CRISPRCasdb

CRISPRCasdb acts as a gateway to a publicly accessible database and software to enable the easy detection of CRISPR sequences in locally-produced data and the consultation of CRISPR sequence data present in the database. It also gives information on the presence of CRISPR-associated (cas) genes when they have been annotated as such.

Webpage:

https://crisprcas.i2bc.paris-saclay.fr/

Licence:

Name: CRISPRcasDB terms of use
URL: https://bioweb.i2bc.paris-saclay.fr/use.htm

Publications:

Publications
More detailed information about this field from each metasource.

CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats
PMID: 17537822
metasource: Fairsharing.org
version: FAIRsharing.org: CRISPRCasdb; CRISPRCasdb; DOI: https://doi.org/10.25504/FAIRsharing.QMGzTm; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins
PMID: 29790974
metasource: Fairsharing.org
version: FAIRsharing.org: CRISPRCasdb; CRISPRCasdb; DOI: https://doi.org/10.25504/FAIRsharing.QMGzTm; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

metasource: Fairsharing.org
version: FAIRsharing.org: CRISPRCasdb; CRISPRCasdb; DOI: https://doi.org/10.25504/FAIRsharing.QMGzTm; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems
PMID: 25330359
metasource: Fairsharing.org
version: FAIRsharing.org: CRISPRCasdb; CRISPRCasdb; DOI: https://doi.org/10.25504/FAIRsharing.QMGzTm; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

CRISPRCasdb a successor of CRISPRdb containing CRISPR arrays and cas genes from complete genome sequences, and tools to download and query lists of repeats and spacers
PMID: 31624845
metasource: Fairsharing.org
version: FAIRsharing.org: CRISPRCasdb; CRISPRCasdb; DOI: https://doi.org/10.25504/FAIRsharing.QMGzTm; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats PubMed citations: 994.

994 articles citing: CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats

Anaerococcus ihuae sp. nov. and Mediannikoviicoccus vaginalis gen. nov., sp. nov., two new bacteria isolated from human vaginal samples. PMID:35859139
Genome Analysis Coupled With Transcriptomics Reveals the Reduced Fitness of a Hot Spring Cyanobacterium Mastigocladus laminosus UU774 Under Exogenous Nitrogen Supplement. PMID:35847102
Features and Colonization Strategies of Enterococcus faecalis in the Gut of Bombyx mori. PMID:35814682
Genomic and proteomic characterization of two strains of Shigella flexneri 2 isolated from infants' stool samples in Argentina. PMID:35804311
Genomic analysis of a novel active prophage of Hafnia paralvei. PMID:35752683
Genome Mining Approach Reveals the Occurrence and Diversity Pattern of Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-Associated Systems in Lactobacillus brevis Strains. PMID:35722276
Theragnostic application of nanoparticle and CRISPR against food-borne multi-drug resistant pathogens. PMID:35711292
Complete genome sequence of the Pogostemon cablin bacterial wilt pathogen Ralstonia solanacearum strain SY1. PMID:35670995
Complete Genome Sequence of Weissella cibaria NH9449 and Comprehensive Comparative-Genomic Analysis: Genomic Diversity and Versatility Trait Revealed. PMID:35663880
Bio-informatic analysis of CRISPR protospacer adjacent motifs (PAMs) in T4 genome. PMID:35655130
KPC-3-, GES-5-, and VIM-1-Producing Enterobacterales Isolated from Urban Ponds. PMID:35627386
Use of 6 Nucleotide Length Words to Study the Complexity of Gene Sequences from Different Organisms. PMID:35626518
Genomic Insights into Omega-3 Polyunsaturated Fatty Acid Producing Shewanella sp. N2AIL from Fish Gut. PMID:35625360
CrisprVi: a software for visualizing and analyzing CRISPR sequences of prokaryotes. PMID:35610585
Oceanisphaera pacifica sp. nov., isolated from the intestine of Trichiurus japonicus. PMID:35590019
Complete Genome Sequence of Paenibacillus polymyxa DSM 365, a Soil Bacterium of Agricultural and Industrial Importance. PMID:35575559
Complete Genome Analysis Reveals the Quorum Sensing-Related Spoilage Potential of Pseudomonas fluorescens PF08, a Specific Spoilage Organism of Turbot (Scophthalmus maximus). PMID:35516425
An Insight into Modern Targeted Genome-Editing Technologies with a Special Focus on CRISPR/Cas9 and its Applications. PMID:35474409
Amplification of the Chromosomal blaCTX-M-14 Gene in Escherichia coli Expanding the Spectrum of Resistance under Antimicrobial Pressure. PMID:35467393
Bioprospecting of Ribosomally Synthesized and Post-translationally Modified Peptides Through Genome Characterization of a Novel Probiotic Lactiplantibacillus plantarum UTNGt21A Strain: A Promising Natural Antimicrobials Factory. PMID:35464932
Comparative Genomics Assisted Functional Characterization of Rahnella aceris ZF458 as a Novel Plant Growth Promoting Rhizobacterium. PMID:35444623
Multidrug-Resistant Klebsiella variicola Isolated in the Urine of Healthy Bovine Heifers, a Potential Risk as an Emerging Human Pathogen. PMID:35416681
CRISPRs in the human genome are differentially expressed between malignant and normal adjacent to tumor tissue. PMID:35396392
CRISPR-Cas System: An Adaptive Immune System's Association with Antibiotic Resistance in Salmonella enterica Serovar Enteritidis. PMID:35386307
Exploring the genome of Lactobacillaceae spp. Sy-1 isolated from Heterotrigona itama honey. PMID:35345581
Genomic and Functional Variation of the Chlorophyll d-Producing Cyanobacterium Acaryochloris marina. PMID:35336144
Escherichia coli and Pseudomonas aeruginosa Isolated From Urine of Healthy Bovine Have Potential as Emerging Human and Bovine Pathogens. PMID:35330764
Whole genome sequencing of Klebsiella pneumoniae clinical isolates sequence type 627 isolated from Egyptian patients. PMID:35320327
Methanosaeta and "Candidatus Velamenicoccus archaeovorus". PMID:35311510
Genotyping Based on CRISPR Loci Diversity and Pathogenic Potential of Diarrheagenic Escherichia coli. PMID:35308371
A high-quality reference genome for the fish pathogen Streptococcus iniae. PMID:35229712
Genomic Comparisons and Phenotypic Diversity of Dickeya zeae Strains Causing Bacterial Soft Rot of Banana in China. PMID:35222482
Exploration of Diverse Secondary Metabolites From Streptomyces sp. YINM00001, Using Genome Mining and One Strain Many Compounds Approach. PMID:35222341
A Novel Freshwater Cyanophage, Mae-Yong924-1, Reveals a New Family. PMID:35215876
Quorum Sensing Controls the CRISPR and Type VI Secretion Systems in Aliivibrio wodanis 06/09/139. PMID:35211539
Complete genome sequence of biocontrol strain Paenibacillus peoriae HJ-2 and further analysis of its biocontrol mechanism. PMID:35209846
Genome Characterization and Probiotic Potential of Corynebacterium amycolatum Human Vaginal Isolates. PMID:35208706
How to Find the Right RNA-Sensing CRISPR-Cas System for an In Vitro Application. PMID:35200314
Heat-Killed Lacticaseibacillus paracasei GMNL-653 Exerts Antiosteoporotic Effects by Restoring the Gut Microbiota Dysbiosis in Ovariectomized Mice. PMID:35187034
Crop Quality Improvement Through Genome Editing Strategy. PMID:35174353
Distribution, Diversity and Roles of CRISPR-Cas Systems in Human and Animal Pathogenic Streptococci. PMID:35173702
Investigation and characterization of human gut phageome in advanced liver cirrhosis of defined etiologies. PMID:35168645
Complete genome sequence of the kiwifruit bacterial canker pathogen Pseudomonas savastanoi strain MHT1. PMID:35120460
Using metagenomic data to boost protein structure prediction and discovery. PMID:35070166
Application of Bacteriophages to Limit Campylobacter in Poultry Production. PMID:35069459
Analysis of Probiotic Bacteria Genomes: Comparison of CRISPR/Cas Systems and Spacer Acquisition Diversity. PMID:35068602
Genomic, Antimicrobial, and Aphicidal Traits of Bacillus velezensis ATR2, and Its Biocontrol Potential against Ginger Rhizome Rot Disease Caused by Bacillus pumilus. PMID:35056513
Structural basis of cyclic oligoadenylate binding to the transcription factor Csa3 outlines cross talk between type III and type I CRISPR systems. PMID:35038453
Comparative genomics and proteomics of Eubacterium maltosivorans: functional identification of trimethylamine methyltransferases and bacterial microcompartments in a human intestinal bacterium with a versatile lifestyle. PMID:34978130
Probiotic Potential Analysis and Safety Evaluation of Enterococcus durans A8-1 Isolated From a Healthy Chinese Infant. PMID:34970251
Highly efficient genome editing in Xanthomonas oryzae pv. oryzae through repurposing the endogenous type I-C CRISPR-Cas system. PMID:34954876
Comparative genomics of Photobacterium species from terrestrial and marine habitats. PMID:34950912
Genomic and Metabolic Features of an Unexpectedly Predominant, Thermophilic, Assistant Starter Microorganism, Thermus thermophilus, in Chinese Inner Mongolian Cheese. PMID:34945513
Comparative Genomics and Physiological Investigation of a New Arthrospira/Limnospira Strain O9.13F Isolated from an Alkaline, Winter Freezing, Siberian Lake. PMID:34943919
Amycolatopsis aidingensis sp. nov., a Halotolerant Actinobacterium, Produces New Secondary Metabolites. PMID:34938275
High-Level Quinolone-Resistant Haemophilus haemolyticus in Pediatric Patient with No History of Quinolone Exposure. PMID:34932443
Lactiplantibacillus plantarum LRCC5314 includes a gene for serotonin biosynthesis via the tryptophan metabolic pathway. PMID:34865198
Phylogenetic Distribution of CRISPR-Cas Systems in Staphylococcus lugdunensis. PMID:34851176
Virulence Comparison of Salmonella enterica Subsp. enterica Isolates from Chicken and Whole Genome Analysis of the High Virulent Strain S. Enteritidis 211. PMID:34835366
Enterococcus faecium Regulates Honey Bee Developmental Genes. PMID:34829986
CRISPR Element Patterns vs. Pathoadaptability of Clinical Pseudomonas aeruginosa Isolates from a Medical Center in Moscow, Russia. PMID:34827239
Draft Genome Sequence of a Poly-γ-Glutamic Acid-Producing Isolate, Bacillus paralicheniformis Strain bcasdu2018/01. PMID:34792384
A Campylobacter integrative and conjugative element with a CRISPR-Cas9 system targeting competing plasmids: a history of plasmid warfare? PMID:34766904
Down in the pond: Isolation and characterization of a new Serratia marcescens strain (LVF3) from the surface water near frog's lettuce (Groenlandia densa). PMID:34748577
Characterization of Blf4, an Archaeal Lytic Virus Targeting a Member of the Methanomicrobiales. PMID:34696364
Distribution and genomic characterization of tigecycline-resistant tet(X4)-positive Escherichia coli of swine farm origin. PMID:34693904
Genomic insights into biocontrol potential of Bacillus stercoris LJBS06. PMID:34692367
Rubber Degrading Strains: Microtetraspora and Dactylosporangium. PMID:34685283
Genomic Characterization of a Prophage, Smhb1, That Infects Salinivibrio kushneri BNH Isolated from a Namib Desert Saline Spring. PMID:34683373
Genomic Analysis of Limosilactobacillus fermentum ATCC 23271, a Potential Probiotic Strain with Anti-Candida Activity. PMID:34682216
Rossellomorea arthrocnemi sp. nov., a novel plant growth-promoting bacterium used in heavy metal polluted soils as a phytoremediation tool. PMID:34665118
Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types. PMID:34606606
Evolution of Type IV CRISPR-Cas Systems: Insights from CRISPR Loci in Integrative Conjugative Elements of Acidithiobacillia. PMID:34582696
Identification of FadT as a Novel Quorum Quenching Enzyme for the Degradation of Diffusible Signal Factor in Cupriavidus pinatubonensis Strain HN-2. PMID:34576026
Description, Taxonomy, and Comparative Genomics of a Novel species, Thermoleptolyngbya sichuanensis sp. nov., Isolated From Hot Springs of Ganzi, Sichuan, China. PMID:34566907
Genomic Stability and Genetic Defense Systems in Dolosigranulum pigrum, a Candidate Beneficial Bacterium from the Human Microbiome. PMID:34546072
Comprehensive genome analysis of a novel actinobacterium with high potential for biotechnological applications, Nonomuraea aridisoli sp. nov., isolated from desert soil. PMID:34529164
Genetic Diversity of Clinical Bordetella Pertussis ST2 Strains in comparison with Vaccine Reference Strains of India. PMID:34527084
Evaluation of probiotic characteristics and whole genome analysis of Pediococcus pentosaceus MR001 for use as probiotic bacteria in shrimp aquaculture. PMID:34526534
Detection of Campylobacter jejuni diversity by clustered regularly interspaced short palindromic repeats (CRISPR) from an animal farm. PMID:34510794
Characterization of Emerging Pathogens Carrying bla KPC-2 Gene in IncP-6 Plasmids Isolated From Urban Sewage in Argentina. PMID:34504809
Functional Identification of the Xanthomonas oryzae pv. oryzae Type I-C CRISPR-Cas System and Its Potential in Gene Editing Application. PMID:34475857
Endophytes from African Rice (Oryza glaberrima L.) Efficiently Colonize Asian Rice (Oryza sativa L.) Stimulating the Activity of Its Antioxidant Enzymes and Increasing the Content of Nitrogen, Carbon, and Chlorophyll. PMID:34442793
Complete genome sequence of Trueperella pyogenes strain Arash114, isolated from the uterus of a water buffalo (Bubalus bubalis) in Iran. PMID:34425879
Whole genome analysis unveils genetic diversity and potential virulence determinants in Vibrio parahaemolyticus associated with disease outbreak among cultured Litopenaeus vannamei (Pacific white shrimp) in India. PMID:34415829
A Type I Restriction Modification System Influences Genomic Evolution Driven by Horizontal Gene Transfer in Paenibacillus polymyxa. PMID:34413842
CASPredict: a web service for identifying Cas proteins. PMID:34395100
A genomic perspective on the potential of termite-associated Cellulosimicrobium cellulans MP1 as producer of plant biomass-acting enzymes and exopolysaccharides. PMID:34395081
New Insights on Streptococcus dysgalactiae subsp. dysgalactiae Isolates. PMID:34335512
Phylogenomic disentangling of the Bifidobacterium longum subsp. infantis taxon. PMID:34319225
Deciphering Symbiotic Interactions of "Candidatus Aenigmarchaeota" with Inferred Horizontal Gene Transfers and Co-occurrence Networks. PMID:34313464
High-risk clones of extended-spectrum β-lactamase-producing Klebsiella pneumoniae isolated from the University Hospital Establishment of Oran, Algeria (2011-2012). PMID:34310625
Complete Genome Sequence of the Anabaena Myophage Elbi. PMID:34292064
Comprehensive Molecular Dissection of Dermatophilus congolensis Genome and First Observation of tet(Z) Tetracycline Resistance. PMID:34281179
Analysis of the Taxonomy and Pathogenic Factors of Pectobacterium aroidearum L6 Using Whole-Genome Sequencing and Comparative Genomics. PMID:34276610
Genome Features and In Vitro Activity against Influenza A and SARS-CoV-2 Viruses of Six Probiotic Strains. PMID:34258278
Whole-Genome Sequence Data Analysis of Anoxybacillus kamchatkensis NASTPD13 Isolated from Hot Spring of Myagdi, Nepal. PMID:34258259
Genomic Analysis of Delftia tsuruhatensis Strain TR1180 Isolated From A Patient From China With In4-Like Integron-Associated Antimicrobial Resistance. PMID:34222039
Antimicrobial Resistance and Genomic Characterization of Two mcr-1-Harboring Foodborne Salmonella Isolates Recovered in China, 2016. PMID:34211439
CRISPR loci-PCR as Tool for Tracking Azospirillum sp. Strain B510. PMID:34206618
Unexpected Discovery of Hypermutator Phenotype Sounds the Alarm for Quality Control Strains. PMID:34180992
Next-Generation Sequencing for Whole-Genome Characterization of Weissella cibaria UTNGt21O Strain Originated From Wild Solanum quitoense Lam. Fruits: An Atlas of Metabolites With Biotechnological Significance. PMID:34163450
Genomic analysis of halophilic bacterium, Lentibacillus sp. CBA3610, derived from human feces. PMID:34162403
Phenotypic and genomic hallmarks of a novel, potentially pathogenic rapidly growing Mycobacterium species related to the Mycobacterium fortuitum complex. PMID:34155223
Identification and Characterization of the CRISPR/Cas System in Staphylococcus aureus Strains From Diverse Sources. PMID:34149645
Pan-Genome Analysis of Vibrio cholerae and Vibrio metschnikovii Strains Isolated From Migratory Birds at Dali Nouer Lake in Chifeng, China. PMID:34136552
Characterization of a bacterial strain Lactobacillus paracasei LP10266 recovered from an endocarditis patient in Shandong, China. PMID:34134621
Genome analysis of Bacteroides sp.CACC 737 isolated from feline for its potential application. PMID:33987575
Ecophysiological Features Shape the Distribution of Prophages and CRISPR in Sulfate Reducing Prokaryotes. PMID:33925267
Characterisation of Phage Susceptibility Variation in Salmonellaenterica Serovar Typhimurium DT104 and DT104b. PMID:33920555
The Development of Bacteriophage Resistance in Vibrio alginolyticus Depends on a Complex Metabolic Adaptation Strategy. PMID:33920240
Pikeienuella piscinae gen. nov., sp. nov., a novel genus in the family Rhodobacteraceae. PMID:33877579
Lytic Bacteriophage EFA1 Modulates HCT116 Colon Cancer Cell Growth and Upregulates ROS Production in an Enterococcus faecalis Co-culture System. PMID:33868210
Genomic and phenotypic diversity of Enterococcus faecalis isolated from endophthalmitis. PMID:33852628
Detection of Highly Divergent Tandem Repeats in the Rice Genome. PMID:33806152
Characterization of CRISPR Spacer and Protospacer Sequences in Paenibacillus larvae and Its Bacteriophages. PMID:33799666
Prevalence and Genetic Diversity of Listeria monocytogenes Isolated From Retail Pork in Wuhan, China. PMID:33767677
Genomic Insights Into the Pathogenicity of a Novel Biofilm-Forming Enterococcus sp. Bacteria (Enterococcus lacertideformus) Identified in Reptiles. PMID:33737921
Streamlining CRISPR spacer-based bacterial host predictions to decipher the viral dark matter. PMID:33677572
CRISPRbuilder-TB: "CRISPR-builder for tuberculosis". Exhaustive reconstruction of the CRISPR locus in mycobacterium tuberculosis complex using SRA. PMID:33667225
Interaction dynamics and virus-host range for estuarine actinophages captured by epicPCR. PMID:33633401
A comparison of fourteen fully characterized mammalian-associated Campylobacter fetus isolates suggests that loss of defense mechanisms contribute to high genomic plasticity and subspecies evolution. PMID:33628630
CasCollect: targeted assembly of CRISPR-associated operons from high-throughput sequencing data. PMID:33575613
Host and body site-specific adaptation of Lactobacillus crispatus genomes. PMID:33575551
Mobile element warfare via CRISPR and anti-CRISPR in Pseudomonas aeruginosa. PMID:33544853
Distinct clonal lineages and within-host diversification shape invasive Staphylococcus epidermidis populations. PMID:33544760
A multiplex CRISPR interference tool for virulence gene interrogation in Legionella pneumophila. PMID:33542442
Whole-Genome Sequence of Bioactive Compound-Producing Pseudomonas aeruginosa Strain LV. PMID:33414299
Comprehensive genomic analysis reveals virulence factors and antibiotic resistance genes in Pantoea agglomerans KM1, a potential opportunistic pathogen. PMID:33406073
Description and genomic characterization of Streptococcus symci sp. nov., isolated from a child's oropharynx. PMID:33387140
Genomic Insight into Pediococcus acidilactici HN9, a Potential Probiotic Strain Isolated from the Traditional Thai-Style Fermented Beef Nhang. PMID:33375492
Assessment of Safety and Probiotic Traits of Enterococcus durans OSY-EGY, Isolated From Egyptian Artisanal Cheese, Using Comparative Genomics and Phenotypic Analyses. PMID:33362752
Comparative genomics of Klebsiella michiganensis BD177 and related members of Klebsiella sp. reveal the symbiotic relationship with Bactrocera dorsalis. PMID:33339499
Various Aspects of a Gene Editing System-CRISPR-Cas9. PMID:33339441
Comparative Pathogenomics of Aeromonas veronii from Pigs in South Africa: Dominance of the Novel ST657 Clone. PMID:33339176
Whole-Genome Sequencing of Bradyrhizobium diazoefficiens 113-2 and Comparative Genomic Analysis Provide Molecular Insights Into Species Specificity and Host Specificity. PMID:33329441
Distribution of Important Probiotic Genes and Identification of the Biogenic Amines Produced by Lactobacillus acidophilus PNW3. PMID:33321968
The State of the Art in Biodefense Related Bacterial Pathogen Detection Using Bacteriophages: How It Started and How It's Going. PMID:33291831
The Surface Protein Fructose-1, 6 Bisphosphate Aldolase of Klebsiella pneumoniae Serotype K1: Role of Interaction with Neutrophils. PMID:33266305
Unexpected diversity of CRISPR unveils some evolutionary patterns of repeated sequences in Mycobacterium tuberculosis. PMID:33256602
Genome Sequence of Klebsiella pneumoniae YBQ, a Clinical Strain Isolated from the Sputum of a Patient with Severe Pneumonia. PMID:33214313
CRISPR sequences are sometimes erroneously translated and can contaminate public databases with spurious proteins containing spaced repeats. PMID:33206958
Complete Genomic Analysis of VRE From a Cattle Feedlot: Focus on 2 Antibiotic Resistance. PMID:33178155
Transcription termination and antitermination of bacterial CRISPR arrays. PMID:33124980
In silico Method in CRISPR/Cas System: An Expedite and Powerful Booster. PMID:33123486
Genomic divergence between Dickeya zeae strain EC2 isolated from rice and previously identified strains, suggests a different rice foot rot strain. PMID:33079956
Clinical and molecular characteristics of carbapenem non-susceptible Escherichia coli: A nationwide survey from Oman. PMID:33036018
First hybrid complete genome of Aeromonas veronii reveals chromosome-mediated novel structural variant mcr-3.30 from a human clinical sample. PMID:33005867
Genome sequence and annotation of Streptomyces tendae UTMC 3329, acid and alkaline tolerant actinobacterium. PMID:32994907
Biochemical and Taxonomic Characterization of Novel Haloarchaeal Strains and Purification of the Recombinant Halotolerant α-Amylase Discovered in the Isolate. PMID:32983058
The Genome of Staphylococcus epidermidis O47. PMID:32983045
Whole-Genome Sequencing Analysis of Quorum Quenching Bacterial Strain Acinetobacter lactucae QL-1 Identifies the FadY Enzyme for Degradation of the Diffusible Signal Factor. PMID:32937869
Identification of a Type IV-A CRISPR-Cas System Located Exclusively on IncHI1B/IncFIB Plasmids in Enterobacteriaceae. PMID:32903441
Whole-genome sequence of multi-drug resistant Pseudomonas aeruginosa strains UY1PSABAL and UY1PSABAL2 isolated from human broncho-alveolar lavage, Yaoundé, Cameroon. PMID:32886694
Genomic Signatures of Honey Bee Association in an Acetic Acid Symbiont. PMID:32870981
Virulence genes and previously unexplored gene clusters in four commensal Neisseria spp. isolated from the human throat expand the neisserial gene repertoire. PMID:32845827
Complete Genome and Comparative Genome Analysis of Lactobacillus reuteri YSJL-12, a Potential Probiotics Strain Isolated From Healthy Sow Fresh Feces. PMID:32782425
Streptobacillus felis, a member of the oropharynx microbiota of the Felidae, isolated from a tropical rusty-spotted cat. PMID:32776203
Genomic Insights of Cryobacterium Isolated From Ice Core Reveal Genome Dynamics for Adaptation in Glacier. PMID:32765445
Development and Application of CRISPR/Cas in Microbial Biotechnology. PMID:32695770
Integrated genome-based probiotic relevance and safety evaluation of Lactobacillus reuteri PNW1. PMID:32687505
Complete genome sequences of Streptococcus pyogenes type strain reveal 100%-match between PacBio-solo and Illumina-Oxford Nanopore hybrid assemblies. PMID:32669560
Source Tracking Based on Core Genome SNV and CRISPR Typing of Salmonella enterica Serovar Heidelberg Isolates Involved in Foodborne Outbreaks in Québec, 2012. PMID:32625190
Genome-Wide Analysis Reveals Genetic Potential for Aromatic Compounds Biodegradation of Sphingopyxis. PMID:32596333
Diversity of Pectobacteriaceae Species in Potato Growing Regions in Northern Morocco. PMID:32545839
Campylobacter bacteriophage DA10: an excised temperate bacteriophage targeted by CRISPR-cas. PMID:32532247
Introducing Lu-1, a Novel Lactobacillus jensenii Phage Abundant in the Urogenital Tract. PMID:32525961
Draft Genome Sequence of Actinomyces neuii UMB1295, Isolated from the Female Urinary Tract. PMID:32499345
Searching for a Bacteriophage Lysin to Treat Corynebacterium bovis in Immunocompromised Mice. PMID:32471521
Draft Genome Sequence of Enterococcus faecalis UMB7780, Isolated from the Female Urinary Tract. PMID:32467278
Characterization of a potential probiotic bacterium Lactococcus raffinolactis WiKim0068 isolated from fermented vegetable using genomic and in vitro analyses. PMID:32460704
Draft Genome Sequence of Lactobacillus jensenii Strain UMB7766, Isolated from the Female Bladder. PMID:32409549
Draft Genome Sequence of Proteus mirabilis UMB1310, Isolated from the Female Urinary Tract. PMID:32409548
Comprehensive Mining and Characterization of CRISPR-Cas Systems in Bifidobacterium. PMID:32408568
High Synteny and Sequence Identity between Genomes of Nitrosococcus oceani Strains Isolated from Different Oceanic Gyres Reveals Genome Economization and Autochthonous Clonal Evolution. PMID:32397339
Comparative genomics of whole-cell pertussis vaccine strains from India. PMID:32381023
Pseudoalteromonas rhizosphaerae sp. nov., a novel plant growth-promoting bacterium with potential use in phytoremediation. PMID:32375987
Complete genome sequencing and comparative genomic analyses of Bacillus sp. S3, a novel hyper Sb(III)-oxidizing bacterium. PMID:32354325
Novel Genus of Phages Infecting Streptococcus thermophilus: Genomic and Morphological Characterization. PMID:32303549
Draft Genome Sequence of Pseudarthrobacter phenanthrenivorans Strain MHSD1, a Bacterial Endophyte Isolated From the Medicinal Plant Pellaea calomelanos. PMID:32284671
Genotyping of Campylobacter jejuni Isolates from Poultry by Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR). PMID:32279188
Genomic investigation of emerging zoonotic pathogen Shewanella xiamenensis. PMID:32269948
Genomic Epidemiology of Vancomycin-Resistant Enterococcus faecium (VREfm) in Latin America: Revisiting The Global VRE Population Structure. PMID:32221315
Bacteriophage-Insensitive Mutants of Antimicrobial-Resistant Salmonella Enterica are Altered in their Tetracycline Resistance and Virulence in Caco-2 Intestinal Cells. PMID:32164202
Applications of the CRISPR/Cas system beyond gene editing. PMID:32161796
The CRISPR-Cas systems were selectively inactivated during evolution of Bacillus cereus group for adaptation to diverse environments. PMID:32132663
Micromonospora zhangzhouensis sp. nov., a Novel Actinobacterium Isolated from Mangrove Soil, Exerts a Cytotoxic Activity in vitro. PMID:32127574
Novel Bacteriophages Capable of Disrupting Biofilms From Clinical Strains of Aeromonas hydrophila. PMID:32117183
Comparative Insights Into the Complete Genome Sequence of Highly Metal Resistant Cupriavidus metallidurans Strain BS1 Isolated From a Gold-Copper Mine. PMID:32117100
Whole-Genome Sequencing of Lactobacillus helveticus D75 and D76 Confirms Safety and Probiotic Potential. PMID:32111071
Comparative genomics of the fish pathogens Edwardsiella ictaluri 93-146 and Edwardsiella piscicida C07-087. PMID:32108566
Analysis of the Complete Genome of the Alkaliphilic and Phototrophic Firmicute Heliorestis convoluta Strain HHT. PMID:32106460
Draft genome sequence of Actinocorallia populi A251T, an actinomycetes producing polyketides and nonribosomal polypeptides. PMID:32099730
Genome Analysis of Lactobacillus plantarum Isolated From Some Indian Fermented Foods for Bacteriocin Production and Probiotic Marker Genes. PMID:32063893
Characterization and whole genome sequencing of a novel strain of Bergeyella cardium related to infective endocarditis. PMID:32050896
Plasmids Shaped the Recent Emergence of the Major Nosocomial Pathogen Enterococcus faecium. PMID:32047136
RNA-Targeting CRISPR-Cas Systems and Their Applications. PMID:32046217
Biocontrol Potential of a Novel Endophytic Bacterium From Mulberry (Morus) Tree. PMID:32039187
Pathogenomic Analysis of a Novel Extensively Drug-Resistant Citrobacter freundii Isolate Carrying a blaNDM-1 Carbapenemase in South Africa. PMID:32024012
Draft Genome Sequences of Eight Strains of Campylobacter helveticus Isolated from Cats and a Dog in New Zealand. PMID:32001558
Genomic Characterization of a Novel Gut Symbiont From the Hadal Snailfish. PMID:31998265
CRISPR-Cas System in Antibiotic Resistance Plasmids in Klebsiella pneumoniae. PMID:31998256
Defining the Environmental Adaptations of Genus Devosia: Insights into its Expansive Short Peptide Transport System and Positively Selected Genes. PMID:31980727
Comparative genomics of multidrug-resistant Enterococcus spp. isolated from wastewater treatment plants. PMID:31980014
Draft genome sequence and nomenclature adjustment of Rhodococcus qingshengii CS98, a cesium-accumulating strain isolated in Japan. PMID:31956519
Comparative Genomics of Streptococcus thermophilus Support Important Traits Concerning the Evolution, Biology and Technological Properties of the Species. PMID:31956321
CRISPR/Cas9: targeted genome editing for the treatment of hereditary hearing loss. PMID:31912450
The complete genome sequence of the nitrile biocatalyst Rhodocccus rhodochrous ATCC BAA-870. PMID:31898479
Genomic dissection of the most prevalent Listeria monocytogenes clone, sequence type ST87, in China. PMID:31870294
Draft Genome Sequence of Thermophilic Bacillus sp. TYF-LIM-B05 Directly Producing Ethanol from Various Carbon Sources Including Lignocellulose. PMID:31832840
Draft Genome Sequence of a Wohlfahrtiimonas chitiniclastica Strain Isolated from Frozen Chicken in Rio De Janeiro, Brazil. PMID:31806738
Draft Genome Sequence of Enterobacter hormaechei Strain MHSD6, a Plant Endophyte Isolated from Medicinal Plant Pellaea calomelanos. PMID:31776223
Draft Genome Sequence of Bacillus safensis Strain Sami, Isolated from Leaf Veins of Ficus religiosa. PMID:31753935
CRISPR-Cas influences the acquisition of antibiotic resistance in Klebsiella pneumoniae. PMID:31747398
Draft Genome Sequence of Bacillus velezensis Strain ZeaDK315Endo16. PMID:31727695
Comparative Analysis of Whole-Genome and Methylome Profiles of a Smooth and a Rough Mycobacterium abscessus Clinical Strain. PMID:31719113
Endogenous CRISPR-Cas System-Based Genome Editing and Antimicrobials: Review and Prospects. PMID:31708910
Genomic and phenotypic insights point to diverse ecological strategies by facultative anaerobes obtained from subsurface coal seams. PMID:31700097
Complete Genome Sequence of Strain YCSC6, a Marine Bacterium Isolated from Saturated Saltpan with Activity Against Uronema marinum. PMID:31691022
Genomic comparison of diverse Salmonella serovars isolated from swine. PMID:31675365
Red-Brown Pigmentation of Acidipropionibacterium jensenii Is Tied to Haemolytic Activity and cyl-Like Gene Cluster. PMID:31671651
Complete Genome of the Chitin-Degrading Bacterium, Paenibacillus xylanilyticus W4. PMID:31670768
Microevolution within ST11 group Clostridioides difficile isolates through mobile genetic elements based on complete genome sequencing. PMID:31666016
Characterization and repurposing of the endogenous Type I-F CRISPR-Cas system of Zymomonas mobilis for genome engineering. PMID:31647102
Horizontal gene transfer contributes to virulence and antibiotic resistance of Vibrio harveyi 345 based on complete genome sequence analysis. PMID:31640552
CRISPRCasdb a successor of CRISPRdb containing CRISPR arrays and cas genes from complete genome sequences, and tools to download and query lists of repeats and spacers. PMID:31624845
Comparative genomic analyses reveal diverse virulence factors and antimicrobial resistance mechanisms in clinical Elizabethkingia meningoseptica strains. PMID:31600234
Complete genome sequence of Rhodococcus sp. NJ-530, a DMSP-degrading actinobacterium isolated from Antarctic sea ice. PMID:31576282
Genome Mining and Comparative Pathogenomic Analysis of An Endemic Methicillin-Resistant Staphylococcus Aureus (MRSA) Clone, ST612-CC8-t1257-SCCmec_IVd(2B), Isolated in South Africa. PMID:31569754
Characterization of CRISPR-Cas Systems in Serratia marcescens Isolated from Rhynchophorus ferrugineus (Olivier, 1790) (Coleoptera: Curculionidae). PMID:31546915
Complete Genome Sequence of a Pseudomonas aeruginosa Isolate from a Kidney Stone. PMID:31537684
Draft Genome Sequence of Ciprofloxacin and Ceftriaxone Resistant Campylobacter jejuni MM26-781 Assigned to Novel ST Isolated From Common Pigeon in Lithuania. PMID:31523125
Genomic Analysis of γ-Hexachlorocyclohexane-Degrading Sphingopyxis lindanitolerans WS5A3p Strain in the Context of the Pangenome of Sphingopyxis. PMID:31500174
Cas9 Contributes to Group B Streptococcal Colonization and Disease. PMID:31497003
Genome sequence of Shewanella corallii strain A687 isolated from pufferfish (Sphoeroides spengleri). PMID:31479095
Comparative genomics of Aeromonas veronii: Identification of a pathotype impacting aquaculture globally. PMID:31465454
Draft Genome Sequence of Bifidobacterium longum ZJ1, Isolated from a Centenarian in Anhui, China. PMID:31416881
Draft Genome Sequence of Bacillus thuringiensis DPC6431, Producer of the Bacteriocin Thuricin CD. PMID:31416857
CasPDB: an integrated and annotated database for Cas proteins from bacteria and archaea. PMID:31411686
Complete genome sequence analysis of the thermoacidophilic verrucomicrobial methanotroph "Candidatus Methylacidiphilum kamchatkense" strain Kam1 and comparison with its closest relatives. PMID:31399023
Whole-genome sequence data and analysis of Lactobacillus delbrueckii subsp. lactis ACA-DC 178 isolated from Greek Kasseri cheese. PMID:31388525
Draft Genome Sequence of Rummeliibacillus sp. Strain TYF005, a Physiologically Recalcitrant Bacterium with High Ethanol and Salt Tolerance Isolated from Spoilage Vinegar. PMID:31371531
Comparative genomics and functional analysis of a highly adhesive dairy Lactobacillus paracasei subsp. paracasei IBB3423 strain. PMID:31359102
Next Generation DNA-Seq and Differential RNA-Seq Allow Re-annotation of the Pyrococcus furiosus DSM 3638 Genome and Provide Insights Into Archaeal Antisense Transcription. PMID:31354685
Draft Genome Sequence of Deinococcus sp. Strain S9, Isolated from Microbial Mat Deposits of Hot Springs Located atop the Himalayan Ranges at Manikaran, India. PMID:31296675
Draft Genome Sequence of an Escherichia coli Sequence Type 155 Strain Isolated from Sewage in Kerala, India. PMID:31270207
Characterization of a NDM-7 carbapenemase-producing Escherichia coli ST410 clinical strain isolated from a urinary tract infection in China. PMID:31239731
Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system. PMID:31238873
Genomic, morphological and functional characterisation of novel bacteriophage FNU1 capable of disrupting Fusobacterium nucleatum biofilms. PMID:31235721
Comparative genomic analysis of Pectobacterium carotovorum subsp. brasiliense SX309 provides novel insights into its genetic and phenotypic features. PMID:31195968
Complete genome sequence and phylogenetic analysis of nosocomial pathogen Acinetobacter nosocomialis strain NCTC 8102. PMID:31177378
Complete Genome Sequence of Qipengyuania sediminis CGMCC 1.12928T, Shed Light on Its Role in Matter-Cycle and Cold Adaption Mechanism of the Genus Qipengyuania. PMID:31172271
Draft Genome Sequence of Bacillus coagulans MA-13, a Thermophilic Lactic Acid Producer from Lignocellulose. PMID:31171617
Gut Microbiota and Colonization Resistance against Bacterial Enteric Infection. PMID:31167904
An overview of designing and selection of sgRNAs for precise genome editing by the CRISPR-Cas9 system in plants. PMID:31139538
Diversity of CRISPR/Cas system in Clostridium perfringens. PMID:31134321
Carbohydrate metabolic systems present on genomic islands are lost and gained in Vibrio parahaemolyticus. PMID:31133029
Genomic insights into a robust gamma-aminobutyric acid-producer Lactobacillus brevis CD0817. PMID:31127390
Draft Genome Sequence of Providencia rettgeri APW139_S1, an NDM-18-Producing Clinical Strain Originating from Hospital Effluent in South Africa. PMID:31123013
Complete genome sequence of Salmonella enterica serovar Sendai shows H antigen convergence with S. Miami and recent divergence from S. Paratyphi A. PMID:31117944
Interspaced Repeat Sequences Confer the Regulatory Functions of AtXTH10, Important for Root Growth in Arabidopsis. PMID:31100875
Analysis of direct repeats and spacers of CRISPR/Cas systems type I-F in Brazilian clinical strains of Pseudomonas aeruginosa. PMID:31098740
Comparative Genomic Analysis of Lactobacillus plantarum: An Overview. PMID:31093491
Comparative Genomics of the Genus Methanohalophilus, Including a Newly Isolated Strain From Kebrit Deep in the Red Sea. PMID:31068917
Remarkable Genome Stability among emm1 Group A Streptococcus in Belgium over 19 Years. PMID:31065672
Complete Genome Sequence of Spiroplasma alleghenense PLHS-1T (ATCC 51752), a Bacterium Isolated from Scorpion Fly (Panorpa helena). PMID:31023800
Characterization of an NDM-5 carbapenemase-producing Escherichia coli ST156 isolate from a poultry farm in Zhejiang, China. PMID:31023222
CRISPRdisco: An Automated Pipeline for the Discovery and Analysis of CRISPR-Cas Systems. PMID:31021201
Complete genome sequence of natural rubber-degrading, gram-negative bacterium, Rhizobacter gummiphilus strain NS21T. PMID:31011550
Draft Genome Sequence of Multidrug-Resistant Enterococcus faecium Strain E1298, with a Sequence Type 1274 Profile, Recovered from the Cloacal Microbiome of a Tropical Screech Owl (Megascops choliba) in Rio de Janeiro, Brazil. PMID:31000546
Draft Genome Sequence of Rhodoplanes sp. Strain T2.26MG-98, Isolated from 492.6 Meters Deep on the Subsurface of the Iberian Pyrite Belt. PMID:31000538
Genomic and Functional Characterization of Enterococcus mundtii QAUEM2808, Isolated From Artisanal Fermented Milk Product Dahi. PMID:30972030
Comparative genomic analysis unravels the transmission pattern and intra-species divergence of acute hepatopancreatic necrosis disease (AHPND)-causing Vibrio parahaemolyticus strains. PMID:30968246
Primed adaptation tolerates extensive structural and size variations of the CRISPR RNA guide in Haloarcula hispanica. PMID:30957847
Independent Microevolution Mediated by Mobile Genetic Elements of Individual Clostridium difficile Isolates from Clade 4 Revealed by Whole-Genome Sequencing. PMID:30944881
In Silico Identification of Three Types of Integrative and Conjugative Elements in Elizabethkingia anophelis Strains Isolated from around the World. PMID:30944210
Draft Genome Sequence of an Enterococcus faecalis Strain (24FS) That Was Isolated from Healthy Infant Feces and Exhibits High Antibacterial Activity, Multiple-Antibiotic Resistance, and Multiple Virulence Factors. PMID:30923239
Just the Two of Us? A Family of Pseudomonas Megaplasmids Offers a Rare Glimpse into the Evolution of Large Mobile Elements. PMID:30918968
CRISPR-Cas immunity leads to a coevolutionary arms race between Streptococcus thermophilus and lytic phage. PMID:30905285
Domestication of previously uncultivated Candidatus Desulforudis audaxviator from a deep aquifer in Siberia sheds light on its physiology and evolution. PMID:30899075
Insight into the genome and brackish water adaptation strategies of toxic and bloom-forming Baltic Sea Dolichospermum sp. UHCC 0315. PMID:30894564
CRISPR-Cas, a highly effective tool for genome editing in Clostridium saccharoperbutylacetonicum N1-4(HMT). PMID:30874768
CRISPR-Cas in Streptococcus pyogenes. PMID:30856357
CRISPR Spacers Indicate Preferential Matching of Specific Virioplankton Genes. PMID:30837341
Survival Mechanisms of Campylobacter hepaticus Identified by Genomic Analysis and Comparative Transcriptomic Analysis of in vivo and in vitro Derived Bacteria. PMID:30804905
Draft Genome Sequence of Heavy Metal-Resistant Bacillus cereus NWUAB01. PMID:30801070
Draft genome sequence of Enterococcus faecium SP15, a potential probiotic strain isolated from spring water. PMID:30795795
Endogenous Gene Regulation as a Predicted Main Function of Type I-E CRISPR/Cas System in E. coli. PMID:30795631
Comparative Genomic Analyses Reveal Core-Genome-Wide Genes Under Positive Selection and Major Regulatory Hubs in Outlier Strains of Pseudomonas aeruginosa. PMID:30787911
Unveiling Genomic Diversity among Members of the Species Bifidobacterium pseudolongum, a Widely Distributed Gut Commensal of the Animal Kingdom. PMID:30737347
Enhanced mammalian genome editing by new Cas12a orthologs with optimized crRNA scaffolds. PMID:30717767
CRISPR-Cas systems are present predominantly on mobile genetic elements in Vibrio species. PMID:30717668
Complete Genome Sequence of Streptomyces olivoreticuli ATCC 31159 Which can Produce Anticancer Bestatin and Show Diverse Secondary Metabolic Potentials. PMID:30706083
Marine biofilms constitute a bank of hidden microbial diversity and functional potential. PMID:30705275
Draft Genome Sequence of Bacillus coagulans ZB29, a Commercial Probiotic Strain. PMID:30687815
Genomic Insights Into A Novel, Alkalitolerant Nitrogen Fixing Bacteria, Azonexus sp. Strain ZS02. PMID:30662569
Detection and variability analyses of CRISPR-like loci in the H. pylori genome. PMID:30648020
Genomic characterisation of the new Dickeya fangzhongdai species regrouping plant pathogens and environmental isolates. PMID:30634913
Bacterial and Archaeal Viruses of Himalayan Hot Springs at Manikaran Modulate Host Genomes. PMID:30619174
Evolution of the Population Structure of Staphylococcus pseudintermedius in France. PMID:30619143
Complete Genome Sequence and Comparative Analysis of Synechococcus sp. CS-601 (SynAce01), a Cold-Adapted Cyanobacterium from an Oligotrophic Antarctic Habitat. PMID:30609821
Genotypic differences between strains of the opportunistic pathogen Corynebacterium bovis isolated from humans, cows, and rodents. PMID:30586440
Bacterial Small RNAs in the Genus Herbaspirillum spp. PMID:30583511
Phenotypic and genomic analyses of bacteriophages targeting environmental and clinical CS3-expressing enterotoxigenic Escherichia coli (ETEC) strains. PMID:30571788
Complete Genome Sequence of Saccharospirillum mangrovi HK-33T Sheds Light on the Ecological Role of a Bacterium in Mangrove Sediment Environment. PMID:30564885
Complete genome of Rhizobium leguminosarum Norway, an ineffective Lotus micro-symbiont. PMID:30534351
Draft Genome Sequence of a Tetracycline-Resistant Plesiomonas shigelloides Strain Isolated from Aquaculture-Reared Tilapia. PMID:30533804
Draft Whole-Genome Shotgun Sequence of Streptomyces sp. Strain ETH9427. PMID:30533680
Draft genome sequence of a uropathogenic Escherichia coli isolate (ST38 O1:H15) from Pakistan, an emerging multidrug-resistant sequence type with a high virulence profile. PMID:30510766
Phenotypic and genomic comparison of Photorhabdus luminescens subsp. laumondii TT01 and a widely used rifampicin-resistant Photorhabdus luminescens laboratory strain. PMID:30497380
Capsular Switching and ICE Transformation Occurred in Human Streptococcus agalactiae ST19 With High Pathogenicity to Fish. PMID:30483518
On the reconstruction of the ancestral bacterial genomes in genus Mycobacterium and Brucella. PMID:30458842
Organic Particles: Heterogeneous Hubs for Microbial Interactions in Aquatic Ecosystems. PMID:30416497
Therapeutic Potential of a New Jumbo Phage That Infects Vibrio coralliilyticus, a Widespread Coral Pathogen. PMID:30405564
CRISPRminer is a knowledge base for exploring CRISPR-Cas systems in microbe and phage interactions. PMID:30393777
High-quality-draft genome sequence of the multiple heavy metal resistant bacterium Pseudaminobacter manganicus JH-7T. PMID:30386456
In silico Analysis Suggests Common Appearance of scaRNAs in Type II Systems and Their Association With Bacterial Virulence. PMID:30386377
Comparative genomic and methylome analysis of non-virulent D74 and virulent Nagasaki Haemophilus parasuis isolates. PMID:30383795
Genomic analysis of the Phalaenopsis pathogen Dickeya sp. PA1, representing the emerging species Dickeya fangzhongdai. PMID:30373513
Genomic Characterization of Cyanophage vB_AphaS-CL131 Infecting Filamentous Diazotrophic Cyanobacterium Aphanizomenon flos-aquae Reveals Novel Insights into Virus-Bacterium Interactions. PMID:30367000
Comparative genomics of the Komagataeibacter strains-Efficient bionanocellulose producers. PMID:30365246
Draft genome sequence data of a tigecycline-resistant Enterobacter cloacae ST93 clinical strain isolated from bloodstream infection. PMID:30364805
Investigation of direct repeats, spacers and proteins associated with clustered regularly interspaced short palindromic repeat (CRISPR) system of Vibrio parahaemolyticus. PMID:30357478
Complete Genomic Analysis of a Kingdom-Crossing Klebsiella variicola Isolate. PMID:30356723
Draft genomes of "Pectobacterium peruviense" strains isolated from fresh water in France. PMID:30344890
Insights into the draft genome sequence of bioactives-producing Bacillus thuringiensis DNG9 isolated from Algerian soil-oil slough. PMID:30344888
Cupriavidus metallidurans Strains with Different Mobilomes and from Distinct Environments Have Comparable Phenomes. PMID:30340417
Programmed DNA destruction by miniature CRISPR-Cas14 enzymes. PMID:30337455
Sulfur Respiration in a Group of Facultatively Anaerobic Natronoarchaea Ubiquitous in Hypersaline Soda Lakes. PMID:30333814
Comparative Genomics of Degradative Novosphingobium Strains With Special Reference to Microcystin-Degrading Novosphingobium sp. THN1. PMID:30319567
Fast and global detection of periodic sequence repeats in large genomic resources. PMID:30304510
Genome analyses of uncultured TG2/ZB3 bacteria in 'Margulisbacteria' specifically attached to ectosymbiotic spirochetes of protists in the termite gut. PMID:30287885
Phylogenetic, comparative genomic and structural analyses of human Streptococcus agalactiae ST485 in China. PMID:30261834
Complete genome sequence of the Robinia pseudoacacia L. symbiont Mesorhizobium amorphae CCNWGS0123. PMID:30250634
Thermosipho spp. Immune System Differences Affect Variation in Genome Size and Geographical Distributions. PMID:30239713
Spread of Carbapenem Resistance by Transposition and Conjugation Among Pseudomonas aeruginosa. PMID:30233535
Active Crossfire Between Cyanobacteria and Cyanophages in Phototrophic Mat Communities Within Hot Springs. PMID:30233525
Genomic Insights Into the Acid Adaptation of Novel Methanotrophs Enriched From Acidic Forest Soils. PMID:30210468
Insights into the Human Virome Using CRISPR Spacers from Microbiomes. PMID:30205462
Evaluating the Safety of Potential Probiotic Enterococcus durans KLDS6.0930 Using Whole Genome Sequencing and Oral Toxicity Study. PMID:30186262
Distinct Genomic Features Characterize Two Clades of Corynebacterium diphtheriae: Proposal of Corynebacterium diphtheriae Subsp. diphtheriae Subsp. nov. and Corynebacterium diphtheriae Subsp. lausannense Subsp. nov. PMID:30174653
Construction and Characterization of Synthetic Bacterial Community for Experimental Ecology and Evolution. PMID:30154827
Evolution of the U.S. Biological Select Agent Rathayibacter toxicus. PMID:30154261
Complete genome of streamlined marine actinobacterium Pontimonas salivibrio strain CL-TW6T adapted to coastal planktonic lifestyle. PMID:30134835
CRISPR Visualizer: rapid identification and visualization of CRISPR loci via an automated high-throughput processing pipeline. PMID:30130453
Comparative genomic analysis of Staphylococcus lugdunensis shows a closed pan-genome and multiple barriers to horizontal gene transfer. PMID:30126366
Novel phages of healthy skin metaviromes from South Africa. PMID:30115980
PAM identification by CRISPR-Cas effector complexes: diversified mechanisms and structures. PMID:30109815
Comparative genomics and evolution of trans-activating RNAs in Class 2 CRISPR-Cas systems. PMID:30103650
Study the Features of 57 Confirmed CRISPR Loci in 38 Strains of Staphylococcus aureus. PMID:30093886
Characterization of CRISPR-Cas Systems in Clinical Klebsiella pneumoniae Isolates Uncovers Its Potential Association With Antibiotic Susceptibility. PMID:30061876
Genomic and Biotechnological Characterization of the Heavy-Metal Resistant, Arsenic-Oxidizing Bacterium Ensifer sp. M14. PMID:30060533
Complete Genome Sequence of Industrial Biocontrol Strain Paenibacillus polymyxa HY96-2 and Further Analysis of Its Biocontrol Mechanism. PMID:30050512
Genetics of CRISPR arrays in Salmonella Typhimurium 14028 associated with foreign DNA decay. PMID:30047111
Defining the Species Micromonospora saelicesensis and Micromonospora noduli Under the Framework of Genomics. PMID:29988535
Whole-Genome Sequence of Salmonella enterica subsp. enterica Serovar Typhimurium Strain WG49 and Escherichia coli Strain WG5 Used in South Africa for Phage Detection in Water Samples. PMID:29954884
Comparative Genomics of Lactobacillus acidipiscis ACA-DC 1533 Isolated From Traditional Greek Kopanisti Cheese Against Species Within the Lactobacillus salivarius Clade. PMID:29942291
Landscape of the genome and host cell response of Mycobacterium shigaense reveals pathogenic features. PMID:29934568
Genome Sequences of Shewanella baltica and Shewanella morhuae Strains Isolated from the Gastrointestinal Tract of Freshwater Fish. PMID:29930054
Genomic variation and biogeography of Antarctic haloarchaea. PMID:29925429
Whole genome shotgun sequences of Streptococcus pyogenes causing acute pharyngitis from India. PMID:29900313
Reemergence of human plague in Yunnan, China in 2016. PMID:29897940
Complete genome sequence of uropathogenic Escherichia coli isolate UPEC 26-1. PMID:29892948
Complete genome sequence of the sesame pathogen Ralstonia solanacearum strain SEPPX 05. PMID:29892946
Proteiniphilum saccharofermentans str. M3/6T isolated from a laboratory biogas reactor is versatile in polysaccharide and oligopeptide utilization as deduced from genome-based metabolic reconstructions. PMID:29892569
Genome-based population structure analysis of the strawberry plant pathogen Xanthomonas fragariae reveals two distinct groups that evolved independently before its species description. PMID:29874158
Distinctive characters of Nostoc genomes in cyanolichens. PMID:29866043
Burkholderia cenocepacia Prophages-Prevalence, Chromosome Location and Major Genes Involved. PMID:29857552
Comparative genomic analysis of a naturally competent Elizabethkingia anophelis isolated from an eye infection. PMID:29855598
Draft Genome Sequences of Enterococcus mundtii Strains Isolated from Beef Slaughterhouses in Kenya. PMID:29798926
CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. PMID:29790974
Systematic prediction of genes functionally linked to CRISPR-Cas systems by gene neighborhood analysis. PMID:29784811
Genus-wide comparison of Pseudovibrio bacterial genomes reveal diverse adaptations to different marine invertebrate hosts. PMID:29775460
Complete genome sequence of "Thiodictyon syntrophicum" sp. nov. strain Cad16T, a photolithoautotrophic purple sulfur bacterium isolated from the alpine meromictic Lake Cadagno. PMID:29774086
Bacterial CRISPR Regions: General Features and their Potential for Epidemiological Molecular Typing Studies. PMID:29755603
Microbial Diversity and Toxin Risk in Tropical Freshwater Reservoirs of Cape Verde. PMID:29734762
High quality draft genome sequences of Mycoplasma agassizii strains PS6T and 723 isolated from Gopherus tortoises with upper respiratory tract disease. PMID:29725499
Complete Genome Sequence of Spiroplasma monobiae MQ-1T (ATCC 33825), a Bacterium Isolated from the Vespid Wasp (Monobia quadridens). PMID:29724836
Strategies for high-altitude adaptation revealed from high-quality draft genome of non-violacein producing Janthinobacterium lividum ERGS5:01. PMID:29721151
Peptoniphilus lacydonensis sp. nov., a new human-associated species isolated from a patient with chronic refractory sinusitis. PMID:29707211
Genomic characterization of Nitrospirillum amazonense strain CBAmC, a nitrogen-fixing bacterium isolated from surface-sterilized sugarcane stems. PMID:29696375
Genome comparison of different Zymomonas mobilis strains provides insights on conservation of the evolution. PMID:29694430
Bifidobacteria isolated from vaginal and gut microbiomes are indistinguishable by comparative genomics. PMID:29684056
High quality draft genome sequence of Mycoplasma testudineum strain BH29T, isolated from the respiratory tract of a desert tortoise. PMID:29682170
Complete Genome Sequence of Spiroplasma floricola 23-6T (ATCC 29989), a Bacterium Isolated from a Tulip Tree (Liriodendron tulipifera L.). PMID:29674553
Complete Genome Sequence of Shewanella sp. WE21, a Rare Isolate with Multiple Novel Large Genomic Islands. PMID:29674546
Characterization of Extensively Drug-Resistant or Pandrug-Resistant Sequence Type 147 and 101 OXA-48-Producing Klebsiella pneumoniae Causing Bloodstream Infections in Patients in an Intensive Care Unit. PMID:29661874
Complete Genome Sequence of Streptococcus ruminantium sp. nov. GUT-187T (=DSM 104980T =JCM 31869T), the Type Strain of S. ruminantium, and Comparison with Genome Sequences of Streptococcus suis Strains. PMID:29659811
Pan-Genome Analysis Links the Hereditary Variation of Leptospirillum ferriphilum With Its Evolutionary Adaptation. PMID:29636744
Genome Sequences of Apibacter spp., Gut Symbionts of Asian Honey Bees. PMID:29635372
A Retrospective Review of Microbiological Methods Applied in Studies Following the Deepwater Horizon Oil Spill. PMID:29628913
Applications of CRISPR/Cas System to Bacterial Metabolic Engineering. PMID:29621180
Ten years of surveillance of the Yulong plague focus in China and the molecular typing and source tracing of the isolates. PMID:29601573
Draft Genome Sequence of Bacillus paralicheniformis F47, Isolated from an Algerian Salty Lake. PMID:29599156
Complete Genome Sequence of Microcystis aeruginosa NIES-2481 and Common Genomic Features of Group G M. aeruginosa. PMID:29576807
Incomplete Selective Sweeps of Microcystis Population Detected by the Leader-End CRISPR Fragment Analysis in a Natural Pond. PMID:29568293
Comparative Genomics of Environmental and Clinical Burkholderia cenocepacia Strains Closely Related to the Highly Transmissible Epidemic ET12 Lineage. PMID:29559964
Comparative genomic and metabolic analysis of three Lactobacillus paracasei cheese isolates reveals considerable genomic differences in strains from the same niche. PMID:29554864
Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors. PMID:29551272
Resolving the complete genome of Kuenenia stuttgartiensis from a membrane bioreactor enrichment using Single-Molecule Real-Time sequencing. PMID:29545612
Reconstituting the History of Cronobacter Evolution Driven by Differentiated CRISPR Activity. PMID:29523551
Whole-Genome Sequence of Phage-Resistant Strain Escherichia coli DH5α. PMID:29519826
Complete Genome Sequence of a Ciprofloxacin-Resistant Salmonella enterica subsp. enterica Serovar Kentucky Sequence Type 198 Strain, PU131, Isolated from a Human Patient in Washington State. PMID:29496839
Bacteriophage Interactions with Marine Pathogenic Vibrios: Implications for Phage Therapy. PMID:29495270
Complete genome sequence of Lactobacillus rhamnosus Pen, a probiotic component of a medicine used in prevention of antibiotic-associated diarrhoea in children. PMID:29483943
Pseudomonas orientalis F9: A Potent Antagonist against Phytopathogens with Phytotoxic Effect in the Apple Flower. PMID:29479340
Complete Genome Sequence and Genomic Characterization of Lactobacillus acidophilus LA1 (11869BP). PMID:29472862
Comparative genomic analysis of the multispecies probiotic-marketed product VSL#3. PMID:29451876
Comparative Genomics of Completely Sequenced Lactobacillus helveticus Genomes Provides Insights into Strain-Specific Genes and Resolves Metagenomics Data Down to the Strain Level. PMID:29441050
Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome. PMID:29434576
Comparative genomic analysis reveals the evolution and environmental adaptation strategies of vibrios. PMID:29433445
Comparative genomics reveals new single-nucleotide polymorphisms that can assist in identification of adherent-invasive Escherichia coli. PMID:29426864
Updating the genomic taxonomy and epidemiology of Campylobacter hyointestinalis. PMID:29403020
Genome analysis of Mycoplasma synoviae strain MS-H, the most common M. synoviae strain with a worldwide distribution. PMID:29394882
Genomic Analysis of Two Phylogenetically Distinct Nitrospira Species Reveals Their Genomic Plasticity and Functional Diversity. PMID:29375506
Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains. PMID:29338683
Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential. PMID:29323202
Genome sequence of Acuticoccus yangtzensis JL1095T (DSM 28604T) isolated from the Yangtze Estuary. PMID:29299111
Complete genome sequence of esterase-producing bacterium Croceicoccus marinus E4A9T. PMID:29299108
Genome sequence of the model plant pathogen Pectobacterium carotovorum SCC1. PMID:29276572
Toward Understanding Phage:Host Interactions in the Rumen; Complete Genome Sequences of Lytic Phages Infecting Rumen Bacteria. PMID:29259581
The Emerging Fish Pathogen Flavobacterium spartansii Isolated from Chinook Salmon: Comparative Genome Analysis and Molecular Manipulation. PMID:29250046
First Report of a Whole-Genome Shotgun Sequence of a Clinical Enterococcus faecalis Sequence Type 6 Strain from South Africa. PMID:29242225
Genomic features of "Candidatus Venteria ishoeyi", a new sulfur-oxidizing macrobacterium from the Humboldt Sulfuretum off Chile. PMID:29236755
Draft genome sequence of Bacillus velezensis 2A-2B strain: a rhizospheric inhabitant of Sporobolus airoides (Torr.) Torr., with antifungal activity against root rot causing phytopathogens. PMID:29225729
CRISPR-Cas Systems in Bacteroides fragilis, an Important Pathobiont in the Human Gut Microbiome. PMID:29218031
Genome overview of eight Candida boidinii strains isolated from human activities and wild environments. PMID:29213357
Emergence and Spread of Epidemic Multidrug-Resistant Pseudomonas aeruginosa. PMID:29202180
Draft Genome Sequence of a Clinical Enterococcus faecium Sequence Type 18 Strain from South Africa. PMID:29192087
Genomic Analysis of a Pathogenic Bacterium, Paeniclostridium sordellii CBA7122 Containing the Highest Number of rRNA Operons, Isolated from a Human Stool Sample. PMID:29187822
Generation of Bacteriophage-Insensitive Mutants of Streptococcus thermophilus via an Antisense RNA CRISPR-Cas Silencing Approach. PMID:29180373
Genomic characterization of a local epidemic Pseudomonas aeruginosa reveals specific features of the widespread clone ST395. PMID:29177088
CRISPR-like sequences in Helicobacter pylori and application in genotyping. PMID:29177012
Genomic Comparison of Two Family-Level Groups of the Uncultivated NAG1 Archaeal Lineage from Chemically and Geographically Disparate Hot Springs. PMID:29163388
Sporulation capability and amylosome conservation among diverse human colonic and rumen isolates of the keystone starch-degrader Ruminococcus bromii. PMID:29159997
Prevailing clone (ST69) of Vibrio cholerae O139 in India over 10 years. PMID:29142593
New eight genes identified at the clinical multidrug-resistant Acinetobacter baumannii DMS06669 strain in a Vietnam hospital. PMID:29137647
Benefits of Genomic Insights and CRISPR-Cas Signatures to Monitor Potential Pathogens across Drinking Water Production and Distribution Systems. PMID:29097994
Analysis of the CRISPR-Cas system in bacteriophages active on epidemic strains of Vibrio cholerae in Bangladesh. PMID:29093571
Genomic Analysis of Bacillus licheniformis CBA7126 Isolated from a Human Fecal Sample. PMID:29081747
Genome Sequence of Geobacillus stearothermophilus DSM 458, an Antimicrobial-Producing Thermophilic Bacterium, Isolated from a Sugar Beet Factory. PMID:29074660
Complete Genome Sequence and Comparative Analysis of Staphylococcus condimenti DSM 11674, a Potential Starter Culture Isolated from Soy Sauce Mash. PMID:29057223
Pathogenicity of Human ST23 Streptococcus agalactiae to Fish and Genomic Comparison of Pathogenic and Non-pathogenic Isolates. PMID:29056932
The Enigmatic Genome of an Obligate Ancient Spiroplasma Symbiont in a Hadal Holothurian. PMID:29054873
Genomic Analysis of Bacillus sp. Strain B25, a Biocontrol Agent of Maize Pathogen Fusarium verticillioides. PMID:29051980
Draft Genome Sequence of a Novel Chitinophaga sp. Strain, MD30, Isolated from a Biofilm in an Air Conditioner Condensate Pipe. PMID:29051259
Complete genome sequence of Thermotoga sp. strain RQ7. PMID:29046741
Draft genome sequence and characterization of commensal Escherichia coli strain BG1 isolated from bovine gastro-intestinal tract. PMID:29046740
De novo assembly of genomes from long sequence reads reveals uncharted territories of Propionibacterium freudenreichii. PMID:29037147
DNA-Sequence Based Typing of the Cronobacter Genus Using MLST, CRISPR-cas Array and Capsular Profiling. PMID:29033918
Characterization and Exploitation of CRISPR Loci in Bifidobacterium longum. PMID:29033911
Diversity and microevolution of CRISPR loci in Helicobacter cinaedi. PMID:29028814
Whole genome shotgun sequencing of Indian strains of Streptococcus agalactiae. PMID:29021957
Population-Genomic Insights into Variation in Prevotella intermedia and Prevotella nigrescens Isolates and Its Association with Periodontal Disease. PMID:28983469
Glimpse into the genome sequence of a multidrug-resistant Acinetobacter pittii ST950 clinical isolate carrying the blaOXA-72 and blaOXA-533 genes in China. PMID:28954001
Safety Assessment of Lactobacillus helveticus KLDS1.8701 Based on Whole Genome Sequencing and Oral Toxicity Studies. PMID:28946645
Restriction-modification mediated barriers to exogenous DNA uptake and incorporation employed by Prevotella intermedia. PMID:28934361
The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes. PMID:28928211
Complete Genome Sequence of Spiroplasma corruscae EC-1T (DSM 19793), a Bacterium Isolated from a Lampyrid Beetle (Ellychnia corrusca). PMID:28912320
MetaCRAST: reference-guided extraction of CRISPR spacers from unassembled metagenomes. PMID:28894651
Genome sequence of the sulfur-oxidizing Bathymodiolus thermophilus gill endosymbiont. PMID:28878861
Draft genome sequences of two opportunistic pathogenic strains of Staphylococcus cohnii isolated from human patients. PMID:28878860
CRISPR-Cas Systems Features and the Gene-Reservoir Role of Coagulase-Negative Staphylococci. PMID:28861060
Genomic, Physiologic, and Symbiotic Characterization of Serratia marcescens Strains Isolated from the Mosquito Anopheles stephensi. PMID:28861046
Whole-Genome Sequence of the Anaerobic Isosaccharinic Acid Degrading Isolate, Macellibacteroides fermentans Strain HH-ZS. PMID:28859355
Comparative Genomic Analysis Identifies a Campylobacter Clade Deficient in Selenium Metabolism. PMID:28854596
Complete Genome Sequence of the Yogurt Isolate Lactobacillus delbrueckii subsp. bulgaricus ACA-DC 87. PMID:28839034
In silico analysis of protein toxin and bacteriocins from Lactobacillus paracasei SD1 genome and available online databases. PMID:28837656
Comparative Genomic and Regulatory Analyses of Natamycin Production of Streptomyces lydicus A02. PMID:28831190
Draft Genome Sequence of Chilean Antarctic Pseudomonas sp. Strain K2I15. PMID:28818894
Comparative Genome Analysis of Rathayibacter tritici NCPPB 1953 with Rathayibacter toxicus Strains Can Facilitate Studies on Mechanisms of Nematode Association and Host Infection. PMID:28811754
Recruitment of CRISPR-Cas systems by Tn7-like transposons. PMID:28811374
Genomic Analysis of the Evolution of Phototrophy among Haloalkaliphilic Rhodobacterales. PMID:28810712
Microbial Community Structure and the Persistence of Cyanobacterial Populations in Salt Crusts of the Hyperarid Atacama Desert from Genome-Resolved Metagenomics. PMID:28804480
Comparative pathogenomics of Clostridium tetani. PMID:28800585
Genomic insights into the pathogenicity and environmental adaptability of Enterococcus hirae R17 isolated from pork offered for retail sale. PMID:28799224
Complete Genome Analysis of Thermus parvatiensis and Comparative Genomics of Thermus spp. Provide Insights into Genetic Variability and Evolution of Natural Competence as Strategic Survival Attributes. PMID:28798737
Whole genome sequence of two Rathayibacter toxicus strains reveals a tunicamycin biosynthetic cluster similar to Streptomyces chartreusis. PMID:28796837
Comparative Analysis of the Flavobacterium columnare Genomovar I and II Genomes. PMID:28790987
Emergence of a Streptococcus dysgalactiae subspecies equisimilis stG62647-lineage associated with severe clinical manifestations. PMID:28790435
Functional analysis of the first complete genome sequence of a multidrug resistant sequence type 2 Staphylococcus epidermidis. PMID:28785416
Complete genome sequence of the sand-sediment actinobacterium Nocardioides dokdonensis FR1436T. PMID:28770029
First draft genome sequence of a strain from the genus Fusibacter isolated from Salar de Ascotán in Northern Chile. PMID:28770028
The genome of the cotton bacterial blight pathogen Xanthomonas citri pv. malvacearum strain MSCT1. PMID:28770027
Neisseria lactamica Y92-1009 complete genome sequence. PMID:28770026
Complete genome sequence of a commensal bacterium, Hafnia alvei CBA7124, isolated from human feces. PMID:28770009
Draft Genome Sequence of Enterococcus faecalis DD14, a Bacteriocinogenic Lactic Acid Bacterium with Anti-Clostridium Activity. PMID:28751398
Genome Sequence of Zymomonas mobilis subsp. mobilis NRRL B-1960. PMID:28751381
Complete Genome Sequence of Mycoplasma capricolum subsp. capripneumoniae Strain zly1309F, Isolated from Endangered Tibetan Antelope. PMID:28729256
Molecular Characterization of Corynebacterium diphtheriae Outbreak Isolates, South Africa, March-June 2015. PMID:28726616
Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium. PMID:28706512
Complete genome sequence of the Bifidobacterium animalis subspecies lactis BL3, preventive probiotics for acute colitis and colon cancer. PMID:28702200
Complete Genome Sequence and Comparative Genomics of a Streptococcus pyogenes emm3 Strain M3-b isolated from a Japanese Patient with Streptococcal Toxic Shock Syndrome. PMID:28698738
Draft Genome Sequence of a Virulent Strain of Pasteurella Multocida Isolated From Alpaca. PMID:28698737
On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires. PMID:28698278
Whole Genome Sequencing of Mycobacterium tuberculosis Isolates From Extrapulmonary Sites. PMID:28692415
Genomic and transcriptomic analyses of Agrobacterium tumefaciens S33 reveal the molecular mechanism of a novel hybrid nicotine-degrading pathway. PMID:28684751
Draft Genome Sequence of Staphylococcus epidermidis (Winslow and Winslow) Evans (ATCC 14990). PMID:28684584
Draft Genome Sequences of Two ATCC Staphylococcus aureus subsp. aureus Strains. PMID:28684583
Draft Genome Sequence of Micrococcus luteus (Schroeter) Cohn (ATCC 12698). PMID:28684577
Draft Genome Sequence of Enterococcus faecalis ATCC BAA-2128. PMID:28684576
Draft Genome Sequence of Escherichia coli K-12 (ATCC 29425). PMID:28684575
Draft Genome Sequence of Escherichia coli K-12 (ATCC 10798). PMID:28684574
Clostridium chauvoei, an Evolutionary Dead-End Pathogen. PMID:28649238
Comparative Genomics of All Three Campylobacter sputorum Biovars and a Novel Cattle-Associated C. sputorum Clade. PMID:28633450
Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum YT. PMID:28623373
Genome Sequencing of Ralstonia solanacearum CQPS-1, a Phylotype I Strain Collected from a Highland Area with Continuous Cropping of Tobacco. PMID:28620361
Genome Mining and Predictive Functional Profiling of Acidophilic Rhizobacterium Pseudomonas fluorescens Pt14. PMID:28611492
Genomic and transcriptomic analyses reveal distinct biological functions for cold shock proteins (VpaCspA and VpaCspD) in Vibrio parahaemolyticus CHN25 during low-temperature survival. PMID:28583064
Genomic and transcriptomic analyses reveal adaptation mechanisms of an Acidithiobacillus ferrivorans strain YL15 to alpine acid mine drainage. PMID:28542527
Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain. PMID:28537263
Differentiation and Structure in Sulfolobus islandicus Rod-Shaped Virus Populations. PMID:28534836
Stumbling across the Same Phage: Comparative Genomics of Widespread Temperate Phages Infecting the Fish Pathogen Vibrio anguillarum. PMID:28531104
Comparative genomic analysis reveals the environmental impacts on two Arcticibacter strains including sixteen Sphingobacteriaceae species. PMID:28515455
Genome sequence of Shigella flexneri strain SP1, a diarrheal isolate that encodes an extended-spectrum β-lactamase (ESBL). PMID:28499446
Chromosomal features of Escherichia coli serotype O2:K2, an avian pathogenic E. coli. PMID:28496941
Comparative Genomics and Transcriptional Analysis of Flavobacterium columnare Strain ATCC 49512. PMID:28469601
CRISPR-Cpf1 assisted genome editing of Corynebacterium glutamicum. PMID:28469274
microTaboo: a general and practical solution to the k-disjoint problem. PMID:28464826
CRF: detection of CRISPR arrays using random forest. PMID:28462029
Pacmanvirus, a New Giant Icosahedral Virus at the Crossroads between Asfarviridae and Faustoviruses. PMID:28446673
Genome Sequencing Reveals the Complex Polysaccharide-Degrading Ability of Novel Deep-Sea Bacterium Flammeovirga pacifica WPAGA1. PMID:28443080
Emergence and Evolution of Multidrug-Resistant Klebsiella pneumoniae with both blaKPC and blaCTX-M Integrated in the Chromosome. PMID:28438939
Disruption of tetR type regulator adeN by mobile genetic element confers elevated virulence in Acinetobacter baumannii. PMID:28436748
Pan genome and CRISPR analyses of the bacterial fish pathogen Moritella viscosa. PMID:28427330
Genomic analyses of the ancestral Manila family of Mycobacterium tuberculosis. PMID:28394899
Draft Genome Sequences of Six Strains of Streptococcus pneumoniae from Serotypes 5, 6A, 6B, 18C, 19A, and 23F. PMID:28385844
Genome Sequences of Two Naphthalene-Degrading Strains of Pseudomonas balearica, Isolated from Polluted Marine Sediment and from an Oil Refinery Site. PMID:28385841
Unravelling the Complete Genome of Archangium gephyra DSM 2261T and Evolutionary Insights into Myxobacterial Chitinases. PMID:28379546
A Locus Encoding Variable Defense Systems against Invading DNA Identified in Streptococcus suis. PMID:28379509
Draft Genome Sequence of the Murine Bacterial Isolate Lactobacillus murinus EF-1. PMID:28336601
Distribution of antimicrobial resistance determinants, virulence-associated factors and clustered regularly interspaced palindromic repeats loci in isolates of Enterococcus faecalis from various settings and genetic lineages. PMID:28334141
Complete genome sequence of Pseudomonas citronellolis P3B5, a candidate for microbial phyllo-remediation of hydrocarbon-contaminated sites. PMID:28300228
Comparative genome analyses of mycobacteria give better insights into their evolution. PMID:28291784
Whole-Genome Shotgun Sequencing of Cephalosporin-Resistant Salmonella enterica Serovar Typhi. PMID:28280021
Complete Genome Sequence of Spiroplasma sp. NBRC 100390. PMID:28280009
Comparative genomics of Enterococcus spp. isolated from bovine feces. PMID:28270110
Genome Sequence of Desulfurella amilsii Strain TR1 and Comparative Genomics of Desulfurellaceae Family. PMID:28265263
CRISPR-Cas and Contact-Dependent Secretion Systems Present on Excisable Pathogenicity Islands with Conserved Recombination Modules. PMID:28264992
Genomic analysis of a Streptococcus pyogenes strain causing endocarditis in a child. PMID:28239478
Comparative pan genome analysis of oral Prevotella species implicated in periodontitis. PMID:28236274
Draft Genome Sequences of Dermacoccus nishinomiyaensis Strains UCD-KPL2534 and UCD-KPL2528 Isolated from an Indoor Track Facility. PMID:28232444
Genome Sequence of Rhodoferax antarcticus ANT.BRT; A Psychrophilic Purple Nonsulfur Bacterium from an Antarctic Microbial Mat. PMID:28230808
Genome sequence of three Psychrobacter sp. strains with potential applications in bioremediation. PMID:28229046
Genomic Characterization of Dairy Associated Leuconostoc Species and Diversity of Leuconostocs in Undefined Mixed Mesophilic Starter Cultures. PMID:28217118
Non-classical phase diagram for virus bacterial coevolution mediated by clustered regularly interspaced short palindromic repeats. PMID:28202591
Comparative Genomic Analysis of Two Vibrio toranzoniae Strains with Different Virulence Capacity Reveals Clues on Its Pathogenicity for Fish. PMID:28194141
Database of Periodic DNA Regions in Major Genomes. PMID:28182099
Not all predicted CRISPR-Cas systems are equal: isolated cas genes and classes of CRISPR like elements. PMID:28166719
The complete genome sequence of the yogurt isolate Streptococcus thermophilus ACA-DC 2. PMID:28163827
Draft genome sequence of Lactobacillus plantarum strains E2C2 and E2C5 isolated from human stool culture. PMID:28163824
Genome Sequence of Lactobacillus paracasei Strain LC-Ikematsu, Isolated from a Pineapple in Okinawa, Japan. PMID:28153910
Genome sequence of a high agarase-producing strain Flammeovirga sp. SJP92. PMID:28138357
Genome features of moderately halophilic polyhydroxyalkanoate-producing Yangia sp. CCB-MM3. PMID:28138356
Diversity and evolution of class 2 CRISPR-Cas systems. PMID:28111461
Comprehensive analysis of draft genomes of two closely related pseudomonas syringae phylogroup 2b strains infecting mono- and dicotyledon host plants. PMID:28105943
Mosaic structure of Mycobacterium bovis BCG genomes as a representation of phage sequences' mobility. PMID:28105923
Staphylococcus aureus CC395 harbours a novel composite staphylococcal cassette chromosome mec element. PMID:28088766
Population genomic insights into variation and evolution of Xanthomonas oryzae pv. oryzae. PMID:28084432
Complete Genome Sequence of Spiroplasma sp. TU-14. PMID:28082500
Whole-Genome Sequence of Streptococcus parauberis Strain SP-llh, Isolated from Cows with Mastitis in Western China. PMID:28082485
Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates. PMID:28073918
Comparative Genomic Analysis of Two Serotype 1/2b Listeria monocytogenes Isolates from Analogous Environmental Niches Demonstrates the Influence of Hypervariable Hotspots in Defining Pathogenesis. PMID:28066772
Comparative Genomics of the Listeria monocytogenes ST204 Subgroup. PMID:28066377
The Complete Genome Sequence of Hyperthermophile Dictyoglomus turgidum DSM 6724™ Reveals a Specialized Carbohydrate Fermentor. PMID:28066333
The driving force of prophages and CRISPR-Cas system in the evolution of Cronobacter sakazakii. PMID:28057934
Networking in microbes: conjugative elements and plasmids in the genus Alteromonas. PMID:28056800
Inhibition of CRISPR-Cas9 with Bacteriophage Proteins. PMID:28041849
Draft genome sequence of a multidrug-resistant beta-lactamase OXA-357-producing Acinetobacter pittii ST865 clinical isolate from China. PMID:28034597
New CRISPR-Cas systems from uncultivated microbes. PMID:28005056
Genome sequence and overview of Oligoflexus tunisiensis Shr3T in the eighth class Oligoflexia of the phylum Proteobacteria. PMID:27999625
Draft Genome Sequences of Type Strains Bacillus drentensis DSM 15600T and Bacillus novalis DSM 15603T. PMID:27979958
Complete Genome Sequence of Trueperella pyogenes, Isolated from Infected Farmland Goats. PMID:27979957
Draft Genome Sequence of Cloacibacterium normanense NRS-1 Isolated from Municipal Wastewater. PMID:27979947
The genome of Rhizobiales bacteria in predatory ants reveals urease gene functions but no genes for nitrogen fixation. PMID:27976703
Genome Sequencing of Sulfolobus sp. A20 from Costa Rica and Comparative Analyses of the Putative Pathways of Carbon, Nitrogen, and Sulfur Metabolism in Various Sulfolobus Strains. PMID:27965637
Use of single molecule sequencing for comparative genomics of an environmental and a clinical isolate of Clostridium difficile ribotype 078. PMID:27964731
Genome Sequence of the Fish Pathogen Yersinia ruckeri Strain 150, Isolated from Diseased Rainbow Trout. PMID:27908991
Draft Genome Sequence of a Urinary Isolate of Lactobacillus crispatus. PMID:27908986
Complete Genome Sequence of Clostridium estertheticum DSM 8809, a Microbe Identified in Spoiled Vacuum Packed Beef. PMID:27891116
Draft Genome Sequence of Salmonella enterica subsp. diarizonae Serovar 61:k:1,5,(7) Strain CRJJGF_00165 (Phylum Gammaproteobacteria). PMID:27881547
An Enrichment of CRISPR and Other Defense-Related Features in Marine Sponge-Associated Microbial Metagenomes. PMID:27877161
Draft Genome Sequence for a Urinary Isolate of Nosocomiicoccus ampullae. PMID:27856579
Two Novel Myoviruses from the North of Iraq Reveal Insights into Clostridium difficile Phage Diversity and Biology. PMID:27854339
Whole-Genome Sequence Analysis of Bombella intestini LMG 28161T, a Novel Acetic Acid Bacterium Isolated from the Crop of a Red-Tailed Bumble Bee, Bombus lapidarius. PMID:27851750
A genomic island in Vibrio cholerae with VPI-1 site-specific recombination characteristics contains CRISPR-Cas and type VI secretion modules. PMID:27845364
Genomic Analysis of Phylotype I Strain EP1 Reveals Substantial Divergence from Other Strains in the Ralstonia solanacearum Species Complex. PMID:27833603
Cedratvirus, a Double-Cork Structured Giant Virus, is a Distant Relative of Pithoviruses. PMID:27827884
Deciphering the virulence factors of the opportunistic pathogen Mycobacterium colombiense. PMID:27818776
Genome of 'Ca. Desulfovibrio trichonymphae', an H2-oxidizing bacterium in a tripartite symbiotic system within a protist cell in the termite gut. PMID:27801909
Complete Genome Sequence of Spiroplasma helicoides TABS-2T (DSM 22551), a Bacterium Isolated from a Horsefly (Tabanus abactor). PMID:27795290
Draft Genome Sequence of Extremely Drug-Resistant Pseudomonas aeruginosa (ST357) Strain CMC_VB_PA_B22862 Isolated from a Community-Acquired Bloodstream Infection. PMID:27795257
Draft Genome Sequence of Curtobacterium sp. Strain UCD-KPL2560 (Phylum Actinobacteria). PMID:27795241
Genome sequences and annotation of two urinary isolates of E. coli. PMID:27777649
A genomic view of food-related and probiotic Enterococcus strains. PMID:27773878
Altered stoichiometry Escherichia coli Cascade complexes with shortened CRISPR RNA spacers are capable of interference and primed adaptation. PMID:27738137
Whole genome shotgun sequence of Bacillus amyloliquefaciens TF28, a biocontrol entophytic bacterium. PMID:27688836
Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Orion Strain CRJJGF_00093 (Phylum Gammaproteobacteria). PMID:27688320
Complete Genome Sequence of Gordonia terrae 3612. PMID:27688316
Comparative Genome Analysis of the Daptomycin-Resistant Streptococcus anginosus Strain J4206 Associated with Breakthrough Bacteremia. PMID:27678123
Complete Genome Sequence of Spiroplasma turonicum Tab4cT, a Bacterium Isolated from Horse Flies (Haematopota sp.). PMID:27660788
The complete genome sequences of sulfur-oxidizing Gammaproteobacteria Sulfurifustis variabilis skN76(T) and Sulfuricaulis limicola HA5(T). PMID:27651857
Genome-directed analysis of prophage excision, host defence systems, and central fermentative metabolism in Clostridium pasteurianum. PMID:27641836
Comparison of Intracellular "Ca. Endomicrobium Trichonymphae" Genomovars Illuminates the Requirement and Decay of Defense Systems against Foreign DNA. PMID:27635050
Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Bardo Strain CRJJGF_00099 (Phylum Gammaproteobacteria). PMID:27634995
Dynamics of genome change among Legionella species. PMID:27633769
The Complete Genome Sequence of the Nicotine-Degrading Bacterium Shinella sp. HZN7. PMID:27625640
Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers. PMID:27611571
Draft genome sequence of Lampropedia cohaerens strain CT6(T) isolated from arsenic rich microbial mats of a Himalayan hot water spring. PMID:27610214
Draft genome sequence of Enterococcus faecium strain LMG 8148. PMID:27610213
Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Blockley Strain CRJJGF_00147 (Phylum Gammaproteobacteria). PMID:27609923
Comparative Genomics of Campylobacter iguaniorum to Unravel Genetic Regions Associated with Reptilian Hosts. PMID:27604878
CRISPRdigger: detecting CRISPRs with better direct repeat annotations. PMID:27596864
Draft genome sequence of Acinetobacter baumannii strain NCTC 13423, a multidrug-resistant clinical isolate. PMID:27594976
Complete Genome Sequence of Mycobacterium avium, Isolated from Commercial Domestic Pekin Ducks (Anas platyrhynchos domestica), Determined Using PacBio Single-Molecule Real-Time Technology. PMID:27587804
Anti-cas spacers in orphan CRISPR4 arrays prevent uptake of active CRISPR-Cas I-F systems. PMID:27573106
Global occurrence and heterogeneity of the Roseobacter-clade species Ruegeria mobilis. PMID:27552638
CRISPR System Acquisition and Evolution of an Obligate Intracellular Chlamydia-Related Bacterium. PMID:27516530
Complete Genome Sequence of Serratia marcescens U36365, a Green Pigment-Producing Strain Isolated from a Patient with Urinary Tract Infection. PMID:27516523
Evolution and Diversity of Listeria monocytogenes from Clinical and Food Samples in Shanghai, China. PMID:27499751
Comparative evaluation of the genomes of three common Drosophila-associated bacteria. PMID:27493201
Lactobacillus oligofermentans glucose, ribose and xylose transcriptomes show higher similarity between glucose and xylose catabolism-induced responses in the early exponential growth phase. PMID:27487841
Comparative genomic analysis of Lactobacillus plantarum ZJ316 reveals its genetic adaptation and potential probiotic profiles. PMID:27487802
Genome sequence of OXA-23 producing Acinetobacter baumannii IHIT7853, a carbapenem-resistant strain from a cat belonging to international clone IC1. PMID:27471549
Complete Genome Sequence of Moraxella osloensis Strain KMC41, a Producer of 4-Methyl-3-Hexenoic Acid, a Major Malodor Compound in Laundry. PMID:27445387
Genome Sequence of the Uncommon Streptococcus pyogenes M/emm66 Strain STAB13021, Isolated from Clonal Clustered Cases in French Brittany. PMID:27445380
Complete Genome Sequence of Highly Virulent Haemophilus parasuis Serotype 11 Strain SC1401. PMID:27445368
Draft Genome Sequence of an Enterococcus thailandicus Strain Isolated from Bovine Feces. PMID:27445365
Genome-sequence analysis of Acinetobacter johnsonii MB44 reveals potential nematode-virulent factors. PMID:27429894
Draft Genome Sequence of the Bacteriocinogenic Strain Enterococcus faecalis DBH18, Isolated from Mallard Ducks (Anas platyrhynchos). PMID:27417838
Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Widemarsh Strain CRJJGF_00058 (Phylum Gammaproteobacteria). PMID:27417830
Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Lille Strain CRJJGF_000101 (Phylum Gammaproteobacteria). PMID:27417829
A computational strategy for the search of regulatory small RNAs in Actinobacillus pleuropneumoniae. PMID:27402897
A Broad Overview and Review of CRISPR-Cas Technology and Stem Cells. PMID:27398291
Speciation and ecological success in dimly lit waters: horizontal gene transfer in a green sulfur bacteria bloom unveiled by metagenomic assembly. PMID:27392085
Reannotation of Yersinia pestis Strain 91001 Based on Omics Data. PMID:27382076
Comparative Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) of Streptococcus thermophilus St-I and its Bacteriophage-Insensitive Mutants (BIM) Derivatives. PMID:27378131
Complete Genome of the Starch-Degrading Myxobacteria Sandaracinus amylolyticus DSM 53668T. PMID:27358428
Comparative genomics analysis of the companion mechanisms of Bacillus thuringiensis Bc601 and Bacillus endophyticus Hbe603 in bacterial consortium. PMID:27353048
Draft Genome Sequence of Bacillus simplex DSM 1321 for Setting Up Phylogenomics in Genomic Taxonomy of the Bacillus-Like Bacteria. PMID:27340061
Comparative Genomics of Campylobacter fetus from Reptiles and Mammals Reveals Divergent Evolution in Host-Associated Lineages. PMID:27333878
Isolation and complete genome sequencing of Mimivirus bombay, a Giant Virus in sewage of Mumbai, India. PMID:27330993
Whole genomic DNA sequencing and comparative genomic analysis of Arthrospira platensis: high genome plasticity and genetic diversity. PMID:27330141
Genome Editing by CRISPR/Cas9: A Game Change in the Genetic Manipulation of Protists. PMID:27315329
Draft Genome Sequence of Bacillus mesonae FJAT-13985T (=DSM 25968T) for Setting Up Phylogenomics in Genomic Taxonomy of the Bacillus-Like Bacteria. PMID:27313309
Whole-Genome Sequencing Analysis of Methicillin-Resistant Staphylococcus simulans Causing Surgical Site Infection. PMID:27313298
Draft Genome Sequence of Moraxella catarrhalis Type Strain CCUG 353T. PMID:27313296
Draft Genome Sequence of a Copper-Resistant Marine Bacterium, Pantoea agglomerans Strain LMAE-2, a Bacterial Strain with Potential Use in Bioremediation. PMID:27313292
Complete Genome Sequence of a New Megavirus Family Member Isolated from an Inland Water Lake for the First Time in India. PMID:27313286
Viruses Infecting a Freshwater Filamentous Cyanobacterium (Nostoc sp.) Encode a Functional CRISPR Array and a Proteobacterial DNA Polymerase B. PMID:27302758
Comparing polysaccharide decomposition between the type strains Gramella echinicola KMM 6050(T) (DSM 19838(T)) and Gramella portivictoriae UST040801-001(T) (DSM 23547(T)), and emended description of Gramella echinicola Nedashkovskaya et al. 2005 emend. Shahina et al. 2014 and Gramella portivictoriae Lau et al. 2005. PMID:27274783
Complete genome sequence of Leuconostoc gelidum subsp. gasicomitatum KG16-1, isolated from vacuum-packaged vegetable sausages. PMID:27274361
RepeatAnalyzer: a tool for analysing and managing short-sequence repeat data. PMID:27260942
Complete Genomes of Bacillus coagulans S-lac and Bacillus subtilis TO-A JPC, Two Phylogenetically Distinct Probiotics. PMID:27258038
First Draft Genome Sequence of Staphylococcus condimenti F-2T. PMID:27257207
Peeping into genomic architecture by re-sequencing of Ochrobactrum intermedium M86 strain during laboratory adapted conditions. PMID:27222803
A Comprehensive Curation Shows the Dynamic Evolutionary Patterns of Prokaryotic CRISPRs. PMID:27195295
CRISPRDetect: A flexible algorithm to define CRISPR arrays. PMID:27184979
Complete genome sequence of 'Halanaeroarchaeum sulfurireducens' M27-SA2, a sulfur-reducing and acetate-oxidizing haloarchaeon from the deep-sea hypersaline anoxic lake Medee. PMID:27182430
Complete genome sequence of an agr-dysfunctional variant of the ST239 lineage of the methicillin-resistant Staphylococcus aureus strain GV69 from Brazil. PMID:27152133
Draft Genome Sequence of Bacillus clausii UBBC07, a Spore-Forming Probiotic Strain. PMID:27103711
Genome Sequence of Salegentibacter mishustinae KCTC 12263, Containing a Complete Subtype I-B CRISPR-Cas System. PMID:27081136
Comparative Genome Analysis Provides Insights into the Pathogenicity of Flavobacterium psychrophilum. PMID:27071075
A barrier to homologous recombination between sympatric strains of the cooperative soil bacterium Myxococcus xanthus. PMID:27046334
Comparative Genomic Analysis Reveals a Possible Novel Non-Tuberculous Mycobacterium Species with High Pathogenic Potential. PMID:27035710
Genetic and life-history traits associated with the distribution of prophages in bacteria. PMID:27015004
Genomic Insight into the Host-Endosymbiont Relationship of Endozoicomonas montiporae CL-33(T) with its Coral Host. PMID:27014194
Draft Genome Sequence of Streptococcus gordonii Type Strain CCUG 33482T. PMID:27013051
Complete Genome Sequence of Arthrobacter sp. ATCC 21022, a Host for Bacteriophage Discovery. PMID:27013048
Draft Genome Sequence of the Bacteriocin-Producing Strain Enterococcus faecium M3K31, Isolated from Griffon Vultures (Gyps fulvus subsp. fulvus). PMID:27013035
Comparative Screening of Digestion Tract Toxic Genes in Proteus mirabilis. PMID:27010388
Horizontal Gene Acquisitions, Mobile Element Proliferation, and Genome Decay in the Host-Restricted Plant Pathogen Erwinia Tracheiphila. PMID:26992913
Complete Genome Sequence of emm28 Type Streptococcus pyogenes MEW123, a Streptomycin-Resistant Derivative of a Clinical Throat Isolate Suitable for Investigation of Pathogenesis. PMID:26988051
Complete Genome Sequence of emm4 Streptococcus pyogenes MEW427, a Throat Isolate from a Child Meeting Clinical Criteria for Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcus (PANDAS). PMID:26988046
Draft genome of Leisingera aquaemixtae CECT 8399(T), a member of the Roseobacter clade isolated from a junction of fresh and ocean water in Jeju Island, South Korea. PMID:26981415
Global MLST of Salmonella Typhi Revisited in Post-genomic Era: Genetic Conservation, Population Structure, and Comparative Genomics of Rare Sequence Types. PMID:26973639
Genome Analysis of Listeria monocytogenes Sequence Type 8 Strains Persisting in Salmon and Poultry Processing Environments and Comparison with Related Strains. PMID:26953695
Draft genome sequences of Pantoea agglomerans and Pantoea vagans isolates associated with termites. PMID:26937267
Evolution of Chromosomal Clostridium botulinum Type E Neurotoxin Gene Clusters: Evidence Provided by Their Rare Plasmid-Borne Counterparts. PMID:26936890
Active and adaptive Legionella CRISPR-Cas reveals a recurrent challenge to the pathogen. PMID:26936325
Genome analysis of Listeria ivanovii strain G770 that caused a deadly aortic prosthesis infection. PMID:26933501
Draft genomic sequence of Nereida ignava CECT 5292(T), a marine bacterium of the family Rhodobacteraceae. PMID:26929790
Genome sequence of Escherichia coli NCCP15653, a group D strain isolated from a diarrhea patient. PMID:26913081
Draft Genome Sequence of Acinetobacter johnsonii MB44, Exhibiting Nematicidal Activity against Caenorhabditis elegans. PMID:26893438
Draft Genome Sequence of "Candidatus Methanomethylophilus" sp. 1R26, Enriched from Bovine Rumen, a Methanogenic Archaeon Belonging to the Methanomassiliicoccales Order. PMID:26893425
Draft Genome Sequence of Desulfitobacterium hafniense Strain DH, a Sulfate-Reducing Bacterium Isolated from Paddy Soils. PMID:26868389
Genomic analysis of the nitrate-respiring Sphingopyxis granuli (formerly Sphingomonas macrogoltabida) strain TFA. PMID:26847793
Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems. PMID:26837824
Draft Genome Sequence of Pannonibacter phragmitetus Strain CGMCC9175, a Halotolerant Polycyclic Aromatic Hydrocarbon-Degrading Bacterium. PMID:26823598
Complete Genome Sequence of the Exopolysaccharide-Producing Burkholderia caribensis Type Strain MWAP64. PMID:26823586
The Complete Genome Sequence of the Murine Pathobiont Helicobacter typhlonius. PMID:26779178
Acidianus Tailed Spindle Virus: a New Archaeal Large Tailed Spindle Virus Discovered by Culture-Independent Methods. PMID:26763997
Nuclease Target Site Selection for Maximizing On-target Activity and Minimizing Off-target Effects in Genome Editing. PMID:26750397
A quick guide to CRISPR sgRNA design tools. PMID:26745836
Complete Genome Sequence of Streptomyces sp. Strain CCM_MD2014, Isolated from Topsoil in Woods Hole, Massachusetts. PMID:26722012
Complete Genome Sequence of Curtobacterium sp. Strain MR_MD2014, Isolated from Topsoil in Woods Hole, Massachusetts. PMID:26722011
Clustered Regularly Interspaced Short Palindromic Repeats Are emm Type-Specific in Highly Prevalent Group A Streptococci. PMID:26710228
Exploring the genomic traits of fungus-feeding bacterial genus Collimonas. PMID:26704531
SMRT sequencing of the Campylobacter coli BfR-CA-9557 genome sequence reveals unique methylation motifs. PMID:26689587
Complete Genome Sequence of Streptococcus anginosus J4211, a Clinical Isolate. PMID:26679576
Complete genome sequence of and proposal of Thermofilum uzonense sp. nov. a novel hyperthermophilic crenarchaeon and emended description of the genus Thermofilum. PMID:26664700
Draft genome sequence of Halopiger salifodinae KCY07-B2(T), an extremly halophilic archaeon isolated from a salt mine. PMID:26664653
Computational approaches to predict bacteriophage-host relationships. PMID:26657537
A New N-Acyl Homoserine Lactone Synthase in an Uncultured Symbiont of the Red Sea Sponge Theonella swinhoei. PMID:26655754
Draft genome of Gemmata massiliana sp. nov, a water-borne Planctomycetes species exhibiting two variants. PMID:26649148
Complete genome sequence and characterization of the haloacid-degrading Burkholderia caribensis MBA4. PMID:26629309
The pan-genome of Lactobacillus reuteri strains originating from the pig gastrointestinal tract. PMID:26626322
Whole genome sequencing provides possible explanations for the difference in phage susceptibility among two Salmonella Typhimurium phage types (DT8 and DT30) associated with a single foodborne outbreak. PMID:26613761
Genome Analysis of Staphylococcus agnetis, an Agent of Lameness in Broiler Chickens. PMID:26606420
Draft genome sequence of Janthinobacterium lividum strain MTR reveals its mechanism of capnophilic behavior. PMID:26605004
Incidence of Type II CRISPR1-Cas Systems in Enterococcus Is Species-Dependent. PMID:26600384
Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems. PMID:26593719
Complete genome sequence of Bacillus cereus FORC_005, a food-borne pathogen from the soy sauce braised fish-cake with quail-egg. PMID:26566422
Draft Genome Sequence of Porphyromonas gingivalis Strain Ando Expressing a 53-Kilodalton-Type Fimbrilin Variant of Mfa1 Fimbriae. PMID:26543123
Comparative genome analysis identifies two large deletions in the genome of highly-passaged attenuated Streptococcus agalactiae strain YM001 compared to the parental pathogenic strain HN016. PMID:26537657
A newly discovered Bordetella species carries a transcriptionally active CRISPR-Cas with a small Cas9 endonuclease. PMID:26502932
Genome Sequence of Flavobacterium akiainvivens IK-1T, Isolated from Decaying Wikstroemia oahuensis, an Endemic Hawaiian Shrub. PMID:26494668
Draft genome sequence of Mesotoga strain PhosAC3, a mesophilic member of the bacterial order Thermotogales, isolated from a digestor treating phosphogypsum in Tunisia. PMID:26464750
Comparative genome analysis of the candidate functional starter culture strains Lactobacillus fermentum 222 and Lactobacillus plantarum 80 for controlled cocoa bean fermentation processes. PMID:26459565
The bacterial pangenome as a new tool for analysing pathogenic bacteria. PMID:26442149
Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. PMID:26422227
Genome sequence of Anoxybacillus ayderensis AB04(T) isolated from the Ayder hot spring in Turkey. PMID:26413199
Complete Genome Sequence of Bifidobacterium actinocoloniiforme Type Strain DSM 22766T, Isolated from Bumblebee Digestive Tracts. PMID:26404606
Draft Genome Sequence of Bacillus sp. FJAT-27238 for Setting up Phylogenomic Analysis of Genomic Taxonomy of Bacillus-Like Bacteria. PMID:26404591
High quality draft genomic sequence of Flavihumibacter solisilvae 3-3(T). PMID:26388970
Genome Sequence of Rough and Smooth Variants of Pleomorphic Strain Lactobacillus farciminis CNCM-I-3699. PMID:26383668
Complete genome sequence of Bacillus thuringiensis strain HD521. PMID:26380647
Differential Distribution of Type II CRISPR-Cas Systems in Agricultural and Nonagricultural Campylobacter coli and Campylobacter jejuni Isolates Correlates with Lack of Shared Environments. PMID:26338188
Draft Genome Sequence of Aquamicrobium defluvii Strain W13Z1, a Psychrotolerant Halotolerant Hydrocarbon-Degrading Bacterium. PMID:26316640
Complete Genome Sequence of Acinetobacter baumannii Strain B8300, Which Displays High Twitching Motility. PMID:26294640
Complete Genome Sequence of Acinetobacter baumannii Strain B8342, a Motility-Positive Clinical Isolate. PMID:26294630
Knowledge-based discovery for designing CRISPR-CAS systems against invading mobilomes in thermophiles. PMID:26279704
Intraspecies Genomic Diversity and Long-Term Persistence of Bifidobacterium longum. PMID:26275230
Survey of clustered regularly interspaced short palindromic repeats and their associated Cas proteins (CRISPR/Cas) systems in multiple sequenced strains of Klebsiella pneumoniae. PMID:26238567
Draft Genome Sequence of Ochrobactrum anthropi Strain W13P3, a Halotolerant Polycyclic Aromatic Hydrocarbon-Degrading Bacterium. PMID:26227610
Draft Genome Sequence of Lactobacillus sp. Strain TCF032-E4, Isolated from Fermented Radish. PMID:26227596
Draft genome sequence and characterization of Desulfitobacterium hafniense PCE-S. PMID:26203328
Comparative Genomic Analyses of Multiple Pseudomonas Strains Infecting Corylus avellana Trees Reveal the Occurrence of Two Genetic Clusters with Both Common and Distinctive Virulence and Fitness Traits. PMID:26147218
Whole-Genome Sequence of Multidrug-Resistant Staphylococcus caprae Strain 9557, Isolated from Cerebrospinal Fluid. PMID:26139720
CRISPR Content Correlates with the Pathogenic Potential of Escherichia coli. PMID:26136211
Antarctic archaea-virus interactions: metaproteome-led analysis of invasion, evasion and adaptation. PMID:26125682
The Contribution of Genetic Recombination to CRISPR Array Evolution. PMID:26085541
Genome informatics and vaccine targets in Corynebacterium urealyticum using two whole genomes, comparative genomics, and reverse vaccinology. PMID:26041051
Lifestyle evolution in cyanobacterial symbionts of sponges. PMID:26037118
Comparative genomics reveals diversified CRISPR-Cas systems of globally distributed Microcystis aeruginosa, a freshwater bloom-forming cyanobacterium. PMID:26029174
As Clear as Mud? Determining the Diversity and Prevalence of Prophages in the Draft Genomes of Estuarine Isolates of Clostridium difficile. PMID:26019165
Functional Analysis of Porphyromonas gingivalis W83 CRISPR-Cas Systems. PMID:26013482
Genomic analysis of a ginger pathogen Bacillus pumilus providing the understanding to the pathogenesis and the novel control strategy. PMID:25989507
Elemental sulfur and acetate can support life of a novel strictly anaerobic haloarchaeon. PMID:25978546
Genomes of sequence type 121 Listeria monocytogenes strains harbor highly conserved plasmids and prophages. PMID:25972859
Functionally Structured Genomes in Lactobacillus kunkeei Colonizing the Honey Crop and Food Products of Honeybees and Stingless Bees. PMID:25953738
CRISPR Diversity in E. coli Isolates from Australian Animals, Humans and Environmental Waters. PMID:25946192
Virulence related sequences; insights provided by comparative genomics of Streptococcus uberis of differing virulence. PMID:25898893
Isolation and characterization of a native avirulent strain of Streptococcus suis serotype 2: a perspective for vaccine development. PMID:25891917
Extensive intra-phylotype diversity in lactobacilli and bifidobacteria from the honeybee gut. PMID:25880915
Complete genome sequence and analysis of Lactobacillus hokkaidonensis LOOC260(T), a psychrotrophic lactic acid bacterium isolated from silage. PMID:25879859
Draft Genome Sequence of Lactobacillus kunkeei AR114 Isolated from Honey Bee Gut. PMID:25792062
Genome Sequence of the Solvent-Producing Clostridium beijerinckii Strain 59B, Isolated from Staffordshire Garden Soil. PMID:25792046
Complete genome sequence of Ornithobacterium rhinotracheale strain ORT-UMN 88. PMID:25780507
Non-contiguous finished genome sequence of Ornithobacterium rhinotracheale strain H06-030791. PMID:25780505
Genomic and phenotypic differentiation among Methanosarcina mazei populations from Columbia River sediment. PMID:25756680
Comparative genome analysis reveals the molecular basis of nicotine degradation and survival capacities of Arthrobacter. PMID:25721465
CRISPR-cas subtype I-Fb in Acinetobacter baumannii: evolution and utilization for strain subtyping. PMID:25706932
Comparative genomic analysis of seven Mycoplasma hyosynoviae strains. PMID:25693846
Complete genome sequence of the fish pathogen Flavobacterium psychrophilum ATCC 49418(T.). PMID:25685258
Genome Sequence of the Clinical Isolate Staphylococcus aureus subsp. aureus Strain UAMS-1. PMID:25676774
Genome Sequence of the Sulfate-Reducing Thermophilic Bacterium Thermodesulfovibrio yellowstonii Strain DSM 11347T (Phylum Nitrospirae). PMID:25635016
Genome Sequences of the Listeria ivanovii subsp. ivanovii Type Strain and Two Listeria ivanovii subsp. londoniensis Strains. PMID:25614561
Genomic analysis of three African strains of Bacillus anthracis demonstrates that they are part of the clonal expansion of an exclusively pathogenic bacterium. PMID:25566394
Transcriptomic and proteomic dynamics in the metabolism of a diazotrophic cyanobacterium, Cyanothece sp. PCC 7822 during a diurnal light-dark cycle. PMID:25547186
Comparative genomic analysis of Acinetobacter baumannii clinical isolates reveals extensive genomic variation and diverse antibiotic resistance determinants. PMID:25534766
Comparative genomic analysis of clinical and environmental strains provides insight into the pathogenicity and evolution of Vibrio parahaemolyticus. PMID:25518728
Draft Genome Sequence of the Mannitol-Producing Strain Lactobacillus mucosae CRL573. PMID:25502678
Bacteriophage resistance mechanisms in the fish pathogen Flavobacterium psychrophilum: linking genomic mutations to changes in bacterial virulence factors. PMID:25480749
COSMID: A Web-based Tool for Identifying and Validating CRISPR/Cas Off-target Sites. PMID:25462530
Genomics-Based Exploration of Virulence Determinants and Host-Specific Adaptations of Pseudomonas syringae Strains Isolated from Grasses. PMID:25437611
Plasmids of psychrophilic and psychrotolerant bacteria and their role in adaptation to cold environments. PMID:25426110
Comparative genomic analysis of nine Sphingobium strains: insights into their evolution and hexachlorocyclohexane (HCH) degradation pathways. PMID:25418849
The Geoglobus acetivorans genome: Fe(III) reduction, acetate utilization, autotrophic growth, and degradation of aromatic compounds in a hyperthermophilic archaeon. PMID:25416759
Draft genome sequence analysis of a Pseudomonas putida W15Oct28 strain with antagonistic activity to Gram-positive and Pseudomonas sp. pathogens. PMID:25369289
TALEN and CRISPR/Cas Genome Editing Systems: Tools of Discovery. PMID:25349712
CRISPR-Cas systems in the marine actinomycete Salinispora: linkages with phage defense, microdiversity and biogeography. PMID:25344663
MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems. PMID:25330359
Genome analysis of environmental and clinical P. aeruginosa isolates from sequence type-1146. PMID:25329302
Draft Genome Sequence of Halotolerant Polycyclic Aromatic Hydrocarbon-Degrading Pseudomonas bauzanensis Strain W13Z2. PMID:25323719
Draft Genome Sequence of Necropsobacter rosorum Strain P709T. PMID:25301642
Adaptation to environmental factors shapes the organization of regulatory regions in microbial communities. PMID:25294412
Genome Sequence of Actinobacillus suis Type Strain ATCC 33415T. PMID:25237027
Draft Genome Sequence of Brachybacterium phenoliresistens Strain W13A50, a Halotolerant Hydrocarbon-Degrading Bacterium. PMID:25237019
Mycobacteriophage-drived diversification of Mycobacterium abscessus. PMID:25224692
Genome information of Methylobacterium oryzae, a plant-probiotic methylotroph in the phyllosphere. PMID:25211235
Genome Sequencing of a Mung Bean Plant Growth Promoting Strain of P. aeruginosa with Biocontrol Ability. PMID:25184130
Draft Genome Sequence of Lactobacillus oryzae Strain SG293T. PMID:25169865
Draft Genome Sequence of Staphylococcus aureus subsp. aureus Strain HG003, an NCTC8325 Derivative. PMID:25169861
CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci. PMID:25161238
Abundant and diverse clustered regularly interspaced short palindromic repeat spacers in Clostridium difficile strains and prophages target multiple phage types within this pathogen. PMID:25161187
Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine. PMID:25124552
Motif depletion in bacteriophages infecting hosts with CRISPR systems. PMID:25103210
Genomic encyclopedia of type strains of the genus Bifidobacterium. PMID:25085493
Improved Draft Genome Sequence of Probiotic Strain Lactobacillus gasseri K7. PMID:25059871
Draft Genome Sequence of Enterococcus hirae Strain INF E1 Isolated from Cultured Milk. PMID:25035319
CRISPR-induced distributed immunity in microbial populations. PMID:25000306
Genome sequence of Candidatus Nitrososphaera evergladensis from group I.1b enriched from Everglades soil reveals novel genomic features of the ammonia-oxidizing archaea. PMID:24999826
Draft Genome Sequence of a Novel Streptomyces griseorubens Strain, JSD-1, Active in Carbon and Nitrogen Recycling. PMID:24994798
Priming in the Type I-F CRISPR-Cas system triggers strand-independent spacer acquisition, bi-directionally from the primed protospacer. PMID:24990370
Genomewide comparison and novel ncRNAs of Aquificales. PMID:24965762
Genomes of Alteromonas australica, a world apart. PMID:24942065
Comparative genome analysis reveals metabolic versatility and environmental adaptations of Sulfobacillus thermosulfidooxidans strain ST. PMID:24940621
Comparative genomic analysis of Mycobacterium tuberculosis clinical isolates. PMID:24923884
CRISPR/Cas9-mediated phage resistance is not impeded by the DNA modifications of phage T4. PMID:24886988
Genomes of two new ammonia-oxidizing archaea enriched from deep marine sediments. PMID:24798206
Genome Sequences of Three Frequently Used Listeria monocytogenes and Listeria ivanovii Strains. PMID:24786957
Prophage induction and differential RecA and UmuDAb transcriptome regulation in the DNA damage responses of Acinetobacter baumannii and Acinetobacter baylyi. PMID:24709747
Genome Sequence of a Hyperthermophilic Archaeon, Thermococcus nautili 30-1, That Produces Viral Vesicles. PMID:24675865
Draft genome comparison of representatives of the three dominant genotype groups of dairy Bacillus licheniformis strains. PMID:24657871
Comparative analysis of CRISPR cassettes from the human gut metagenomic contigs. PMID:24628983
How to kill the honey bee larva: genomic potential and virulence mechanisms of Paenibacillus larvae. PMID:24599066
A genomic perspective on a new bacterial genus and species from the Alcaligenaceae family, Basilea psittacipulmonis. PMID:24581117
Complete genome sequence of Enterococcus mundtii QU 25, an efficient L-(+)-lactic acid-producing bacterium. PMID:24568933
Progenitor “Mycobacterium canettii” clone responsible for lymph node tuberculosis epidemic, Djibouti. PMID:24520560
Phylogenomics of "Candidatus Hepatoplasma crinochetorum," a lineage of mollicutes associated with noninsect arthropods. PMID:24482531
Draft Genome Sequence of Gordonia alkanivorans Strain CGMCC6845, a Halotolerant Hydrocarbon-Degrading Bacterium. PMID:24482528
Draft Genome Sequence of Advenella kashmirensis Strain W13003, a Polycyclic Aromatic Hydrocarbon-Degrading Bacterium. PMID:24482505
Genomic analysis of Chthonomonas calidirosea, the first sequenced isolate of the phylum Armatimonadetes. PMID:24477196
Draft Genome Sequence of Brevibacillus panacihumi Strain W25, a Halotolerant Hydrocarbon-Degrading Bacterium. PMID:24459276
Halorhabdus tiamatea: proteogenomics and glycosidase activity measurements identify the first cultivated euryarchaeon from a deep-sea anoxic brine lake as potential polysaccharide degrader. PMID:24428220
Analysis of the complete genome of Fervidococcus fontis confirms the distinct phylogenetic position of the order Fervidicoccales and suggests its environmental function. PMID:24366681
Phylogenetic relationship and virulence inference of Streptococcus Anginosus Group: curated annotation and whole-genome comparative analysis support distinct species designation. PMID:24341328
Association of clustered regularly interspaced short palindromic repeat (CRISPR) elements with specific serotypes and virulence potential of shiga toxin-producing Escherichia coli. PMID:24334663
Strain-level genomic variation in natural populations of Lebetimonas from an erupting deep-sea volcano. PMID:24257443
Architecture and gene repertoire of the flexible genome of the extreme acidophile Acidithiobacillus caldus. PMID:24250794
Comparative genomics analysis of Streptococcus agalactiae reveals that isolates from cultured tilapia in China are closely related to the human strain A909. PMID:24215651
Predominant Acidilobus-like populations from geothermal environments in yellowstone national park exhibit similar metabolic potential in different hypoxic microbial communities. PMID:24162572
Structure and RNA-binding properties of the type III-A CRISPR-associated protein Csm3. PMID:24157656
Genome analysis coupled with physiological studies reveals a diverse nitrogen metabolism in Methylocystis sp. strain SC2. PMID:24130670
RNA-Seq reveals differential gene expression in Staphylococcus aureus with single-nucleotide resolution. PMID:24116120
Genomic adaptation of the Lactobacillus casei group. PMID:24116025
In and out: an analysis of epibiotic vs periplasmic bacterial predators. PMID:24088628
Comparative phenotypic analysis and genome sequence of Clostridium beijerinckii SA-1, an offspring of NCIMB 8052. PMID:24068240
Characterization of a novel composite staphylococcal cassette chromosome mec (SCCmec-SCCcad/ars/cop) in the neonatal sepsis-associated Staphylococcus capitis pulsotype NRCS-A. PMID:24060879
Draft Genome Sequence of a Hexachlorocyclohexane-Degrading Bacterium, Sphingobium baderi Strain LL03T. PMID:24051322
The Genomic Blueprint of Salmonella enterica subspecies enterica serovar Typhi P-stx-12. PMID:24019994
Comparative analysis of the complete genome of an epidemic hospital sequence type 203 clone of vancomycin-resistant Enterococcus faecium. PMID:24004955
Bifidobacterium animalis subsp. lactis ATCC 27673 is a genomically unique strain within its conserved subspecies. PMID:23995933
Structure and genetic content of the megaplasmids of neurotoxigenic clostridium butyricum type E strains from Italy. PMID:23967192
Emergence of epidemic multidrug-resistant Enterococcus faecium from animal and commensal strains. PMID:23963180
Comparative genomic and transcriptome analyses of pathotypes of Xanthomonas citri subsp. citri provide insights into mechanisms of bacterial virulence and host range. PMID:23941402
Complete genome sequence of Streptococcus dysgalactiae subsp. equisimilis 167 carrying Lancefield group C antigen and comparative genomics of S. dysgalactiae subsp. equisimilis strains. PMID:23918808
Complete genome sequence and comparative analysis of Acetobacter pasteurianus 386B, a strain well-adapted to the cocoa bean fermentation ecosystem. PMID:23902333
Variation of the virus-related elements within syntenic genomes of the hyperthermophilic Archaeon Aeropyrum. PMID:23872576
CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems. PMID:23863837
Exploiting CRISPR/Cas: interference mechanisms and applications. PMID:23857052
Genome Sequence of "Candidatus Methanomassiliicoccus intestinalis" Issoire-Mx1, a Third Thermoplasmatales-Related Methanogenic Archaeon from Human Feces. PMID:23846268
Complete genome analysis of three Acinetobacter baumannii clinical isolates in China for insight into the diversification of drug resistance elements. PMID:23826102
Genome of a SAR116 bacteriophage shows the prevalence of this phage type in the oceans. PMID:23798439
Antibiotic Resistance in Salmonella enterica Serovar Typhimurium Associates with CRISPR Sequence Type. PMID:23796925
Genome Sequence of the Banana Pathogen Dickeya zeae Strain MS1, Which Causes Bacterial Soft Rot. PMID:23766402
Mechanistic model of Rothia mucilaginosa adaptation toward persistence in the CF lung, based on a genome reconstructed from metagenomic data. PMID:23737977
Comparative genomics of Salmonella enterica serovars Derby and Mbandaka, two prevalent serovars associated with different livestock species in the UK. PMID:23725633
Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry. PMID:23720654
Complete genomes of two dipteran-associated spiroplasmas provided insights into the origin, dynamics, and impacts of viral invasion in spiroplasma. PMID:23711669
CRISPR regulation of intraspecies diversification by limiting IS transposition and intercellular recombination. PMID:23661565
The susceptibility of Pseudomonas aeruginosa strains from cystic fibrosis patients to bacteriophages. PMID:23637754
Pan-genome and comparative genome analyses of propionibacterium acnes reveal its genomic diversity in the healthy and diseased human skin microbiome. PMID:23631911
Evidence for the widespread distribution of CRISPR-Cas system in the Phylum Cyanobacteria. PMID:23628889
Genomics and genetics of Sulfolobus islandicus LAL14/1, a model hyperthermophilic archaeon. PMID:23594878
The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems. PMID:23563642
Genomic analysis by deep sequencing of the probiotic Lactobacillus brevis KB290 harboring nine plasmids reveals genomic stability. PMID:23544154
CRISPRs of Enterococcus faecalis and E. hirae isolates from pig feces have species-specific repeats but share some common spacer sequences. PMID:23535981
Comparative genome analysis of Streptococcus infantarius subsp. infantarius CJ18, an African fermented camel milk isolate with adaptations to dairy environment. PMID:23521820
A method to find palindromes in nucleic acid sequences. PMID:23515654
Crass: identification and reconstruction of CRISPR from unassembled metagenomic data. PMID:23511966
Physical model of the immune response of bacteria against bacteriophage through the adaptive CRISPR-Cas immune system. PMID:23492852
CRISPRTarget: bioinformatic prediction and analysis of crRNA targets. PMID:23492433
The CRISPR-associated gene cas2 of Legionella pneumophila is required for intracellular infection of amoebae. PMID:23481601
Snapshot of haloarchaeal tailed virus genomes. PMID:23470522
CRISPR-spacer integration reporter plasmids reveal distinct genuine acquisition specificities among CRISPR-Cas I-E variants of Escherichia coli. PMID:23445770
Probabilistic models for CRISPR spacer content evolution. PMID:23442002
Comparative genomic analysis of phylogenetically closely related Hydrogenobaculum sp. isolates from Yellowstone National Park. PMID:23435891
Complete genome sequence of Pyrobaculum oguniense. PMID:23407329
Genome analysis and phylogenetic relatedness of Gallibacterium anatis strains from poultry. PMID:23359626
Propionibacterium acnes strain populations in the human skin microbiome associated with acne. PMID:23337890
Genomic analysis of Melioribacter roseus, facultatively anaerobic organotrophic bacterium representing a novel deep lineage within Bacteriodetes/Chlorobi group. PMID:23301019
Genomic sequence analysis and characterization of Sneathia amnii sp. nov. PMID:23281612
Molecular identification and characterization of clustered regularly interspaced short palindromic repeat (CRISPR) gene cluster in Taylorella equigenitalis. PMID:23275249
Characterization of CRISPR RNA biogenesis and Cas6 cleavage-mediated inhibition of a provirus in the haloarchaeon Haloferax mediterranei. PMID:23243301
Genomic analysis of cold-active Colwelliaphage 9A and psychrophilic phage-host interactions. PMID:23224375
Genome sequence of "Candidatus Methanomethylophilus alvus" Mx1201, a methanogenic archaeon from the human gut belonging to a seventh order of methanogens. PMID:23209209
Function and regulation of clustered regularly interspaced short palindromic repeats (CRISPR) / CRISPR associated (Cas) systems. PMID:23202464
Genomic insights into strategies used by Xanthomonas albilineans with its reduced artillery to spread within sugarcane xylem vessels. PMID:23171051
Emergence of sequence type 779 methicillin-resistant Staphylococcus aureus harboring a novel pseudo staphylococcal cassette chromosome mec (SCCmec)-SCC-SCCCRISPR composite element in Irish hospitals. PMID:23147725
Genome sequence of "Candidatus Microthrix parvicella" Bio17-1, a long-chain-fatty-acid-accumulating filamentous actinobacterium from a biological wastewater treatment plant. PMID:23144412
Genome sequence of Halorubrum sp. strain T3, an extremely halophilic archaeon harboring a virus-like element. PMID:23144373
Genome sequence of the thermophile Bacillus coagulans Hammer, the type strain of the species. PMID:23105047
The genome sequence of Propionibacterium acidipropionici provides insights into its biotechnological and industrial potential. PMID:23083487
Genome sequence of Pseudomonas aeruginosa strain AH16, isolated from a patient with chronic pneumonia in China. PMID:23045492
Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation. PMID:23035691
An evolutionary link between natural transformation and CRISPR adaptive immunity. PMID:23033473
Cas5d processes pre-crRNA and is a member of a larger family of CRISPR RNA endonucleases. PMID:23006625
Massive gene acquisitions in Mycobacterium indicus pranii provide a perspective on mycobacterial evolution. PMID:22965120
Complete genome sequence of Streptococcus pyogenes M1 476, isolated from a patient with streptococcal toxic shock syndrome. PMID:22965090
A novel link between Campylobacter jejuni bacteriophage defence, virulence and Guillain-Barré syndrome. PMID:22945471
Double-stranded endonuclease activity in Bacillus halodurans clustered regularly interspaced short palindromic repeats (CRISPR)-associated Cas2 protein. PMID:22942283
Comparative genomics of the Staphylococcus intermedius group of animal pathogens. PMID:22919635
Complete genome sequence of Streptococcus mutans GS-5, a serotype c strain. PMID:22887682
Complete genome sequence of the hyperthermophilic archaeon Thermococcus sp. strain CL1, isolated from a Paralvinella sp. polychaete worm collected from a hydrothermal vent. PMID:22887670
Complete genome sequence of the opportunistic food-borne pathogen Cronobacter sakazakii ES15. PMID:22843579
Draft genome sequence of Ureibacillus thermosphaericus strain thermo-BF, isolated from Ramsar hot springs in Iran. PMID:22843574
Staphylococcus epidermidis pan-genome sequence analysis reveals diversity of skin commensal and hospital infection-associated isolates. PMID:22830599
Genomic and transcriptomic insights into the thermo-regulated biosynthesis of validamycin in Streptomyces hygroscopicus 5008. PMID:22827618
Comparative genome analysis of the high pathogenicity Salmonella Typhimurium strain UK-1. PMID:22792393
Comparative genomics of plant-associated Pseudomonas spp.: insights into diversity and inheritance of traits involved in multitrophic interactions. PMID:22792073
Genome sequence of an oligohaline hyperthermophilic archaeon, Thermococcus zilligii AN1, isolated from a terrestrial geothermal freshwater spring. PMID:22740682
Complete genome sequence of Helicobacter cinaedi strain PAGU611, isolated in a case of human bacteremia. PMID:22740670
Diverse CRISPRs evolving in human microbiomes. PMID:22719260
Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill. PMID:22717885
Complete genome sequencing and analysis of Saprospira grandis str. Lewin, a predatory marine bacterium. PMID:22675601
Intricate interactions between the bloom-forming cyanobacterium Microcystis aeruginosa and foreign genetic elements, revealed by diversified clustered regularly interspaced short palindromic repeat (CRISPR) signatures. PMID:22636003
Metagenomics - a guide from sampling to data analysis. PMID:22587947
Tandem repeats discovery service (TReaDS) applied to finding novel cis-acting factors in repeat expansion diseases. PMID:22536970
Complete genome sequence of the serotype k Streptococcus mutans strain LJ23. PMID:22535936
Complete genome sequence, lifestyle, and multi-drug resistance of the human pathogen Corynebacterium resistens DSM 45100 isolated from blood samples of a leukemia patient. PMID:22524407
Pangenomic study of Corynebacterium diphtheriae that provides insights into the genomic diversity of pathogenic isolates from cases of classical diphtheria, endocarditis, and pneumonia. PMID:22505676
Reconstructing viral genomes from the environment using fosmid clones: the case of haloviruses. PMID:22479446
Genome sequence of "Candidatus Nitrosopumilus salaria" BD31, an ammonia-oxidizing archaeon from the San Francisco Bay estuary. PMID:22461555
Genome sequence of "Candidatus Nitrosoarchaeum limnia" BG20, a low-salinity ammonia-oxidizing archaeon from the San Francisco Bay estuary. PMID:22461554
The automatic annotation of bacterial genomes. PMID:22408191
Characterization of the CRISPR/Cas subtype I-A system of the hyperthermophilic crenarchaeon Thermoproteus tenax. PMID:22408157
Identification of novel positive-strand RNA viruses by metagenomic analysis of archaea-dominated Yellowstone hot springs. PMID:22379100
Characterization of species-specific repeats in 613 prokaryotic species. PMID:22368180
Comparative analysis of the first complete Enterococcus faecium genome. PMID:22366422
Yersinia pestis lineages in Mongolia. PMID:22363455
RNA-guided genetic silencing systems in bacteria and archaea. PMID:22337052
Complete genome sequence of the beer spoilage organism Pediococcus claussenii ATCC BAA-344T. PMID:22328764
Genomic characterization of the Taylorella genus. PMID:22235352
Legionella pneumophila sequence type 1/Paris pulsotype subtyping by spoligotyping. PMID:22205819
Is the genetic landscape of the deep subsurface biosphere affected by viruses? PMID:22084639
The UCSC Archaeal Genome Browser: 2012 update. PMID:22080555
Genomic analysis reveals Lactobacillus sanfranciscensis as stable element in traditional sourdoughs. PMID:21995419
Complete genome sequence of the fish pathogen Flavobacterium branchiophilum. PMID:21926215
Complete genome sequence of Alicyclobacillus acidocaldarius strain Tc-4-1. PMID:21914900
Draft genome sequence of Nesterenkonia sp. strain F, isolated from Aran-Bidgol Salt Lake in Iran. PMID:21914888
Complete genome analysis of Sulfobacillus acidophilus strain TPY, isolated from a hydrothermal vent in the Pacific Ocean. PMID:21914875
Genomic analysis and temperature-dependent transcriptome profiles of the rhizosphere originating strain Pseudomonas aeruginosa M18. PMID:21884571
The human gut virome: inter-individual variation and dynamic response to diet. PMID:21880779
Transcriptomes of Frankia sp. strain CcI3 in growth transitions. PMID:21867524
Comparative analysis of two complete Corynebacterium ulcerans genomes and detection of candidate virulence factors. PMID:21801446
Complete genome sequence of the bacterium Porphyromonas gingivalis TDC60, which causes periodontal disease. PMID:21705612
Crystal structure of clustered regularly interspaced short palindromic repeats (CRISPR)-associated Csn2 protein revealed Ca2+-dependent double-stranded DNA binding activity. PMID:21697083
Genome Sequence of Campylobacter jejuni strain 327, a strain isolated from a turkey slaughterhouse. PMID:21677848
Sequencing and comparative genome analysis of two pathogenic Streptococcus gallolyticus subspecies: genome plasticity, adaptation and virulence. PMID:21633709
CRISPR inhibition of prophage acquisition in Streptococcus pyogenes. PMID:21573110
Clostridium botulinum group III: a group with dual identity shaped by plasmids, phages and mobile elements. PMID:21486474
Diversity, evolution, and functionality of clustered regularly interspaced short palindromic repeat (CRISPR) regions in the fire blight pathogen Erwinia amylovora. PMID:21460108
Complete genome sequence of the pathogenic bacterium Riemerella anatipestifer strain RA-GD. PMID:21441509
The CRISPR/Cas immune system is an operon regulated by LeuO, H-NS, and leucine-responsive regulatory protein in Salmonella enterica serovar Typhi. PMID:21398529
Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis. PMID:21364937
Metagenomic analysis of kimchi, a traditional Korean fermented food. PMID:21317261
Comparative analysis and supragenome modeling of twelve Moraxella catarrhalis clinical isolates. PMID:21269504
Envelope stress is a trigger of CRISPR RNA-mediated DNA silencing in Escherichia coli. PMID:21255106
Complete genome sequencing and analysis of a Lancefield group G Streptococcus dysgalactiae subsp. equisimilis strain causing streptococcal toxic shock syndrome (STSS). PMID:21223537
Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. PMID:21169198
Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss. PMID:21126366
A genomic perspective on the potential of Actinobacillus succinogenes for industrial succinate production. PMID:21118570
Multidrug-resistant enterococci lack CRISPR-cas. PMID:21060735
Complete genome sequence of strain HTCC2503T of Parvularcula bermudensis, the type species of the order "Parvularculales" in the class Alphaproteobacteria. PMID:21037002
The complete genome of Propionibacterium freudenreichii CIRM-BIA1, a hardy actinobacterium with food and probiotic applications. PMID:20668525
Viruses in the faecal microbiota of monozygotic twins and their mothers. PMID:20631792
Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions. PMID:20627862
Comparative genome analysis of Prevotella ruminicola and Prevotella bryantii: insights into their environmental niche. PMID:20585943
Genome analysis of Moraxella catarrhalis strain BBH18, [corrected] a human respiratory tract pathogen. PMID:20453089
Meeting report: a workshop on Best Practices in Genome Annotation. PMID:20428316
Pyrosequencing-based comparative genome analysis of the nosocomial pathogen Enterococcus faecium and identification of a large transferable pathogenicity island. PMID:20398277
Livestock-associated methicillin-resistant Staphylococcus aureus sequence type 398 in humans, Canada. PMID:20350371
CRISPR-mediated phage resistance and the ghost of coevolution past. PMID:20236977
Bacterial lifestyle in a deep-sea hydrothermal vent chimney revealed by the genome sequence of the thermophilic bacterium Deferribacter desulfuricans SSM1. PMID:20189949
Complete genome sequence and lifestyle of black-pigmented Corynebacterium aurimucosum ATCC 700975 (formerly C. nigricans CN-1) isolated from a vaginal swab of a woman with spontaneous abortion. PMID:20137072
Evolutionary dynamics of clustered irregularly interspaced short palindromic repeat systems in the ocean metagenome. PMID:20118362
Phage resistance of a marine bacterium, Roseobacter denitrificans OCh114, as revealed by comparative proteomics. PMID:20107991
Comparative genomics of green sulfur bacteria. PMID:20099081
CRISPI: a CRISPR interactive database. PMID:19846435
Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific content. PMID:19656368
Metabolic versatility and indigenous origin of the archaeon Thermococcus sibiricus, isolated from a siberian oil reservoir, as revealed by genome analysis. PMID:19447963
The complete genome and proteome of Laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats. PMID:19283063
Germ warfare in a microbial mat community: CRISPRs provide insights into the co-evolution of host and viral genomes. PMID:19132092
The genome of Thermosipho africanus TCF52B: lateral genetic connections to the Firmicutes and Archaea. PMID:19124572
Complete genome sequence of the anaerobic, protein-degrading hyperthermophilic crenarchaeon Desulfurococcus kamchatkensis. PMID:19114480
Interaction between bacteriophage DMS3 and host CRISPR region inhibits group behaviors of Pseudomonas aeruginosa. PMID:18952788
Genome sequence of a nephritogenic and highly transformable M49 strain of Streptococcus pyogenes. PMID:18820018
Analysis of the Pseudoalteromonas tunicata genome reveals properties of a surface-associated life style in the marine environment. PMID:18813346
Genome sequence of a Lancefield group C Streptococcus zooepidemicus strain causing epidemic nephritis: new information about an old disease. PMID:18716664
Insight into microevolution of Yersinia pestis by clustered regularly interspaced short palindromic repeats. PMID:18612419
CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats. PMID:18442988
Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus. PMID:18065539
CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins PubMed citations: 329.

329 articles citing: CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins

Investigation of memory-enhancing effects of Streptococcus thermophilus EG007 in mice and elucidating molecular and metagenomic characteristics using nanopore sequencing. PMID:35918353
Characterization of Marinilongibacter aquaticus gen. nov., sp. nov., a unique marine bacterium harboring four CRISPR-Cas systems in the phylum Bacteroidota. PMID:35913596
Comparative Genomic Analysis of the Human Pathogen Wohlfahrtiimonas Chitiniclastica Provides Insight Into the Identification of Antimicrobial Resistance Genotypes and Potential Virulence Traits. PMID:35873140
Genomic Insights Into the Interspecific Diversity and Evolution of Mobiluncus, a Pathogen Associated With Bacterial Vaginosis. PMID:35865929
CRISPR-Cas12a nucleases function with structurally engineered crRNAs: SynThetic trAcrRNA. PMID:35842430
Genomic Insights of Enterococcus faecium UC7251, a Multi-Drug Resistant Strain From Ready-to-Eat Food, Highlight the Risk of Antimicrobial Resistance in the Food Chain. PMID:35814695
CRISPR-Based Approaches for Gene Regulation in Non-Model Bacteria. PMID:35813973
Genomic characterization of Streptococcus parasuis, a close relative of Streptococcus suis and also a potential opportunistic zoonotic pathogen. PMID:35752768
Pangenome Evolution in Environmentally Transmitted Symbionts of Deep-Sea Mussels Is Governed by Vertical Inheritance. PMID:35731940
Comparative Genomics Provides Insights Into Genetic Diversity of Clostridium tyrobutyricum and Potential Implications for Late Blowing Defects in Cheese. PMID:35722315
Genome Mining Approach Reveals the Occurrence and Diversity Pattern of Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-Associated Systems in Lactobacillus brevis Strains. PMID:35722276
Health-Promoting Nature of Lactococcus lactis IBB109 and Lactococcus lactis IBB417 Strains Exhibiting Proliferation Inhibition and Stimulation of Interleukin-18 Expression in Colorectal Cancer Cells. PMID:35694291
UG/Abi: a highly diverse family of prokaryotic reverse transcriptases associated with defense functions. PMID:35648479
PADLOC: a web server for the identification of antiviral defence systems in microbial genomes. PMID:35639517
Antimicrobial Resistance and Comparative Genomic Analysis of Elizabethkingia anophelis subsp. endophytica Isolated from Raw Milk. PMID:35625292
Genomic characterization of lytic bacteriophages targeting genetically diverse Pseudomonas aeruginosa clinical isolates. PMID:35620437
Pangenome analyses of Bacillus pumilus, Bacillus safensis, and Priestia megaterium exploring the plant-associated features of bacilli strains isolated from canola. PMID:35612623
CrisprVi: a software for visualizing and analyzing CRISPR sequences of prokaryotes. PMID:35610585
Genome sequence and Carbohydrate Active Enzymes (CAZymes) repertoire of the thermophilic Caldicoprobacter algeriensis TH7C1T. PMID:35598016
Draft Genome Sequence of Geobacillus stearothermophilus Strain K4E3_SPR_NPP, Isolated from Kasol Hot Spring, Himachal Pradesh, India. PMID:35587782
Streptomyces marincola sp. nov., a Novel Marine Actinomycete, and Its Biosynthetic Potential of Bioactive Natural Products. PMID:35572650
Comparative Genomic Analysis of Vibrio cincinnatiensis Provides Insights into Genetic Diversity, Evolutionary Dynamics, and Pathogenic Traits of the Species. PMID:35562911
Systematic and quantitative view of the antiviral arsenal of prokaryotes. PMID:35538097
Draft Genome Sequence of a Lactobacillus gasseri Strain Isolated from the Catheterized Urine of a Healthy Postmenopausal Woman. PMID:35532533
First Identification of a Multidrug-Resistant Pseudomonas putida Co-Carrying Five β-Lactam Resistance Genes Recovered from a Urinary Tract Infection in China. PMID:35510158
Host-Associated Phages Disperse across the Extraterrestrial Analogue Antarctica. PMID:35499326
Complete Genome Sequence of Methanofollis formosanus DSM 15483T, Isolated from an Aquaculture Fish Pond. PMID:35481773
Polyphasic Identification and Genomic Insights of Leptothermofonsia sichuanensis gen. sp. nov., a Novel Thermophilic Cyanobacteria Within Leptolyngbyaceae. PMID:35418964
Emergence of a Multidrug-Resistant Escherichia coli Co-Carrying a New mcr-1.33 Variant and bla NDM-5 Genes Recovered from a Urinary Tract Infection. PMID:35411158
Significance of both alkB and P450 alkane-degrading systems in Tsukamurella tyrosinosolvens: proteomic evidence. PMID:35396956
Critical Assessment of Metagenome Interpretation: the second round of challenges. PMID:35396482
CRISPRs in the human genome are differentially expressed between malignant and normal adjacent to tumor tissue. PMID:35396392
Genome sequence of Corynebacterium amycolatum ICIS 99 isolated from human vagina reveals safety and beneficial properties. PMID:35352202
Draft Genome Sequence of Lactococcus lactis Subsp. cremoris WA2-67: A Promising Nisin-Producing Probiotic Strain Isolated from the Rearing Environment of a Spanish Rainbow Trout (Oncorhynchus mykiss, Walbaum) Farm. PMID:35336097
CRISPR-Cas Systems in Gut Microbiome of Children with Autism Spectrum Disorders. PMID:35330117
FrCas9 is a CRISPR/Cas9 system with high editing efficiency and fidelity. PMID:35301321
Precipitous Increase of Bacterial CRISPR-Cas Abundance at Around 45°C. PMID:35300480
Isomaltooligosaccharides utilization and genomic characterization of human infant anti-inflammatory Bifidobacterium longum and Bifidobacterium breve strains. PMID:35299989
Virulence and Antibiotic Resistance Genes in Listeria monocytogenes Strains Isolated From Ready-to-Eat Foods in Chile. PMID:35299835
The core and accessory Hfq interactomes across Pseudomonas aeruginosa lineages. PMID:35273147
A Comparative Genomic and Safety Assessment of Six Lactiplantibacillus plantarum subsp. argentoratensis Strains Isolated from Spontaneously Fermented Greek Wheat Sourdoughs for Potential Biotechnological Application. PMID:35269627
Spacer2PAM: A computational framework to guide experimental determination of functional CRISPR-Cas system PAM sequences. PMID:35258601
Integrative Assessments on Molecular Taxonomy of Acidiferrobacter thiooxydans ZJ and Its Environmental Adaptation Based on Mobile Genetic Elements. PMID:35250944
Genomic Analysis of Molecular Bacterial Mechanisms of Resistance to Phage Infection. PMID:35250902
Endogenous CRISPR-Cas Systems in Group I Clostridium botulinum and Clostridium sporogenes Do Not Directly Target the Botulinum Neurotoxin Gene Cluster. PMID:35222299
Quorum Sensing Controls the CRISPR and Type VI Secretion Systems in Aliivibrio wodanis 06/09/139. PMID:35211539
Metagenomic Assessment of DNA Viral Diversity in Freshwater Sponges, Baikalospongia bacillifera. PMID:35208935
Distribution, Diversity and Roles of CRISPR-Cas Systems in Human and Animal Pathogenic Streptococci. PMID:35173702
Draft Genome Sequences of Four Strains of Campylobacter jejuni Isolated from Patients with Axonal Variant of Guillain-Barré Syndrome in Bangladesh. PMID:35142550
Isolation, characterization and comparative genomics of potentially probiotic Lactiplantibacillus plantarum strains from Indian foods. PMID:35121802
Draft Genome Sequence of Oceanobacillus jordanicus Strain GSFE11, a Halotolerant Plant Growth-Promoting Bacterial Endophyte Isolated From the Jordan Valley. PMID:35095268
Genomic and functional characterization of bacteriocinogenic lactic acid bacteria isolated from Boza, a traditional cereal-based beverage. PMID:35087086
Using metagenomic data to boost protein structure prediction and discovery. PMID:35070166
Complete Genome Sequencing and Comparative Genomics of Three Potential Probiotic Strains, Lacticaseibacillus casei FBL6, Lacticaseibacillus chiayiensis FBL7, and Lacticaseibacillus zeae FBL8. PMID:35069490
Isolation and characterization of Streptomyces bacteriophages and Streptomyces strains encoding biosynthetic arsenals. PMID:35061755
Genetic Potential of Dissulfurimicrobium hydrothermale, an Obligate Sulfur-Disproportionating Thermophilic Microorganism. PMID:35056509
Evolutionary and mechanistic diversity of Type I-F CRISPR-associated transposons. PMID:35051352
Cas11 enables genome engineering in human cells with compact CRISPR-Cas3 systems. PMID:35051351
Genomic evolution of the globally disseminated multidrug-resistant Klebsiella pneumoniae clonal group 147. PMID:35019836
Phylogeny and potential virulence of cryptic clade Escherichia coli species complex isolates derived from an arable field trial. PMID:35005658
Genomic Characterization of Streptococcus suis Serotype 24 Clonal Complex 221/234 From Human Patients. PMID:35003043
Paenibacillus albicereus sp. nov. and Niallia alba sp. nov., isolated from digestive syrup. PMID:34997867
Genomic Analyses of Pediococcus pentosaceus ST65ACC, a Bacteriocinogenic Strain Isolated from Artisanal Raw-Milk Cheese. PMID:34984631
Spontaneous Phage Resistance in Avian Pathogenic Escherichia coli. PMID:34966369
Presence and Persistence of Putative Lytic and Temperate Bacteriophages in Vaginal Metagenomes from South African Adolescents. PMID:34960611
Genome-Based Characterization of a Plasmid-Associated Micrococcin P1 Biosynthetic Gene Cluster and Virulence Factors in Mammaliicoccus sciuri IMDO-S72. PMID:34936836
Genomic Analysis of Global Staphylococcus argenteus Strains Reveals Distinct Lineages With Differing Virulence and Antibiotic Resistance Gene Content. PMID:34925305
Complete Genome Sequence of the Type Strain Tepidimonas taiwanensis LMG 22826T, a Thermophilic Alkaline Protease and Polyhydroxyalkanoate Producer. PMID:34908127
Draft Genome Sequence of Weissella cibaria P71, a Promising Aquaculture Probiotic Strain Isolated from Common Octopus (Octopus vulgaris). PMID:34881980
Engineered CRISPR-Cas systems for the detection and control of antibiotic-resistant infections. PMID:34863214
CRISPR Element Patterns vs. Pathoadaptability of Clinical Pseudomonas aeruginosa Isolates from a Medical Center in Moscow, Russia. PMID:34827239
Complete Genome Sequence of Two Deep-Sea Streptomyces Isolates from Madeira Archipelago and Evaluation of Their Biosynthetic Potential. PMID:34822492
Prophage integration into CRISPR loci enables evasion of antiviral immunity in Streptococcus pyogenes. PMID:34819640
Genomic Insights Into New Species of the Genus Halomicroarcula Reveals Potential for New Osmoadaptative Strategies in Halophilic Archaea. PMID:34803972
Phylogenetic Analysis Reveals Distinct Evolutionary Trajectories of the Fluoroquinolones-Resistant Escherichia coli ST1193 From Fuzhou, China. PMID:34803966
High-quality whole-genome sequence analysis of Lactobacillus paragasseri UBLG-36 reveals oxalate-degrading potential of the strain. PMID:34797858
Deciphering Multidrug-Resistant Acinetobacter baumannii from a Pediatric Cancer Hospital in Egypt. PMID:34787450
Cadmium stress triggers significant metabolic reprogramming in Enterococcus faecium CX 2-6. PMID:34765088
Complete Genome Sequence of Bacillus badius NBPM-293, a Plant Growth-Promoting Strain Isolated from Rhizosphere Soil. PMID:34761955
Characterization of 67 Confirmed Clustered Regularly Interspaced Short Palindromic Repeats Loci in 52 Strains of Staphylococci. PMID:34751223
Comparative Genomic Analysis and a Novel Set of Missense Mutation of the Leptospira weilii Serogroup Mini From the Urine of Asymptomatic Dogs in Thailand. PMID:34733249
Evolutionary genomics and biosynthetic potential of novel environmental Actinobacteria. PMID:34716462
The widespread presence of a family of fish virulence plasmids in Vibrio vulnificus stresses its relevance as a zoonotic pathogen linked to fish farms. PMID:34702148
Characterization of Blf4, an Archaeal Lytic Virus Targeting a Member of the Methanomicrobiales. PMID:34696364
Comparative Genomic Analysis of Bifidobacterium bifidum Strains Isolated from Different Niches. PMID:34680899
Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types. PMID:34606606
CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids. PMID:34606604
Antimicrobial Resistance and CRISPR Typing Among Salmonella Isolates From Poultry Farms in China. PMID:34603259
PAM-repeat associations and spacer selection preferences in single and co-occurring CRISPR-Cas systems. PMID:34593010
Exploration of the Diversity of Clustered Regularly Interspaced Short Palindromic Repeats-Cas Systems in Clostridium novyi sensu lato. PMID:34589070
Complete Genome Sequencing of Leptospira interrogans Isolates from Malaysia Reveals Massive Genome Rearrangement but High Conservation of Virulence-Associated Genes. PMID:34578230
Comparative Genomics and Specific Functional Characteristics Analysis of Lactobacillus acidophilus. PMID:34576887
Comparative Genomic Analysis Uncovered Evolution of Pathogenicity Factors, Horizontal Gene Transfer Events, and Heavy Metal Resistance Traits in Citrus Canker Bacterium Xanthomonas citri subsp. citri. PMID:34557177
A Novel Miniature CRISPR-Cas13 System for SARS-CoV-2 Diagnostics. PMID:34546709
Genomes of Novel Myxococcota Reveal Severely Curtailed Machineries for Predation and Cellular Differentiation. PMID:34524899
Enhanced Recovery of Microbial Genes and Genomes From a Marine Water Column Using Long-Read Metagenomics. PMID:34512586
Characterization of Emerging Pathogens Carrying bla KPC-2 Gene in IncP-6 Plasmids Isolated From Urban Sewage in Argentina. PMID:34504809
Enhanced Cas12a multi-gene regulation using a CRISPR array separator. PMID:34499031
Brevibacterium limosum sp. nov., Brevibacterium pigmenatum sp. nov., and Brevibacterium atlanticum sp. nov., three novel dye decolorizing actinobacteria isolated from ocean sediments. PMID:34491521
Programmable RNA targeting with the single-protein CRISPR effector Cas7-11. PMID:34489594
Highly diverse flavobacterial phages isolated from North Sea spring blooms. PMID:34475519
Draft Genome Sequence of Enterobacter oligotrophicus, Isolated from the Microbiome of a Lizard in the Caribbean. PMID:34472977
Genome-driven elucidation of phage-host interplay and impact of phage resistance evolution on bacterial fitness. PMID:34465897
Genomic and Phenotypic Biology of Novel Strains of Dickeya zeae Isolated From Pineapple and Taro in Hawaii: Insights Into Genome Plasticity, Pathogenicity, and Virulence Determinants. PMID:34456933
Comparative Genomics Analyses Reveal the Differences between B. longum subsp. infantis and B. longum subsp. longum in Carbohydrate Utilisation, CRISPR-Cas Systems and Bacteriocin Operons. PMID:34442792
Comment on Tanmoy et al. CRISPR-Cas Diversity in Clinical Salmonella enterica Serovar Typhi Isolates from South Asian Countries. Genes 2020, 11, 1365. PMID:34440320
Diversity of International High-Risk Clones of Acinetobacter baumannii Revealed in a Russian Multidisciplinary Medical Center during 2017-2019. PMID:34439060
CRISPRclassify: Repeat-Based Classification of CRISPR Loci. PMID:34406047
Safety Evaluation of Lactobacillus delbrueckii subsp. lactis CIDCA 133: a Health-Promoting Bacteria. PMID:34403080
CASPredict: a web service for identifying Cas proteins. PMID:34395100
Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures. PMID:34363005
Insights from Bacteroides Species in Children with Type 1 Diabetes. PMID:34361871
Physiological and Genomic Characterization of a Hyperthermophilic Archaeon Archaeoglobus neptunius sp. nov. Isolated From a Deep-Sea Hydrothermal Vent Warrants the Reclassification of the Genus Archaeoglobus. PMID:34335500
Lytic archaeal viruses infect abundant primary producers in Earth's crust. PMID:34330907
Comprehensive Molecular Dissection of Dermatophilus congolensis Genome and First Observation of tet(Z) Tetracycline Resistance. PMID:34281179
Profiling the Virulence and Antibiotic Resistance Genes of Cronobacter sakazakii Strains Isolated From Powdered and Dairy Formulas by Whole-Genome Sequencing. PMID:34276629
At the Gate of Mutualism: Identification of Genomic Traits Predisposing to Insect-Bacterial Symbiosis in Pathogenic Strains of the Aphid Symbiont Serratia symbiotica. PMID:34268133
Draft Genome Sequence of Enterobacter hormaechei subsp. steigerwaltii Strain BEI01. PMID:34264109
Draft Genome Sequences of Seven Cronobacter sakazakii Strains Carrying the mcr 9.1 Gene Isolated in Chile. PMID:34264101
Comparative Genomics of Closely Related Tetragenococcus halophilus Strains Elucidate the Diversity and Microevolution of CRISPR Elements. PMID:34220781
Comprehensive pan-genome analysis of Lactiplantibacillus plantarum complete genomes. PMID:34216519
The First Data on the Complete Genome of a Tetrodotoxin-Producing Bacterium. PMID:34207879
Pangenomics reveals alternative environmental lifestyles among chlamydiae. PMID:34188040
Genomic Analysis of Family UBA6911 (Group 18 Acidobacteria) Expands the Metabolic Capacities of the Phylum and Highlights Adaptations to Terrestrial Habitats. PMID:34160232
Genome analysis of Pseudomonas sp. OF001 and Rubrivivax sp. A210 suggests multicopper oxidases catalyze manganese oxidation required for cylindrospermopsin transformation. PMID:34157973
A transferrable and integrative type I-F Cascade for heterologous genome editing and transcription modulation. PMID:34157103
Identification and Characterization of the CRISPR/Cas System in Staphylococcus aureus Strains From Diverse Sources. PMID:34149645
CRISPRloci: comprehensive and accurate annotation of CRISPR-Cas systems. PMID:34133710
Legionella pneumophila CRISPR-Cas Suggests Recurrent Encounters with One or More Phages in the Family Microviridae. PMID:34132590
Genome analysis to decipher syntrophy in the bacterial consortium 'SCP' for azo dye degradation. PMID:34116639
Pan-Genome Analysis Reveals Host-Specific Functional Divergences in Burkholderia gladioli. PMID:34067383
Microbial Hotspots in Lithic Microhabitats Inferred from DNA Fractionation and Metagenomics in the Atacama Desert. PMID:34065975
Comprehensive Scanning of Prophages in Lactobacillus: Distribution, Diversity, Antibiotic Resistance Genes, and Linkages with CRISPR-Cas Systems. PMID:34060909
A global metagenomic map of urban microbiomes and antimicrobial resistance. PMID:34043940
Analysis of Genome Sequences of Coagulase-Negative Staphylococci Isolates from South Africa and Nigeria Highlighted Environmentally Driven Heterogeneity. PMID:34025805
Diverse Viruses Carrying Genes for Microbial Extremotolerance in the Atacama Desert Hyperarid Soil. PMID:34006626
De novo genome assembly and analysis unveil biosynthetic and metabolic potentials of Pseudomonas fragi A13BB. PMID:34006216
Comparative genomics analysis of Pediococcus acidilactici species. PMID:33990913
Draft Genome Sequence of Deefgea sp. Strain CFH1-16, Isolated from the Intestine of the Freshwater Fish Hypomesus nipponensis. PMID:33986104
Comparative Genomics, from the Annotated Genome to Valuable Biological Information: A Case Study. PMID:33961220
Complete genome sequence of Streptomyces sp. HSG2 from rhizosphere soil of mangrove in Qingmei Gang, Sanya. PMID:33932153
Cocultivation of an ultrasmall environmental parasitic bacterium with lytic ability against bacteria associated with wastewater foams. PMID:33927381
Ecophysiological Features Shape the Distribution of Prophages and CRISPR in Sulfate Reducing Prokaryotes. PMID:33925267
Characterisation of Phage Susceptibility Variation in Salmonellaenterica Serovar Typhimurium DT104 and DT104b. PMID:33920555
Genome Characterization of Lactiplantibacillus plantarum Strain UTNGt2 Originated from Theobroma grandiflorum (White Cacao) of Ecuadorian Amazon: Antimicrobial Peptides from Safety to Potential Applications. PMID:33916842
Polyphasic characterization of and genomic insights into a haloalkali-tolerant Saccharibacillus alkalitolerans sp. nov., that produces three cellulase isozymes and several antimicrobial compounds. PMID:33913068
Reductive evolution and unique predatory mode in the CPR bacterium Vampirococcus lugosii. PMID:33911080
Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom. PMID:33902727
Genome analysis provides insights into the biocontrol ability of Mitsuaria sp. strain TWR114. PMID:33880605
Genomic and phenotypic diversity of Enterococcus faecalis isolated from endophthalmitis. PMID:33852628
Diversity of the type I-U CRISPR-Cas system in Bifidobacterium. PMID:33837440
Modeling the ecology of parasitic plasmids. PMID:33833414
Genome-Wide Identification and Analysis of Chromosomally Integrated Putative Prophages Associated with Clinical Klebsiella pneumoniae Strains. PMID:33813641
Whole-Genome Sequencing and Comparative Genomics of Three Helicobacter pylori Strains Isolated from the Stomach of a Patient with Adenocarcinoma. PMID:33809022
Genetic Basis of Antimicrobial Resistant Gram-Negative Bacteria Isolated From Bloodstream in Brazil. PMID:33791325
Cooperation between Different CRISPR-Cas Types Enables Adaptation in an RNA-Targeting System. PMID:33785624
Isolation and Characterization of Gardnerella Phage vB_Gva_AB1, a Bacteriophage Infecting a Clinical Strain of Gardnerella vaginalis. PMID:33766896
Whole-genome analysis of probiotic product isolates reveals the presence of genes related to antimicrobial resistance, virulence factors, and toxic metabolites, posing potential health risks. PMID:33761872
Hybrid genome de novo assembly with methylome analysis of the anaerobic thermophilic subsurface bacterium Thermanaerosceptrum fracticalcis strain DRI-13T. PMID:33757423
Genetic characteristics and phylogenetic analysis of Brazilian clinical strains of Pseudomonas aeruginosa harboring CRISPR/Cas systems. PMID:33751147
Complete Genome Sequence of Sinorhizobium meliloti S35m, a Salt-Tolerant Isolate from Alfalfa Rhizosphere in Soil Native to the Caucasus Region. PMID:33737367
crRNA complementarity shifts endogenous CRISPR-Cas systems between transcriptional repression and DNA defense. PMID:33733999
Genomics of an endemic cystic fibrosis Burkholderia multivorans strain reveals low within-patient evolution but high between-patient diversity. PMID:33720991
Binnacle: Using Scaffolds to Improve the Contiguity and Quality of Metagenomic Bins. PMID:33717033
Description and genomic insights into a multidrug resistant novel bacterium Savagea serpentis sp. nov., isolated from the scats of a vine snake (Ahaetulla nasuta). PMID:33715106
Streamlining CRISPR spacer-based bacterial host predictions to decipher the viral dark matter. PMID:33677572
Genomic and Phenotypic Analysis of Multidrug-Resistant Acinetobacter baumannii Clinical Isolates Carrying Different Types of CRISPR/Cas Systems. PMID:33668622
CRISPRbuilder-TB: "CRISPR-builder for tuberculosis". Exhaustive reconstruction of the CRISPR locus in mycobacterium tuberculosis complex using SRA. PMID:33667225
Characterization of multidrug-resistant Acinetobacter baumannii strain ATCC BAA1605 using whole-genome sequencing. PMID:33663564
CRISPR-SE: a brute force search engine for CRISPR design. PMID:33655210
Natural Competence and Horizontal Gene Transfer in Campylobacter. PMID:33620655
Massive expansion of human gut bacteriophage diversity. PMID:33606979
CasCollect: targeted assembly of CRISPR-associated operons from high-throughput sequencing data. PMID:33575613
Pangenome analysis reveals genetic isolation in Campylobacter hyointestinalis subspecies adapted to different mammalian hosts. PMID:33564053
Vagococcus fluvialis isolation and sequencing from urine of healthy cattle. PMID:33561240
Phylogeny of Salmonella enterica subspecies arizonae by whole-genome sequencing reveals high incidence of polyphyly and low phase 1 H antigen variability. PMID:33539276
Evaluation of CRISPR Diversity in the Human Skin Microbiome for Personal Identification. PMID:33531409
Lactic Acid Bacteria in Wine: Technological Advances and Evaluation of Their Functional Role. PMID:33519768
Comparative Genomics of Leuconostoc carnosum. PMID:33505375
Genomic and Functional Characterization of Enterococcus faecalis Isolates Recovered From the International Space Station and Their Potential for Pathogenicity. PMID:33505359
Peeling the Layers Away: The Genomic Characterization of Bacillus pumilus 64-1, an Isolate With Antimicrobial Activity From the Marine Sponge Plakina cyanorosea (Porifera, Homoscleromorpha). PMID:33488540
Comparative Genomic Analysis of Mycobacteriaceae Reveals Horizontal Gene Transfer-Mediated Evolution of the CRISPR-Cas System in the Mycobacterium tuberculosis Complex. PMID:33468705
Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics. PMID:33446769
Complete Genome Sequence of Ovine Mycobacterium avium subsp. paratuberculosis Strain JIII-386 (MAP-S/type III) and Its Comparison to MAP-S/type I, MAP-C, and M. avium Complex Genomes. PMID:33383865
Molecular Characterization of Cronobacter sakazakii Strains Isolated from Powdered Milk. PMID:33374633
Survey and Sequence Characterization of Bovine Mastitis-Associated Escherichia coli in Dairy Herds. PMID:33365333
CRISPR-Cas systems restrict horizontal gene transfer in Pseudomonas aeruginosa. PMID:33349652
Genomic Investigation into the Virulome, Pathogenicity, Stress Response Factors, Clonal Lineages, and Phylogenetic Relationship of Escherichia coli Strains Isolated from Meat Sources in Ghana. PMID:33327465
Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome. PMID:33323122
NCBI's Virus Discovery Codeathon: Building "FIVE" -The Federated Index of Viral Experiments API Index. PMID:33322070
Comparative genome analyses of Mycobacteroides immunogenum reveals two potential novel subspecies. PMID:33295861
The State of the Art in Biodefense Related Bacterial Pathogen Detection Using Bacteriophages: How It Started and How It's Going. PMID:33291831
CRISPRidentify: identification of CRISPR arrays using machine learning approach. PMID:33290505
Antimicrobial Resistance and Genomic Characterization of OXA-48- and CTX-M-15-Co-Producing Hypervirulent Klebsiella pneumoniae ST23 Recovered from Nosocomial Outbreak. PMID:33287207
Diversity and Distribution of a Novel Genus of Hyperthermophilic Aquificae Viruses Encoding a Proof-Reading Family-A DNA Polymerase. PMID:33281778
Prophages and Past Prophage-Host Interactions Revealed by CRISPR Spacer Content in a Fish Pathogen. PMID:33276599
The phylogenomics of CRISPR-Cas system and revelation of its features in Salmonella. PMID:33273523
Comparative genomics in "Candidatus Kuenenia stuttgartiensis" reveal high genomic plasticity in the overall genome structure, CRISPR loci and surface proteins. PMID:33261555
Genomic Characterization of a Novel Tenericutes Bacterium from Deep-Sea Holothurian Intestine. PMID:33260795
Unravelling the Features of Success of VIM-Producing ST111 and ST235 Pseudomonas aeruginosa in a Greek Hospital. PMID:33260774
Unexpected diversity of CRISPR unveils some evolutionary patterns of repeated sequences in Mycobacterium tuberculosis. PMID:33256602
Casboundary: automated definition of integral Cas cassettes. PMID:33226067
Prophages are associated with extensive CRISPR-Cas auto-immunity. PMID:33219687
CRISPR-Cas Diversity in Clinical Salmonella enterica Serovar Typhi Isolates from South Asian Countries. PMID:33218076
Characterization of Clinical and Carrier Streptococcus agalactiae and Prophage Contribution to the Strain Variability. PMID:33217933
Identification of Spacer and Protospacer Sequence Requirements in the Vibrio cholerae Type I-E CRISPR/Cas System. PMID:33208517
CRISPR sequences are sometimes erroneously translated and can contaminate public databases with spurious proteins containing spaced repeats. PMID:33206958
Insights into the Metabolism and Evolution of the Genus Acidiphilium, a Typical Acidophile in Acid Mine Drainage. PMID:33203689
Multidrug-Resistant Proteus mirabilis Strain with Cointegrate Plasmid. PMID:33198099
There're CRISPRs in My Yogurt: A Discovery-Based CURE at the Intersection of Industrial Food Production and the Human Microbiome. PMID:33193202
Heavily Armed Ancestors: CRISPR Immunity and Applications in Archaea with a Comparative Analysis of CRISPR Types in Sulfolobales. PMID:33172134
Discovery of multiple anti-CRISPRs highlights anti-defense gene clustering in mobile genetic elements. PMID:33159058
Genome mining and UHPLC-QTOF-MS/MS to identify the potential antimicrobial compounds and determine the specificity of biosynthetic gene clusters in Bacillus subtilis NCD-2. PMID:33153447
Decoding the Genomic Variability among Members of the Bifidobacterium dentium Species. PMID:33152994
Plasmid- and strain-specific factors drive variation in ESBL-plasmid spread in vitro and in vivo. PMID:33149210
Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics. PMID:33139880
In silico Method in CRISPR/Cas System: An Expedite and Powerful Booster. PMID:33123486
Draft Genome Sequences of Cronobacter muytjensii Cr150, Cronobacter turicensis Cr170, and Cronobacter sakazakii Cr611. PMID:33122419
Repurposing the Native Type I-F CRISPR-Cas System in Pseudomonas aeruginosa for Genome Editing. PMID:33111087
Integrated Phenotypic-Genotypic Analysis of Candidate Probiotic Weissella Cibaria Strains Isolated from Dairy Cows in Kuwait. PMID:33085038
AcrDB: a database of anti-CRISPR operons in prokaryotes and viruses. PMID:33068435
Long-run bacteria-phage coexistence dynamics under natural habitat conditions in an environmental biotechnology system. PMID:33067586
Clinical and molecular characteristics of carbapenem non-susceptible Escherichia coli: A nationwide survey from Oman. PMID:33036018
Complete Genome Sequence of Yellow Pigment-Producing Sphingobium sp. Strain HAL-16. PMID:33033136
Draft Genome Sequence of Escherichia coli Strain Tj, Isolated from the Varzob River in Tajikistan. PMID:33033128
Genomic analysis reveals high virulence and antibiotic resistance amongst phage susceptible Acinetobacter baumannii. PMID:32999368
Complete genome sequence of fish-pathogenic Aeromonas hydrophila HX-3 and a comparative analysis: insights into virulence factors and quorum sensing. PMID:32968153
Genome-Assisted Characterization of Lactobacillus fermentum, Weissella cibaria, and Weissella confusa Strains Isolated from Sorghum as Starters for Sourdough Fermentation. PMID:32927810
Identification of a Type IV-A CRISPR-Cas System Located Exclusively on IncHI1B/IncFIB Plasmids in Enterobacteriaceae. PMID:32903441
Investigation of a Staphylococcus argenteus Strain Involved in a Chronic Prosthetic-Joint Infection. PMID:32872360
The Impact of Mercury Selection and Conjugative Genetic Elements on Community Structure and Resistance Gene Transfer. PMID:32849443
Comprehensive genome data analysis establishes a triple whammy of carbapenemases, ICEs and multiple clinically relevant bacteria. PMID:32841111
Complete Genome Sequence of Streptococcus mutans Strain MD, Which Produces Highly Potent Mutacins. PMID:32817148
Complete Genomic Analysis of Enterococcus faecium Heat-Resistant Strain Developed by Two-Step Adaptation Laboratory Evolution Method. PMID:32793575
Characterization of a SPM-1 metallo-beta-lactamase-producing Pseudomonas aeruginosa by comparative genomics and phenotypic analysis. PMID:32764694
Draft Genome Sequence of Ligilactobacillus salivarius TUCO-L2, Isolated from Lama glama Milk. PMID:32763947
The Isolation and Genome Sequencing of Five Novel Bacteriophages From the Rumen Active Against Butyrivibrio fibrisolvens. PMID:32760371
ICEs Are the Main Reservoirs of the Ciprofloxacin-Modifying crpP Gene in Pseudomonas aeruginosa. PMID:32759827
Modular prophage interactions driven by capsule serotype select for capsule loss under phage predation. PMID:32732904
DNA targeting and interference by a bacterial Argonaute nuclease. PMID:32731256
Genomic Characterization and Environmental Distribution of a Thermophilic Anaerobe Dissulfurirhabdus thermomarina SH388T Involved in Disproportionation of Sulfur Compounds in Shallow Sea Hydrothermal Vents. PMID:32727039
High diversity and variability of pipolins among a wide range of pathogenic Escherichia coli strains. PMID:32719405
Completed Genomic Sequence of Bacillus thuringiensis HER1410 Reveals a Cry-Containing Chromosome, Two Megaplasmids, and an Integrative Plasmidial Prophage. PMID:32690586
Insights into the dynamics between viruses and their hosts in a hot spring microbial mat. PMID:32661357
Comparative Genomic Analysis Reveals the Metabolism and Evolution of the Thermophilic Archaeal Genus Metallosphaera. PMID:32655516
Single-Cell Genomics of Novel Actinobacteria With the Wood-Ljungdahl Pathway Discovered in a Serpentinizing System. PMID:32655506
A Genomic Perspective on the Potential of Wild-Type Rumen Bacterium Enterobacter sp. LU1 as an Industrial Platform for Bio-Based Succinate Production. PMID:32650546
Genomic characterization of the most barotolerant Listeria monocytogenes RO15 strain compared to reference strains used to evaluate food high pressure processing. PMID:32615922
Genomic analyses of multidrug-resistant Salmonella Indiana, Typhimurium, and Enteritidis isolates using MinION and MiSeq sequencing technologies. PMID:32614888
Determining the Genetic Characteristics of Resistance and Virulence of the "Epidermidis Cluster Group" Through Pan-Genome Analysis. PMID:32596166
Draft Genome Sequence of Bifidobacterium pseudocatenulatum Bif4, Isolated from Healthy Infant Feces. PMID:32586871
The Basis for Natural Multiresistance to Phage in Pseudomonas aeruginosa. PMID:32570896
CRISPRcasIdentifier: Machine learning for accurate identification and classification of CRISPR-Cas systems. PMID:32556168
Dual-Seq reveals genome and transcriptome of Caedibacter taeniospiralis, obligate endosymbiont of Paramecium. PMID:32546745
Initial Mapping of the New York City Wastewater Virome. PMID:32546676
Campylobacter bacteriophage DA10: an excised temperate bacteriophage targeted by CRISPR-cas. PMID:32532247
Bio-Layer Interferometry Analysis of the Target Binding Activity of CRISPR-Cas Effector Complexes. PMID:32528975
The Diversity of the CRISPR-Cas System and Prophages Present in the Genome Reveals the Co-evolution of Bifidobacterium pseudocatenulatum and Phages. PMID:32528454
Alteromonas Myovirus V22 Represents a New Genus of Marine Bacteriophages Requiring a Tail Fiber Chaperone for Host Recognition. PMID:32518192
Draft Genome Sequence of Escherichia coli UMB9246, Isolated from the Bladder of a Woman with Recurrent Urinary Tract Infection. PMID:32499352
Exploring potential of vaginal Lactobacillus isolates from South African women for enhancing treatment for bacterial vaginosis. PMID:32497109
Parallel reductive genome evolution in Desulfovibrio ectosymbionts independently acquired by Trichonympha protists in the termite gut. PMID:32483307
Draft Genome Sequence of Lactobacillus mulieris UMB7784, Isolated from the Female Urinary Tract. PMID:32439675
Genome Sequences of Burkholderia thailandensis Strains E421, E426, and DW503. PMID:32439666
Draft Genome Sequence of Lactobacillus mulieris UMB9245, Isolated from the Female Bladder. PMID:32409555
Whole Genome Sequencing and Comparative Genomic Analyses of Lysinibacillus pakistanensis LZH-9, a Halotolerant Strain with Excellent COD Removal Capability. PMID:32408484
AcrFinder: genome mining anti-CRISPR operons in prokaryotes and their viruses. PMID:32402073
Comparative Genomic Analysis Provides Insights into the Phylogeny, Resistome, Virulome, and Host Adaptation in the Genus Ewingella. PMID:32354059
Niche specialization and spread of Staphylococcus capitis involved in neonatal sepsis. PMID:32341568
Exploring the success of Brazilian endemic clone Pseudomonas aeruginosa ST277 and its association with the CRISPR-Cas system type I-C. PMID:32293244
Draft Genome Sequence of Pseudarthrobacter phenanthrenivorans Strain MHSD1, a Bacterial Endophyte Isolated From the Medicinal Plant Pellaea calomelanos. PMID:32284671
Complete Genome Sequence of Moraxella osloensis Strain YV1, Isolated from an Australian Wastewater Treatment Plant. PMID:32273350
Honey bees harbor a diverse gut virome engaging in nested strain-level interactions with the microbiota. PMID:32179689
Comparative Genomics of Pediococcus pentosaceus Isolated From Different Niches Reveals Genetic Diversity in Carbohydrate Metabolism and Immune System. PMID:32174896
Functional Genomics Insights Into the Pathogenicity, Habitat Fitness, and Mechanisms Modifying Plant Development of Rhodococcus sp. PBTS1 and PBTS2. PMID:32082278
Prophage-Mediated Disruption of Genetic Competence in Staphylococcus pseudintermedius. PMID:32071159
Genome analysis of a wild rumen bacterium Enterobacter aerogenes LU2 - a novel bio-based succinic acid producer. PMID:32029880
Characterization of Staphylococcus intermedius Group Isolates Associated with Animals from Antarctica and Emended Description of Staphylococcus delphini. PMID:32024111
Comparative analysis of Lactobacillus gasseri from Chinese subjects reveals a new species-level taxa. PMID:32013858
Targeting of temperate phages drives loss of type I CRISPR-Cas systems. PMID:31969710
Draft Genome Sequence of the Non-Microcystin-Producing Microcystis aeruginosa Strain KLA2, Isolated from a Freshwater Reservoir in Northern California, USA. PMID:31948955
Comparative Genomics Analysis of Lactobacillus mucosae from Different Niches. PMID:31947593
Type I-F CRISPR-Cas Distribution and Array Dynamics in Legionella pneumophila. PMID:31937548
Campylobacter portucalensis sp. nov., a new species of Campylobacter isolated from the preputial mucosa of bulls. PMID:31923228
Composition and Diversity of CRISPR-Cas13a Systems in the Genus Leptotrichia. PMID:31921024
The complete genome sequence of the nitrile biocatalyst Rhodocccus rhodochrous ATCC BAA-870. PMID:31898479
Genomic Characteristics of the Toxic Bloom-Forming Cyanobacterium Microcystis aeruginosa NIES-102. PMID:31892993
Type IV CRISPR-Cas systems are highly diverse and involved in competition between plasmids. PMID:31879772
Multiple Origins and Specific Evolution of CRISPR/Cas9 Systems in Minimal Bacteria (Mollicutes). PMID:31824468
Draft Genome Sequence of Enterobacter hormaechei Strain MHSD6, a Plant Endophyte Isolated from Medicinal Plant Pellaea calomelanos. PMID:31776223
Genome-Wide Analyses Revealed Remarkable Heterogeneity in Pathogenicity Determinants, Antimicrobial Compounds, and CRISPR-Cas Systems of Complex Phytopathogenic Genus Pectobacterium. PMID:31756888
Novel Sulfolobus Fuselloviruses with Extensive Genomic Variations. PMID:31748395
Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile genetic elements. PMID:31745554
Genomic Insights into the Carbon and Energy Metabolism of a Thermophilic Deep-Sea Bacterium Deferribacter autotrophicus Revealed New Metabolic Traits in the Phylum Deferribacteres. PMID:31717820
Prokaryotic Genome Expansion Is Facilitated by Phages and Plasmids but Impaired by CRISPR. PMID:31681190
International Spread of Multidrug-Resistant Campylobacter coli in Men Who Have Sex With Men in Washington State and Québec, 2015-2018. PMID:31665255
Maintenance of Sympatric and Allopatric Populations in Free-Living Terrestrial Bacteria. PMID:31662456
MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis. PMID:31647104
Characterization and repurposing of the endogenous Type I-F CRISPR-Cas system of Zymomonas mobilis for genome engineering. PMID:31647102
Pangenome of Acinetobacter baumannii uncovers two groups of genomes, one of them with genes involved in CRISPR/Cas defence systems associated with the absence of plasmids and exclusive genes for biofilm formation. PMID:31626589
CRISPRCasdb a successor of CRISPRdb containing CRISPR arrays and cas genes from complete genome sequences, and tools to download and query lists of repeats and spacers. PMID:31624845
PADS Arsenal: a database of prokaryotic defense systems related genes. PMID:31620779
Genomic Insights Into Five Strains of Lactobacillus plantarum With Biotechnological Potential Isolated From chicha, a Traditional Maize-Based Fermented Beverage From Northwestern Argentina. PMID:31611862
Complete Genome Sequence of the Biocontrol Agent Bacillus velezensis UFLA258 and Its Comparison with Related Species: Diversity within the Commons. PMID:31580420
Cronobacter sakazakii, Cronobacter malonaticus, and Cronobacter dublinensis Genotyping Based on CRISPR Locus Diversity. PMID:31555228
A Simple Criterion for Inferring CRISPR Array Direction. PMID:31551987
Using the Endogenous CRISPR-Cas System of Heliobacterium modesticaldum To Delete the Photochemical Reaction Center Core Subunit Gene. PMID:31540988
Bioinformatics Identification of Anti-CRISPR Loci by Using Homology, Guilt-by-Association, and CRISPR Self-Targeting Spacer Approaches. PMID:31506266
CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog. PMID:31492655
Draft Genome Sequences of 11 Lactobacillus jensenii Strains Isolated from the Female Bladder. PMID:31467111
Genome Sequence of a Novel Enterococcus faecalis Sequence Type 922 Strain Isolated from a Door Handle in the Intensive Care Unit of a District Hospital in Durban, South Africa. PMID:31467094
CasPDB: an integrated and annotated database for Cas proteins from bacteria and archaea. PMID:31411686
Genomic analysis of Staphylococcus capitis isolated from blood cultures in neonates at a neonatal intensive care unit in Sweden. PMID:31396832
Whole-Genome Sequences of Four Indian Isolates of Azospirillum brasilense. PMID:31371541
Genome sequencing and analysis of Salmonella enterica subsp. enterica serovar Stanley UPM 517: Insights on its virulence-associated elements and their potentials as vaccine candidates. PMID:31293824
Genomic Comparison of Lactobacillus helveticus Strains Highlights Probiotic Potential. PMID:31293536
Genetic and Phenotypic Features of a Novel Acinetobacter Species, Strain A47, Isolated From the Clinical Setting. PMID:31275288
Mobilome of Brevibacterium aurantiacum Sheds Light on Its Genetic Diversity and Its Adaptation to Smear-Ripened Cheeses. PMID:31244798
Diversity of CRISPR/Cas system in Clostridium perfringens. PMID:31134321
Draft Genome Sequence of a Medium- and Long-Chain n-Alkane-Degrading Bacterium, Tsukamurella tyrosinosolvens Strain PS2, with Two Genetic Systems for Alkane Degradation. PMID:31023793
Accessory genome of the multi-drug resistant ocular isolate of Pseudomonas aeruginosa PA34. PMID:30986237
Just the Two of Us? A Family of Pseudomonas Megaplasmids Offers a Rare Glimpse into the Evolution of Large Mobile Elements. PMID:30918968
A matter of background: DNA repair pathways as a possible cause for the sparse distribution of CRISPR-Cas systems in bacteria. PMID:30905287
Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species. PMID:30905286
Insight into the genome and brackish water adaptation strategies of toxic and bloom-forming Baltic Sea Dolichospermum sp. UHCC 0315. PMID:30894564
Pseudomonas Diversity Within Urban Freshwaters. PMID:30828321
Draft Genome Sequence of Chromatium okenii Isolated from the Stratified Alpine Lake Cadagno. PMID:30760771
Genotypic differences between strains of the opportunistic pathogen Corynebacterium bovis isolated from humans, cows, and rodents. PMID:30586440
CRISPRminer is a knowledge base for exploring CRISPR-Cas systems in microbe and phage interactions. PMID:30393777
MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems PubMed citations: 104.

104 articles citing: MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems

Analysis of the Taxonomy, Synteny, and Virulence Factors for Soft Rot Pathogen Pectobacterium aroidearum in Amorphophallus konjac Using Comparative Genomics. PMID:35910650
The Di-Symbiotic Systems in the Aphids Sipha maydis and Periphyllus lyropictus Provide a Contrasting Picture of Recent Co-Obligate Nutritional Endosymbiosis in Aphids. PMID:35889078
The evolutionary origin of host association in the Rickettsiales. PMID:35798888
Phage-host coevolution in natural populations. PMID:35760840
Isolation of Listeria ivanovii from Bulk-Tank Milk of Sheep and Goat Farms-From Clinical Work to Bioinformatics Studies: Prevalence, Association with Milk Quality, Antibiotic Susceptibility, Predictors, Whole Genome Sequence and Phylogenetic Relationships. PMID:35741392
Host control and the evolution of cooperation in host microbiomes. PMID:35732630
Evolution of Plasmid Mobility: Origin and Fate of Conjugative and Nonconjugative Plasmids. PMID:35639760
PADLOC: a web server for the identification of antiviral defence systems in microbial genomes. PMID:35639517
Genomic characterization of lytic bacteriophages targeting genetically diverse Pseudomonas aeruginosa clinical isolates. PMID:35620437
Comprehensive Analysis Reveals the Genetic and Pathogenic Diversity of Ralstonia solanacearum Species Complex and Benefits Its Taxonomic Classification. PMID:35602040
Comparative Genomic Analysis of Vibrio cincinnatiensis Provides Insights into Genetic Diversity, Evolutionary Dynamics, and Pathogenic Traits of the Species. PMID:35562911
FirmiData: a set of 40 genomes of Firmicutes with a curated annotation of ICEs and IMEs. PMID:35538580
Systematic and quantitative view of the antiviral arsenal of prokaryotes. PMID:35538097
Long-Term Stability of Bacterial Associations in a Microcosm of Ostreococcus tauri (Chlorophyta, Mamiellophyceae). PMID:35463414
Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance. PMID:35379360
Engineering selectivity of Cutibacterium acnes phages by epigenetic imprinting. PMID:35344565
Phages and their satellites encode hotspots of antiviral systems. PMID:35316646
Pan-Genome Analysis of Delftia tsuruhatensis Reveals Important Traits Concerning the Genetic Diversity, Pathogenicity, and Biotechnological Properties of the Species. PMID:35230132
Strategies for High-Efficiency Mutation Using the CRISPR/Cas System. PMID:35198566
The "Other" Rickettsiales: an Overview of the Family "Candidatus Midichloriaceae". PMID:35108076
Isolation and characterization of Streptomyces bacteriophages and Streptomyces strains encoding biosynthetic arsenals. PMID:35061755
Bacteroidales species in the human gut are a reservoir of antibiotic resistance genes regulated by invertible promoters. PMID:35013297
A catalogue of 1,167 genomes from the human gut archaeome. PMID:34969981
Genomic Analysis of Global Staphylococcus argenteus Strains Reveals Distinct Lineages With Differing Virulence and Antibiotic Resistance Gene Content. PMID:34925305
The Facts and Family Secrets of Plasmids That Replicate via the Rolling-Circle Mechanism. PMID:34878299
Characterization of Blf4, an Archaeal Lytic Virus Targeting a Member of the Methanomicrobiales. PMID:34696364
Comparative Genomic Analysis of Bifidobacterium bifidum Strains Isolated from Different Niches. PMID:34680899
Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types. PMID:34606606
CASPredict: a web service for identifying Cas proteins. PMID:34395100
At the Gate of Mutualism: Identification of Genomic Traits Predisposing to Insect-Bacterial Symbiosis in Pathogenic Strains of the Aphid Symbiont Serratia symbiotica. PMID:34268133
Identification and Characterization of the CRISPR/Cas System in Staphylococcus aureus Strains From Diverse Sources. PMID:34149645
Molecular Analysis of Bacterial Isolates From Necrotic Wheat Leaf Lesions Caused by Xanthomonas translucens, and Description of Three Putative Novel Species, Sphingomonas albertensis sp. nov., Pseudomonas triticumensis sp. nov. and Pseudomonas foliumensis sp. nov. PMID:34093484
SepF is the FtsZ anchor in archaea, with features of an ancestral cell division system. PMID:34088904
Comprehensive Scanning of Prophages in Lactobacillus: Distribution, Diversity, Antibiotic Resistance Genes, and Linkages with CRISPR-Cas Systems. PMID:34060909
Comparative Genomics, from the Annotated Genome to Valuable Biological Information: A Case Study. PMID:33961220
Complete Genome Sequences of Francisella marina Strains E95-16 and E103-15, Isolated from Maricultured Spotted Rose Snapper (Lutjanus guttatus) on the Pacific Coast of Central America. PMID:33958406
Genome analysis provides insights into the biocontrol ability of Mitsuaria sp. strain TWR114. PMID:33880605
Population genomics and antimicrobial resistance dynamics of Escherichia coli in wastewater and river environments. PMID:33846529
A novel approach to teaching Hidden Markov Models to a diverse undergraduate population. PMID:33748491
Bacteria have numerous distinctive groups of phage-plasmids with conserved phage and variable plasmid gene repertoires. PMID:33590101
Comparative genomics of Flavobacterium columnare unveils novel insights in virulence and antimicrobial resistance mechanisms. PMID:33579339
Pathogenic Determinants of the Mycobacterium kansasii Complex: An Unsuspected Role for Distributive Conjugal Transfer. PMID:33578772
CasCollect: targeted assembly of CRISPR-associated operons from high-throughput sequencing data. PMID:33575613
The State of the Art in Biodefense Related Bacterial Pathogen Detection Using Bacteriophages: How It Started and How It's Going. PMID:33291831
Prophages are associated with extensive CRISPR-Cas auto-immunity. PMID:33219687
In silico Method in CRISPR/Cas System: An Expedite and Powerful Booster. PMID:33123486
Genome-wide analysis of the Firmicutes illuminates the diderm/monoderm transition. PMID:33077930
Ancestral Reconstructions Decipher Major Adaptations of Ammonia-Oxidizing Archaea upon Radiation into Moderate Terrestrial and Marine Environments. PMID:33051370
Comprehensive genome data analysis establishes a triple whammy of carbapenemases, ICEs and multiple clinically relevant bacteria. PMID:32841111
Autotransporters Drive Biofilm Formation and Autoaggregation in the Diderm Firmicute Veillonella parvula. PMID:32817093
ICEs Are the Main Reservoirs of the Ciprofloxacin-Modifying crpP Gene in Pseudomonas aeruginosa. PMID:32759827
Chromosome Architecture and Gene Content of the Emergent Pathogen Acinetobacter haemolyticus. PMID:32670207
CRISPRcasIdentifier: Machine learning for accurate identification and classification of CRISPR-Cas systems. PMID:32556168
Phylogenetic background and habitat drive the genetic diversification of Escherichia coli. PMID:32530914
Virulence Potential of a Multidrug-Resistant Escherichia coli Strain Belonging to the Emerging Clonal Group ST101-B1 Isolated from Bloodstream Infection. PMID:32486334
Identification of integrative and conjugative elements in pathogenic and commensal Neisseriaceae species via genomic distributions of DNA uptake sequence dialects. PMID:32375974
The Potato Yam Phyllosphere Ectosymbiont Paraburkholderia sp. Msb3 Is a Potent Growth Promotor in Tomato. PMID:32373084
Comparative Genomic Analysis Provides Insights into the Phylogeny, Resistome, Virulome, and Host Adaptation in the Genus Ewingella. PMID:32354059
Repeated horizontal gene transfers triggered parallel evolution of magnetotaxis in two evolutionary divergent lineages of magnetotactic bacteria. PMID:32296121
Draft Genome Sequence of Pseudarthrobacter phenanthrenivorans Strain MHSD1, a Bacterial Endophyte Isolated From the Medicinal Plant Pellaea calomelanos. PMID:32284671
The major subunit of widespread competence pili exhibits a novel and conserved type IV pilin fold. PMID:32273343
Comparative Genomic Analysis Confirms Five Genetic Populations of the Select Agent, Rathayibacter toxicus. PMID:32150860
Comparative genomics of the fish pathogens Edwardsiella ictaluri 93-146 and Edwardsiella piscicida C07-087. PMID:32108566
Comparative Genomic Analysis of Citrobacter and Key Genes Essential for the Pathogenicity of Citrobacter koseri. PMID:31866966
Draft Genome Sequence of Enterobacter hormaechei Strain MHSD6, a Plant Endophyte Isolated from Medicinal Plant Pellaea calomelanos. PMID:31776223
Comparative genomics reveals a novel genetic organization of the sad cluster in the sulfonamide-degrader 'Candidatus Leucobacter sulfamidivorax' strain GP. PMID:31752666
Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile genetic elements. PMID:31745554
Pan-genome analysis of Riemerella anatipestifer reveals its genomic diversity and acquired antibiotic resistance associated with genomic islands. PMID:31654228
MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis. PMID:31647104
Comparative genomic analysis of the Hafnia genus reveals an explicit evolutionary relationship between the species alvei and paralvei and provides insights into pathogenicity. PMID:31646960
CRISPRCasdb a successor of CRISPRdb containing CRISPR arrays and cas genes from complete genome sequences, and tools to download and query lists of repeats and spacers. PMID:31624845
Implications of Mobile Genetic Elements for Salmonella enterica Single-Nucleotide Polymorphism Subtyping and Source Tracking Investigations. PMID:31585993
Comparative genomics of Aeromonas veronii: Identification of a pathotype impacting aquaculture globally. PMID:31465454
An archaeal origin of the Wood-Ljungdahl H4MPT branch and the emergence of bacterial methylotrophy. PMID:31451772
Evolution of a family of molecular Rube Goldberg contraptions. PMID:31415567
Comparative genome analysis of Lactobacillus mudanjiangensis, an understudied member of the Lactobacillus plantarum group. PMID:31368886
Population gene introgression and high genome plasticity for the zoonotic pathogen Streptococcus agalactiae. PMID:31350563
Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility. PMID:31323028
Ubiquinone Biosynthesis over the Entire O2 Range: Characterization of a Conserved O2-Independent Pathway. PMID:31289180
First Report of Integrative Conjugative Elements in Riemerella anatipestifer Isolates From Ducks in China. PMID:31069241
Just the Two of Us? A Family of Pseudomonas Megaplasmids Offers a Rare Glimpse into the Evolution of Large Mobile Elements. PMID:30918968
The effect of bacterial mutation rate on the evolution of CRISPR-Cas adaptive immunity. PMID:30905293
A matter of background: DNA repair pathways as a possible cause for the sparse distribution of CRISPR-Cas systems in bacteria. PMID:30905287
Insight into the genome and brackish water adaptation strategies of toxic and bloom-forming Baltic Sea Dolichospermum sp. UHCC 0315. PMID:30894564
Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea. PMID:30833729
Comparative genomics of Paraburkholderia kururiensis and its potential in bioremediation, biofertilization, and biocontrol of plant pathogens. PMID:30811107
Comparative Genomics of Aeromonas hydrophila Secretion Systems and Mutational Analysis of hcp1 and vgrG1 Genes From T6SS. PMID:30687246
Genetic exchanges are more frequent in bacteria encoding capsules. PMID:30576310
Host Range and Genetic Plasticity Explain the Coexistence of Integrative and Extrachromosomal Mobile Genetic Elements. PMID:29905872
CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. PMID:29790974
The Genome Sequence of "Candidatus Fokinia solitaria": Insights on Reductive Evolution in Rickettsiales. PMID:29659807
Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome. PMID:29434576
Inhibition of NHEJ repair by type II-A CRISPR-Cas systems in bacteria. PMID:29234047
The chromosomal organization of horizontal gene transfer in bacteria. PMID:29018197
The Type IX Secretion System Is Required for Virulence of the Fish Pathogen Flavobacterium columnare. PMID:28939608
Integrative and conjugative elements and their hosts: composition, distribution and organization. PMID:28911112
Comparative Analysis of the Flavobacterium columnare Genomovar I and II Genomes. PMID:28790987
Abundance and co-occurrence of extracellular capsules increase environmental breadth: Implications for the emergence of pathogens. PMID:28742161
Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain. PMID:28537263
Comparative Genomics and Transcriptional Analysis of Flavobacterium columnare Strain ATCC 49512. PMID:28469601
Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis. PMID:27461509
Genetic and life-history traits associated with the distribution of prophages in bacteria. PMID:27015004
Identification of protein secretion systems in bacterial genomes. PMID:26979785
Bacteria in Ostreococcus tauri cultures - friends, foes or hitchhikers? PMID:25426102
CRISPRCasdb a successor of CRISPRdb containing CRISPR arrays and cas genes from complete genome sequences, and tools to download and query lists of repeats and spacers PubMed citations: 34.

34 articles citing: CRISPRCasdb a successor of CRISPRdb containing CRISPR arrays and cas genes from complete genome sequences, and tools to download and query lists of repeats and spacers

Interaction of Proteins with Inverted Repeats and Cruciform Structures in Nucleic Acids. PMID:35682854
CrisprVi: a software for visualizing and analyzing CRISPR sequences of prokaryotes. PMID:35610585
The Virome of Healthy Honey Bee Colonies: Ubiquitous Occurrence of Known and New Viruses in Bee Populations. PMID:35532210
Prediction of Prophages and Their Host Ranges in Pathogenic and Commensal Neisseria Species. PMID:35418239
CRISPR-Cas Systems in Gut Microbiome of Children with Autism Spectrum Disorders. PMID:35330117
viralFlye: assembling viruses and identifying their hosts from long-read metagenomics data. PMID:35189932
An Interplay between Viruses and Bacteria Associated with the White Sea Sponges Revealed by Metagenomics. PMID:35054418
Spontaneous Phage Resistance in Avian Pathogenic Escherichia coli. PMID:34966369
Colistin Resistance Onset Strategies and Genomic Mosaicism in Clinical Acinetobacter baumannii Lineages. PMID:34832671
CRISPR Element Patterns vs. Pathoadaptability of Clinical Pseudomonas aeruginosa Isolates from a Medical Center in Moscow, Russia. PMID:34827239
High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems. PMID:34758284
CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids. PMID:34606604
PAM-repeat associations and spacer selection preferences in single and co-occurring CRISPR-Cas systems. PMID:34593010
Mechanism for Cas4-assisted directional spacer acquisition in CRISPR-Cas. PMID:34588691
CRISPR/Cas9: Principle, Applications, and Delivery through Extracellular Vesicles. PMID:34199901
Comparative genomic analysis of Mycoplasma anatis strains. PMID:34181213
Distribution and phasing of sequence motifs that facilitate CRISPR adaptation. PMID:34174210
Genome analysis of Pseudomonas sp. OF001 and Rubrivivax sp. A210 suggests multicopper oxidases catalyze manganese oxidation required for cylindrospermopsin transformation. PMID:34157973
Identification and Characterization of the CRISPR/Cas System in Staphylococcus aureus Strains From Diverse Sources. PMID:34149645
Pruning and Tending Immune Memories: Spacer Dynamics in the CRISPR Array. PMID:33868219
Genomic and Phenotypic Analysis of Multidrug-Resistant Acinetobacter baumannii Clinical Isolates Carrying Different Types of CRISPR/Cas Systems. PMID:33668622
Phageome Analysis of Bifidobacteria-Rich Samples. PMID:33649949
Vagococcus fluvialis isolation and sequencing from urine of healthy cattle. PMID:33561240
Evaluation of CRISPR Diversity in the Human Skin Microbiome for Personal Identification. PMID:33531409
CRISPR-Cas Diversity in Clinical Salmonella enterica Serovar Typhi Isolates from South Asian Countries. PMID:33218076
Identification of Natural CRISPR Systems and Targets in the Human Microbiome. PMID:33217332
CRISPR sequences are sometimes erroneously translated and can contaminate public databases with spurious proteins containing spaced repeats. PMID:33206958
Heavily Armed Ancestors: CRISPR Immunity and Applications in Archaea with a Comparative Analysis of CRISPR Types in Sulfolobales. PMID:33172134
Transcription termination and antitermination of bacterial CRISPR arrays. PMID:33124980
In silico Method in CRISPR/Cas System: An Expedite and Powerful Booster. PMID:33123486
Csx3 is a cyclic oligonucleotide phosphodiesterase associated with type III CRISPR-Cas that degrades the second messenger cA4. PMID:32826317
New virus isolates from Italian hydrothermal environments underscore the biogeographic pattern in archaeal virus communities. PMID:32322010
Detection of CRISPR adaptation. PMID:32010936
The 27th annual Nucleic Acids Research database issue and molecular biology database collection. PMID:31906604

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version: FAIRsharing.org: CRISPRCasdb; CRISPRCasdb; DOI: https://doi.org/10.25504/FAIRsharing.QMGzTm; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

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version: FAIRsharing.org: CRISPRCasdb; CRISPRCasdb; DOI: https://doi.org/10.25504/FAIRsharing.QMGzTm; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

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version: FAIRsharing.org: CRISPRCasdb; CRISPRCasdb; DOI: https://doi.org/10.25504/FAIRsharing.QMGzTm; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

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version: FAIRsharing.org: CRISPRCasdb; CRISPRCasdb; DOI: https://doi.org/10.25504/FAIRsharing.QMGzTm; Last edited: Jan. 25, 2021, 4:27 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

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