FAIRsharing.2wb6fv; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

Other names: rrnDB

The ribosomal RNA operon copy number database is a publicly available, curated resource for ribosomal operon (rrn) copy number information for Bacteria and Archaea.

Webpage:

http://rrndb.umms.med.umich.edu/

Publications:

Publications
More detailed information about this field from each metasource.

rrndb: the Ribosomal RNA Operon Copy Number Database
PMID: 11125085
metasource: Fairsharing.org
version: FAIRsharing.org: rrnDB; The ribosomal RNA operon copy number database; DOI: https://doi.org/10.25504/FAIRsharing.2wb6fv; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development
PMID: 25414355
metasource: Fairsharing.org
version: FAIRsharing.org: rrnDB; The ribosomal RNA operon copy number database; DOI: https://doi.org/10.25504/FAIRsharing.2wb6fv; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea
PMID: 18948294
metasource: Fairsharing.org
version: FAIRsharing.org: rrnDB; The ribosomal RNA operon copy number database; DOI: https://doi.org/10.25504/FAIRsharing.2wb6fv; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

rrndb: the Ribosomal RNA Operon Copy Number Database PubMed citations: 296.

296 articles citing: rrndb: the Ribosomal RNA Operon Copy Number Database

Estuarine plastisphere as an overlooked source of N2O production. PMID:35794126
Identification of housekeeping genes of Candidatus Branchiomonas cysticola associated with epitheliocystis in Atlantic salmon (Salmo salar L.). PMID:35661924
Effects of broad-spectrum antibiotics on the colonisation of probiotic yeast Saccharomyces boulardii in the murine gastrointestinal tract. PMID:35614092
Microfluidic One-Pot Digital Droplet FISH Using LNA/DNA Molecular Beacons for Bacteria Detection and Absolute Quantification. PMID:35448297
Morphological characteristics and abundance of prokaryotes associated with gills in mangrove brachyuran crabs living along a tidal gradient. PMID:35421185
Comparison of Automated Ribotyping, spa Typing, and MLST in 108 Clinical Isolates of Staphylococcus aureus from Orthopedic Infections. PMID:35163582
Dysbiotic microbes and how to find them: a review of microbiome profiling in prostate cancer. PMID:35065652
Cerebrospinal Fluid from Healthy Pregnant Women Does Not Harbor a Detectable Microbial Community. PMID:34908504
Improved quantitative microbiome profiling for environmental antibiotic resistance surveillance. PMID:34794510
The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole. PMID:34531387
Ribosome Biogenesis in Archaea. PMID:34367089
Ultra-accurate microbial amplicon sequencing with synthetic long reads. PMID:34090540
Analysis of microbiota in the stomach and midgut of two penaeid shrimps during probiotic feeding. PMID:33976316
High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers. PMID:33953314
Influence of Temperature and Sulfate Concentration on the Sulfate/Sulfite Reduction Prokaryotic Communities in the Tibetan Hot Springs. PMID:33809110
R/G Value-A Numeric Index of Individual Periodontal Health and Oral Microbiome Dynamics. PMID:33777830
Toward Best Practice in Livestock Microbiota Research: A Comprehensive Comparison of Sample Storage and DNA Extraction Strategies. PMID:33708184
Molecular Detection of Campylobacter Species: Comparision of 16SrRNA with slyD, cadF, rpoA, and dnaJ Sequencing. PMID:33649718
Primer, Pipelines, Parameters: Issues in 16S rRNA Gene Sequencing. PMID:33627512
The gut microbiome of horses: current research on equine enteral microbiota and future perspectives. PMID:33499951
TIPP2: metagenomic taxonomic profiling using phylogenetic markers. PMID:33471121
Wide distribution of the Ustilago maydis-bacterium endosymbiosis in naturally infected maize plants. PMID:33356903
Effect of diet and intestinal AhR expression on fecal microbiome and metabolomic profiles. PMID:33256731
Comparison of the Performance and Microbial Community Structure of Two Outdoor Pilot-Scale Photobioreactors Treating Digestate. PMID:33171685
Response of Salivary Microbiota to Caries Preventive Treatment in Aboriginal and Torres Strait Islander Children. PMID:33149844
Evaluating the Potential Antibiotic Resistance Status in Environment Based on the Trait of Microbial Community. PMID:33123107
Regeneration of unconventional natural gas by methanogens co-existing with sulfate-reducing prokaryotes in deep shale wells in China. PMID:32994524
Antifungal Potential of the Skin Microbiota of Hibernating Big Brown Bats (Eptesicus fuscus) Infected With the Causal Agent of White-Nose Syndrome. PMID:32793178
Prevalence of Antibiotic Resistome in Ready-to-Eat Salad. PMID:32269985
Quantification and Phylogenetic Analysis of Ammonia Oxidizers on Biofilm Carriers in a Full-Scale Wastewater Treatment Plant. PMID:32249239
Multitarget Approaches against Multiresistant Superbugs. PMID:32156116
Effects of Composting Different Types of Organic Fertilizer on the Microbial Community Structure and Antibiotic Resistance Genes. PMID:32079314
Phylogenomic analysis of novel Diaforarchaea is consistent with sulfite but not sulfate reduction in volcanic environments on early Earth. PMID:32066874
Molecular Biomarkers and Influential Factors of Denitrification in a Full-Scale Biological Nitrogen Removal Plant. PMID:31861619
First-tier detection of intragenomic 16S rRNA gene variation in culturable endophytic bacteria from cacao seeds. PMID:31768299
Relative Abundance of Ammonia Oxidizing Archaea and Bacteria Influences Soil Nitrification Responses to Temperature. PMID:31690001
Accurate and Strict Identification of Probiotic Species Based on Coverage of Whole-Metagenome Shotgun Sequencing Data. PMID:31440213
Influence of environment on the pathogenesis of Ostreid herpesvirus-1 (OsHV-1) infections in Pacific oysters (Crassostrea gigas) through differential microbiome responses. PMID:31372553
Spatial ecology of a wastewater network defines the antibiotic resistance genes in downstream receiving waters. PMID:31295654
Sewage effluent from an Indian hospital harbors novel carbapenemases and integron-borne antibiotic resistance genes. PMID:31248462
Deconstructing the Polymerase Chain Reaction II: an improved workflow and effects on artifact formation and primer degeneracy. PMID:31231597
Detection of respiratory pathogens in clinical samples using metagenomic shotgun sequencing. PMID:31136295
Pseudomonas putida rDNA is a favored site for the expression of biosynthetic genes. PMID:31065014
Genetic diversity and multiple antibiotic resistance index study of bacterial pathogen, Klebsiella pneumoniae strains isolated from diseased Indian major carps. PMID:31020632
ANCHOR: a 16S rRNA gene amplicon pipeline for microbial analysis of multiple environmental samples. PMID:30990927
Quantitative and qualitative evaluation of the impact of the G2 enhancer, bead sizes and lysing tubes on the bacterial community composition during DNA extraction from recalcitrant soil core samples based on community sequencing and qPCR. PMID:30973938
16S rRNA/rRNA Gene Ratios and Cell Activity Staining Reveal Consistent Patterns of Microbial Activity in Plant-Associated Soil. PMID:30944883
Polyclonal symbiont populations in hydrothermal vent tubeworms and the environment. PMID:30887877
Fate of Antibiotic Resistant Pseudomonas putida and Broad Host Range Plasmid in Natural Soil Microcosms. PMID:30881351
Prediction and large-scale analysis of primary operons in plastids reveals unique genetic features in the evolution of chloroplasts. PMID:30828719
Population Structure and Morphotype Analysis of "Candidatus Accumulibacter" Using Fluorescence In Situ Hybridization-Staining-Flow Cytometry. PMID:30824450
Deletion of rRNA Operons of Sinorhizobium fredii Strain NGR234 and Impact on Symbiosis With Legumes. PMID:30814981
Detecting antibiotic resistance genes and human potential pathogenic Bacteria in fishmeal by culture-independent method. PMID:30707381
Contributions and Challenges of High Throughput qPCR for Determining Antimicrobial Resistance in the Environment: A Critical Review. PMID:30609875
Water Quality and Total Microbial Load: A Double-Threshold Identification Procedure Intended for Space Applications. PMID:30574126
Towards Quantitative Microbiome Community Profiling Using Internal Standards. PMID:30552195
Shotgun Metagenomics Reveals Taxonomic and Functional Shifts in Hot Water Microbiome Due to Temperature Setting and Stagnation. PMID:30542327
Long-term succession in a coal seam microbiome during in situ biostimulation of coalbed-methane generation. PMID:30323265
Effect of a butyrate-fortified milk replacer on gastrointestinal microbiota and products of fermentation in artificially reared dairy calves at weaning. PMID:30297834
G3 PhyloChip Analysis Confirms the Promise of Plant-Based Culture Media for Unlocking the Composition and Diversity of the Maize Root Microbiome and for Recovering Unculturable Candidate Divisions/Phyla. PMID:30210099
Extraction of Biofilms From Ureteral Stents for Quantification and Cultivation-Dependent and -Independent Analyses. PMID:30050505
Highlighting Clinical Metagenomics for Enhanced Diagnostic Decision-making: A Step Towards Wider Implementation. PMID:30026887
Anaerobic bacteria cultured from cystic fibrosis airways correlate to milder disease: a multisite study. PMID:29946004
Multiple Ribosomal RNA Operons in Bacteria; Their Concerted Evolution and Potential Consequences on the Rate of Evolution of Their 16S rRNA. PMID:29937760
A CAZyme-Rich Genome of a Taxonomically Novel Rhodophyte-Associated Carrageenolytic Marine Bacterium. PMID:29936557
Brucella abortus: determination of survival times and evaluation of methods for detection in several matrices. PMID:29871600
Metagenomic Approaches to Investigate the Contribution of the Vineyard Environment to the Quality of Wine Fermentation: Potentials and Difficulties. PMID:29867889
Chronic rhinosinusitis with nasal polyps is characterized by dysbacteriosis of the nasal microbiota. PMID:29784985
Does intra-ruminal nitrogen recycling waste valuable resources? A review of major players and their manipulation. PMID:29721317
The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool. PMID:29609653
Impact of Wastewater Treatment on the Prevalence of Integrons and the Genetic Diversity of Integron Gene Cassettes. PMID:29475864
Nitrifier Gene Abundance and Diversity in Sediments Impacted by Acid Mine Drainage. PMID:29209281
High reactivity of deep biota under anthropogenic CO2 injection into basalt. PMID:29051484
Ecological strategies and metabolic trade-offs of complex environmental biofilms. PMID:28955480
Depth Distribution and Assembly of Sulfate-Reducing Microbial Communities in Marine Sediments of Aarhus Bay. PMID:28939599
Nutrient and acetate amendment leads to acetoclastic methane production and microbial community change in a non-producing Australian coal well. PMID:28925579
Ecotoxicity and antibiotic resistance of a mixture of hospital and urban sewage in a wastewater treatment plant. PMID:28875281
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. PMID:28787424
Metagenomics of urban sewage identifies an extensively shared antibiotic resistome in China. PMID:28724443
Deciphering biodiversity and interactions between bacteria and microeukaryotes within epilithic biofilms from the Loue River, France. PMID:28659582
A Robust Framework for Microbial Archaeology. PMID:28460196
Simulated rRNA/DNA Ratios Show Potential To Misclassify Active Populations as Dormant. PMID:28363969
Improvement of identification methods for honeybee specific Lactic Acid Bacteria; future approaches. PMID:28346815
A Numbers Game: Ribosome Densities, Bacterial Growth, and Antibiotic-Mediated Stasis and Death. PMID:28174311
Capturing Compositional Variation in Denitrifying Communities: a Multiple-Primer Approach That Includes Epsilonproteobacteria. PMID:28087525
Diversity, abundance and activity of ammonia-oxidizing microorganisms in fine particulate matter. PMID:27941955
Potential role of anammox in nitrogen removal in a freshwater reservoir, Jiulonghu Reservoir (China). PMID:27905043
Association of running manner with bacterial community dynamics in a partial short-term nitrifying bioreactor for treatment of piggery wastewater with high ammonia content. PMID:27637946
Microbial Diagnostic Microarrays for the Detection and Typing of Food- and Water-Borne (Bacterial) Pathogens. PMID:27605332
Abundance of Class 1 Integron-Integrase and Sulfonamide Resistance Genes in River Water and Sediment Is Affected by Anthropogenic Pressure and Environmental Factors. PMID:27599709
The Microbiome and Immune Regulation After Transplantation. PMID:27517729
Molecular Evidence for Metabolically Active Bacteria in the Atmosphere. PMID:27252689
Graph mining for next generation sequencing: leveraging the assembly graph for biological insights. PMID:27154001
Diversity of gene cassettes and the abundance of the class 1 integron-integrase gene in sediment polluted by metals. PMID:26961777
Restriction Profiling of 23S Microheterogenic Ribosomal Repeats for Detection and Characterizing of E. coli and Their Clonal, Pathogenic, and Phylogroups. PMID:26885397
Consistent 1,3-propanediol production from glycerol in mixed culture fermentation over a wide range of pH. PMID:26855671
Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria. PMID:26814838
Yersinia spp. Identification Using Copy Diversity in the Chromosomal 16S rRNA Gene Sequence. PMID:26808495
Variability of rRNA Operon Copy Number and Growth Rate Dynamics of Bacillus Isolated from an Extremely Oligotrophic Aquatic Ecosystem. PMID:26779143
Development of a point-of-care-device for fast detection of periodontal pathogens. PMID:26702613
Subseafloor microbial communities in hydrogen-rich vent fluids from hydrothermal systems along the Mid-Cayman Rise. PMID:26663423
Bacterial overgrowth and diversification of microbiota in gastric cancer. PMID:26657453
Metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities. PMID:26579098
Decreases in average bacterial community rRNA operon copy number during succession. PMID:26565722
Microbial diversity in a submarine carbonate edifice from the serpentinizing hydrothermal system of the Prony Bay (New Caledonia) over a 6-year period. PMID:26379636
Effect of Agricultural Amendments on Cajanus cajan (Pigeon Pea) and Its Rhizospheric Microbial Communities--A Comparison between Chemical Fertilizers and Bioinoculants. PMID:26231030
Illumina MiSeq Phylogenetic Amplicon Sequencing Shows a Large Reduction of an Uncharacterised Succinivibrionaceae and an Increase of the Methanobrevibacter gottschalkii Clade in Feed Restricted Cattle. PMID:26226343
The Bacterial Communities of Full-Scale Biologically Active, Granular Activated Carbon Filters Are Stable and Diverse and Potentially Contain Novel Ammonia-Oxidizing Microorganisms. PMID:26209671
Functional gene pyrosequencing reveals core proteobacterial denitrifiers in boreal lakes. PMID:26191058
Abundant Trimethylornithine Lipids and Specific Gene Sequences Are Indicative of Planctomycete Importance at the Oxic/Anoxic Interface in Sphagnum-Dominated Northern Wetlands. PMID:26150465
Detection and Enumeration of Streptococcus agalactiae from Bovine Milk Samples by Real-Time Polymerase Chain Reaction. PMID:26134534
Excretion of Host DNA in Feces Is Associated with Risk of Clostridium difficile Infection. PMID:26090486
Genome Wide Analysis for Searching Novel Markers to Rapidly Identify Clostridium Strains. PMID:26063934
The human microbiome in hematopoiesis and hematologic disorders. PMID:26012569
A preliminary and qualitative study of resource ratio theory to nitrifying lab-scale bioreactors. PMID:25874592
Metaproteomics of complex microbial communities in biogas plants. PMID:25874383
Microbial abundance in surface ice on the Greenland Ice Sheet. PMID:25852678
Insights into the Origin of Clostridium botulinum Strains: Evolution of Distinct Restriction Endonuclease Sites in rrs (16S rRNA gene). PMID:25805900
Quo vadis? Microbial profiling revealed strong effects of cleanroom maintenance and routes of contamination in indoor environments. PMID:25778463
Study of rumen metagenome community using qPCR under different diets. PMID:25606402
Ancient and modern environmental DNA. PMID:25487334
Effects of sample handling and cultivation bias on the specificity of bacterial communities in keratose marine sponges. PMID:25477868
rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development. PMID:25414355
Nitrogen-converting communities in aerobic granules at different hydraulic retention times (HRTs) and operational modes. PMID:25367416
Seasonality and depth distribution of the abundance and activity of ammonia oxidizing microorganisms in marine coastal sediments (North Sea). PMID:25250020
Disturbance and temporal partitioning of the activated sludge metacommunity. PMID:25126758
Phylogenetics and the human microbiome. PMID:25102857
Gene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human Microbiome Project's Most Wanted taxa. PMID:24965364
Distinct diversity of the czcA gene in two sedimentary horizons from a contaminated estuarine core. PMID:24894751
Quantification of encapsulated bioburden in spacecraft polymer materials by cultivation-dependent and molecular methods. PMID:24736730
Impacts of an ethanol-blended fuel release on groundwater and fate of produced methane: Simulation of field observations. PMID:24678130
Mycoplasma salivarium as a dominant coloniser of Fanconi anaemia associated oral carcinoma. PMID:24642836
Impacts of bioturbation on temporal variation in bacterial and archaeal nitrogen-cycling gene abundance in coastal sediments. PMID:24596269
Microbial community structure in lake and wetland sediments from a high Arctic polar desert revealed by targeted transcriptomics. PMID:24594936
Ecological succession and stochastic variation in the assembly of Arabidopsis thaliana phyllosphere communities. PMID:24449749
Watershed-scale fungal community characterization along a pH gradient in a subsurface environment cocontaminated with uranium and nitrate. PMID:24389927
Assessment of viral community functional potential from viral metagenomes may be hampered by contamination with cellular sequences. PMID:24335607
A simple one-step PCR walking method and its application of bacterial rRNA for sequencing identification. PMID:24322403
More than meets the eye: associations of vaginal bacteria with gram stain morphotypes using molecular phylogenetic analysis. PMID:24302980
Diversity and abundance of the arsenite oxidase gene aioA in geothermal areas of Tengchong, Yunnan, China. PMID:24292445
Mycobacterium avium complex in day care hot water systems, and persistence of live cells and DNA in hot water pipes. PMID:24272032
A treatment plant receiving waste water from multiple bulk drug manufacturers is a reservoir for highly multi-drug resistant integron-bearing bacteria. PMID:24204801
Quantitative and qualitative impact of hospital effluent on dissemination of the integron pool. PMID:24152716
Systematic identification of gene families for use as "markers" for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups. PMID:24146954
Metagenomic species profiling using universal phylogenetic marker genes. PMID:24141494
A simple one-step PCR walking method and its application of bacterial rRNA for sequencing identification. PMID:24126601
Rapid detection and identification of nontuberculous mycobacterial pathogens in fish by using high-resolution melting analysis. PMID:24123734
Molecular diagnosis of Actinomadura madurae infection by 16S rRNA deep sequencing. PMID:24108607
Abundance, activity, and diversity of archaeal and bacterial communities in both uncontaminated and highly copper-contaminated marine sediments. PMID:24072336
Linking N2O emissions from biochar-amended soil to the structure and function of the N-cycling microbial community. PMID:24067258
Standard inocula preparations reduce the bacterial diversity and reliability of regulatory biodegradation tests. PMID:24043502
Patterns and processes of microbial community assembly. PMID:24006468
The human urinary microbiome; bacterial DNA in voided urine of asymptomatic adults. PMID:23967406
Effect of leaf type and pesticide exposure on abundance of bacterial taxa in mosquito larval habitats. PMID:23940789
Primer evaluation and adaption for cost-efficient SYBR Green-based qPCR and its applicability for specific quantification of methanogens. PMID:23918633
Microbial community structure across a wastewater-impacted riparian buffer zone in the southeastern coastal plain. PMID:23894260
Intragenomic heterogeneity of 16S rRNA genes causes overestimation of prokaryotic diversity. PMID:23872556
Description of an unusual Neisseria meningitidis isolate containing and expressing Neisseria gonorrhoeae-Specific 16S rRNA gene sequences. PMID:23863567
The unique hmuY gene sequence as a specific marker of Porphyromonas gingivalis. PMID:23844074
Archaea on human skin. PMID:23776475
Ecological drivers of biogeographic patterns of soil archaeal community. PMID:23717418
Investigating the diversity of pseudomonas spp. in soil using culture dependent and independent techniques. PMID:23677146
Bacterial monitoring with adhesive sheet in the international space station-"Kibo", the Japanese experiment module. PMID:23603802
A duplex PCR-based assay for measuring the amount of bacterial contamination in a nucleic acid extract from a culture of free-living protists. PMID:23593495
Ribonucleoproteins in archaeal pre-rRNA processing and modification. PMID:23554567
Characterizing the distribution and rates of microbial sulfate reduction at Middle Valley hydrothermal vents. PMID:23535916
The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses. PMID:23460914
Microbiome of the upper troposphere: species composition and prevalence, effects of tropical storms, and atmospheric implications. PMID:23359712
rRNA (rrn) operon-engineered Bacillus subtilis as a feasible test organism for antibiotic discovery. PMID:23335737
Design and Construction of a Single-Tube, LATE-PCR, Multiplex Endpoint Assay with Lights-On/Lights-Off Probes for the Detection of Pathogens Associated with Sepsis. PMID:23326668
Similar gene estimates from circular and linear standards in quantitative PCR analyses using the prokaryotic 16S rRNA gene as a model. PMID:23284822
The ecological roles of bacterial populations in the surface sediments of coastal lagoon environments in Japan as revealed by quantification and qualification of 16S rDNA. PMID:23264132
Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm. PMID:23178669
Interaction of operational and physicochemical factors leading to Gordonia amarae-like foaming in an incompletely nitrifying activated sludge plant. PMID:22983974
Bacterial and archaeal phylogenetic diversity associated with swine sludge from an anaerobic treatment lagoon. PMID:22828793
Homogeneity and synchronous dynamics of microbial communities in particulate biofilms: from major populations to minor groups. PMID:22791046
Emergent macrophytes act selectively on ammonia-oxidizing bacteria and archaea. PMID:22706066
Effect of volumetric water content and clover (Trifolium incarnatum) on the survival of Escherichia coli O157:H7 in a soil matrix. PMID:22669252
Bacterial communities in different sections of a municipal wastewater treatment plant revealed by 16S rDNA 454 pyrosequencing. PMID:22555912
Variable copy number, intra-genomic heterogeneities and lateral transfers of the 16S rRNA gene in Pseudomonas. PMID:22545126
Using high throughput sequencing to explore the biodiversity in oral bacterial communities. PMID:22520388
Integron involvement in environmental spread of antibiotic resistance. PMID:22509175
Distribution of genetic marker concentrations for fecal indicator bacteria in sewage and animal feces. PMID:22504809
Impacts of nitrogen application rates on the activity and diversity of denitrifying bacteria in the Broadbalk Wheat Experiment. PMID:22451109
Community structure and in situ activity of nitrifying bacteria in Phragmites root-associated biofilms. PMID:22446303
Biodiversity in Oscypek, a traditional Polish cheese, determined by culture-dependent and -independent approaches. PMID:22247135
Identification and characterization of psychrotolerant sporeformers associated with fluid milk production and processing. PMID:22247129
Abundance, diversity and activity of sulfate-reducing prokaryotes in heavy metal-contaminated sediment from a salt marsh in the Medway Estuary (UK). PMID:22124626
Abundance and composition of epiphytic bacterial and archaeal ammonia oxidizers of marine red and brown macroalgae. PMID:22081571
The Western English Channel contains a persistent microbial seed bank. PMID:22071345
Molecular techniques in the biotechnological fight against halogenated compounds in anoxic environments. PMID:22070763
Development and application of an enzymatic and cell flotation treatment for the recovery of viable microbial cells from environmental matrices such as anaerobic sludge. PMID:22003005
Low-dissolved-oxygen nitrifying systems exploit ammonia-oxidizing bacteria with unusually high yields. PMID:21926211
Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation. PMID:21872475
Identification of new single nucleotide polymorphism-based markers for inter- and intraspecies discrimination of obligate bacterial parasites (Pasteuria spp.) of invertebrates. PMID:21803895
Abundance and diversity of Sphingomonas in Shenfu petroleum-wastewater irrigation zone, China. PMID:21735160
Ammonia-oxidizing archaea and ammonia-oxidizing bacteria in six full-scale wastewater treatment bioreactors. PMID:21706171
In search of an uncultured human-associated TM7 bacterium in the environment. PMID:21701585
Comparison of innovative molecular approaches and standard spore assays for assessment of surface cleanliness. PMID:21652744
Overestimation of the abundance of sulfate-reducing bacteria in human feces by quantitative PCR targeting the Desulfovibrio 16S rRNA gene. PMID:21460115
Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees. PMID:21437252
Increment in anaerobic hydrocarbon degradation activity of Halic Bay sediments via nutrient amendment. PMID:21390532
Effect of nitrate, acetate, and hydrogen on native perchlorate-reducing microbial communities and their activity in vadose soil. PMID:21284679
Influence of plant polymers on the distribution and cultivation of bacteria in the phylum Acidobacteria. PMID:21097594
Culturable Rhodobacter and Shewanella species are abundant in estuarine turbidity maxima of the Columbia River. PMID:20977571
Distribution of high bacterial taxa across the chronosequence of two alpine glacier forelands. PMID:20936406
Characterization of bacterial community structure in a drinking water distribution system during an occurrence of red water. PMID:20851995
Obstacles of Multiplex Real-Time PCR for Bacterial 16S rDNA: Primer Specifity and DNA Decontamination of Taq Polymerase. PMID:20737013
Archaea in artificial environments: their presence in global spacecraft clean rooms and impact on planetary protection. PMID:20703318
Determinants of the distribution of nitrogen-cycling microbial communities at the landscape scale. PMID:20703315
Coupled arsenotrophy in a hot spring photosynthetic biofilm at Mono Lake, California. PMID:20511421
Different atmospheric methane-oxidizing communities in European beech and Norway spruce soils. PMID:20348309
A primer on metagenomics. PMID:20195499
Quantification of burkholderia coxL genes in Hawaiian volcanic deposits. PMID:20139318
Performance assessment PCR-based assays targeting bacteroidales genetic markers of bovine fecal pollution. PMID:20061457
Archaeal and bacterial communities respond differently to environmental gradients in anoxic sediments of a California hypersaline lake, the Salton Sea. PMID:19948847
Detection of Catabacter hongkongensis in polluted European water samples. PMID:19946949
Mapping the tree of life: progress and prospects. PMID:19946133
Visualization of ribosomal RNA operon copy number distribution. PMID:19781086
Application of clone library analysis and real-time PCR for comparison of microbial communities in a low-grade copper sulfide ore bioheap leachate. PMID:19669184
Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults. PMID:19508560
Diversity of 23S rRNA genes within individual prokaryotic genomes. PMID:19415112
Approaches to analyse dynamic microbial communities such as those seen in cystic fibrosis lung. PMID:19403459
High-throughput quantitative analysis of the human intestinal microbiota with a phylogenetic microarray. PMID:19363078
Impact of deoxynivalenol on the intestinal microflora of pigs. PMID:19333431
Estimation of pig fecal contamination in a river catchment by real-time PCR using two pig-specific Bacteroidales 16S rRNA genetic markers. PMID:19329663
Effect of lake trophic status and rooted macrophytes on community composition and abundance of ammonia-oxidizing prokaryotes in freshwater sediments. PMID:19304820
The human vaginal bacterial biota and bacterial vaginosis. PMID:19282975
Characterization of a Dehalobacter coculture that dechlorinates 1,2-dichloroethane to ethene and identification of the putative reductive dehalogenase gene. PMID:19270140
Change in the community structure of ammonia-oxidizing bacteria in activated sludge during selective incubation for MPN determination. PMID:19229575
Quantitative community fingerprinting methods for estimating the abundance of operational taxonomic units in natural microbial communities. PMID:19201961
Prokaryotic genomes and diversity in surface ocean waters: interrogating the global ocean sampling metagenome. PMID:19201952
Selective control of the Prorocentrum minimum harmful algal blooms by a novel algal-lytic bacterium Pseudoalteromonas haloplanktis AFMB-008041. PMID:19048341
rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea. PMID:18948294
A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library. PMID:18682527
Monitoring abundance and expression of "Dehalococcoides" species chloroethene-reductive dehalogenases in a tetrachloroethene-dechlorinating flow column. PMID:18676701
Probiotic Lactobacillus plantarum 299v does not counteract unfavorable phytohemagglutinin-induced changes in the rat intestinal microbiota. PMID:18606805
Quantitative microbial community analysis of three different sulfidic mine tailing dumps generating acid mine drainage. PMID:18586975
Field-based stable isotope probing reveals the identities of benzoic acid-metabolizing microorganisms and their in situ growth in agricultural soil. PMID:18469130
Molecular insight into activated sludge producing polyhydroxyalkanoates under aerobic-anaerobic conditions. PMID:18418634
Molecular genetic basis of ribotyping. PMID:18400796
Archaea dominate the ammonia-oxidizing community in the rhizosphere of the freshwater macrophyte Littorella uniflora. PMID:18344332
Quantitative PCR for detection and enumeration of genetic markers of bovine fecal pollution. PMID:18065617
Genetic selection of low fertile Onchocerca volvulus by ivermectin treatment. PMID:17989786
Quantitative distributions of Epsilonproteobacteria and a Sulfurimonas subgroup in pelagic redoxclines of the central Baltic Sea. PMID:17921285
Monitoring and source tracking of tetracycline resistance genes in lagoons and groundwater adjacent to swine production facilities over a 3-year period. PMID:17545324
Serial analysis of rRNA genes and the unexpected dominance of rare members of microbial communities. PMID:17526780
Molecular approaches: advantages and artifacts in assessing bacterial diversity. PMID:17476541
Bacterial diversity associated with Blood Falls, a subglacial outflow from the Taylor Glacier, Antarctica. PMID:17468282
Nitric oxide reductase-targeted real-time PCR quantification of denitrifier populations in soil. PMID:17449686
A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. PMID:17391789
Unravelling microbial communities with DNA-microarrays: challenges and future directions. PMID:17345135
The Dehalococcoides population in sediment-free mixed cultures metabolically dechlorinates the commercial polychlorinated biphenyl mixture aroclor 1260. PMID:17308182
Isolation and characterization of soil bacteria that define Terriglobus gen. nov., in the phylum Acidobacteria. PMID:17293520
Performance of the translational apparatus varies with the ecological strategies of bacteria. PMID:17277058
Monitoring bacterial communities in raw milk and cheese by culture-dependent and -independent 16S rRNA gene-based analyses. PMID:17259356
Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. PMID:17071787
The mosaic nature of intergenic 16S-23S rRNA spacer regions suggests rRNA operon copy number variation in Clostridium difficile strains. PMID:16980415
Comparison of two fingerprinting techniques, terminal restriction fragment length polymorphism and automated ribosomal intergenic spacer analysis, for determination of bacterial diversity in aquatic environments. PMID:16957219
Temperature gradient gel electrophoresis of fecal 16S rRNA reveals active Escherichia coli in the microbiota of patients with ulcerative colitis. PMID:16954244
Toward a census of bacteria in soil. PMID:16848637
The fate of laterally transferred genes: life in the fast lane to adaptation or death. PMID:16651664
Development and characterization of stable sediment-free anaerobic bacterial enrichment cultures that dechlorinate aroclor 1260. PMID:16597944
Rapid quantitative profiling of complex microbial populations. PMID:16407321
Effect of inhibition of acetoclastic methanogenesis on growth of archaeal populations in an anoxic model environment. PMID:16391040
Heterogeneous macrolide resistance and gene conversion in the pneumococcus. PMID:16377711
Specific and sensitive detection of Neisseria gonorrhoeae in clinical specimens by real-time PCR. PMID:16272500
Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays. PMID:16000830
Development and application of an insertional system for gene delivery and expression in Campylobacter jejuni. PMID:16000815
Genomic and phylogenetic characterization of luminous bacteria symbiotic with the deep-sea fish Chlorophthalmus albatrossis (Aulopiformes: Chlorophthalmidae). PMID:15691950
Variation in 16S-23S rRNA intergenic spacer regions in Photobacterium damselae: a mosaic-like structure. PMID:15691912
Differences in codon bias cannot explain differences in translational power among microbes. PMID:15636642
Life history implications of rRNA gene copy number in Escherichia coli. PMID:15528533
Comparison of different primer sets for use in automated ribosomal intergenic spacer analysis of complex bacterial communities. PMID:15466561
Bacterial overgrowth in the cystic fibrosis transmembrane conductance regulator null mouse small intestine. PMID:15385508
Development and application of a real-time PCR approach for quantification of uncultured bacteria in the central Baltic Sea. PMID:15294837
Diversity and dynamics of a north atlantic coastal Vibrio community. PMID:15240289
Characterization of bacterial communities in feces from healthy elderly volunteers and hospitalized elderly patients by using real-time PCR and effects of antibiotic treatment on the fecal microbiota. PMID:15184159
Recovery of GFP-labeled bacteria for culturing and molecular analysis after cell sorting using a benchtop flow cytometer. PMID:15164239
Spatial distribution and stability of the eight microbial species of the altered schaedler flora in the mouse gastrointestinal tract. PMID:15128534
Gram-positive bacteria are a major reservoir of Class 1 antibiotic resistance integrons in poultry litter. PMID:15107498
Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. PMID:15090503
Real-time quantitative PCR for assessment of abundance of Pseudoalteromonas species in marine samples. PMID:15066834
Direct quantification of Campylobacter jejuni and Campylobacter lanienae in feces of cattle by real-time quantitative PCR. PMID:15066825
Occurrence and phylogenetic diversity of Sphingomonas strains in soils contaminated with polycyclic aromatic hydrocarbons. PMID:15066784
Description of Treponema azotonutricium sp. nov. and Treponema primitia sp. nov., the first spirochetes isolated from termite guts. PMID:15006748
Power analysis for real-time PCR quantification of genes in activated sludge and analysis of the variability introduced by DNA extraction. PMID:14602618
Phylogenetic analysis of anaerobic psychrophilic enrichment cultures obtained from a greenland glacier ice core. PMID:12676695
Rates and consequences of recombination between rRNA operons. PMID:12533472
Competitive PCR for quantitation of a Cytophaga-Flexibacter-Bacteroides phylum bacterium associated with the Tuber borchii Vittad. mycelium. PMID:12450871
Coexistence of multiple proteobacterial endosymbionts in the gills of the wood-boring Bivalve Lyrodus pedicellatus (Bivalvia: Teredinidae). PMID:12450854
Simultaneous determination of different DNA sequences by mass spectrometric evaluation of Sanger sequencing reactions. PMID:12409476
Diversity and abundance of bacteria in an underground oil-storage cavity. PMID:12197947
Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited. PMID:11823207
Quantification of Nitrosomonas oligotropha-like ammonia-oxidizing bacteria and Nitrospira spp. from full-scale wastewater treatment plants by competitive PCR. PMID:11772633
The RDP-II (Ribosomal Database Project). PMID:11125082
rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development PubMed citations: 253.

253 articles citing: rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development

Microbial Diversity in Groundwater and Its Response to Seawater Intrusion in Beihai City, Southern China. PMID:35910635
Long-term nitrogen deposition enhances microbial capacities in soil carbon stabilization but reduces network complexity. PMID:35902889
Strategy to Evaluate Changes in Bacterial Community Profiles and Bacterial Pathogen Load Reduction After Sewage Disinfection. PMID:35898906
Ecosystem-specific microbiota and microbiome databases in the era of big data. PMID:35842686
A Comparative Perspective on Ribosome Biogenesis: Unity and Diversity Across the Tree of Life. PMID:35796979
A Bayesian method for identifying associations between response variables and bacterial community composition. PMID:35793382
Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data. PMID:35773532
Coastal Microbial Communities Disrupted During the 2018 Hurricane Season in Outer Banks, North Carolina. PMID:35756005
Microbiome assembly on Drosophila body surfaces benefits the flies to combat fungal infections. PMID:35663020
Feed Insects as a Reservoir of Granadaene-Producing Lactococci. PMID:35615513
Gut microbiota predicts body fat change following a low-energy diet: a PREVIEW intervention study. PMID:35599315
Integrated analysis of microbe-host interactions in Crohn's disease reveals potential mechanisms of microbial proteins on host gene expression. PMID:35479407
Short-Chain Fatty Acids Modulate Healthy Gut Microbiota Composition and Functional Potential. PMID:35287182
Biofilms in Water Hoses of a Meat Processing Environment Harbor Complex Microbial Communities. PMID:35237250
Obesity Reshapes the Microbial Population Structure along the Gut-Liver-Lung Axis in Mice. PMID:35203702
High-throughput identification and quantification of single bacterial cells in the microbiota. PMID:35194029
Response of Total (DNA) and Metabolically Active (RNA) Microbial Communities in Miscanthus × Giganteus Cultivated Soil to Different Nitrogen Fertilization Rates. PMID:35170997
Comparison of Automated Ribotyping, spa Typing, and MLST in 108 Clinical Isolates of Staphylococcus aureus from Orthopedic Infections. PMID:35163582
The mosquito microbiome includes habitat-specific but rare symbionts. PMID:35140881
High-throughput qPCR and 16S rRNA gene amplicon sequencing as complementary methods for the investigation of the cheese microbiota. PMID:35130830
Vertical Distribution of Soil Bacterial Communities in Different Forest Types Along an Elevation Gradient. PMID:35083529
MinION™ Nanopore Sequencing of Skin Microbiome 16S and 16S-23S rRNA Gene Amplicons. PMID:35071053
High molecular weight DNA extraction strategies for long-read sequencing of complex metagenomes. PMID:35068060
Nutrient supply controls the linkage between species abundance and ecological interactions in marine bacterial communities. PMID:35013303
A Novel qPCR Method for the Detection of Lactic Acid Bacteria in Fermented Milk. PMID:34945617
Complete Genome Analysis of Undecylprodigiosin Pigment Biosynthesizing Marine Streptomyces Species Displaying Potential Bioactive Applications. PMID:34835376
Effect of the Manufacturing Process on the Microbiota, Organoleptic Properties and Volatilome of Three Salmon-Based Products. PMID:34828798
Temporal variability in quantitative human gut microbiome profiles and implications for clinical research. PMID:34795283
Improved quantitative microbiome profiling for environmental antibiotic resistance surveillance. PMID:34794510
Detecting Flavobacterial Fish Pathogens in the Environment via High-Throughput Community Analysis. PMID:34788066
Capacity of soil bacteria to reach the phyllosphere and convergence of floral communities despite soil microbiota variation. PMID:34620708
Current Applications of Absolute Bacterial Quantification in Microbiome Studies and Decision-Making Regarding Different Biological Questions. PMID:34576694
Characterizing the molecular composition and diagnostic potential of Mycobacterium tuberculosis urinary cell-free DNA using next-generation sequencing. PMID:34562627
In vitro Colon Fermentation of Soluble Arabinoxylan Is Modified Through Milling and Extrusion. PMID:34513901
Aberrant gut-microbiota-immune-brain axis development in premature neonates with brain damage. PMID:34480872
Linkage of community composition and function over short response time in anaerobic digestion systems with food fermentation wastewater. PMID:34466784
Phagotrophic Protists and Their Associates: Evidence for Preferential Grazing in an Abiotically Driven Soil Ecosystem. PMID:34442632
Resource-diversity relationships in bacterial communities reflect the network structure of microbial metabolism. PMID:34413507
The allometry of cellular DNA and ribosomal gene content among microbes and its use for the assessment of microbiome community structure. PMID:34404486
Honeybee Exposure to Veterinary Drugs: How Is the Gut Microbiota Affected? PMID:34378962
Ribosome Biogenesis in Archaea. PMID:34367089
Amplicon Sequence Variants Artificially Split Bacterial Genomes into Separate Clusters. PMID:34287003
Benchmark of 16S rRNA gene amplicon sequencing using Japanese gut microbiome data from the V1-V2 and V3-V4 primer sets. PMID:34246242
Reply to: "Re-evaluating the evidence for a universal genetic boundary among microbial species". PMID:34234115
Lipoplexes to Deliver Oligonucleotides in Gram-Positive and Gram-Negative Bacteria: Towards Treatment of Blood Infections. PMID:34210111
Metagenomics and Other Omics Approaches to Bacterial Communities and Antimicrobial Resistance Assessment in Aquacultures. PMID:34203511
Novel insights into the genetically obese (ob/ob) and diabetic (db/db) mice: two sides of the same coin. PMID:34183063
Ecological Divergence Within the Enterobacterial Genus Sodalis: From Insect Symbionts to Inhabitants of Decomposing Deadwood. PMID:34177846
Long-Term Biocide Efficacy and Its Effect on a Souring Microbial Community. PMID:34160245
No re-calibration required? Stability of a bioelectrochemical sensor for biodegradable organic matter over 800 days. PMID:34153826
Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases. PMID:34117246
Binary Metabolic Phenotypes and Phenotype Diversity Metrics for the Functional Characterization of Microbial Communities. PMID:34113324
General Unified Microbiome Profiling Pipeline (GUMPP) for Large Scale, Streamlined and Reproducible Analysis of Bacterial 16S rRNA Data to Predicted Microbial Metagenomes, Enzymatic Reactions and Metabolic Pathways. PMID:34074026
Honeybees Exposure to Natural Feed Additives: How Is the Gut Microbiota Affected? PMID:34067140
Human Pathogenic Bacteria Detected in Rainwater: Risk Assessment and Correlation to Microbial Source Tracking Markers and Traditional Indicators. PMID:34025613
Cell size, genome size, and maximum growth rate are near-independent dimensions of ecological variation across bacteria and archaea. PMID:33976787
Compartmentalization of bacterial and fungal microbiomes in the gut of adult honeybees. PMID:33963194
High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers. PMID:33953314
Land use in urban areas impacts the composition of soil bacterial communities involved in nitrogen cycling. A case study from Lefkosia (Nicosia) Cyprus. PMID:33854127
The Oral Microbiome in Periodontal Health. PMID:33828997
Habitat Elevation Shapes Microbial Community Composition and Alter the Metabolic Functions in Wild Sable (Martes zibellina) Guts. PMID:33803658
Reduced metagenome sequencing for strain-resolution taxonomic profiles. PMID:33781324
R/G Value-A Numeric Index of Individual Periodontal Health and Oral Microbiome Dynamics. PMID:33777830
Longitudinal Study of the Bulk Tank Milk Microbiota Reveals Major Temporal Shifts in Composition. PMID:33708181
Assessment of Bacterial Community Composition and Dynamics in Alfalfa Silages With and Without Lactobacillus plantarum Inoculation Using Absolute Quantification 16S rRNA Sequencing. PMID:33584594
Antibiotics and the developing intestinal microbiome, metabolome and inflammatory environment in a randomized trial of preterm infants. PMID:33479274
Comparative Genomics of Marine Bacteria from a Historically Defined Plastic Biodegradation Consortium with the Capacity to Biodegrade Polyhydroxyalkanoates. PMID:33467086
Changes in Bacterial and Chemical Components and Growth Prediction for Lactobacillus sakei during Kimoto-Style Fermentation Starter Preparation in Sake Brewing: a Comprehensive Analysis. PMID:33452026
Simulation of Microbial Response to Accidental Diesel Spills in Basins Containing Brackish Sea Water and Sediment. PMID:33424796
A Slimy Business: the Future of Fish Skin Microbiome Studies. PMID:33410931
Host-Associated Quantitative Abundance Profiling Reveals the Microbial Load Variation of Root Microbiome. PMID:33404537
A Multi-Omics Protocol for Swine Feces to Elucidate Longitudinal Dynamics in Microbiome Structure and Function. PMID:33260576
Analysis of relative bacterial activity and lactate dehydrogenase gene expression of caries-associated bacteria in a site-specific natural biofilm: an ex vivo study. PMID:33226500
Microbiome Composition and Borrelia Detection in Ixodes scapularis Ticks at the Northwestern Edge of Their Range. PMID:33218113
Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline. PMID:33193131
BIOCOM-PIPE: a new user-friendly metabarcoding pipeline for the characterization of microbial diversity from 16S, 18S and 23S rRNA gene amplicons. PMID:33129268
The Role of Phosphorus Limitation in Shaping Soil Bacterial Communities and Their Metabolic Capabilities. PMID:33109755
phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes. PMID:33109753
Termites Are Associated with External Species-Specific Bacterial Communities. PMID:33097518
Efficient and cost-effective bacterial mRNA sequencing from low input samples through ribosomal RNA depletion. PMID:33066726
Sensitive Identification of Bacterial DNA in Clinical Specimens by Broad-Range 16S rRNA Gene Enrichment. PMID:33028602
The Effect of Coconut Oil Addition to Feed of Pigs on Rectal Microbial Diversity and Bacterial Abundance. PMID:33003372
Phylogenetic and genomic analysis reveals high genomic openness and genetic diversity of Clostridium perfringens. PMID:32975504
16S rRNA Gene Copy Number Normalization Does Not Provide More Reliable Conclusions in Metataxonomic Surveys. PMID:32862246
Evaluation of Enzymatic Cleaning on Food Processing Installations and Food Products Bacterial Microflora. PMID:32849429
Niche Partitioning between Coastal and Offshore Shelf Waters Results in Differential Expression of Alkane and Polycyclic Aromatic Hydrocarbon Catabolic Pathways. PMID:32843540
The human gut archaeome: identification of diverse haloarchaea in Korean subjects. PMID:32753050
Diversity of Gut Microbiota and Bifidobacterial Community of Chinese Subjects of Different Ages and from Different Regions. PMID:32722057
Propolis Envelope Promotes Beneficial Bacteria in the Honey Bee (Apis mellifera) Mouthpart Microbiome. PMID:32708479
Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses. PMID:32706331
Microbial diversity drives carbon use efficiency in a model soil. PMID:32703952
Assessment of Gram- and Viability-Staining Methods for Quantifying Bacterial Community Dynamics Using Flow Cytometry. PMID:32676069
The sources and transmission routes of microbial populations throughout a meat processing facility. PMID:32651393
A prospective longitudinal study on the microbiota composition in amyotrophic lateral sclerosis. PMID:32546239
A synthesis of bacterial and archaeal phenotypic trait data. PMID:32503990
Unraveling the Diversity of Eukaryotic Microplankton in a Large and Deep Perialpine Lake Using a High Throughput Sequencing Approach. PMID:32457713
Long-Term Nutrient Enrichment of an Oligotroph-Dominated Wetland Increases Bacterial Diversity in Bulk Soils and Plant Rhizospheres. PMID:32434837
Modeling microbial growth in carpet dust exposed to diurnal variations in relative humidity using the "Time-of-Wetness" framework. PMID:32403157
Modeling the Growth and Interaction Between Brochothrix thermosphacta, Pseudomonas spp., and Leuconostoc gelidum in Minced Pork Samples. PMID:32328055
Perturbed Mitochondrial Dynamics Is a Novel Feature of Colitis That Can Be Targeted to Lessen Disease. PMID:32298841
Profiling of Oral Bacterial Communities. PMID:32286907
Metagenomic views of microbial dynamics influenced by hydrocarbon seepage in sediments of the Gulf of Mexico. PMID:32238866
New strategies and structural considerations in development of therapeutics for carbapenem-resistant Enterobacteriaceae. PMID:32201344
The ecology of heterogeneity: soil bacterial communities and C dynamics. PMID:32200737
Linking Human Milk Oligosaccharides, Infant Fecal Community Types, and Later Risk To Require Antibiotics. PMID:32184252
Temperature and Nutrient Levels Correspond with Lineage-Specific Microdiversification in the Ubiquitous and Abundant Freshwater Genus Limnohabitans. PMID:32169939
pH and Phosphate Induced Shifts in Carbon Flow and Microbial Community during Thermophilic Anaerobic Digestion. PMID:32093251
Insights into the Identification of the Specific Spoilage Organisms in Chicken Meat. PMID:32093245
Assessment of Spoilage Bacterial Communities in Food Wrap and Modified Atmospheres-Packed Minced Pork Meat Samples by 16S rDNA Metagenetic Analysis. PMID:32038536
Molecular sequencing and morphological identification reveal similar patterns in native bee communities across public and private grasslands of eastern North Dakota. PMID:31971987
The absence of intact polar lipid-derived GDGTs in marine waters dominated by Marine Group II: Implications for lipid biosynthesis in Archaea. PMID:31941956
Quantitative PCR provides a simple and accessible method for quantitative microbiota profiling. PMID:31940382
Reuterin Demonstrates Potent Antimicrobial Activity Against a Broad Panel of Human and Poultry Meat Campylobacter spp. Isolates. PMID:31935889
The complete genome sequence of the nitrile biocatalyst Rhodocccus rhodochrous ATCC BAA-870. PMID:31898479
Characterization of the Cultivable Microbiota in Fresh and Stored Mature Human Breast Milk. PMID:31824453
Successive passaging of a plant-associated microbiome reveals robust habitat and host genotype-dependent selection. PMID:31806755
Patterns of PCR Amplification Artifacts of the Fungal Barcode Marker in a Hybrid Mushroom. PMID:31803173
Potential clinical utility of multiple target quantitative polymerase chain reaction (qPCR) array to detect microbial pathogens in patients with chronic obstructive pulmonary disease (COPD). PMID:31737352
Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. PMID:31695033
Effects of Habitat Partitioning on the Distribution of Bacterioplankton in Deep Lakes. PMID:31636614
Spatial and temporal dynamics of a freshwater eukaryotic plankton community revealed via 18S rRNA gene metabarcoding. PMID:31595089
OutbreakFinder: a visualization tool for rapid detection of bacterial strain clusters based on optimized multidimensional scaling. PMID:31523522
Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data. PMID:31488068
Historical Drought Affects Microbial Population Dynamics and Activity During Soil Drying and Re-Wet. PMID:31482287
Fishing in the Soup - Pathogen Detection in Food Safety Using Metabarcoding and Metagenomic Sequencing. PMID:31447815
An expectation-maximization algorithm enables accurate ecological modeling using longitudinal microbiome sequencing data. PMID:31439018
Archaeal Communities in Deep Terrestrial Subsurface Underneath the Deccan Traps, India. PMID:31379755
B-Vitamin Sharing Promotes Stability of Gut Microbial Communities. PMID:31333610
Predominance of Cand. Patescibacteria in Groundwater Is Caused by Their Preferential Mobilization From Soils and Flourishing Under Oligotrophic Conditions. PMID:31281301
Micronutrient Requirements and Sharing Capabilities of the Human Gut Microbiome. PMID:31275260
High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution. PMID:31269198
Time Series Genome-Centric Analysis Unveils Bacterial Response to Operational Disturbance in Activated Sludge. PMID:31266798
Sewage effluent from an Indian hospital harbors novel carbapenemases and integron-borne antibiotic resistance genes. PMID:31248462
Dynamic Modulation of the Gut Microbiota and Metabolome by Bacteriophages in a Mouse Model. PMID:31175044
Predictive genomic traits for bacterial growth in culture versus actual growth in soil. PMID:31053828
Exploring the piezotolerant/piezophilic microbial community and genomic basis of piezotolerance within the deep subsurface Deccan traps. PMID:31049708
Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains. PMID:31046679
Marine Deep Biosphere Microbial Communities Assemble in Near-Surface Sediments in Aarhus Bay. PMID:31031732
Microbial iron metabolism as revealed by gene expression profiles in contrasted Southern Ocean regimes. PMID:30958628
16S rRNA/rRNA Gene Ratios and Cell Activity Staining Reveal Consistent Patterns of Microbial Activity in Plant-Associated Soil. PMID:30944883
Metatranscriptomic exploration of microbial functioning in clouds. PMID:30867542
Divergent microbial communities in groundwater and overlying soils exhibit functional redundancy for plant-polysaccharide degradation. PMID:30865693
The Active Sulfate-Reducing Microbial Community in Littoral Sediment of Oligotrophic Lake Constance. PMID:30814991
Compositional changes to the ileal microbiome precede the onset of spontaneous ileitis in SHIP deficient mice. PMID:30760087
Long-Term Transcriptional Activity at Zero Growth of a Cosmopolitan Rare Biosphere Member. PMID:30755506
Unicellular Cyanobacteria Are Important Components of Phytoplankton Communities in Australia's Northern Oceanic Ecoregions. PMID:30728821
Trait-based community assembly and succession of the infant gut microbiome. PMID:30710083
Mapping the Surface Microbiome and Metabolome of Brown Seaweed Fucus vesiculosus by Amplicon Sequencing, Integrated Metabolomics and Imaging Techniques. PMID:30705420
Mycobacterial species and their contribution to cholesterol degradation in wastewater treatment plants. PMID:30696864
Acetate promotes microbial reductive debromination of tetrabromobisphenol A during the startup phase of anaerobic wastewater sludge bioreactors. PMID:30625682
Towards Quantitative Microbiome Community Profiling Using Internal Standards. PMID:30552195
Corrigendum: A Comparison of Techniques for Collecting Skin Microbiome Samples: Swabbing Versus Tape-Stripping. PMID:30519225
Exploration of deep terrestrial subsurface microbiome in Late Cretaceous Deccan traps and underlying Archean basement, India. PMID:30498254
Assessment and application of host-specific Bacteroidales genetic markers for microbial source tracking of river water in Japan. PMID:30444920
Heterogeneity of Microbial Communities on Deep-Sea Ferromanganese Crusts in the Takuyo-Daigo Seamount. PMID:30381615
Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes. PMID:30352611
A Comparison of Techniques for Collecting Skin Microbiome Samples: Swabbing Versus Tape-Stripping. PMID:30333815
Long-term succession in a coal seam microbiome during in situ biostimulation of coalbed-methane generation. PMID:30323265
From proteins to polysaccharides: lifestyle and genetic evolution of Coprothermobacter proteolyticus. PMID:30315317
Alterations in the Abundance and Co-occurrence of Akkermansia muciniphila and Faecalibacterium prausnitzii in the Colonic Mucosa of Inflammatory Bowel Disease Subjects. PMID:30245977
Abundance and distribution of Archaea in the subseafloor sedimentary biosphere. PMID:30116037
Community dynamics and functional characteristics of naphthalene-degrading populations in contaminated surface sediments and hypoxic/anoxic groundwater. PMID:30051558
Functional Microbial Features Driving Community Assembly During Seed Germination and Emergence. PMID:30008730
Stochastic processes govern invasion success in microbial communities when the invader is phylogenetically close to resident bacteria. PMID:30002504
Multiple Ribosomal RNA Operons in Bacteria; Their Concerted Evolution and Potential Consequences on the Rate of Evolution of Their 16S rRNA. PMID:29937760
RNase III Processing of rRNA in the Lyme Disease Spirochete Borrelia burgdorferi. PMID:29632096
riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions. PMID:29608703
Investigating Colonization of the Healthy Adult Gastrointestinal Tract by Fungi. PMID:29600282
Assessment of Fecal Indicator Bacteria and Potential Pathogen Co-Occurrence at a Shellfish Growing Area. PMID:29593669
Large Blooms of Bacillales (Firmicutes) Underlie the Response to Wetting of Cyanobacterial Biocrusts at Various Stages of Maturity. PMID:29511079
Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem. PMID:29482646
The Madness of Microbiome: Attempting To Find Consensus "Best Practice" for 16S Microbiome Studies. PMID:29427429
Community and Proteomic Analysis of Anaerobic Consortia Converting Tetramethylammonium to Methane. PMID:29391857
Taxonomy of anaerobic digestion microbiome reveals biases associated with the applied high throughput sequencing strategies. PMID:29386622
Translational Selection for Speed Is Not Sufficient to Explain Variation in Bacterial Codon Usage Bias. PMID:29385509
Phylogenetic Network Analysis Revealed the Occurrence of Horizontal Gene Transfer of 16S rRNA in the Genus Enterobacter. PMID:29180992
Statistical analysis of co-occurrence patterns in microbial presence-absence datasets. PMID:29145425
Quantitative microbiome profiling links gut community variation to microbial load. PMID:29143816
Dynamic integration and excision of filamentous phage XacF1 in Xanthomonas citri pv. citri, the causative agent of citrus canker disease. PMID:29123980
Abundance and Multilocus Sequence Analysis of Vibrio Bacteria Associated with Diseased Elkhorn Coral (Acropora palmata) of the Florida Keys. PMID:29079623
Draft genome sequence and characterization of commensal Escherichia coli strain BG1 isolated from bovine gastro-intestinal tract. PMID:29046740
Comparison of Thaumarchaeotal populations from four deep sea basins. PMID:29029137
Geobiological feedbacks and the evolution of thermoacidophiles. PMID:29028004
Ecological strategies and metabolic trade-offs of complex environmental biofilms. PMID:28955480
Microbial communities in placentas from term normal pregnancy exhibit spatially variable profiles. PMID:28894161
Microbial functional trait of rRNA operon copy numbers increases with organic levels in anaerobic digesters. PMID:28841202
Influence of Igneous Basement on Deep Sediment Microbial Diversity on the Eastern Juan de Fuca Ridge Flank. PMID:28824568
Active microorganisms thrive among extremely diverse communities in cloud water. PMID:28792539
A clinician's guide to microbiome analysis. PMID:28790452
Differentiating Botulinum Neurotoxin-Producing Clostridia with a Simple, Multiplex PCR Assay. PMID:28733282
Four-year bacterial monitoring in the International Space Station-Japanese Experiment Module "Kibo" with culture-independent approach. PMID:28725725
Mucin Cross-Feeding of Infant Bifidobacteria and Eubacterium hallii. PMID:28721502
Persistence of antibiotic resistance plasmids in bacterial biofilms. PMID:28616070
Nutrient Stoichiometry Shapes Microbial Community Structure in an Evaporitic Shallow Pond. PMID:28611750
Tomato root microbiota and Phytophthora parasitica-associated disease. PMID:28511691
Single Cell Analysis Linking Ribosomal (r)DNA and rRNA Copy Numbers to Cell Size and Growth Rate Provides Insights into Molecular Protistan Ecology. PMID:28499076
Diversity of Metabolically Active Bacteria in Water-Flooded High-Temperature Heavy Oil Reservoir. PMID:28487680
Streptococcus tigurinus is frequent among gtfR-negative Streptococcus oralis isolates and in the human oral cavity, but highly virulent strains are uncommon. PMID:28473881
A Robust Framework for Microbial Archaeology. PMID:28460196
Comparative genomics of Burkholderia multivorans, a ubiquitous pathogen with a highly conserved genomic structure. PMID:28430818
Short-Term Exposure of Paddy Soil Microbial Communities to Salt Stress Triggers Different Transcriptional Responses of Key Taxonomic Groups. PMID:28400748
Application of hierarchical oligonucleotide primer extension (HOPE) to assess relative abundances of ammonia- and nitrite-oxidizing bacteria. PMID:28376730
Microbial Biogeography and Core Microbiota of the Rat Digestive Tract. PMID:28374781
Cooperative growth of Geobacter sulfurreducens and Clostridium pasteurianum with subsequent metabolic shift in glycerol fermentation. PMID:28287150
Phylogenetic diversity and in situ detection of eukaryotes in anaerobic sludge digesters. PMID:28264042
Archaeal and bacterial communities in deep-sea hydrogenetic ferromanganese crusts on old seamounts of the northwestern Pacific. PMID:28235095
Annual community patterns are driven by seasonal switching between closely related marine bacteria. PMID:28234350
Differences in Gut Metabolites and Microbial Composition and Functions between Egyptian and U.S. Children Are Consistent with Their Diets. PMID:28191503
A Numbers Game: Ribosome Densities, Bacterial Growth, and Antibiotic-Mediated Stasis and Death. PMID:28174311
Characterisation of microbial communities within aggressive prostate cancer tissues. PMID:28101126
Comparative Analysis of Methanogenic Communities in Different Laboratory-Scale Anaerobic Digesters. PMID:28074084
Molecular-based detection of potentially pathogenic bacteria in membrane bioreactor (MBR) systems treating municipal wastewater: a case study. PMID:28013467
Oligofructose as an adjunct in treatment of diabetes in NOD mice. PMID:27874076
A High-Fat High-Sucrose Diet Rapidly Alters Muscle Integrity, Inflammation and Gut Microbiota in Male Rats. PMID:27853291
Community Composition and Abundance of Bacterial, Archaeal and Nitrifying Populations in Savanna Soils on Contrasting Bedrock Material in Kruger National Park, South Africa. PMID:27807431
Bacterial evolution: Genomics of metabolic trade-offs. PMID:27782136
Genome sequences and annotation of two urinary isolates of E. coli. PMID:27777649
Virus-mediated archaeal hecatomb in the deep seafloor. PMID:27757416
Novel and Unexpected Microbial Diversity in Acid Mine Drainage in Svalbard (78° N), Revealed by Culture-Independent Approaches. PMID:27682111
Diversity is the question, not the answer. PMID:27636395
Exploiting rRNA operon copy number to investigate bacterial reproductive strategies. PMID:27617693
Absolute quantification of microbial taxon abundances. PMID:27612291
Ketogenic diet modifies the gut microbiota in a murine model of autism spectrum disorder. PMID:27594980
Regional Variation of CH4 and N2 Production Processes in the Deep Aquifers of an Accretionary Prism. PMID:27592518
High Prevalence of Diverse Insertion Sequences within the rRNA Operons of Mycoplasma bovis. PMID:27542937
PCR detection of Burkholderia multivorans in water and soil samples. PMID:27514367
Dynamics of the Fouling Layer Microbial Community in a Membrane Bioreactor. PMID:27399199
Adjusting microbiome profiles for differences in microbial load by spike-in bacteria. PMID:27329048
Metatranscriptomics reveals the molecular mechanism of large granule formation in granular anammox reactor. PMID:27319320
Draft Genome Sequence of "Rathayibacter tanaceti" Strain VKM Ac-2596 Isolated from Tanacetum vulgare Infested by a Foliar Nematode. PMID:27313291
Microbial Inventory of Deeply Buried Oceanic Crust from a Young Ridge Flank. PMID:27303398
Underestimation of ammonia-oxidizing bacteria abundance by amplification bias in amoA-targeted qPCR. PMID:27166579
Consortia of low-abundance bacteria drive sulfate reduction-dependent degradation of fermentation products in peat soil microcosms. PMID:27015005
Survival of Antibiotic Resistant Bacteria and Horizontal Gene Transfer Control Antibiotic Resistance Gene Content in Anaerobic Digesters. PMID:27014196
RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to metagenomes. PMID:26984526
Evaluation of Enrichment Protocols for Bacterial Endosymbionts of Ciliates by Real-Time PCR. PMID:26894821
Variability of rRNA Operon Copy Number and Growth Rate Dynamics of Bacillus Isolated from an Extremely Oligotrophic Aquatic Ecosystem. PMID:26779143
Assessing Bacterial Diversity in the Rhizosphere of Thymus zygis Growing in the Sierra Nevada National Park (Spain) through Culture-Dependent and Independent Approaches. PMID:26741495
Oxygen Affects Gut Bacterial Colonization and Metabolic Activities in a Gnotobiotic Cockroach Model. PMID:26637604
Prokaryotes in Subsoil-Evidence for a Strong Spatial Separation of Different Phyla by Analysing Co-occurrence Networks. PMID:26635741
Assessing the Groundwater Quality at a Saudi Arabian Agricultural Site and the Occurrence of Opportunistic Pathogens on Irrigated Food Produce. PMID:26445052
Complete Genome Sequence of Pelosinus fermentans JBW45, a Member of a Remarkably Competitive Group of Negativicutes in the Firmicutes Phylum. PMID:26404608
16Stimator: statistical estimation of ribosomal gene copy numbers from draft genome assemblies. PMID:26359911
Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, and Treponema denticola / Prevotella intermedia Co-Infection Are Associated with Severe Periodontitis in a Thai Population. PMID:26313005
Mucosa-associated Faecalibacterium prausnitzii phylotype richness is reduced in patients with inflammatory bowel disease. PMID:26296733
Complex coupled metabolic and prokaryotic community responses to increasing temperatures in anaerobic marine sediments: critical temperatures and substrate changes. PMID:26207045
Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota. PMID:26140533
Detection and Enumeration of Streptococcus agalactiae from Bovine Milk Samples by Real-Time Polymerase Chain Reaction. PMID:26134534
MiDAS: the field guide to the microbes of activated sludge. PMID:26120139
Penile Microbiota and Female Partner Bacterial Vaginosis in Rakai, Uganda. PMID:26081632
Databases for Microbiologists. PMID:26013493
Phylum level change in the cecal and fecal gut communities of rats fed diets containing different fermentable substrates supports a role for nitrogen as a factor contributing to community structure. PMID:25954902
Structure, mineralogy, and microbial diversity of geothermal spring microbialites associated with a deep oil drilling in Romania. PMID:25870594
rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea PubMed citations: 170.

170 articles citing: rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea

Long-term nitrogen deposition enhances microbial capacities in soil carbon stabilization but reduces network complexity. PMID:35902889
Comparison of an automated DNA extraction and 16S rDNA real time PCR/sequencing diagnostic method using optimized reagents with culture during a 15-month study using specimens from sterile body sites. PMID:35501697
Antibiotic Exposure, Common Morbidities and Main Intestinal Microbial Groups in Very Preterm Neonates: A Pilot Study. PMID:35203839
Metagenomic community composition and resistome analysis in a full-scale cold climate wastewater treatment plant. PMID:35033203
Going Beyond Bacteria: Uncovering the Role of Archaeome and Mycobiome in Inflammatory Bowel Disease. PMID:34938203
Evolutionary characteristics and phylogeny of cotton chloroplast tRNAs. PMID:34750674
Restoration, conservation and phytoplankton hysteresis. PMID:34394942
Honeybee Exposure to Veterinary Drugs: How Is the Gut Microbiota Affected? PMID:34378962
Characterizing Microbiomes via Sequencing of Marker Loci: Techniques To Improve Throughput, Account for Cross-Contamination, and Reduce Cost. PMID:34254828
Honeybees Exposure to Natural Feed Additives: How Is the Gut Microbiota Affected? PMID:34067140
Microbiome Aggregated Traits and Assembly Are More Sensitive to Soil Management than Diversity. PMID:34042469
Lipoptena fortisetosa as a vector of Bartonella bacteria in Japanese sika deer (Cervus nippon). PMID:33482884
Regeneration of unconventional natural gas by methanogens co-existing with sulfate-reducing prokaryotes in deep shale wells in China. PMID:32994524
Complete genome sequence of the biocontrol agent Serratia marcescens strain N4-5 uncovers an assembly artefact. PMID:32965626
Plant growth promoting rhizobacteria isolated from halophytes and drought-tolerant plants: genomic characterisation and exploration of phyto-beneficial traits. PMID:32908201
The host-associated archaeome. PMID:32690877
A prospective longitudinal study on the microbiota composition in amyotrophic lateral sclerosis. PMID:32546239
Ribosome engineering reveals the importance of 5S rRNA autonomy for ribosome assembly. PMID:32518240
Temporal variations in bacterial community diversity and composition throughout intensive care unit renovations. PMID:32513256
Genome Insights of the Plant-Growth Promoting Bacterium Cronobacter muytjensii JZ38 With Volatile-Mediated Antagonistic Activity Against Phytophthora infestans. PMID:32218777
A bird's-eye view of phylosymbiosis: weak signatures of phylosymbiosis among all 15 species of cranes. PMID:32183630
Bacterial and Eukaryotic Small-Subunit Amplicon Data Do Not Provide a Quantitative Picture of Microbial Communities, but They Are Reliable in the Context of Ecological Interpretations. PMID:32132159
Functional Genomics Insights Into the Pathogenicity, Habitat Fitness, and Mechanisms Modifying Plant Development of Rhodococcus sp. PBTS1 and PBTS2. PMID:32082278
Promiscuous Ribozymes and Their Proposed Role in Prebiotic Evolution. PMID:32011135
Time Series Genome-Centric Analysis Unveils Bacterial Response to Operational Disturbance in Activated Sludge. PMID:31266798
Seasonal development of a coastal microbial mat. PMID:31227767
Arsenic and high affinity phosphate uptake gene distribution in shallow submarine hydrothermal sediments. PMID:30956374
16S rRNA/rRNA Gene Ratios and Cell Activity Staining Reveal Consistent Patterns of Microbial Activity in Plant-Associated Soil. PMID:30944883
Feeding Rapidly Alters Microbiome Composition and Gene Transcription in the Clownfish Gut. PMID:30446559
Impact of DNA extraction method and targeted 16S-rRNA hypervariable region on oral microbiota profiling. PMID:30397210
Probiotics in human gut microbiota can degrade host glycosaminoglycans. PMID:30006634
Synchrony of Eukaryotic and Prokaryotic Planktonic Communities in Three Seasonally Sampled Austrian Lakes. PMID:29963032
Trait-based patterns of microbial dynamics in dormancy potential and heterotrophic strategy: case studies of resource-based and post-press succession. PMID:29959406
Three-Month Feeding Integration With Bifidobacterium Strains Prevents Gastrointestinal Symptoms in Healthy Newborns. PMID:29888226
Human Activity Determines the Presence of Integron-Associated and Antibiotic Resistance Genes in Southwestern British Columbia. PMID:29765365
In vivo expression of proteases and protease inhibitor, a serpin, by periodontal pathogens at teeth and implants. PMID:29498485
A historical legacy of antibiotic utilization on bacterial seed banks in sediments. PMID:29312823
Quantitative Detection of Active Vibrios Associated with White Plague Disease in Mussismilia braziliensis Corals. PMID:29204142
Progressive Colonization of Bacteria and Degradation of Rice Straw in the Rumen by Illumina Sequencing. PMID:29163444
Complete Genome Sequence Analysis of Enterobacter sp. SA187, a Plant Multi-Stress Tolerance Promoting Endophytic Bacterium. PMID:29163376
Modes of carbon fixation in an arsenic and CO2-rich shallow hydrothermal ecosystem. PMID:29089625
Analysis of airborne microbial communities using 16S ribosomal RNA: Potential bias due to air sampling stress. PMID:29079080
Comparison of Thaumarchaeotal populations from four deep sea basins. PMID:29029137
DNA accumulation on ventilation system filters in university buildings in Singapore. PMID:29023520
Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine. PMID:28924494
Microbial functional trait of rRNA operon copy numbers increases with organic levels in anaerobic digesters. PMID:28841202
Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment. PMID:28821012
Bacterial Community Associated with Healthy and Diseased Pacific White Shrimp (Litopenaeus vannamei) Larvae and Rearing Water across Different Growth Stages. PMID:28769916
In vitro evaluation of the prebiotic effect of red and white grape polyphenolic extracts. PMID:28677073
DNA extraction replicates improve diversity and compositional dissimilarity in metabarcoding of eukaryotes in marine sediments. PMID:28622351
Analysis of complete genome sequence and major surface antigens of Neorickettsia helminthoeca, causative agent of salmon poisoning disease. PMID:28585301
A Robust Framework for Microbial Archaeology. PMID:28460196
Simulated rRNA/DNA Ratios Show Potential To Misclassify Active Populations as Dormant. PMID:28363969
Complete Genome Sequence of Bacillus subtilis Strain 29R7-12, a Piezophilic Bacterium Isolated from Coal-Bearing Sediment 2.4 Kilometers below the Seafloor. PMID:28232436
Microbial Typing by Machine Learned DNA Melt Signatures. PMID:28165067
Non-selective Separation of Bacterial Cells with Magnetic Nanoparticles Facilitated by Varying Surface Charge. PMID:27990136
Presence does not imply activity: DNA and RNA patterns differ in response to salt perturbation in anaerobic digestion. PMID:27843490
Effect of Bifidobacterium breve on the Intestinal Microbiota of Coeliac Children on a Gluten Free Diet: A Pilot Study. PMID:27782071
Identification and Analysis of Informative Single Nucleotide Polymorphisms in 16S rRNA Gene Sequences of the Bacillus cereus Group. PMID:27582514
Complete genome sequence of thermophilic Bacillus smithii type strain DSM 4216(T). PMID:27559429
A comprehensive method for amplicon-based and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples. PMID:27391119
Performance of 16s rDNA Primer Pairs in the Study of Rhizosphere and Endosphere Bacterial Microbiomes in Metabarcoding Studies. PMID:27242686
MetaTrans: an open-source pipeline for metatranscriptomics. PMID:27211518
Identification of syntrophic acetate-oxidizing bacteria in anaerobic digesters by combined protein-based stable isotope probing and metagenomics. PMID:27128991
Characterization of the gut microbiome in epidemiologic studies: the multiethnic cohort experience. PMID:27039047
Estimates of Soil Bacterial Ribosome Content and Diversity Are Significantly Affected by the Nucleic Acid Extraction Method Employed. PMID:26896137
Effect of organic carbon and metal accumulation on the bacterial communities in sulphidogenic sediments. PMID:26780045
The musk chemical composition and microbiota of Chinese forest musk deer males. PMID:26744067
A Comprehensive tRNA Genomic Survey Unravels the Evolutionary History of tRNA Arrays in Prokaryotes. PMID:26710853
Comparative Analysis of Prokaryotic Communities Associated with Organic and Conventional Farming Systems. PMID:26684619
Metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities. PMID:26579098
16Stimator: statistical estimation of ribosomal gene copy numbers from draft genome assemblies. PMID:26359911
Membrane biofilm development improves COD removal in anaerobic membrane bioreactor wastewater treatment. PMID:26238293
Microbial Population Differentials between Mucosal and Submucosal Intestinal Tissues in Advanced Crohn's Disease of the Ileum. PMID:26222621
Detection and Enumeration of Streptococcus agalactiae from Bovine Milk Samples by Real-Time Polymerase Chain Reaction. PMID:26134534
Stone-dwelling actinobacteria Blastococcus saxobsidens, Modestobacter marinus and Geodermatophilus obscurus proteogenomes. PMID:26125681
Novel insights into the pathogenicity of epidemic Aeromonas hydrophila ST251 clones from comparative genomics. PMID:26014286
Deconstructing the polymerase chain reaction: understanding and correcting bias associated with primer degeneracies and primer-template mismatches. PMID:25996930
Under-detection of endospore-forming Firmicutes in metagenomic data. PMID:25973144
Does the arthropod microbiota impact the establishment of vector-borne diseases in mammalian hosts? PMID:25856431
Microbial communities in dark oligotrophic volcanic ice cave ecosystems of Mt. Erebus, Antarctica. PMID:25814983
Biogeochemical insights into microbe-mineral-fluid interactions in hydrothermal chimneys using enrichment culture. PMID:25778451
Insights from 20 years of bacterial genome sequencing. PMID:25722247
The interaction of Saccharomyces paradoxus with its natural competitors on oak bark. PMID:25706044
Polar front associated variation in prokaryotic community structure in Arctic shelf seafloor. PMID:25667586
Quantitative real-time polymerase chain reaction for detecting Mycoplasma hyosynoviae and Mycoplasma hyorhinis in pen-based oral, tonsillar, and nasal fluids. PMID:25643803
rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development. PMID:25414355
Distribution and respiratory activity of mycobacteria in household water system of healthy volunteers in Japan. PMID:25350137
Draft Genome Sequences of Two Ulvan-Degrading Isolates, Strains LTR and LOR, That Belong to the Alteromonas Genus. PMID:25342689
Disturbance and temporal partitioning of the activated sludge metacommunity. PMID:25126758
Draft Genome Sequence of Nonlabens ulvanivorans, an Ulvan-Degrading Bacterium. PMID:25125644
Quantitative molecular detection of putative periodontal pathogens in clinically healthy and periodontally diseased subjects. PMID:25029268
Exploration of bacterial community classes in major human habitats. PMID:24887286
Quantification of encapsulated bioburden in spacecraft polymer materials by cultivation-dependent and molecular methods. PMID:24736730
CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction. PMID:24708850
Mycoplasma salivarium as a dominant coloniser of Fanconi anaemia associated oral carcinoma. PMID:24642836
Vibrio diversity and dynamics in the Monterey Bay upwelling region. PMID:24575086
Survival of prokaryotes in a polluted waste dump during remediation by alkaline hydrolysis. PMID:24532314
Draft Genome Sequence of Williamsia sp. Strain D3, Isolated From the Darwin Mountains, Antarctica. PMID:24459282
Hot-alkaline DNA extraction method for deep-subseafloor archaeal communities. PMID:24441163
Surprising abundance of Gallionella-related iron oxidizers in creek sediments at pH 4.4 or at high heavy metal concentrations. PMID:24385973
Mycobacterium avium complex in day care hot water systems, and persistence of live cells and DNA in hot water pipes. PMID:24272032
Stability of the maternal gut microbiota during late pregnancy and early lactation. PMID:24258611
Analysis of the gull fecal microbial community reveals the dominance of Catellicoccus marimammalium in relation to culturable Enterococci. PMID:24242244
Release of free DNA by membrane-impaired bacterial aerosols due to aerosolization and air sampling. PMID:24096426
Use of quantitative 16S rRNA PCR to determine bacterial load does not augment conventional cerebrospinal fluid (CSF) cultures among children undergoing treatment for CSF shunt infection. PMID:23953744
A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets. PMID:23915218
Analysis of the airway microbiota of healthy individuals and patients with chronic obstructive pulmonary disease by T-RFLP and clone sequencing. PMID:23874580
Functional gene analysis of freshwater iron-rich flocs at circumneutral pH and isolation of a stalk-forming microaerophilic iron-oxidizing bacterium. PMID:23811518
Quantification of endospore-forming firmicutes by quantitative PCR with the functional gene spo0A. PMID:23811505
pH gradient and distribution of streptococci, lactobacilli, prevotellae, and fusobacteria in carious dentine. PMID:23771212
Gut microbiota composition in male rat models under different nutritional status and physical activity and its association with serum leptin and ghrelin levels. PMID:23724144
Ecological drivers of biogeographic patterns of soil archaeal community. PMID:23717418
CLUSTOM: a novel method for clustering 16S rRNA next generation sequences by overlap minimization. PMID:23650520
Characteristics of microbial communities in crustal fluids in a deep-sea hydrothermal field of the suiyo seamount. PMID:23626587
Mobile elements in a single-filament orange Guaymas Basin Beggiatoa ("Candidatus Maribeggiatoa") sp. draft genome: evidence for genetic exchange with cyanobacteria. PMID:23603674
Ribonucleoproteins in archaeal pre-rRNA processing and modification. PMID:23554567
Culture-independent analysis of aerosol microbiology in a metropolitan subway system. PMID:23542619
Characterizing the distribution and rates of microbial sulfate reduction at Middle Valley hydrothermal vents. PMID:23535916
Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana. PMID:23457551
Enrichment of specific protozoan populations during in situ bioremediation of uranium-contaminated groundwater. PMID:23446832
Gut microbiota in children with type 1 diabetes differs from that in healthy children: a case-control study. PMID:23433344
Fundamentals of microbial community resistance and resilience. PMID:23267351
Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm. PMID:23178669
Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance. PMID:23133348
Intrinsic and acquired resistance mechanisms in enterococcus. PMID:23076243
Ribosomal multi-operon diversity: an original perspective on the genus Aeromonas. PMID:23032081
Evidence for a bacterial mechanism for group-specific social odors among hyenas. PMID:22937224
Genometa--a fast and accurate classifier for short metagenomic shotgun reads. PMID:22927906
Genetic diversity within the genus Francisella as revealed by comparative analyses of the genomes of two North American isolates from environmental sources. PMID:22920915
Gene copy number variation and its significance in cyanobacterial phylogeny. PMID:22894826
Bacterial and archaeal phylogenetic diversity associated with swine sludge from an anaerobic treatment lagoon. PMID:22828793
Diversity of 5S rRNA genes within individual prokaryotic genomes. PMID:22765222
Bacterial communities in different sections of a municipal wastewater treatment plant revealed by 16S rDNA 454 pyrosequencing. PMID:22555912
Leaf microbiota in an agroecosystem: spatiotemporal variation in bacterial community composition on field-grown lettuce. PMID:22534606
Human occupancy as a source of indoor airborne bacteria. PMID:22529946
BactQuant: an enhanced broad-coverage bacterial quantitative real-time PCR assay. PMID:22510143
Characterization and identification of productivity-associated rhizobacteria in wheat. PMID:22504815
Evaluation of methods for the extraction and purification of DNA from the human microbiome. PMID:22457796
Large variations in bacterial ribosomal RNA genes. PMID:22446745
Size-resolved emission rates of airborne bacteria and fungi in an occupied classroom. PMID:22257156
Application of phylogenetic microarrays to interrogation of human microbiota. PMID:22092522
Molecular techniques in the biotechnological fight against halogenated compounds in anoxic environments. PMID:22070763
Fecal indicators and zoonotic pathogens in household drinking water taps fed from rainwater tanks in Southeast Queensland, Australia. PMID:22020514
Growth of Chlorella vulgaris and associated bacteria in photobioreactors. PMID:21936882
The quantitative significance of Syntrophaceae and syntrophic partnerships in methanogenic degradation of crude oil alkanes. PMID:21914097
Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance. PMID:21833332
Identification of new single nucleotide polymorphism-based markers for inter- and intraspecies discrimination of obligate bacterial parasites (Pasteuria spp.) of invertebrates. PMID:21803895
Comparison of innovative molecular approaches and standard spore assays for assessment of surface cleanliness. PMID:21652744
Overestimation of the abundance of sulfate-reducing bacteria in human feces by quantitative PCR targeting the Desulfovibrio 16S rRNA gene. PMID:21460115
A closer look at bacteroides: phylogenetic relationship and genomic implications of a life in the human gut. PMID:21222211
Optimizing the analysis of human intestinal microbiota with phylogenetic microarray. PMID:21155851
Abundance and diversity of biofilms in natural and artificial aquifers of the Äspö Hard Rock Laboratory, Sweden. PMID:21132427
Influence of plant polymers on the distribution and cultivation of bacteria in the phylum Acidobacteria. PMID:21097594
Influence of external resistance on electrogenesis, methanogenesis, and anode prokaryotic communities in microbial fuel cells. PMID:21075886
Archaea in artificial environments: their presence in global spacecraft clean rooms and impact on planetary protection. PMID:20703318
The complete genome of Propionibacterium freudenreichii CIRM-BIA1, a hardy actinobacterium with food and probiotic applications. PMID:20668525
Resistance and resilience of benthic biofilm communities from a temperate saltmarsh to desiccation and rewetting. PMID:20596071
A 'rare biosphere' microorganism contributes to sulfate reduction in a peatland. PMID:20535221
Diversity of 16S rRNA genes within individual prokaryotic genomes. PMID:20418441
Biogeography and biodiversity in sulfide structures of active and inactive vents at deep-sea hydrothermal fields of the Southern Mariana Trough. PMID:20228114
Transposases are the most abundant, most ubiquitous genes in nature. PMID:20215432
Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PMID:20140211
Quantification of burkholderia coxL genes in Hawaiian volcanic deposits. PMID:20139318
Novel real-time PCR assay for simultaneous detection and differentiation of Clostridium chauvoei and Clostridium septicum in clostridial myonecrosis. PMID:20129968
The systemic imprint of growth and its uses in ecological (meta)genomics. PMID:20090831
Complete genomic structure of the cultivated rice endophyte Azospirillum sp. B510. PMID:20047946
Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent. PMID:19840106
Visualization of ribosomal RNA operon copy number distribution. PMID:19781086
Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009. PMID:19033364

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gene
metasource: Fairsharing.org
version: FAIRsharing.org: rrnDB; The ribosomal RNA operon copy number database; DOI: https://doi.org/10.25504/FAIRsharing.2wb6fv; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

genome
metasource: Fairsharing.org
version: FAIRsharing.org: rrnDB; The ribosomal RNA operon copy number database; DOI: https://doi.org/10.25504/FAIRsharing.2wb6fv; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

nucleic acid sequence
metasource: Fairsharing.org
version: FAIRsharing.org: rrnDB; The ribosomal RNA operon copy number database; DOI: https://doi.org/10.25504/FAIRsharing.2wb6fv; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

operon
metasource: Fairsharing.org
version: FAIRsharing.org: rrnDB; The ribosomal RNA operon copy number database; DOI: https://doi.org/10.25504/FAIRsharing.2wb6fv; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

ribosomal rna
metasource: Fairsharing.org
version: FAIRsharing.org: rrnDB; The ribosomal RNA operon copy number database; DOI: https://doi.org/10.25504/FAIRsharing.2wb6fv; Last edited: Jan. 8, 2019, 1:21 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

gene genome nucleic acid sequence operon ribosomal rna

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5S Ribosomal RNA Database

Prokaryotic Operon DataBase

PreOpDB

Database of Aligned Ribosomal Complexes

SILVA

Eukaryotic Ribosomal Internal Transcribed Spacer 1 Database

CaSNP

RPG - Ribosomal Protein Gene database

CNVIntegrate

16S and 23S Ribosomal RNA Mutation Database

CanGEM

Progenetix - genomic copy number aberrations in cancer

IRESite

Ribosomal Database Project (RDP-II)

The UCSC Archaeal Genome Browser

CNV-ETLAI

rPredictor

CNAdbCC

RIDOM - Ribosomal Differentiation of Medical Microorganisms

ODB - Operon database