IMG Genomes

Names
More detailed information about this field from each metasource.

IMG Genomes
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

Integrated Microbial Genomes (IMG)
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:08.890519

img
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:08.890519

Other names: Integrated Microbial Genomes (IMG), img

Since 2016, the IMG/VR database has provided access to the largest collection of viral sequences obtained from (meta)genomes. Here we present the 3rd version of IMG/VR, composed of 18,373 cultivated and 2,314,329 uncultivated viral genomes (UViGs), nearly tripling the total number of sequences compared to the previous version. UViGs in IMG/VR are now reported as single viral contigs, integrated proviruses, or genome bins, and are annotated with a new standardized pipeline including genome quality estimation using CheckV, taxonomic classification reflecting the latest ICTV update, and expanded host taxonomy prediction. The new IMG/VR interface enables users to efficiently browse, search, and select UViGs based on genome features and/or sequence similarity.

Webpage:

http://img.jgi.doe.gov/

Publications:

Publications
More detailed information about this field from each metasource.

IMG: the Integrated Microbial Genomes database and comparative analysis system
PMID: 22194640
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:08.890519

The integrated microbial genomes system: an expanding comparative analysis resource
PMID: 19864254
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:08.890519

http://dx.doi.org/10.1093/nar/gkaa946
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

IMG: the Integrated Microbial Genomes database and comparative analysis system PubMed citations: 652.

652 articles citing: IMG: the Integrated Microbial Genomes database and comparative analysis system

Comparative Genomics of Clostridium baratii Reveals Strain-Level Diversity in Toxin Abundance. PMID:35208668
Contamination detection in genomic data: more is not enough. PMID:35189924
High-Throughput Time-Lapse Fluorescence Microscopy Screening for Heterogeneously Expressed Genes in Bacillus subtilis. PMID:35171018
The Bacteroidetes Aequorivita sp. and Kaistella jeonii Produce Promiscuous Esterases With PET-Hydrolyzing Activity. PMID:35069509
Chronic pancreatitis in a caerulein-induced mouse model is associated with an altered gut microbiome. PMID:34949545
Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes. PMID:34871418
A k-mer based approach for classifying viruses without taxonomy identifies viral associations in human autism and plant microbiomes. PMID:34849195
Metagenomics of Antarctic Marine Sediment Reveals Potential for Diverse Chemolithoautotrophy. PMID:34817234
Contamination in Reference Sequence Databases: Time for Divide-and-Rule Tactics. PMID:34745061
MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes. PMID:34702846
A Tetratricopeptide Repeat Scaffold Couples Signal Detection to OdhI Phosphorylation in Metabolic Control by the Protein Kinase PknG. PMID:34607462
Xanthohumol Requires the Intestinal Microbiota to Improve Glucose Metabolism in Diet-Induced Obese Mice. PMID:34496124
Genomic Variation Influences Methanothermococcus Fitness in Marine Hydrothermal Systems. PMID:34489903
Distribution of Denitrification among Haloarchaea: A Comprehensive Study. PMID:34442748
Using Functional Annotations to Study Pairwise Interactions in Urinary Tract Infection Communities. PMID:34440394
Genome Annotation of Poly(lactic acid) Degrading Pseudomonas aeruginosa, Sphingobacterium sp. and Geobacillus sp. PMID:34299026
Response to substrate limitation by a marine sulfate-reducing bacterium. PMID:34285365
Alterations in bile acid metabolizing gut microbiota and specific bile acid genes as a precision medicine to subclassify NAFLD. PMID:34151600
The extracellular contractile injection system is enriched in environmental microbes and associates with numerous toxins. PMID:34145238
Radical genome remodelling accompanied the emergence of a novel host-restricted bacterial pathogen. PMID:34015034
Programmable RNA editing with compact CRISPR-Cas13 systems from uncultivated microbes. PMID:33941935
Root Exudates Alter the Expression of Diverse Metabolic, Transport, Regulatory, and Stress Response Genes in Rhizosphere Pseudomonas. PMID:33936009
CAZymes in Maribacter dokdonensis 62-1 From the Patagonian Shelf: Genomics and Physiology Compared to Related Flavobacteria and a Co-occurring Alteromonas Strain. PMID:33912144
Genome sequence of Epibacterium ulvae strain DSM 24752T, an indigoidine-producing, macroalga-associated member of the marine Roseobacter group. PMID:33902719
Metaproteogenomic Profiling of Chemosynthetic Microbial Biofilms Reveals Metabolic Flexibility During Colonization of a Shallow-Water Gas Vent. PMID:33889140
Evolutionary stasis of a deep subsurface microbial lineage. PMID:33824425
Differences in the Microbial Composition of Hemodialysis Patients Treated with and without β-Blockers. PMID:33809103
Ultrafine particles altered gut microbial population and metabolic profiles in a sex-specific manner in an obese mouse model. PMID:33767227
Scarcity of scale-free topology is universal across biochemical networks. PMID:33753807
Functional Analysis of Phenazine Biosynthesis Genes in Burkholderia spp. PMID:33741619
Continental-Scale Gene Flow Prevents Allopatric Divergence of Pelagic Freshwater Bacteria. PMID:33674852
Intestinal Dysbiosis in Young Cystic Fibrosis Rabbits. PMID:33669429
Starvation Alters Gut Microbiome in Black Soldier Fly (Diptera: Stratiomyidae) Larvae. PMID:33664713
HoSeIn: A Workflow for Integrating Various Homology Search Results from Metagenomic and Metatranscriptomic Sequence Datasets. PMID:33659350
Draft genome sequences of three filamentous cyanobacteria isolated from brackish habitats. PMID:33613774
Genomic Insights Into the Lifestyles of Thaumarchaeota Inside Sponges. PMID:33537022
Trace gas oxidizers are widespread and active members of soil microbial communities. PMID:33398096
A Pseudoalteromonas Clade with Remarkable Biosynthetic Potential. PMID:33397702
Microbe-set enrichment analysis facilitates functional interpretation of microbiome profiling data. PMID:33293650
Dysbiotic Lesional Microbiome With Filaggrin Missense Variants Associate With Atopic Dermatitis in India. PMID:33282748
Deciphering functional redundancy in the human microbiome. PMID:33277504
Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions. PMID:33230266
In silico analysis of the chemotactic system of Agrobacterium tumefaciens. PMID:33118922
Seeding Biochemistry on Other Worlds: Enceladus as a Case Study. PMID:33064954
Unravelling lactate-acetate and sugar conversion into butyrate by intestinal Anaerobutyricum and Anaerostipes species by comparative proteogenomics. PMID:33001550
Streamlined and Abundant Bacterioplankton Thrive in Functional Cohorts. PMID:32994284
Structural and functional comparison of Saccharomonospora azurea strains in terms of primycin producing ability. PMID:32989522
Compositional and Functional Adaptations of Intestinal Microbiota and Related Metabolites in CKD Patients Receiving Dietary Protein Restriction. PMID:32932711
Molecular Dialogues between Early Divergent Fungi and Bacteria in an Antagonism versus a Mutualism. PMID:32900811
METATRYP v 2.0: Metaproteomic Least Common Ancestor Analysis for Taxonomic Inference Using Specialized Sequence Assemblies-Standalone Software and Web Servers for Marine Microorganisms and Coronaviruses. PMID:32897080
Gut microbiota modulation with long-chain corn bran arabinoxylan in adults with overweight and obesity is linked to an individualized temporal increase in fecal propionate. PMID:32814582
Comparative gut microbiome analysis of the Prakriti and Sasang systems reveals functional level similarities in constitutionally similar classes. PMID:32802721
Prominent members of the human gut microbiota express endo-acting O-glycanases to initiate mucin breakdown. PMID:32782292
Isolation, Characterization, and Pathogenicity of Two Pseudomonas syringae Pathovars from Populus trichocarpa Seeds. PMID:32731357
Plasmids Related to the Symbiotic Nitrogen Fixation Are Not Only Cooperated Functionally but Also May Have Evolved over a Time Span in Family Rhizobiaceae. PMID:32687170
Co-Expression Networks for Causal Gene Identification Based on RNA-Seq Data of Corynebacterium pseudotuberculosis. PMID:32674507
Rhizobium leguminosarum bv. trifolii NodD2 Enhances Competitive Nodule Colonization in the Clover-Rhizobium Symbiosis. PMID:32651206
More P450s Are Involved in Secondary Metabolite Biosynthesis in Streptomyces Compared to Bacillus, Cyanobacteria, and Mycobacterium. PMID:32646068
A scoutRNA Is Required for Some Type V CRISPR-Cas Systems. PMID:32645367
Soil Acidobacteria Strain AB23 Resistance to Oxidative Stress Through Production of Carotenoids. PMID:32617619
Compositional and functional characterisation of biomass-degrading microbial communities in guts of plant fibre- and soil-feeding higher termites. PMID:32576253
Genome and sequence determinants governing the expression of horizontally acquired DNA in bacteria. PMID:32514119
Genetic Redundancy in Iron and Manganese Transport in the Metabolically Versatile Bacterium Rhodopseudomonas palustris TIE-1. PMID:32503905
Uncovering the Core Microbiome and Distribution of Palmerolide in Synoicum adareanum Across the Anvers Island Archipelago, Antarctica. PMID:32498449
Comparative Genomics and Metabolomics in the Genus Nocardia. PMID:32487740
PICRUSt2 for prediction of metagenome functions. PMID:32483366
Global distribution of a chlorophyll f cyanobacterial marker. PMID:32457503
Identification and Characterization of a DmoB Flavin Oxidoreductase from a Putative Two-Component DMS C-Monooxygenase. PMID:32391470
Transcriptomic Study of Substrate-Specific Transport Mechanisms for Iron and Carbon in the Marine Copiotroph Alteromonas macleodii. PMID:32345736
Interactions between DksA and Stress-Responsive Alternative Sigma Factors Control Inorganic Polyphosphate Accumulation in Escherichia coli. PMID:32341074
The Peptidoglycan Biosynthesis Gene murC in Frankia: Actinorhizal vs. Plant Type. PMID:32316316
Effects of Halophyte Root Exudates and Their Components on Chemotaxis, Biofilm Formation and Colonization of the Halophilic Bacterium Halomonas Anticariensis FP35T. PMID:32316222
Genomic investigation of emerging zoonotic pathogen Shewanella xiamenensis. PMID:32269948
The Changes in the Frog Gut Microbiome and Its Putative Oxygen-Related Phenotypes Accompanying the Development of Gastrointestinal Complexity and Dietary Shift. PMID:32194513
Multiple-Disease Detection and Classification across Cohorts via Microbiome Search. PMID:32184368
Complete Genome Sequence of Pseudomonas psychrotolerans CS51, a Plant Growth-Promoting Bacterium, Under Heavy Metal Stress Conditions. PMID:32182882
Metagenome Mining Reveals Hidden Genomic Diversity of Pelagimyophages in Aquatic Environments. PMID:32071164
"Candidatus Galacturonibacter soehngenii" Shows Acetogenic Catabolism of Galacturonic Acid but Lacks a Canonical Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase Complex. PMID:32063897
Gut Microbiota as Diagnostic Tools for Mirroring Disease Progression and Circulating Nephrotoxin Levels in Chronic Kidney Disease: Discovery and Validation Study. PMID:32015679
Comparative genomics of multidrug-resistant Enterococcus spp. isolated from wastewater treatment plants. PMID:31980014
The differential distribution of bacteria between cancerous and noncancerous ovarian tissues in situ. PMID:31954395
Whole genome sequence analysis reveals the broad distribution of the RtxA type 1 secretion system and four novel putative type 1 secretion systems throughout the Legionella genus. PMID:31935215
A Novel Cyanobacterium Synechococcus elongatus PCC 11802 has Distinct Genomic and Metabolomic Characteristics Compared to its Neighbor PCC 11801. PMID:31932622
Comparative Genomic Analysis of Soil Dwelling Bacteria Utilizing a Combinational Codon Usage and Molecular Phylogenetic Approach Accentuating on Key Housekeeping Genes. PMID:31921071
Genome-Scale Metabolic Reconstruction of Acetobacter pasteurianus 386B, a Candidate Functional Starter Culture for Cocoa Bean Fermentation. PMID:31921009
ClC transporter activity modulates histidine catabolism in Lactobacillus reuteri by altering intracellular pH and membrane potential. PMID:31830990
Division of labor in honey bee gut microbiota for plant polysaccharide digestion. PMID:31776248
Comparative Genomics Guides Elucidation of Vitamin B12 Biosynthesis in Novel Human-Associated Akkermansia Strains. PMID:31757822
Genomic Signatures for Sedimentary Microbial Utilization of Phytoplankton Detritus in a Fast-Flowing Estuary. PMID:31749780
Cultivation and functional characterization of 79 planctomycetes uncovers their unique biology. PMID:31740763
Cultivation-Assisted Genome of Candidatus Fukatsuia symbiotica; the Enigmatic "X-Type" Symbiont of Aphids. PMID:31725149
Meta-16S rRNA Gene Phylogenetic Reconstruction Reveals the Astonishing Diversity of Cosmopolitan Myxobacteria. PMID:31717918
Genomic and phenotypic insights point to diverse ecological strategies by facultative anaerobes obtained from subsurface coal seams. PMID:31700097
Improved Draft Genome Sequence of Microbacterium sp. Strain LKL04, a Bacterial Endophyte Associated with Switchgrass Plants. PMID:31699756
Fueling ab initio folding with marine metagenomics enables structure and function predictions of new protein families. PMID:31676016
Microbial Metabolic Capacity for Intestinal Folate Production and Modulation of Host Folate Receptors. PMID:31649646
Herbal Formula-3 ameliorates OVA-induced food allergy in mice may via modulating the gut microbiota. PMID:31632550
Energy-converting hydrogenases: the link between H2 metabolism and energy conservation. PMID:31630229
Genome-resolved metagenomics and metatranscriptomics reveal niche differentiation in functionally redundant microbial communities at deep-sea hydrothermal vents. PMID:31573126
Metatranscriptomic Analyses of Diel Metabolic Functions During a Microcystis Bloom in Western Lake Erie (United States). PMID:31551998
Soil Metatranscriptomes Under Long-Term Experimental Warming and Drying: Fungi Allocate Resources to Cell Metabolic Maintenance Rather Than Decay. PMID:31551941
Phylogenetic microbiota profiling in fecal samples depends on combination of sequencing depth and choice of NGS analysis method. PMID:31527871
Genome Sequence of Bacillus subtilis natto VK161, a Novel Strain That Produces Vitamin K2. PMID:31467091
Gut microbiota and their putative metabolic functions in fragmented Bengal tiger population of Nepal. PMID:31465520
On the evolution and physiology of cable bacteria. PMID:31427514
MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PMID:31388474
Atmospheric carbon monoxide oxidation is a widespread mechanism supporting microbial survival. PMID:31358912
rpoB, a promising marker for analyzing the diversity of bacterial communities by amplicon sequencing. PMID:31357928
Dynamic Metabolic Rewiring Enables Efficient Acetyl Coenzyme A Assimilation in Paracoccus denitrificans. PMID:31289174
The l-Thr Kinase/l-Thr-Phosphate Decarboxylase (CobD) Enzyme from Methanosarcina mazei Gö1 Contains Metallocenters Needed for Optimal Activity. PMID:31268299
Dual pathways of tRNA hydroxylation ensure efficient translation by expanding decoding capability. PMID:31253794
Molecular Epidemiology of Xanthomonas perforans Outbreaks in Tomato Plants from Transplant to Field as Determined by Single-Nucleotide Polymorphism Analysis. PMID:31253682
Proteomic Response of Three Marine Ammonia-Oxidizing Archaea to Hydrogen Peroxide and Their Metabolic Interactions with a Heterotrophic Alphaproteobacterium. PMID:31239395
Whole-Genome Analysis of Halomonas sp. Soap Lake #7 Reveals It Possesses Putative Mrp Antiporter Operon Groups 1 and 2. PMID:31214690
The human gut chemical landscape predicts microbe-mediated biotransformation of foods and drugs. PMID:31184303
Carbohydrate Hydrolytic Potential and Redundancy of an Anaerobic Digestion Microbiome Exposed to Acidosis, as Uncovered by Metagenomics. PMID:31152018
Individual Physiological Adaptations Enable Selected Bacterial Taxa To Prevail during Long-Term Incubations. PMID:31152013
Identification of Resistance Genes and Response to Arsenic in Rhodococcus aetherivorans BCP1. PMID:31133997
Comparative Genomics of Cyanobacterial Symbionts Reveals Distinct, Specialized Metabolism in Tropical Dysideidae Sponges. PMID:31088928
Life at Home and on the Roam: Genomic Adaptions Reflect the Dual Lifestyle of an Intracellular, Facultative Symbiont. PMID:31086829
Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study. PMID:31076212
Physiology, Metabolism, and Fossilization of Hot-Spring Filamentous Microbial Mats. PMID:31038352
Molecular Evolution of Pseudomonas syringae Type III Secreted Effector Proteins. PMID:31024592
Diversity and Distribution of Bacteria Producing Known Secondary Metabolites. PMID:31016338
Asgard archaea capable of anaerobic hydrocarbon cycling. PMID:31015394
Insights into ecological role of a new deltaproteobacterial order Candidatus Acidulodesulfobacterales by metagenomics and metatranscriptomics. PMID:30962514
Characteristic dysbiosis of gut microbiota of Chinese patients with diarrhea-predominant irritable bowel syndrome by an insight into the pan-microbiome. PMID:30958430
Physiological adaptations to serpentinization in the Samail Ophiolite, Oman. PMID:30872803
Pathogenic potential of non-typhoidal Salmonella serovars isolated from aquatic environments in Mexico. PMID:30859492
Potential for Microbially Mediated Natural Attenuation of Diluted Bitumen on the Coast of British Columbia (Canada). PMID:30850431
Inference of Convergent Gene Acquisition Among Pseudomonas syringae Strains Isolated From Watermelon, Cantaloupe, and Squash. PMID:30837979
Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease. PMID:30801026
Cyanobacterial phylogenetic analysis based on phylogenomics approaches render evolutionary diversification and adaptation: an overview of representative orders. PMID:30800598
A New Microbial Pathway for Organophosphonate Degradation Catalyzed by Two Previously Misannotated Non-Heme-Iron Oxygenases. PMID:30789718
Design and Assessment of Species-Level qPCR Primers Targeting Comammox. PMID:30766515
Draft genome sequence data of Lysinibacillus fusiformis strain GM, isolated from potato phyllosphere as a potential probiotic. PMID:30761330
Insights Into the Evolution of Picocyanobacteria and Phycoerythrin Genes (mpeBA and cpeBA). PMID:30761097
A new genomic blueprint of the human gut microbiota. PMID:30745586
Inorganic Polyphosphate Accumulation in Escherichia coli Is Regulated by DksA but Not by (p)ppGpp. PMID:30745375
An N-nitrosating metalloenzyme constructs the pharmacophore of streptozotocin. PMID:30728519
iVikodak-A Platform and Standard Workflow for Inferring, Analyzing, Comparing, and Visualizing the Functional Potential of Microbial Communities. PMID:30692979
Comparative genomics of 16 Microbacterium spp. that tolerate multiple heavy metals and antibiotics. PMID:30671291
Impact of Homologous Recombination on the Evolution of Prokaryotic Core Genomes. PMID:30670614
Proteogenomics Reveals Novel Reductive Dehalogenases and Methyltransferases Expressed during Anaerobic Dichloromethane Metabolism. PMID:30658979
Marine Sponges as Chloroflexi Hot Spots: Genomic Insights and High-Resolution Visualization of an Abundant and Diverse Symbiotic Clade. PMID:30637337
Comparison of Bacillus subtilis transcriptome profiles from two separate missions to the International Space Station. PMID:30623021
Characterization and complete genome analysis of the surfactin-producing, plant-protecting bacterium Bacillus velezensis 9D-6. PMID:30621587
Microbial Synthesis and Transformation of Inorganic and Organic Chlorine Compounds. PMID:30619161
Methanogenesis on Early Stages of Life: Ancient but Not Primordial. PMID:30612264
Recombination of ecologically and evolutionarily significant loci maintains genetic cohesion in the Pseudomonas syringae species complex. PMID:30606234
Freshwater carbon and nutrient cycles revealed through reconstructed population genomes. PMID:30581671
The Prodigal Compound: Return of Ribosyl 1,5-Bisphosphate as an Important Player in Metabolism. PMID:30567937
Comparative Genomics and Proteomic Analysis of Assimilatory Sulfate Reduction Pathways in Anaerobic Methanotrophic Archaea. PMID:30559729
The Ferredoxin-Like Protein FerR Regulates PrbP Activity in Liberibacter asiaticus. PMID:30552192
Proteogenomic Analysis of Burkholderia Species Strains 25 and 46 Isolated from Uraniferous Soils Reveals Multiple Mechanisms to Cope with Uranium Stress. PMID:30545132
Recent Trends in System-Scale Integrative Approaches for Discovering Protective Antigens Against Mycobacterial Pathogens. PMID:30538722
Draft Genome Sequences of Two Bacillus sp. Strains and Four Cellulomonas sp. Strains Isolated from Heavy-Metal-Contaminated Soil. PMID:30533647
Uneven distribution of cobamide biosynthesis and dependence in bacteria predicted by comparative genomics. PMID:30429574
Identifying and Predicting Novelty in Microbiome Studies. PMID:30425147
The Effect of Dietary Mushroom Agaricus bisporus on Intestinal Microbiota Composition and Host Immunological Function. PMID:30424006
Quantifying and comparing bacterial growth dynamics in multiple metagenomic samples. PMID:30420687
Assessment of 16S rRNA gene primers for studying bacterial community structure and function of aging flue-cured tobaccos. PMID:30415449
Genome Features and Biochemical Characteristics of a Robust, Fast Growing and Naturally Transformable Cyanobacterium Synechococcus elongatus PCC 11801 Isolated from India. PMID:30413737
Members of the Genus Methylobacter Are Inferred To Account for the Majority of Aerobic Methane Oxidation in Oxic Soils from a Freshwater Wetland. PMID:30401770
Associations between digital dermatitis lesion grades in dairy cattle and the quantities of four Treponema species. PMID:30373670
Competitive lottery-based assembly of selected clades in the human gut microbiome. PMID:30340536
Programmed DNA destruction by miniature CRISPR-Cas14 enzymes. PMID:30337455
Antifungal Activity of Bacillus Species Against Fusarium and Analysis of the Potential Mechanisms Used in Biocontrol. PMID:30333816
A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.). PMID:30323263
Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community. PMID:30322445
Exploration of the Biosynthetic Potential of the Populus Microbiome. PMID:30320216
acI Actinobacteria Assemble a Functional Actinorhodopsin with Natively Synthesized Retinal. PMID:30315080
Geospatial variation in co-occurrence networks of nitrifying microbial guilds. PMID:30307658
Transcriptomic responses of Serratia liquefaciens cells grown under simulated Martian conditions of low temperature, low pressure, and CO2-enriched anoxic atmosphere. PMID:30297913
Progress of analytical tools and techniques for human gut microbiome research. PMID:30267313
N-Deacetylases required for muramic-δ-lactam production are involved in Clostridium difficile sporulation, germination, and heat resistance. PMID:30266804
Multiscale analysis of autotroph-heterotroph interactions in a high-temperature microbial community. PMID:30260956
The Thaumarchaeon N. gargensis carries functional bioABD genes and has a promiscuous E. coli ΔbioH-complementing esterase EstN1. PMID:30218044
Soil exchange rates of COS and CO18O differ with the diversity of microbial communities and their carbonic anhydrase enzymes. PMID:30214028
Changes in the genetic requirements for microbial interactions with increasing community complexity. PMID:30211673
Web of microbes (WoM): a curated microbial exometabolomics database for linking chemistry and microbes. PMID:30208844
An exploration of microbial and associated functional diversity in the OMZ and non-OMZ areas in the Bay of Bengal. PMID:30207310
Comparative genomics reveals diverse capsular polysaccharide synthesis gene clusters in emerging Raoultella planticola. PMID:30204830
Complete genome sequencing and analysis of endophytic Sphingomonas sp. LK11 and its potential in plant growth. PMID:30175026
An Orphan MbtH-Like Protein Interacts with Multiple Nonribosomal Peptide Synthetases in Myxococcus xanthus DK1622. PMID:30126939
Origin and Evolution of Flavin-Based Electron Bifurcating Enzymes. PMID:30123204
Following the terrestrial tracks of Caulobacter - redefining the ecology of a reputed aquatic oligotroph. PMID:30108303
Biomarker panels for characterizing microbial community biofilm formation as composite molecular process. PMID:30092027
From hairballs to hypotheses-biological insights from microbial networks. PMID:30085090
Genome Variation in the Model Halophilic Bacterium Salinibacter ruber. PMID:30072959
Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size. PMID:30068938
Biochemical and Phylogenetic Study of SltF, a Flagellar Lytic Transglycosylase from Rhodobacter sphaeroides. PMID:30061356
Metagenomic mining of regulatory elements enables programmable species-selective gene expression. PMID:30052624
Identification of Different Putative Outer Membrane Electron Conduits Necessary for Fe(III) Citrate, Fe(III) Oxide, Mn(IV) Oxide, or Electrode Reduction by Geobacter sulfurreducens. PMID:30038047
The Effect of Feeding Cocoa Powder and Lactobacillus rhamnosus on the Composition and Function of Pig Intestinal Microbiome. PMID:30019034
16S rRNA Long-Read Sequencing of the Granulation Tissue from Nonsmokers and Smokers-Severe Chronic Periodontitis Patients. PMID:30013983
An Approach to In Silico Dissection of Bacterial Intelligence Through Selective Genomic Tools. PMID:30013271
Genome analysis of new Blattabacterium spp., obligatory endosymbionts of Periplaneta fuliginosa and P. japonica. PMID:29990378
Body Mass Index Differences in the Gut Microbiota Are Gender Specific. PMID:29988340
Hydrocarbon degradation and response of seafloor sediment bacterial community in the northern Gulf of Mexico to light Louisiana sweet crude oil. PMID:29950702
Rectal and Naris Swabs: Practical and Informative Samples for Analyzing the Microbiota of Critically Ill Patients. PMID:29898981
Genome Sequencing and Comparative Analysis of Stenotrophomonas acidaminiphila Reveal Evolutionary Insights Into Sulfamethoxazole Resistance. PMID:29867899
Metagenomic Approaches to Investigate the Contribution of the Vineyard Environment to the Quality of Wine Fermentation: Potentials and Difficulties. PMID:29867889
Disbiome database: linking the microbiome to disease. PMID:29866037
Comparative genomics reveals phylogenetic distribution patterns of secondary metabolites in Amycolatopsis species. PMID:29859036
Genome Analysis of Multidrug-Resistant Shewanella algae Isolated From Human Soft Tissue Sample. PMID:29755354
Enterococcus faecalis AHG0090 is a Genetically Tractable Bacterium and Produces a Secreted Peptidic Bioactive that Suppresses Nuclear Factor Kappa B Activation in Human Gut Epithelial Cells. PMID:29720977
Polynucleobacter meluiroseus sp. nov., a bacterium isolated from a lake located in the mountains of the Mediterranean island of Corsica. PMID:29688164
Genome sequence of Planktotalea frisia type strain (SH6-1T), a representative of the Roseobacter group isolated from the North Sea during a phytoplankton bloom. PMID:29682168
Draft genome sequence of Bosea sp. WAO an arsenite and sulfide oxidizer isolated from a pyrite rock outcrop in New Jersey. PMID:29682167
Identification of two different chemosensory pathways in representatives of the genus Halomonas. PMID:29669514
Extensive reshaping of bacterial operons by programmed mRNA decay. PMID:29668692
A methanotrophic archaeon couples anaerobic oxidation of methane to Fe(III) reduction. PMID:29662147
Dual Role of Humic Substances As Electron Donor and Shuttle for Dissimilatory Iron Reduction. PMID:29658273
Alfalfa Intervention Alters Rumen Microbial Community Development in Hu Lambs During Early Life. PMID:29636743
Oligotrophic wetland sediments susceptible to shifts in microbiomes and mercury cycling with dissolved organic matter addition. PMID:29632744
The social network of microorganisms - how auxotrophies shape complex communities. PMID:29599459
Homologous Recombination in Core Genomes Facilitates Marine Bacterial Adaptation. PMID:29572211
GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes. PMID:29562347
Sulfate Transporters in Dissimilatory Sulfate Reducing Microorganisms: A Comparative Genomics Analysis. PMID:29551997
Cas13d Is a Compact RNA-Targeting Type VI CRISPR Effector Positively Modulated by a WYL-Domain-Containing Accessory Protein. PMID:29551514
Disease-induced assemblage of a plant-beneficial bacterial consortium. PMID:29520025
Complete Genome Sequences of pLMA1 and pLMA7, Two Large Linear Plasmids of Micrococcus Strains Isolated from a High-Altitude Lake in Argentina. PMID:29472322
Physiological Heterogeneity Triggers Sibling Conflict Mediated by the Type VI Secretion System in an Aggregative Multicellular Bacterium. PMID:29437919
New Insights into the Function and Global Distribution of Polyethylene Terephthalate (PET)-Degrading Bacteria and Enzymes in Marine and Terrestrial Metagenomes. PMID:29427431
Translational Selection for Speed Is Not Sufficient to Explain Variation in Bacterial Codon Usage Bias. PMID:29385509
Systematic discovery of antiphage defense systems in the microbial pangenome. PMID:29371424
Physiological and Comparative Genomic Analysis of Arthrobacter sp. SRS-W-1-2016 Provides Insights on Niche Adaptation for Survival in Uraniferous Soils. PMID:29324691
Identification of Bacterial Species That Can Utilize Fructose-Asparagine. PMID:29269489
Toward Understanding Phage:Host Interactions in the Rumen; Complete Genome Sequences of Lytic Phages Infecting Rumen Bacteria. PMID:29259581
Draft genome sequence of Pseudomonas extremaustralis strain USBA-GBX 515 isolated from Superparamo soil samples in Colombian Andes. PMID:29255573
Gene Graphics: a genomic neighborhood data visualization web application. PMID:29228171
CRISPR-Cas Systems in Bacteroides fragilis, an Important Pathobiont in the Human Gut Microbiome. PMID:29218031
Comparative genomic analysis of Brevibacterium strains: insights into key genetic determinants involved in adaptation to the cheese habitat. PMID:29216827
Atmospheric trace gases support primary production in Antarctic desert surface soil. PMID:29211716
Metagenomics-guided analysis of microbial chemolithoautotrophic phosphite oxidation yields evidence of a seventh natural CO2 fixation pathway. PMID:29183985
Sugar Metabolism of the First Thermophilic Planctomycete Thermogutta terrifontis: Comparative Genomic and Transcriptomic Approaches. PMID:29163426
Multi-omics Reveals the Lifestyle of the Acidophilic, Mineral-Oxidizing Model Species Leptospirillum ferriphilumT. PMID:29150517
Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients. PMID:29142241
A thermostable Cas9 with increased lifetime in human plasma. PMID:29127284
Imaging of Cellular Oxidoreductase Activity Suggests Mixotrophic Metabolisms in Thiomargarita spp. PMID:29114021
Human microbiome signatures of differential colorectal cancer drug metabolism. PMID:29104759
Draft Genome Sequences of Two Lactobacillus casei Strains Isolated from Cheddar Cheese and a Fermented Milk Drink. PMID:29097471
DISARM is a widespread bacterial defence system with broad anti-phage activities. PMID:29085076
Reclassification of a Polynucleobacter cosmopolitanus strain isolated from tropical Lake Victoria as Polynucleobacter victoriensis sp. nov. PMID:29068276
Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents. PMID:29066755
Genomic divergence and cohesion in a species of pelagic freshwater bacteria. PMID:29037158
Benzene and Naphthalene Degrading Bacterial Communities in an Oil Sands Tailings Pond. PMID:29033909
Genomic insights into the thiamin metabolism of Paenibacillus thiaminolyticus NRRL B-4156 and P. apiarius NRRL B-23460. PMID:29026451
Polynucleobacter aenigmaticus sp. nov. isolated from the permanently anoxic monimolimnion of a temperate meromictic lake. PMID:29022553
A Metagenomic Analysis of Bacterial Microbiota in the Digestive Tract of Triatomines. PMID:28989277
Draft genome sequence of Dethiobacter alkaliphilus strain AHT1T, a gram-positive sulfidogenic polyextremophile. PMID:28943998
Genome-wide identification of bacterial plant colonization genes. PMID:28938018
Developing genome-reduced Pseudomonas chlororaphis strains for the production of secondary metabolites. PMID:28893188
Succession and Fermentation Products of Grass Carp (Ctenopharyngodon idellus) Hindgut Microbiota in Response to an Extreme Dietary Shift. PMID:28871246
Optimization of a metatranscriptomic approach to study the lignocellulolytic potential of the higher termite gut microbiome. PMID:28863779
Complete Genome sequence of the nematicidal Bacillus thuringiensis MYBT18246. PMID:28852435
Complete Genome Sequence of Magnetospirillum sp. ME-1, a Novel Magnetotactic Bacterium Isolated from East Lake, Wuhan, China. PMID:28839012
Polynucleobacter sphagniphilus sp. nov. a planktonic freshwater bacterium isolated from an acidic and humic freshwater habitat. PMID:28829016
Infectious polymorphic toxins delivered by outer membrane exchange discriminate kin in myxobacteria. PMID:28820387
Defining Electron Bifurcation in the Electron-Transferring Flavoprotein Family. PMID:28808132
Draft Genome Sequence of Magnetospirillum sp. Strain 15-1, a Denitrifying Toluene Degrader Isolated from a Planted Fixed-Bed Reactor. PMID:28798176
Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. PMID:28776041
Silvanigrella aquatica gen. nov., sp. nov., isolated from a freshwater lake, description of Silvanigrellaceae fam. nov. and Silvanigrellales ord. nov., reclassification of the order Bdellovibrionales in the class Oligoflexia, reclassification of the families Bacteriovoracaceae and Halobacteriovoraceae in the new order Bacteriovoracales ord. nov., and reclassification of the family Pseudobacteriovoracaceae in the order Oligoflexales. PMID:28771119
Novel Pelagic Iron-Oxidizing Zetaproteobacteria from the Chesapeake Bay Oxic-Anoxic Transition Zone. PMID:28769885
The Physiological Functions and Structural Determinants of Catalytic Bias in the [FeFe]-Hydrogenases CpI and CpII of Clostridium pasteurianum Strain W5. PMID:28747909
Nutrient and Rainfall Additions Shift Phylogenetically Estimated Traits of Soil Microbial Communities. PMID:28744266
Draft genome sequences of strains Salinicola socius SMB35T, Salinicola sp. MH3R3-1 and Chromohalobacter sp. SMB17 from the Verkhnekamsk potash mining region of Russia. PMID:28729898
The Electron Bifurcating FixABCX Protein Complex from Azotobacter vinelandii: Generation of Low-Potential Reducing Equivalents for Nitrogenase Catalysis. PMID:28704608
Extensive horizontal gene transfer in cheese-associated bacteria. PMID:28644126
Ehrlichia chaffeensis TRP120 Moonlights as a HECT E3 Ligase Involved in Self- and Host Ubiquitination To Influence Protein Interactions and Stability for Intracellular Survival. PMID:28630068
Genomics and metagenomics of trimethylamine-utilizing Archaea in the human gut microbiome. PMID:28585938
Complete Genome Sequence of Veillonella atypica OK5, the First Transformable Strain in the Species. PMID:28572307
Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches. PMID:28538703
Uncovering the trimethylamine-producing bacteria of the human gut microbiota. PMID:28506279
Genome sequencing and description of Oerskovia enterophila VJag, an agar- and cellulose-degrading bacterium. PMID:28484582
Complete Genome Sequence of Bordetella pertussis Pelita III, the Production Strain for an Indonesian Whole-Cell Pertussis Vaccine. PMID:28450511
CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline. PMID:28449639
Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments. PMID:28439121
β-Carboxysome bioinformatics: identification and evolution of new bacterial microcompartment protein gene classes and core locus constraints. PMID:28419380
Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems. PMID:28396823
High-fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice. PMID:28390422
Second Era of OMICS in Caries Research: Moving Past the Phase of Disillusionment. PMID:28384412
Intestinal microbiome landscaping: insight in community assemblage and implications for microbial modulation strategies. PMID:28364729
Sequence-based analysis of the genus Ruminococcus resolves its phylogeny and reveals strong host association. PMID:28348838
An In vitro Study of Bio-Control and Plant Growth Promotion Potential of Salicaceae Endophytes. PMID:28348550
In search of genome annotation consistency: solid gene clusters and how to use them. PMID:28324432
Enabling comparative modeling of closely related genomes: example genus Brucella. PMID:28324362
Microbial players and processes involved in phytoplankton bloom utilization in the water column of a fast-flowing, river-dominated estuary. PMID:28318115
Genomic diversity within the haloalkaliphilic genus Thioalkalivibrio. PMID:28282461
Genome Sequence of Porphyromonas gingivalis Strain A7A1-28. PMID:28280013
Comparative genomics of Enterococcus spp. isolated from bovine feces. PMID:28270110
Three Novel Species with Peptidoglycan Cell Walls form the New Genus Lacunisphaera gen. nov. in the Family Opitutaceae of the Verrucomicrobial Subdivision 4. PMID:28243229
A Putative O-Linked β-N-Acetylglucosamine Transferase Is Essential for Hormogonium Development and Motility in the Filamentous Cyanobacterium Nostoc punctiforme. PMID:28242721
Draft Genome Sequence of Mycobacterium chimaera Type Strain Fl-0169. PMID:28232435
Integration of Metagenomic and Stable Carbon Isotope Evidence Reveals the Extent and Mechanisms of Carbon Dioxide Fixation in High-Temperature Microbial Communities. PMID:28217111
Resequencing and annotation of the Nostoc punctiforme ATTC 29133 genome: facilitating biofuel and high-value chemical production. PMID:28211005
Elevated Rate of Genome Rearrangements in Radiation-Resistant Bacteria. PMID:28188144
Chemolithotrophic processes in the bacterial communities on the surface of mineral-enriched biochars. PMID:28169988
Draft genome sequences of eight bacteria isolated from the indoor environment: Staphylococcus capitis strain H36, S. capitis strain H65, S. cohnii strain H62, S. hominis strain H69, Microbacterium sp. strain H83, Mycobacterium iranicum strain H39, Plantibacter sp. strain H53, and Pseudomonas oryzihabitans strain H72. PMID:28163826
Genome composition and phylogeny of microbes predict their co-occurrence in the environment. PMID:28152007
Sticking together: inter-species aggregation of bacteria isolated from iron snow is controlled by chemical signaling. PMID:28140394
Draft genome sequence of Arthrobacter sp. strain B6 isolated from the high-arsenic sediments in Datong Basin, China. PMID:28138355
Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts. PMID:28094347
Direct Heme Uptake by Phytoplankton-Associated Roseobacter Bacteria. PMID:28083564
Genome Sequence of Porphyromonas gingivalis Strain 381. PMID:28082501
Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities. PMID:28079128
Asgard archaea illuminate the origin of eukaryotic cellular complexity. PMID:28077874
Fuerstia marisgermanicae gen. nov., sp. nov., an Unusual Member of the Phylum Planctomycetes from the German Wadden Sea. PMID:28066393
Diversity of Phototrophic Genes Suggests Multiple Bacteria May Be Able to Exploit Sunlight in Exposed Soils from the Sør Rondane Mountains, East Antarctica. PMID:28066352
Insights into the lifestyle of uncultured bacterial natural product factories associated with marine sponges. PMID:28049838
Horizontal gene transfer drives the evolution of Rh50 permeases in prokaryotes. PMID:28049420
Phosphoribosyl Diphosphate (PRPP): Biosynthesis, Enzymology, Utilization, and Metabolic Significance. PMID:28031352
Metagenome phylogenetic profiling of microbial community evolution in a tetrachloroethene-contaminated aquifer responding to enhanced reductive dechlorination protocols. PMID:27980706
Genome and Proteome Analysis of Rhodococcus erythropolis MI2: Elucidation of the 4,4´-Dithiodibutyric Acid Catabolism. PMID:27977722
Aerobic Lineage of the Oxidative Stress Response Protein Rubrerythrin Emerged in an Ancient Microaerobic, (Hyper)Thermophilic Environment. PMID:27917155
Polynucleobacter wuianus sp. nov., a free-living freshwater bacterium affiliated with the cryptic species complex PnecC. PMID:27902302
An Enrichment of CRISPR and Other Defense-Related Features in Marine Sponge-Associated Microbial Metagenomes. PMID:27877161
Microdiversification of a Pelagic Polynucleobacter Species Is Mainly Driven by Acquisition of Genomic Islands from a Partially Interspecific Gene Pool. PMID:27836842
Avoiding Pandemic Fears in the Subway and Conquering the Platypus. PMID:27832215
Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. PMID:27774985
IMG/M: integrated genome and metagenome comparative data analysis system. PMID:27738135
Comprehensive genomic and phenotypic metal resistance profile of Pseudomonas putida strain S13.1.2 isolated from a vineyard soil. PMID:27730570
HydDB: A web tool for hydrogenase classification and analysis. PMID:27670643
Peeking under the Iron Curtain: Development of a Microcosm for Imaging the Colonization of Steel Surfaces by Mariprofundus sp. Strain DIS-1, an Oxygen-Tolerant Fe-Oxidizing Bacterium. PMID:27637877
Draft genome sequence of Mameliella alba strain UMTAT08 isolated from clonal culture of toxic dinoflagellate Alexandrium tamiyavanichii. PMID:27625991
Functional Annotations of Paralogs: A Blessing and a Curse. PMID:27618105
Complete genome sequence of Desulfurivibrio alkaliphilus strain AHT2(T), a haloalkaliphilic sulfidogen from Egyptian hypersaline alkaline lakes. PMID:27617057
Near complete genome sequence of the animal feed probiotic, Bacillus amyloliquefaciens H57. PMID:27602182
Phylogeography, Salinity Adaptations and Metabolic Potential of the Candidate Division KB1 Bacteria Based on a Partial Single Cell Genome. PMID:27597842
Long-Term Warming Alters Carbohydrate Degradation Potential in Temperate Forest Soils. PMID:27590813
Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome. PMID:27572443
Orenia metallireducens sp. nov. Strain Z6, a Novel Metal-Reducing Member of the Phylum Firmicutes from the Deep Subsurface. PMID:27565620
The methanogenic redox cofactor F420 is widely synthesized by aerobic soil bacteria. PMID:27505347
Genomic mechanisms for cold tolerance and production of exopolysaccharides in the Arctic cyanobacterium Phormidesmis priestleyi BC1401. PMID:27485510
Systems-level Proteomics of Two Ubiquitous Leaf Commensals Reveals Complementary Adaptive Traits for Phyllosphere Colonization. PMID:27457762
Single-cell Sequencing of Thiomargarita Reveals Genomic Flexibility for Adaptation to Dynamic Redox Conditions. PMID:27446006
Transhydrogenase and Growth Substrate Influence Lipid Hydrogen Isotope Ratios in Desulfovibrio alaskensis G20. PMID:27445998
Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis. PMID:27422831
The Genomic Sequence of the Oral Pathobiont Strain NI1060 Reveals Unique Strategies for Bacterial Competition and Pathogenicity. PMID:27409077
Functional profiling of cyanobacterial genomes and its role in ecological adaptations. PMID:27408818
Genome Evolution in the Obligate but Environmentally Active Luminous Symbionts of Flashlight Fish. PMID:27389687
Stoichiometric modelling of assimilatory and dissimilatory biomass utilisation in a microbial community. PMID:27387069
A catalogue of 136 microbial draft genomes from Red Sea metagenomes. PMID:27377622
Editorial: Transport in Plant Microbe Interactions. PMID:27375662
Genome-Centric Analysis of Microbial Populations Enriched by Hydraulic Fracture Fluid Additives in a Coal Bed Methane Production Well. PMID:27375557
The nature of mutations induced by replication–transcription collisions. PMID:27362223
Cyanobacterial ultrastructure in light of genomic sequence data. PMID:27344651
Complete Genome Sequence of Dyella thiooxydans ATSB10, a Thiosulfate-Oxidizing Bacterium Isolated from Sunflower Fields in South Korea. PMID:27340060
Metagenomic Evidence for the Presence of Comammox Nitrospira-Like Bacteria in a Drinking Water System. PMID:27303675
Gene Loss and Horizontal Gene Transfer Contributed to the Genome Evolution of the Extreme Acidophile "Ferrovum". PMID:27303384
Pseudomonas syringae type III effector HopAF1 suppresses plant immunity by targeting methionine recycling to block ethylene induction. PMID:27274076
A stable genetic polymorphism underpinning microbial syntrophy. PMID:27258948
Deep Subsurface Life from North Pond: Enrichment, Isolation, Characterization and Genomes of Heterotrophic Bacteria. PMID:27242705
Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis. PMID:27199545
OrfM: a fast open reading frame predictor for metagenomic data. PMID:27153669
Ancestral genome reconstruction identifies the evolutionary basis for trait acquisition in polyphosphate accumulating bacteria. PMID:27128993
Term-seq reveals abundant ribo-regulation of antibiotics resistance in bacteria. PMID:27120414
The Intestinal Microbiome and Estrogen Receptor-Positive Female Breast Cancer. PMID:27107051
Energy efficiency trade-offs drive nucleotide usage in transcribed regions. PMID:27098217
EDGAR 2.0: an enhanced software platform for comparative gene content analyses. PMID:27098043
Identification of a Third Mn(II) Oxidase Enzyme in Pseudomonas putida GB-1. PMID:27084014
Differences in stability of seed-associated microbial assemblages in response to invasion by phytopathogenic microorganisms. PMID:27077013
Reclassification of four Polynucleobacter necessarius strains as representatives of Polynucleobacter asymbioticus comb. nov., Polynucleobacter duraquae sp. nov., Polynucleobacter yangtzensis sp. nov. and Polynucleobacter sinensis sp. nov., and emended description of Polynucleobacter necessarius. PMID:27064460
Draft Genome Sequence of Tepidibacillus decaturensis Strain Z9, an Anaerobic, Moderately Thermophilic, and Heterotrophic Bacterium from the Deep Subsurface of the Illinois Basin, USA. PMID:27056217
Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community. PMID:27048805
Differences down-under: alcohol-fueled methanogenesis by archaea present in Australian macropodids. PMID:27022996
Insights into the single cell draft genome of "Candidatus Achromatium palustre". PMID:27014417
Formaldehyde as a carbon and electron shuttle between autotroph and heterotroph populations in acidic hydrothermal vents of Norris Geyser Basin, Yellowstone National Park. PMID:26995682
Draft Genome Sequence of Aliiroseovarius crassostreae CV919-312, the Causative Agent of Roseovarius Oyster Disease (Formerly Juvenile Oyster Disease). PMID:26988054
Methyl-esterified 3-hydroxybutyrate oligomers protect bacteria from hydroxyl radicals. PMID:26974813
The Structural Basis of Coenzyme A Recycling in a Bacterial Organelle. PMID:26959993
Complete ecological isolation and cryptic diversity in Polynucleobacter bacteria not resolved by 16S rRNA gene sequences. PMID:26943621
Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus CFL1, a Lactic Acid Bacterium Isolated from French Handcrafted Fermented Milk. PMID:26941141
Glycan Engineering for Cell and Developmental Biology. PMID:26933739
Influence of whole-wheat consumption on fecal microbial community structure of obese diabetic mice. PMID:26925326
Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children. PMID:26912898
Isolation and genome sequencing of four Arctic marine Psychrobacter strains exhibiting multicopper oxidase activity. PMID:26879123
Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments. PMID:26872043
Evidence for plasmid-mediated salt tolerance in the human gut microbiome and potential mechanisms. PMID:26850157
Vikodak--A Modular Framework for Inferring Functional Potential of Microbial Communities from 16S Metagenomic Datasets. PMID:26848568
Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction. PMID:26824177
Genome Sequence and Analysis of Escherichia coli MRE600, a Colicinogenic, Nonmotile Strain that Lacks RNase I and the Type I Methyltransferase, EcoKI. PMID:26802429
Characterization of Bacterial Communities in Selected Smokeless Tobacco Products Using 16S rDNA Analysis. PMID:26784944
Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria. PMID:26784354
Expanding the World of Marine Bacterial and Archaeal Clades. PMID:26779174
Developing of the Computer Method for Annotation of Bacterial Genes. PMID:26770195
High quality permanent draft genome sequence of Phaseolibacter flectens ATCC 12775(T), a plant pathogen of French bean pods. PMID:26767091
Permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, a thermoacidophilic sulfur-reducing crenarchaeon isolated from acidic hot springs of Hveravellir, Iceland. PMID:26767090
Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations. PMID:26744812
Trace Metal Acquisition by Marine Heterotrophic Bacterioplankton with Contrasting Trophic Strategies. PMID:26729720
High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED. PMID:26682918
MycoCAP - Mycobacterium Comparative Analysis Platform. PMID:26666970
Complete genome of Pseudomonas chlororaphis strain UFB2, a soil bacterium with antibacterial activity against bacterial canker pathogen of tomato. PMID:26634018
The pan-genome of Lactobacillus reuteri strains originating from the pig gastrointestinal tract. PMID:26626322
Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires. PMID:26617277
Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage. PMID:26615204
SymbioGenomesDB: a database for the integration and access to knowledge on host-symbiont relationships. PMID:26607947
Web Resources for Metagenomics Studies. PMID:26602607
Global prevalence and distribution of genes and microorganisms involved in mercury methylation. PMID:26601305
Genome sequence and description of the anaerobic lignin-degrading bacterium Tolumonas lignolytica sp. nov. PMID:26594307
Metabolic and genomic analysis elucidates strain-level variation in Microbacterium spp. isolated from chromate contaminated sediment. PMID:26587353
Comparative metagenomics reveals impact of contaminants on groundwater microbiomes. PMID:26583008
Analysis of cbbL, nifH, and pufLM in Soils from the Sør Rondane Mountains, Antarctica, Reveals a Large Diversity of Autotrophic and Phototrophic Bacteria. PMID:26582318
Genome sequence of Pedobacter glucosidilyticus DD6b, isolated from zooplankton Daphnia magna. PMID:26566425
Genome Sequence of Porphyromonas gingivalis Strain AJW4. PMID:26543127
VarR controls colonization and virulence in the marine macroalgal pathogen Nautella italica R11. PMID:26528274
Bacillus cereus eﬄux protein BC3310 - a multidrug transporter of the unknown major facilitator family, UMF-2. PMID:26528249
Genome Sequence of "Candidatus Thioglobus autotrophica" Strain EF1, a Chemoautotroph from the SUP05 Clade of Marine Gammaproteobacteria. PMID:26494660
Genome Sequence of "Candidatus Thioglobus singularis" Strain PS1, a Mixotroph from the SUP05 Clade of Marine Gammaproteobacteria. PMID:26494659
Metagenomic evidence for reciprocal particle exchange between the mainstem estuary and lateral bay sediments of the lower Columbia River. PMID:26483785
Laboratory-scale bioaugmentation relieves acetate accumulation and stimulates methane production in stalled anaerobic digesters. PMID:26481626
Genome-Wide Analysis of Oceanimonas sp. GK1 Isolated from Gavkhouni Wetland (Iran) Demonstrates Presence of Genes for Virulence and Pathogenicity. PMID:26464816
Draft genome sequence of Mesotoga strain PhosAC3, a mesophilic member of the bacterial order Thermotogales, isolated from a digestor treating phosphogypsum in Tunisia. PMID:26464750
Prediction of microbial phenotypes based on comparative genomics. PMID:26451672
Correcting Inconsistencies and Errors in Bacterial Genome Metadata Using an Automated Curation Tool in Excel (AutoCurE). PMID:26442252
Mining the phytomicrobiome to understand how bacterial coinoculations enhance plant growth. PMID:26442090
PanFP: pangenome-based functional profiles for microbial communities. PMID:26409790
Genome Sequence of Porphyromonas gingivalis Strain A7436. PMID:26404590
Metatranscriptomics reveals metabolic adaptation and induction of virulence factors by Haemophilus parasuis during lung infection. PMID:26395877
High-quality permanent draft genome sequence of the extremely osmotolerant diphenol degrading bacterium Halotalea alkalilenta AW-7(T), and emended description of the genus Halotalea. PMID:26380640
Genome sequence of the pink-pigmented marine bacterium Loktanella hongkongensis type strain (UST950701-009P(T)), a representative of the Roseobacter group. PMID:26380639
Permanent draft genome sequence of Acidiphilium sp. JA12-A1. PMID:26380040
Experimental validation of in silico model-predicted isocitrate dehydrogenase and phosphomannose isomerase from Dehalococcoides mccartyi. PMID:26374290
Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels. PMID:26371554
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PMID:26336640
The green impact: bacterioplankton response toward a phytoplankton spring bloom in the southern North Sea assessed by comparative metagenomic and metatranscriptomic approaches. PMID:26322028
Functional Basis of Microorganism Classification. PMID:26317871
Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe. PMID:26283343
Anaerobic biosynthesis of the lower ligand of vitamin B12. PMID:26246619
Potential Role of Acetyl-CoA Synthetase (acs) and Malate Dehydrogenase (mae) in the Evolution of the Acetate Switch in Bacteria and Archaea. PMID:26235787
Fatty acid profiles and desaturase-encoding genes are different in thermo- and psychrotolerant strains of the Bacillus cereus Group. PMID:26227277
Genome sequence of Clostridium sporogenes DSM 795(T), an amino acid-degrading, nontoxic surrogate of neurotoxin-producing Clostridium botulinum. PMID:26221421
Representing virus-host interactions and other multi-organism processes in the Gene Ontology. PMID:26215368
Draft Genome Sequence of the Cellulolytic and Xylanolytic Thermophile Clostridium clariflavum Strain 4-2a. PMID:26205857
Genome sequence of the Roseovarius mucosus type strain (DSM 17069(T)), a bacteriochlorophyll a-containing representative of the marine Roseobacter group isolated from the dinoflagellate Alexandrium ostenfeldii. PMID:26203330
Interaction networks for identifying coupled molecular processes in microbial communities. PMID:26180552
Arsenophonus and Sodalis Symbionts in Louse Flies: an Analogy to the Wigglesworthia and Sodalis System in Tsetse Flies. PMID:26150448
Microbial species delineation using whole genome sequences. PMID:26150420
Ecophysiology of an uncultivated lineage of Aigarchaeota from an oxic, hot spring filamentous 'streamer' community. PMID:26140529
The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes. PMID:26136581
Engineered and Native Coenzyme B12-dependent Isovaleryl-CoA/Pivalyl-CoA Mutase. PMID:26134562
New Insight into Microbial Iron Oxidation as Revealed by the Proteomic Profile of an Obligate Iron-Oxidizing Chemolithoautotroph. PMID:26092463
Complete Genome Sequence of the Linear Plasmid pJD12 Hosted by Micrococcus sp. D12, Isolated from a High-Altitude Volcanic Lake in Argentina. PMID:26067968
Evolutionary dynamics of rhomboid proteases in Streptomycetes. PMID:26054641
Adaptive Evolution of Thermotoga maritima Reveals Plasticity of the ABC Transporter Network. PMID:26048924
Genomic analysis of six new Geobacillus strains reveals highly conserved carbohydrate degradation architectures and strategies. PMID:26029180
Alarmingly High Segregation Frequencies of Quinolone Resistance Alleles within Human and Animal Microbiomes Are Not Explained by Direct Clinical Antibiotic Exposure. PMID:26019163
Gut microbial succession follows acute secretory diarrhea in humans. PMID:25991682
Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population. PMID:25954269
Genome Sequence of the Acidophilic Iron Oxidizer Ferrimicrobium acidiphilum Strain T23T. PMID:25931604
Genome Sequence of the Acidophilic Ferrous Iron-Oxidizing Isolate Acidithrix ferrooxidans Strain Py-F3, the Proposed Type Strain of the Novel Actinobacterial Genus Acidithrix. PMID:25931603
Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria. PMID:25922666
Integrating chemical mutagenesis and whole-genome sequencing as a platform for forward and reverse genetic analysis of Chlamydia. PMID:25920978
Whole-genome sequencing in outbreak analysis. PMID:25876885
The composition of the global and feature specific cyanobacterial core-genomes. PMID:25852675
Subsistence strategies in traditional societies distinguish gut microbiomes. PMID:25807110
Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. PMID:25780495
Transcriptomics in the tropics: Total RNA-based profiling of Costa Rican bromeliad-associated communities. PMID:25755850
Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes. PMID:25739499
Concordance and discordance of sequence survey methods for molecular epidemiology. PMID:25737810
Closed Genome Sequence of Clostridium pasteurianum ATCC 6013. PMID:25700419
Complete Genome Sequence of the Nitrogen-Fixing and Solvent-Producing Clostridium pasteurianum DSM 525. PMID:25700415
Deconstruction of archaeal genome depict strategic consensus in core pathways coding sequence assembly. PMID:25674789
Role of RNA secondary structure and processing in stability of the nifH1 transcript in the cyanobacterium Anabaena variabilis. PMID:25666132
Genomic and phenotypic insights into the ecology of Arthrobacter from Antarctic soils. PMID:25649291
Reassessment of the transhydrogenase/malate shunt pathway in Clostridium thermocellum ATCC 27405 through kinetic characterization of malic enzyme and malate dehydrogenase. PMID:25616802
YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia. PMID:25591325
Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2. PMID:25566348
Metagenomic evidence for metabolism of trace atmospheric gases by high-elevation desert Actinobacteria. PMID:25566214
A genome-guided analysis of energy conservation in the thermophilic, cytochrome-free acetogenic bacterium Thermoanaerobacter kivui. PMID:25523312
Regulation of Three Nitrogenase Gene Clusters in the Cyanobacterium Anabaena variabilis ATCC 29413. PMID:25513762
Comparison of environmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms. PMID:25511286
Emergence shapes the structure of the seed microbiota. PMID:25501471
The ins and outs of metal homeostasis by the root nodule actinobacterium Frankia. PMID:25495525
AKE - the Accelerated k-mer Exploration web-tool for rapid taxonomic classification and visualization. PMID:25495116
Going from microbial ecology to genome data and back: studies on a haloalkaliphilic bacterium isolated from Soap Lake, Washington State. PMID:25477871
A systematic computational analysis of biosynthetic gene cluster evolution: lessons for engineering biosynthesis. PMID:25474254
Evaluative profiling of arsenic sensing and regulatory systems in the human microbiome project genomes. PMID:25452698
Survival strategies in the aquatic and terrestrial world: the impact of second messengers on cyanobacterial processes. PMID:25411927
Reduced catabolic protein expression in Clostridium butyricum DSM 10702 correlate with reduced 1,3-propanediol synthesis at high glycerol loading. PMID:25401066
The Draft Genome Sequence of Sphingomonas sp. Strain FukuSWIS1, Obtained from Acidic Lake Grosse Fuchskuhle, Indicates Photoheterotrophy and a Potential for Humic Matter Degradation. PMID:25395647
Toxin-antitoxin systems in the mobile genome of Acidithiobacillus ferrooxidans. PMID:25384039
Quantitative and functional characterization of the hyper-conserved protein of Prochlorococcus and marine Synechococcus. PMID:25360678
Comparative transcriptomics between Synechococcus PCC 7942 and Synechocystis PCC 6803 provide insights into mechanisms of stress acclimation. PMID:25340743
A taxonomy of bacterial microcompartment loci constructed by a novel scoring method. PMID:25340524
Complete Genome Sequence of the Solvent Producer Clostridium saccharoperbutylacetonicum Strain DSM 14923. PMID:25323722
All1371 is a polyphosphate-dependent glucokinase in Anabaena sp. PCC 7120. PMID:25320362
Genome-based comparative analyses of Antarctic and temperate species of Paenibacillus. PMID:25285990
VibrioBase: a model for next-generation genome and annotation database development. PMID:25243218
Testing the role of genetic background in parallel evolution using the comparative experimental evolution of antibiotic resistance. PMID:25228081
Genome sequence of the exopolysaccharide-producing Salipiger mucosus type strain (DSM 16094(T)), a moderately halophilic member of the Roseobacter clade. PMID:25197501
Genome sequence of the Thermotoga thermarum type strain (LA3(T)) from an African solfataric spring. PMID:25197486
The complete genome sequence of Clostridium indolis DSM 755(T.). PMID:25197485
Genome sequence of the pink to light reddish-pigmented Rubellimicrobium mesophilum type strain (DSM 19309(T)), a representative of the Roseobacter group isolated from soil, and emended description of the species. PMID:25197472
Genome sequence of the Wenxinia marina type strain (DSM 24838(T)), a representative of the Roseobacter group isolated from oilfield sediments. PMID:25197468
Complete genome sequence of the bacteriochlorophyll a-containing Roseibacterium elongatum type strain (DSM 19469(T)), a representative of the Roseobacter group isolated from Australian coast sand. PMID:25197467
Evolution of the F0F1 ATP synthase complex in light of the patchy distribution of different bioenergetic pathways across prokaryotes. PMID:25188293
Systems biology perspectives on minimal and simpler cells. PMID:25184563
Microbiome analysis - from technical advances to biological relevance. PMID:25184041
Heterologous expression and characterization of the manganese-oxidizing protein from Erythrobacter sp. strain SD21. PMID:25172859
FusoBase: an online Fusobacterium comparative genomic analysis platform. PMID:25149689
Comparative analysis of functional metagenomic annotation and the mappability of short reads. PMID:25148512
A scalable and accurate targeted gene assembly tool (SAT-Assembler) for next-generation sequencing data. PMID:25122209
Identification of a cyclic-di-GMP-modulating response regulator that impacts biofilm formation in a model sulfate reducing bacterium. PMID:25120537
Proteomics-based metabolic modeling and characterization of the cellulolytic bacterium Thermobifida fusca. PMID:25115351
Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage. PMID:25093637
Regulation of nitrogenase gene expression by transcript stability in the cyanobacterium Anabaena variabilis. PMID:25092030
First Insights into the Genome of the Amino Acid-Metabolizing Bacterium Clostridium litorale DSM 5388. PMID:25081264
Bacteriophages as vehicles for antibiotic resistance genes in the environment. PMID:25078987
Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria. PMID:25071821
Improved Draft Genome Sequence of Probiotic Strain Lactobacillus gasseri K7. PMID:25059871
Genome Sequence of Bacillus safensis CFA06, Isolated from Biodegraded Petroleum in Brazil. PMID:25059859
The expanded diversity of methylophilaceae from Lake Washington through cultivation and genomic sequencing of novel ecotypes. PMID:25058595
The structural code of cyanobacterial genomes. PMID:25056315
vanI: a novel D-Ala-D-Lac vancomycin resistance gene cluster found in Desulfitobacterium hafniense. PMID:25042042
Characterization and evolutionary implications of the triad Asp-Xxx-Glu in group II phosphopantetheinyl transferases. PMID:25036863
Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. PMID:25036635
HelicoBase: a Helicobacter genomic resource and analysis platform. PMID:25030426
The long goodbye: the rise and fall of flavodoxin during plant evolution. PMID:25009172
Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology. PMID:25003965
Functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe. PMID:25002542
Leveraging structure for enzyme function prediction: methods, opportunities, and challenges. PMID:24998033
Emergent biosynthetic capacity in simple microbial communities. PMID:24992662
Rhodoluna lacicola gen. nov., sp. nov., a planktonic freshwater bacterium with stream-lined genome. PMID:24984700
Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks. PMID:24980702
Carbadox has both temporary and lasting effects on the swine gut microbiota. PMID:24959163
Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences. PMID:24930142
Complete Genome Sequence of Amino Acid-Utilizing Eubacterium acidaminophilum al-2 (DSM 3953). PMID:24926057
Identification of genes required for the survival of B. fragilis using massive parallel sequencing of a saturated transposon mutant library. PMID:24899126
Proteomic analysis of the Burkholderia pseudomallei type II secretome reveals hydrolytic enzymes, novel proteins, and the deubiquitinase TssM. PMID:24866793
Carbohydrate catabolism in Phaeobacter inhibens DSM 17395, a member of the marine roseobacter clade. PMID:24858085
Syntrophic exchange in synthetic microbial communities. PMID:24778240
Genomic features of a bumble bee symbiont reflect its host environment. PMID:24747890
Draft Genome Sequence of Bacillus pumilus Fairview, an Isolate Recovered from a Microbial Methanogenic Enrichment of Coal Seam Gas Formation Water from Queensland, Australia. PMID:24744330
Diversity and genomic insights into the uncultured Chloroflexi from the human microbiota. PMID:24738594
An expanded genomic representation of the phylum cyanobacteria. PMID:24709563
CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction. PMID:24708850
Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction. PMID:24708835
Comparative genomics for mycobacterial peptidoglycan remodelling enzymes reveals extensive genetic multiplicity. PMID:24661741
Sulfur species as redox partners and electron shuttles for ferrihydrite reduction by Sulfurospirillum deleyianum. PMID:24632263
Genomic and transcriptomic analyses of the facultative methanotroph Methylocystis sp. strain SB2 grown on methane or ethanol. PMID:24610846
Utilization of glyphosate as phosphate source: biochemistry and genetics of bacterial carbon-phosphorus lyase. PMID:24600043
StaphyloBase: a specialized genomic resource for the staphylococcal research community. PMID:24578355
The CasKR two-component system is required for the growth of mesophilic and psychrotolerant Bacillus cereus strains at low temperatures. PMID:24509924
Complete enumeration of elementary flux modes through scalable demand-based subnetwork definition. PMID:24497502
Characterization of cyanobacterial hydrocarbon composition and distribution of biosynthetic pathways. PMID:24475038
CoryneBase: Corynebacterium genomic resources and analysis tools at your fingertips. PMID:24466021
Genome Sequence of the Mycorrhizal Helper Bacterium Pseudomonas fluorescens BBc6R8. PMID:24407649
Analysis of the complete genome of Fervidococcus fontis confirms the distinct phylogenetic position of the order Fervidicoccales and suggests its environmental function. PMID:24366681
Thermoanaerobacter thermohydrosulfuricus WC1 shows protein complement stability during fermentation of key lignocellulose-derived substrates. PMID:24362431
Draft Genome Sequence of the Arsenite-Oxidizing Strain Aliihoeflea sp. 2WW, Isolated from Arsenic-Contaminated Groundwater. PMID:24356838
Listeria monocytogenes, a down-to-earth pathogen. PMID:24350062
Draft Genome Sequence of "Candidatus Halobonum tyrrellensis" Strain G22, Isolated from the Hypersaline Waters of Lake Tyrrell, Australia. PMID:24336364
Diet rapidly and reproducibly alters the human gut microbiome. PMID:24336217
Methanotrophic archaea possessing diverging methane-oxidizing and electron-transporting pathways. PMID:24335827
INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles. PMID:24324765
Fermentation stage-dependent adaptations of Bacillus licheniformis during enzyme production. PMID:24313996
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). PMID:24293654
Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade. PMID:24286338
Complete Genome Sequence of the Solvent Producer Clostridium saccharobutylicum NCP262 (DSM 13864). PMID:24285650
Strain-level genomic variation in natural populations of Lebetimonas from an erupting deep-sea volcano. PMID:24257443
The genome portal of the Department of Energy Joint Genome Institute: 2014 updates. PMID:24225321
Relative amino acid composition signatures of organisms and environments. PMID:24204807
MetaRef: a pan-genomic database for comparative and community microbial genomics. PMID:24203705
Niche specialization of novel Thaumarchaeota to oxic and hypoxic acidic geothermal springs of Yellowstone National Park. PMID:24196321
Life based on phosphite: a genome-guided analysis of Desulfotignum phosphitoxidans. PMID:24180241
Draft Genome Sequence of the Biosurfactant-Producing Bacterium Gordonia amicalis Strain CCMA-559, Isolated from Petroleum-Impacted Sediment. PMID:24179120
Draft Genome Sequence of Pseudomonas azotifigens Strain DSM 17556T (6H33bT), a Nitrogen Fixer Strain Isolated from a Compost Pile. PMID:24179119
IMG 4 version of the integrated microbial genomes comparative analysis system. PMID:24165883
Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla. PMID:24149512
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
Metabolic adaptation and trophic strategies of soil bacteria-C1- metabolism and sulfur chemolithotrophy in Starkeya novella. PMID:24146664
Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution. PMID:24146609
Novel characteristics of succinate coenzyme A (Succinate-CoA) ligases: conversion of malate to malyl-CoA and CoA-thioester formation of succinate analogues in vitro. PMID:24141127
Thermal adaptation of conformational dynamics in ribonuclease H. PMID:24098095
Functional genomics of novel secondary metabolites from diverse cyanobacteria using untargeted metabolomics. PMID:24084783
Trehalose/2-sulfotrehalose biosynthesis and glycine-betaine uptake are widely spread mechanisms for osmoadaptation in the Halobacteriales. PMID:24048226
First Insights into the Genome of the Gram-Negative, Endospore-Forming Organism Sporomusa ovata Strain H1 DSM 2662. PMID:24029766
Draft Genome Sequence of Bacillus pumilus CCMA-560, Isolated from an Oil-Contaminated Mangrove Swamp. PMID:24029758
Draft Genome Sequence of Thermoanaerobacter sp. Strain A7A, Reconstructed from a Metagenome Obtained from a High-Temperature Hydrocarbon Reservoir in the Bass Strait, Australia. PMID:24029756
Microbial life in a fjord: metagenomic analysis of a microbial mat in Chilean patagonia. PMID:24015199
Draft Genome Sequence of Thermotoga maritima A7A Reconstructed from Metagenomic Sequencing Analysis of a Hydrocarbon Reservoir in the Bass Strait, Australia. PMID:24009120
Cumate-inducible gene expression system for sphingomonads and other Alphaproteobacteria. PMID:23995928
Exploring the roles of DNA methylation in the metal-reducing bacterium Shewanella oneidensis MR-1. PMID:23995632
Permanent draft genome sequence of Comamonas testosteroni KF-1. PMID:23991256
Complete genome sequence of Halorhodospira halophila SL1. PMID:23991253
The (d)evolution of methanotrophy in the Beijerinckiaceae--a comparative genomics analysis. PMID:23985741
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. PMID:23975157
Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae. PMID:23949660
Structure and evolution of chlorate reduction composite transposons. PMID:23919996
Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass. PMID:23894306
Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules. PMID:23858463
Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges. PMID:23842652
A cell wall recycling shortcut that bypasses peptidoglycan de novo biosynthesis. PMID:23831760
An ICEBs1-like element may be associated with the extreme radiation and desiccation resistance of Bacillus pumilus SAFR-032 spores. PMID:23812891
Quantification of endospore-forming firmicutes by quantitative PCR with the functional gene spo0A. PMID:23811505
MS/MS networking guided analysis of molecule and gene cluster families. PMID:23798442
Draft Genome Sequence for Caulobacter sp. Strain OR37, a Bacterium Tolerant to Heavy Metals. PMID:23792749
Draft Genome Sequence for Ralstonia sp. Strain OR214, a Bacterium with Potential for Bioremediation. PMID:23792748
How much metagenomic sequencing is enough to achieve a given goal? PMID:23752679
Contrasting genomic properties of free-living and particle-attached microbial assemblages within a coastal ecosystem. PMID:23750156
The abundance and variety of carbohydrate-active enzymes in the human gut microbiota. PMID:23748339
Genome Sequence of Pseudomonas aeruginosa PA45, a Highly Virulent Strain Isolated from a Patient with Bloodstream Infection. PMID:23704188
Draft Genome Sequence of the Cellulolytic, Mesophilic, Anaerobic Bacterium Clostridium termitidis Strain CT1112 (DSM 5398). PMID:23704187
Poles apart: Arctic and Antarctic Octadecabacter strains share high genome plasticity and a new type of xanthorhodopsin. PMID:23671678
Computational meta'omics for microbial community studies. PMID:23670539
Using Bioinformatics to Develop and Test Hypotheses: E. coli-Specific Virulence Determinants. PMID:23653804
The YNP Metagenome Project: Environmental Parameters Responsible for Microbial Distribution in the Yellowstone Geothermal Ecosystem. PMID:23653623
A metagenomic insight into freshwater methane-utilizing communities and evidence for cooperation between the Methylococcaceae and the Methylophilaceae. PMID:23638358
Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices. PMID:23638103
CRISPR-Cas systems target a diverse collection of invasive mobile genetic elements in human microbiomes. PMID:23628424
Towards a predictive systems-level model of the human microbiome: progress, challenges, and opportunities. PMID:23623295
The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. PMID:23587224
Draft Genome Sequence for Desulfovibrio africanus Strain PCS. PMID:23580709
Multiple single-cell genomes provide insight into functions of uncultured Deltaproteobacteria in the human oral cavity. PMID:23555659
MGcV: the microbial genomic context viewer for comparative genome analysis. PMID:23547764
Metabolic model for the filamentous 'Candidatus Microthrix parvicella' based on genomic and metagenomic analyses. PMID:23446830
Genome mining for methanobactins. PMID:23442874
Improving microbial genome annotations in an integrated database context. PMID:23424620
De novo prediction of the genomic components and capabilities for microbial plant biomass degradation from (meta-)genomes. PMID:23414703
Simultaneous quantification of multiple bacteria by the BactoChip microarray designed to target species-specific marker genes. PMID:23409037
Complete Genome Sequence of Bacillus thuringiensis Strain 407 Cry-. PMID:23405326
Draft Genome Sequence of Clostridium sp. Maddingley, Isolated from Coal-Seam Gas Formation Water. PMID:23405323
Draft Genome Sequence of Methanobacterium sp. Maddingley, Reconstructed from Metagenomic Sequencing of a Methanogenic Microbial Consortium Enriched from Coal-Seam Gas Formation Water. PMID:23405289
Use of degradation tags to control protein levels in the Cyanobacterium Synechocystis sp. Strain PCC 6803. PMID:23396339
Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities. PMID:23387867
A cyclic form of N6-threonylcarbamoyladenosine as a widely distributed tRNA hypermodification. PMID:23242255
Evaluation method for the potential functionome harbored in the genome and metagenome. PMID:23234305
Functional Annotation Analytics of Bacillus Genomes Reveals Stress Responsive Acetate Utilization and Sulfate Uptake in the Biotechnologically Relevant Bacillus megaterium. PMID:23226010
OrtholugeDB: a bacterial and archaeal orthology resource for improved comparative genomic analysis. PMID:23203876
By their genes ye shall know them: genomic signatures of predatory bacteria. PMID:23190728
Comparative genomic and phylogenetic approaches to characterize the role of genetic recombination in mycobacterial evolution. PMID:23189179
MBGD update 2013: the microbial genome database for exploring the diversity of microbial world. PMID:23118485
Lateral gene transfer of an ABC transporter complex between major constituents of the human gut microbiome. PMID:23116195
Resuscitation promoting factor (Rpf) from Tomitella biformata AHU 1821(T) promotes growth and resuscitates non-dividing cells. PMID:23100022
Genomic and physiological characterization of the chromate-reducing, aquifer-derived Firmicute Pelosinus sp. strain HCF1. PMID:23064329
Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource. PMID:23061897
Sequence, structure, and evolution of cellulases in glycoside hydrolase family 48. PMID:23055526
Twenty-one genome sequences from Pseudomonas species and 19 genome sequences from diverse bacteria isolated from the rhizosphere and endosphere of Populus deltoides. PMID:23045501
Uncovering the co-evolutionary network among prokaryotic genes. PMID:22962457
Metagenomics and its connection to microbial community organization. PMID:22912649
The Human Microbiome Project: a community resource for the healthy human microbiome. PMID:22904687
Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux. PMID:22848480
Genome sequence of the mesophilic Thermotogales bacterium Mesotoga prima MesG1.Ag.4.2 reveals the largest Thermotogales genome to date. PMID:22798451
IMG/M-HMP: a metagenome comparative analysis system for the Human Microbiome Project. PMID:22792232
Engineering ecosystems and synthetic ecologies. PMID:22722235
Unlocking the potential of metagenomics through replicated experimental design. PMID:22678395
Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory. PMID:22678348
Phenotypic and transcriptomic response of auxotrophic Mycobacterium avium subsp. paratuberculosis leuD mutant under environmental stress. PMID:22675497
Caldicellulosiruptor core and pangenomes reveal determinants for noncellulosomal thermophilic deconstruction of plant biomass. PMID:22636774
MicrobeDB: a locally maintainable database of microbial genomic sequences. PMID:22576174
The integrated microbial genomes system: an expanding comparative analysis resource PubMed citations: 159.

159 articles citing: The integrated microbial genomes system: an expanding comparative analysis resource

Curating COBRA Models of Microbial Metabolism. PMID:34719001
Comparative Genomic Analysis of the DUF34 Protein Family Suggests Role as a Metal Ion Chaperone or Insertase. PMID:34572495
Comparative Genomics Provides Insights into the Genetic Diversity and Evolution of the DPANN Superphylum. PMID:34254817
Bacteremic cholangitis due to Raoultella planticola complicating intrahepatic bile duct stricture 5 years post-laparoscopic cholecystectomy: a case report. PMID:33823908
MogR Is a Ubiquitous Transcriptional Repressor Affecting Motility, Biofilm Formation and Virulence in Bacillus thuringiensis. PMID:33424814
Insights into the Metabolism and Evolution of the Genus Acidiphilium, a Typical Acidophile in Acid Mine Drainage. PMID:33203689
Long inverted repeats around the chromosome replication terminus in the model strain Bacillus thuringiensis serovar israelensis BGSC 4Q7. PMID:33180015
Genomic Characteristics Distinguish Geographically Distributed Dehalococcoidia. PMID:33013780
Amixicile depletes the ex vivo periodontal microbiome of anaerobic bacteria. PMID:32278683
Amixicile targets anaerobic bacteria within the oral microbiome. PMID:31706024
Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. PMID:30345391
MetaHCR: a web-enabled metagenome data management system for hydrocarbon resources. PMID:30212909
Herbaspirillum seropedicae Differentially Expressed Genes in Response to Iron Availability. PMID:30018605
Prediction of enzymatic pathways by integrative pathway mapping. PMID:29377793
Resequencing and annotation of the Nostoc punctiforme ATTC 29133 genome: facilitating biofuel and high-value chemical production. PMID:28211005
Functional Annotations of Paralogs: A Blessing and a Curse. PMID:27618105
Essential Genes for In Vitro Growth of the Endophyte Herbaspirillum seropedicae SmR1 as Revealed by Transposon Insertion Site Sequencing. PMID:27590816
Comparative genomics of an endophytic Pseudomonas putida isolated from mango orchard. PMID:27560648
The Chthonomonas calidirosea Genome Is Highly Conserved across Geographic Locations and Distinct Chemical and Microbial Environments in New Zealand's Taupō Volcanic Zone. PMID:27060125
Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community. PMID:27048805
Comparative metagenomics reveals impact of contaminants on groundwater microbiomes. PMID:26583008
Heterogeneity of the gut microbiome in mice: guidelines for optimizing experimental design. PMID:26323480
Metagenomic insights into S(0) precipitation in a terrestrial subsurface lithoautotrophic ecosystem. PMID:25620962
YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia. PMID:25591325
Genomic and metabolic analysis of fluoranthene degradation pathway in Celeribacter indicus P73T. PMID:25582347
Oil degradation and biosurfactant production by the deep sea bacterium Dietzia maris As-13-3. PMID:25566224
Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities. PMID:25333462
FusoBase: an online Fusobacterium comparative genomic analysis platform. PMID:25149689
Bacterial metabolism of methylated amines and identification of novel methylotrophs in Movile Cave. PMID:25050523
From prediction to function using evolutionary genomics: human-specific ecotypes of Lactobacillus reuteri have diverse probiotic functions. PMID:24951561
Regulation of Hfq mRNA and protein levels in Escherichia coli and Pseudomonas aeruginosa by the Burkholderia cenocepacia MtvR sRNA. PMID:24901988
Pyoverdine synthesis by the Mn(II)-oxidizing bacterium Pseudomonas putida GB-1. PMID:24847318
The prevalence of species and strains in the human microbiome: a resource for experimental efforts. PMID:24827833
New insights into Dehalococcoides mccartyi metabolism from a reconstructed metabolic network-based systems-level analysis of D. mccartyi transcriptomes. PMID:24733489
Identification of a predicted partner-switching system that affects production of the gene transfer agent RcGTA and stationary phase viability in Rhodobacter capsulatus. PMID:24645667
Single cell genomic study of Dehalococcoidetes species from deep-sea sediments of the Peruvian Margin. PMID:24599070
Draft Genome Sequence of Syntrophorhabdus aromaticivorans Strain UI, a Mesophilic Aromatic Compound-Degrading Syntroph. PMID:24503990
Complete genome sequence of Arthrobacter sp. strain FB24. PMID:24501649
Mining locus tags in PubMed Central to improve microbial gene annotation. PMID:24499370
Genomic analysis of Chthonomonas calidirosea, the first sequenced isolate of the phylum Armatimonadetes. PMID:24477196
From meta-omics to causality: experimental models for human microbiome research. PMID:24450613
Diversity and abundance of phosphonate biosynthetic genes in nature. PMID:24297932
Discovery of microorganisms and enzymes involved in high-solids decomposition of rice straw using metagenomic analyses. PMID:24205054
Differential expression of a sodium-phosphate cotransporter among Vibrio vulnificus strains. PMID:24141939
Genome sequence analyses show that Neisseria oralis is the same species as 'Neisseria mucosa var. heidelbergensis'. PMID:24097834
The RclR protein is a reactive chlorine-specific transcription factor in Escherichia coli. PMID:24078635
Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1. PMID:24065962
MLST revisited: the gene-by-gene approach to bacterial genomics. PMID:23979428
The genome of the moderate halophile Amycolicicoccus subflavus DQS3-9A1(T) reveals four alkane hydroxylation systems and provides some clues on the genetic basis for its adaptation to a petroleum environment. PMID:23967144
PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. PMID:23942190
Salmonella utilizes D-glucosaminate via a mannose family phosphotransferase system permease and associated enzymes. PMID:23836865
Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean. PMID:23801761
A meta-analysis of the genomic and transcriptomic composition of complex life. PMID:23759593
The abundance and variety of carbohydrate-active enzymes in the human gut microbiota. PMID:23748339
Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease. PMID:23673380
Insights into the structure and metabolic function of microbes that shape pelagic iron-rich aggregates ("iron snow"). PMID:23645202
Glycolytic strategy as a tradeoff between energy yield and protein cost. PMID:23630264
NemR is a bleach-sensing transcription factor. PMID:23536188
Ecogenomic perspectives on domains of unknown function: correlation-based exploration of marine metagenomes. PMID:23516388
Phylogenetic analysis of erythritol catabolic loci within the Rhizobiales and proteobacteria. PMID:23432981
Whole Genome Sequencing of Thermus oshimai JL-2 and Thermus thermophilus JL-18, Incomplete Denitrifiers from the United States Great Basin. PMID:23405355
The Janthinobacterium sp. HH01 genome encodes a homologue of the V. cholerae CqsA and L. pneumophila LqsA autoinducer synthases. PMID:23405110
Differential requirements for mRNA folding partially explain why highly expressed proteins evolve slowly. PMID:23382244
Variations in the rhythms of respiration and nitrogen fixation in members of the unicellular diazotrophic cyanobacterial genus Cyanothece. PMID:23274238
Evolutionary effects of translocations in bacterial genomes. PMID:23160175
The novel cis-encoded small RNA h2cR is a negative regulator of hfq2 in Burkholderia cenocepacia. PMID:23082228
Convergence of the transcriptional responses to heat shock and singlet oxygen stresses. PMID:23028346
Comparative genomic analysis of the DUF71/COG2102 family predicts roles in diphthamide biosynthesis and B12 salvage. PMID:23013770
Measures of compositional strand bias related to replication machinery and its applications. PMID:22942671
Synthesis of methylphosphonic acid by marine microbes: a source for methane in the aerobic ocean. PMID:22936780
Comparative metagenomics of two microbial mats at Cuatro Ciénegas Basin II: community structure and composition in oligotrophic environments. PMID:22920516
Inability to catabolize galactose leads to increased ability to compete for nodule occupancy in Sinorhizobium meliloti. PMID:22797764
Accessibility and conservation: general features of bacterial small RNA-mRNA interactions? PMID:22767260
Mesophilic and thermophilic conditions select for unique but highly parallel microbial communities to perform carboxylate platform biomass conversion. PMID:22761870
The CanOE strategy: integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes. PMID:22693442
Metagenomic microbial community profiling using unique clade-specific marker genes. PMID:22688413
A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs. PMID:22678431
dbCAN: a web resource for automated carbohydrate-active enzyme annotation. PMID:22645317
Caldicellulosiruptor core and pangenomes reveal determinants for noncellulosomal thermophilic deconstruction of plant biomass. PMID:22636774
The metagenome of an anaerobic microbial community decomposing poplar wood chips. PMID:22629327
Translational web robots for pathogen genome analysis. PMID:22587672
Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus. PMID:22586090
Distribution of nitrogen fixation and nitrogenase-like sequences amongst microbial genomes. PMID:22554235
Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of Verrucomicrobia. PMID:22536372
Characterization of an O-demethylase of Desulfitobacterium hafniense DCB-2. PMID:22522902
Mining genomes of marine cyanobacteria for elements of zinc homeostasis. PMID:22514551
The passive yet successful way of planktonic life: genomic and experimental analysis of the ecology of a free-living polynucleobacter population. PMID:22448227
High expression hampers horizontal gene transfer. PMID:22436996
Insights into the bovine rumen plasmidome. PMID:22431592
A genomic approach to bacterial taxonomy: an examination and proposed reclassification of species within the genus Neisseria. PMID:22422752
The zinc-ribbon domain of Helicobacter pylori HP0958: requirement for RpoN accumulation and possible roles of homologs in other bacteria. PMID:22408721
Genetic analysis of the upper phenylacetate catabolic pathway in the production of tropodithietic acid by Phaeobacter gallaeciensis. PMID:22407685
Metagenomic analysis of a stable trichloroethene-degrading microbial community. PMID:22378537
Growth of aerobic ripening bacteria at the cheese surface is limited by the availability of iron. PMID:22367081
A novel protein kinase-like domain in a selenoprotein, widespread in the tree of life. PMID:22359664
The genome sequence of Polymorphum gilvum SL003B-26A1(T) reveals its genetic basis for crude oil degradation and adaptation to the saline soil. PMID:22359583
Transcriptional response of the sulfur chemolithoautotroph Thiomicrospira crunogena to dissolved inorganic carbon limitation. PMID:22328671
Genome sequence of Desulfitobacterium hafniense DCB-2, a Gram-positive anaerobe capable of dehalogenation and metal reduction. PMID:22316246
The diversity of cyanobacterial metabolism: genome analysis of multiple phototrophic microorganisms. PMID:22300633
A vast collection of microbial genes that are toxic to bacteria. PMID:22300632
Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. PMID:22282518
Genetic co-occurrence network across sequenced microbes. PMID:22219725
IMG: the Integrated Microbial Genomes database and comparative analysis system. PMID:22194640
Complete genome sequence of Mycobacterium sp. strain (Spyr1) and reclassification to Mycobacterium gilvum Spyr1. PMID:22180818
Draft genome sequence of Caminibacter mediatlanticus strain TB-2, an epsilonproteobacterium isolated from a deep-sea hydrothermal vent. PMID:22180817
Accurate genome relative abundance estimation based on shotgun metagenomic reads. PMID:22162995
High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use. PMID:22158395
Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris Hildenborough. PMID:22156435
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. PMID:22135293
The Comprehensive Phytopathogen Genomics Resource: a web-based resource for data-mining plant pathogen genomes. PMID:22120664
Horizontal gene transfer in Histophilus somni and its role in the evolution of pathogenic strain 2336, as determined by comparative genomic analyses. PMID:22111657
IMG/M: the integrated metagenome data management and comparative analysis system. PMID:22086953
Functional Annotation Analytics of Rhodopseudomonas palustris Genomes. PMID:22084572
The UCSC Archaeal Genome Browser: 2012 update. PMID:22080555
FungiDB: an integrated functional genomics database for fungi. PMID:22064857
The Arthrobacter species FB24 Arth_1007 (DnaB) intein is a pseudogene. PMID:22028863
The complete genome sequence of Thermoproteus tenax: a physiologically versatile member of the Crenarchaeota. PMID:22003381
Xenorhodopsins, an enigmatic new class of microbial rhodopsins horizontally transferred between archaea and bacteria. PMID:21985229
The evolution of function in strictosidine synthase-like proteins. PMID:21948213
Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone Spring, Oklahoma). PMID:21908640
CsrA-FliW interaction governs flagellin homeostasis and a checkpoint on flagellar morphogenesis in Bacillus subtilis. PMID:21895793
Evolutionary history and functional characterization of three large genes involved in sporulation in Bacillus cereus group bacteria. PMID:21821775
Potentially pathogenic nontuberculous mycobacteria found in aquatic systems. Analysis from a reclaimed water and water distribution system in Mexico City. PMID:21805195
Mutations in Flavobacterium johnsoniae sprE result in defects in gliding motility and protein secretion. PMID:21784937
Misannotations of rRNA can now generate 90% false positive protein matches in metatranscriptomic studies. PMID:21771858
PGAT: a multistrain analysis resource for microbial genomes. PMID:21765097
Saliva microbiomes distinguish caries-active from healthy human populations. PMID:21716312
De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. PMID:21716304
The Genomic Standards Consortium. PMID:21713030
General metabolism of Laribacter hongkongensis: a genome-wide analysis. PMID:21711917
Genome sequences of eight morphologically diverse Alphaproteobacteria. PMID:21705585
Defining reference sequences for Nocardia species by similarity and clustering analyses of 16S rRNA gene sequence data. PMID:21687706
The evolution of respiratory chain complex I from a smaller last common ancestor consisting of 11 protein subunits. PMID:21597881
Bacterial metallothioneins: past, present, and questions for the future. PMID:21594652
Exploring metabolic pathway reconstruction and genome-wide expression profiling in Lactobacillus reuteri to define functional probiotic features. PMID:21559529
AGeS: a software system for microbial genome sequence annotation. PMID:21408217
Comparative whole genome sequence analysis of the carcinogenic bacterial model pathogen Helicobacter felis. PMID:21402865
The CO2-concentrating mechanism of Synechococcus WH5701 is composed of native and horizontally-acquired components. PMID:21384181
RATT: Rapid Annotation Transfer Tool. PMID:21306991
Meeting report: GSC M5 roundtable at the 13th International Society for Microbial Ecology meeting in Seattle, WA, USA August 22-27, 2010. PMID:21304725
Complete genome sequence of Archaeoglobus profundus type strain (AV18). PMID:21304717
Meeting Report from the Genomic Standards Consortium (GSC) Workshop 8. PMID:21304696
Characterization of the deleted in autism 1 protein family: implications for studying cognitive disorders. PMID:21283809
Genome (re-)annotation and open-source annotation pipelines. PMID:21255336
Fecal contamination of shallow tubewells in Bangladesh inversely related to arsenic. PMID:21226536
BIGSdb: Scalable analysis of bacterial genome variation at the population level. PMID:21143983
Networks of gene sharing among 329 proteobacterial genomes reveal differences in lateral gene transfer frequency at different phylogenetic depths. PMID:21059789
Complete genome sequence of strain HTCC2170, a novel member of the genus Maribacter in the family Flavobacteriaceae. PMID:21037013
Genome sequence of strain HTCC2083, a novel member of the marine clade Roseobacter. PMID:21036993
Genome sequence of Oceanicaulis sp. strain HTCC2633, isolated from the Western Sargasso Sea. PMID:21036991
A widespread peroxiredoxin-like domain present in tumor suppression- and progression-implicated proteins. PMID:20964819
Genome sequence of the marine alphaproteobacterium HTCC2150, assigned to the Roseobacter clade. PMID:20889754
Sequencing of multiple clostridial genomes related to biomass conversion and biofuel production. PMID:20889752
Genome sequence of Fulvimarina pelagi HTCC2506T, a Mn(II)-oxidizing alphaproteobacterium possessing an aerobic anoxygenic photosynthetic gene cluster and Xanthorhodopsin. PMID:20639329
Identification of compounds with bioactivity against the nematode Caenorhabditis elegans by a screen based on the functional genomics of the marine bacterium Pseudoalteromonas tunicata D2. PMID:20601498
Novel α-glucosidase from human gut microbiome: substrate specificities and their switch. PMID:20581222
A computational genomics pipeline for prokaryotic sequencing projects. PMID:20519285
GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. PMID:20436475
The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources. PMID:19965766
http://dx.doi.org/10.1093/nar/gkaa946

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genomics databases (non-vertebrate)
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

prokaryotic genome databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

virology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:08.890519

microbial ecology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:08.890519

genomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:08.890519

metagenomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:08.890519

comparative genomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:08.890519

genomics prokaryotic genome virology microbial ecology genomics metagenomics comparative genomics

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Integrated Microbial Genomes and Microbiomes - Viral Resources

Integrated Microbial Genomes And Microbiomes

IMG-ABC

GenoList Genome Browser

NCBI Viral Genomes Resource

Genomes OnLine Database

An INtegrated Data warehouse of mIcrobial GenOmes

EBI Genomes

UCSC Genome Browser database

Ensembl

Influenza Virus Database

Ensembl Genomes

MBGD - Microbial Genome Database

Entrez Genomes

MycoCosm

Phytozome

GenomeAtlas

Human Endogenous Retrovirus database

Drosophila Species Genomes

PhylomeDB