R31NJMGW last accessed: 2022-11-04

Other names: MicroScope

MicroScope is a web-based platform for microbial comparative genome analysis and manual functional annotation. Its relational database schema stores precalculated results of syntactic and functional annotation pipelines as well as Pathway Tools and metabolic analysis specific to each genome.

Webpage:

http://www.genoscope.cns.fr/agc/microscope/home/

Licence:

Name: CC
URL: https://creativecommons.org/licenses/by/4.0/

Publications:

Publications
More detailed information about this field from each metasource.

MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data
PMID: 23193269
metasource: Fairsharing.org
version: FAIRsharing.org: MicroScope; Microbial Genome Annotation & Analysis Platform; DOI: https://doi.org/10.25504/FAIRsharing.3t5qc3; Last edited: Jan. 8, 2019, 1:23 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

http://dx.doi.org/10.1093/nar/gks1194
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data PubMed citations: 233.

233 articles citing: MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data

Phage-host coevolution in natural populations. PMID:35760840
Reactivity-based screening for natural product discovery. PMID:35379434
Type Strains of Entomopathogenic Nematode-Symbiotic Bacterium Species, Xenorhabdus szentirmaii (EMC) and X. budapestensis (EMA), Are Exceptional Sources of Non-Ribosomal Templated, Large-Target-Spectral, Thermotolerant-Antimicrobial Peptides (by Both), and Iodinin (by EMC). PMID:35335666
Molecular and Genomic Insights of mcr-1-Producing Escherichia coli Isolates from Piglets. PMID:35203760
Identification of Potential Citrate Metabolism Pathways in Carnobacterium maltaromaticum. PMID:34683489
Development of an Illumina-based analysis method to study bradyrhizobial population structure-case study on nitrogen-fixing rhizobia associating with cowpea or peanut. PMID:34453562
Dynamics of extended-spectrum beta-lactamase-producing Enterobacterales colonization in long-term carriers following travel abroad. PMID:34279212
Genome analysis of Pseudomonas sp. OF001 and Rubrivivax sp. A210 suggests multicopper oxidases catalyze manganese oxidation required for cylindrospermopsin transformation. PMID:34157973
A Novel Moderately Thermophilic Facultative Methylotroph within the Class Alphaproteobacteria. PMID:33668875
Draft genome of a novel methanotrophic Methylobacter sp. from the volcanic soils of Pantelleria Island. PMID:33566237
Bioinformatics-Based Activities in High School: Fostering Students' Literacy, Interest, and Attitudes on Gene Regulation, Genomics, and Evolution. PMID:33162959
Nutrient Limitation Causes Differential Expression of Transport- and Metabolism Genes in the Compartmentalized Anammox Bacterium Kuenenia stuttgartiensis. PMID:32903544
The Transcriptomic Landscape of Cupriavidus metallidurans CH34 Acutely Exposed to Copper. PMID:32899882
Exploring the upper pH limits of nitrite oxidation: diversity, ecophysiology, and adaptive traits of haloalkalitolerant Nitrospira. PMID:32709974
New Insight into Antimicrobial Compounds from Food and Marine-Sourced Carnobacterium Species through Phenotype and Genome Analyses. PMID:32708353
Heme Uptake in Lactobacillus sakei Evidenced by a New Energy Coupling Factor (ECF)-Like Transport System. PMID:32680867
The Leader Peptide peTrpL Forms Antibiotic-Containing Ribonucleoprotein Complexes for Posttranscriptional Regulation of Multiresistance Genes. PMID:32546623
Hydrogen and Carbon Monoxide-Utilizing Kyrpidia spormannii Species From Pantelleria Island, Italy. PMID:32508778
Repeated horizontal gene transfers triggered parallel evolution of magnetotaxis in two evolutionary divergent lineages of magnetotactic bacteria. PMID:32296121
Novel heavy metal resistance gene clusters are present in the genome of Cupriavidus neocaledonicus STM 6070, a new species of Mimosa pudica microsymbiont isolated from heavy-metal-rich mining site soil. PMID:32143559
Complete Genome Sequence of Strain BW-2, a Magnetotactic Gammaproteobacterium in the Family Ectothiorhodospiraceae, Isolated from a Brackish Spring in Death Valley, California. PMID:31896630
Casimicrobium huifangae gen. nov., sp. nov., a Ubiquitous "Most-Wanted" Core Bacterial Taxon from Municipal Wastewater Treatment Plants. PMID:31811031
deltaRpkm: an R package for a rapid detection of differential gene presence between related bacterial genomes. PMID:31791245
Magnetosome Gene Duplication as an Important Driver in the Evolution of Magnetotaxis in the Alphaproteobacteria. PMID:31662428
MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis. PMID:31647104
Elucidating Syntrophic Butyrate-Degrading Populations in Anaerobic Digesters Using Stable-Isotope-Informed Genome-Resolved Metagenomics. PMID:31387934
On the Impact of the Pangenome and Annotation Discrepancies While Building Protein Sequence Databases for Bacteria Proteogenomics. PMID:31281302
Species-specific mechanisms of cytotoxicity toward immune cells determine the successful outcome of Vibrio infections. PMID:31221761
Secretion of DNases by Marine Bacteria: A Culture Based and Bioinformatics Approach. PMID:31134017
A Mutagenic Screen Identifies a TonB-Dependent Receptor Required for the Lanthanide Metal Switch in the Type I Methanotroph "Methylotuvimicrobium buryatense" 5GB1C. PMID:31085692
σ54 (σL) plays a central role in carbon metabolism in the industrially relevant Clostridium beijerinckii. PMID:31076628
Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains. PMID:31046679
A Physiological and Genomic Comparison of Nitrosomonas Cluster 6a and 7 Ammonia-Oxidizing Bacteria. PMID:30976841
Widespread soil bacterium that oxidizes atmospheric methane. PMID:30962365
Local Diversification of Methicillin- Resistant Staphylococcus aureus ST239 in South America After Its Rapid Worldwide Dissemination. PMID:30873127
Complete Genome Sequence of Bradyrhizobium sp. Strain ORS3257, an Efficient Nitrogen-Fixing Bacterium Isolated from Cowpea in Senegal. PMID:30687830
Genomic and Transcriptomic Changes that Mediate Increased Platinum Resistance in Cupriavidus metallidurans. PMID:30669395
l-Rhamnose Metabolism in Clostridium beijerinckii Strain DSM 6423. PMID:30578270
The draft genome sequence of "Nitrospira lenta" strain BS10, a nitrite oxidizing bacterium isolated from activated sludge. PMID:30498561
Gene Gangs of the Chloroviruses: Conserved Clusters of Collinear Monocistronic Genes. PMID:30347809
Cupriavidus metallidurans Strains with Different Mobilomes and from Distinct Environments Have Comparable Phenomes. PMID:30340417
One complete and three draft genome sequences of four Brochothrix thermosphacta strains, CD 337, TAP 175, BSAS1 3 and EBP 3070. PMID:30338025
Ancestral gene acquisition as the key to virulence potential in environmental Vibrio populations. PMID:30072747
Transcriptome Profiles of Nod Factor-independent Symbiosis in the Tropical Legume Aeschynomene evenia. PMID:30026595
Draft Genome Sequences of Nine Strains of Brochothrix thermosphacta, Carnobacterium divergens, Lactobacillus algidus, Lactobacillus fuchuensis, Lactococcus piscium, Leuconostoc gelidum subsp. gasicomitatum, Pseudomonas lundensis, and Weissella viridescens, a Collection of Psychrotrophic Species Involved in Meat and Seafood Spoilage. PMID:29903812
The Response of Paraburkholderia terrae Strains to Two Soil Fungi and the Potential Role of Oxalate. PMID:29896162
Parallels between experimental and natural evolution of legume symbionts. PMID:29891837
Novel prosthecate bacteria from the candidate phylum Acetothermia. PMID:29884828
Phylogenomic Analysis of Lactobacillus curvatus Reveals Two Lineages Distinguished by Genes for Fermenting Plant-Derived Carbohydrates. PMID:29850855
Fermentative Spirochaetes mediate necromass recycling in anoxic hydrocarbon-contaminated habitats. PMID:29849169
Enhanced biological fixation of methane for microbial lipid production by recombinant Methylomicrobium buryatense. PMID:29755588
Genome annotation and comparative genomic analysis of Bacillus subtilis MJ01, a new bio-degradation strain isolated from oil-contaminated soil. PMID:29730772
Complete and Draft Genome Sequences of Nine Lactobacillus sakei Strains Selected from the Three Known Phylogenetic Lineages and Their Main Clonal Complexes. PMID:29674528
GROOLS: reactive graph reasoning for genome annotation through biological processes. PMID:29642842
Genome and transcriptome of the natural isopropanol producer Clostridium beijerinckii DSM6423. PMID:29636009
Draft Genome Sequences of Endophytic Isolates of Klebsiella variicola and Klebsiella pneumoniae Obtained from the Same Sugarcane Plant. PMID:29567733
Comparative Genomics of Environmental and Clinical Burkholderia cenocepacia Strains Closely Related to the Highly Transmissible Epidemic ET12 Lineage. PMID:29559964
Resolving the complete genome of Kuenenia stuttgartiensis from a membrane bioreactor enrichment using Single-Molecule Real-Time sequencing. PMID:29545612
Modules of co-occurrence in the cyanobacterial pan-genome reveal functional associations between groups of ortholog genes. PMID:29522508
Draft Genome Sequence of a Multidrug- and Colistin-Resistant mcr-1-Producing Escherichia coli Isolate from a Swine Farm in Mexico. PMID:29519827
Cultivation and Genomic Analysis of "Candidatus Nitrosocaldus islandicus," an Obligately Thermophilic, Ammonia-Oxidizing Thaumarchaeon from a Hot Spring Biofilm in Graendalur Valley, Iceland. PMID:29491853
Genetic Separation of Listeria monocytogenes Causing Central Nervous System Infections in Animals. PMID:29459888
Transcriptomic profiling of Burkholderia phymatum STM815, Cupriavidus taiwanensis LMG19424 and Rhizobium mesoamericanum STM3625 in response to Mimosa pudica root exudates illuminates the molecular basis of their nodulation competitiveness and symbiotic evolutionary history. PMID:29378510
Genomic Analysis of Two Phylogenetically Distinct Nitrospira Species Reveals Their Genomic Plasticity and Functional Diversity. PMID:29375506
Complete Genome Sequence of the Halophilic Methylotrophic Methanogen Archaeon Methanohalophilus portucalensis Strain FDF-1T. PMID:29348351
Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains. PMID:29338683
Draft genome sequences of three fungal-interactive Paraburkholderia terrae strains, BS007, BS110 and BS437. PMID:29270249
Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium. PMID:29220487
An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics. PMID:29141959
Adaptation in toxic environments: comparative genomics of loci carrying antibiotic resistance genes derived from acid mine drainage waters. PMID:29090447
Bacterial SBP56 identified as a Cu-dependent methanethiol oxidase widely distributed in the biosphere. PMID:29064480
The Enigmatic Genome of an Obligate Ancient Spiroplasma Symbiont in a Hadal Holothurian. PMID:29054873
Genomic insights into the thiamin metabolism of Paenibacillus thiaminolyticus NRRL B-4156 and P. apiarius NRRL B-23460. PMID:29026451
Phenotypic and Transcriptomic Responses of Campylobacter jejuni Suspended in an Artificial Freshwater Medium. PMID:28979243
MicroScope-an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data. PMID:28968784
Comparative Genomics of Ralstonia solanacearum Identifies Candidate Genes Associated with Cool Virulence. PMID:28955357
DNA Adenine Methyltransferase (Dam) Overexpression Impairs Photorhabdus luminescens Motility and Virulence. PMID:28919886
Draft Genome Sequence of the Iridescent Marine Bacterium Cellulophaga lytica CECT 8139. PMID:28883133
The Complete Genome Sequence of the Fish Pathogen Tenacibaculum maritimum Provides Insights into Virulence Mechanisms. PMID:28861057
Strand-specific transcriptomes of Enterohemorrhagic Escherichia coli in response to interactions with ground beef microbiota: interactions between microorganisms in raw meat. PMID:28774270
Complete Genome Sequence of Bradyrhizobium sp. ORS285, a Photosynthetic Strain Able To Establish Nod Factor-Dependent or Nod Factor-Independent Symbiosis with Aeschynomene Legumes. PMID:28751380
Whole genome sequencing and annotation of halophilic Salinicoccus sp. BAB 3246 isolated from the coastal region of Gujarat. PMID:28702355
Comparative genomic analysis of Acinetobacter strains isolated from murine colonic crypts. PMID:28697749
Culture-Independent Analyses Reveal Novel Anaerolineaceae as Abundant Primary Fermenters in Anaerobic Digesters Treating Waste Activated Sludge. PMID:28690595
Draft Genome Sequence of Lactobacillus curvatus FLEC03, a Meat-Borne Isolate from Beef Carpaccio Packaged in a Modified Atmosphere. PMID:28663298
Genome Analysis of Endomicrobium proavitum Suggests Loss and Gain of Relevant Functions during the Evolution of Intracellular Symbionts. PMID:28646115
Draft Genome Sequence of Serratia proteamaculans MFPA44A14-05, a Model Organism for the Study of Meat and Seafood Spoilage. PMID:28596408
Variable virulence phenotype of Xenorhabdus bovienii (γ-Proteobacteria: Enterobacteriaceae) in the absence of their vector hosts. PMID:28430102
Conservation and diversity of the IrrE/DdrO-controlled radiation response in radiation-resistant Deinococcus bacteria. PMID:28397370
Identification of Virulent Capnocytophaga canimorsus Isolates by Capsular Typing. PMID:28381610
Comparative Genomic Analysis Reveals Ecological Differentiation in the Genus Carnobacterium. PMID:28337181
Light Modulates Metabolic Pathways and Other Novel Physiological Traits in the Human Pathogen Acinetobacter baumannii. PMID:28289081
An antimicrobial peptide-resistant minor subpopulation of Photorhabdus luminescens is responsible for virulence. PMID:28252016
Complete Genome Sequence of the Hyperthermophilic Piezophilic Archaeon Pyrococcus kukulkanii NCB100 Isolated from the Rebecca's Roost Hydrothermal Vent in the Guaymas Basin. PMID:28209839
Complete Genome Sequence of Methanohalophilus halophilus DSM 3094T, Isolated from a Cyanobacterial Mat and Bottom Deposits at Hamelin Pool, Shark Bay, Northwestern Australia. PMID:28209822
Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis. PMID:28189581
Comparison of biofilm formation and motility processes in arsenic-resistant Thiomonas spp. strains revealed divergent response to arsenite. PMID:28169492
Lifestyle and Horizontal Gene Transfer-Mediated Evolution of Mucispirillum schaedleri, a Core Member of the Murine Gut Microbiota. PMID:28168224
Genome-Wide Transcriptional Start Site Mapping and sRNA Identification in the Pathogen Leptospira interrogans. PMID:28154810
Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks. PMID:28129330
Complete Genome Sequence of Lactococcus piscium CNCM I-4031, a Bioprotective Strain for Seafood Products. PMID:28126939
Insights into the Planktothrix genus: Genomic and metabolic comparison of benthic and planktic strains. PMID:28117406
Microbial Degradation of a Recalcitrant Pesticide: Chlordecone. PMID:28066351
Microbial communities in pyrene amended soil-compost mixture and fertilized soil. PMID:28050848
Single-Molecule Sequencing (PacBio) of the Staphylococcus capitis NRCS-A Clone Reveals the Basis of Multidrug Resistance and Adaptation to the Neonatal Intensive Care Unit Environment. PMID:28018320
New Multilocus Variable-Number Tandem-Repeat Analysis (MLVA) Scheme for Fine-Scale Monitoring and Microevolution-Related Study of Ralstonia pseudosolanacearum Phylotype I Populations. PMID:28003195
Global repositioning of transcription start sites in a plant-fermenting bacterium. PMID:27982035
Identification of the RNA Pyrophosphohydrolase RppH of Helicobacter pylori and Global Analysis of Its RNA Targets. PMID:27974459
Vibrio crassostreae, a benign oyster colonizer turned into a pathogen after plasmid acquisition. PMID:27922600
Ecophysiology and Comparative Genomics of Nitrosomonas mobilis Ms1 Isolated from Autotrophic Nitrifying Granules of Wastewater Treatment Bioreactor. PMID:27920767
MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes. PMID:27899624
Transcriptional Responses of the Bacterium Burkholderia terrae BS001 to the Fungal Host Lyophyllum sp. Strain Karsten under Soil-Mimicking Conditions. PMID:27844108
Global Dynamic Proteome Study of a Pellicle-forming Acinetobacter baumannii Strain. PMID:27799293
Updates in Rhea - an expert curated resource of biochemical reactions. PMID:27789701
Draft Genome Sequence of Carnobacterium divergens V41, a Bacteriocin-Producing Strain. PMID:27738030
A Resource Allocation Trade-Off between Virulence and Proliferation Drives Metabolic Versatility in the Plant Pathogen Ralstonia solanacearum. PMID:27732672
Insights into the Quorum Sensing Regulon of the Acidophilic Acidithiobacillus ferrooxidans Revealed by Transcriptomic in the Presence of an Acyl Homoserine Lactone Superagonist Analog. PMID:27683573
MxaY regulates the lanthanide-mediated methanol dehydrogenase switch in Methylomicrobium buryatense. PMID:27651996
Complete Genome Sequence of Cyanobium sp. NIES-981, a Marine Strain Potentially Useful for Ecotoxicological Bioassays. PMID:27469961
Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis. PMID:27461509
"Candidatus Propionivibrio aalborgensis": A Novel Glycogen Accumulating Organism Abundant in Full-Scale Enhanced Biological Phosphorus Removal Plants. PMID:27458436
Adhesion, Biofilm Formation, and Genomic Features of Campylobacter jejuni Bf, an Atypical Strain Able to Grow under Aerobic Conditions. PMID:27446042
Complete Genome Sequence of the Hyperthermophilic and Piezophilic Archeon Thermococcus piezophilus CDGST, Able To Grow under Extreme Hydrostatic Pressures. PMID:27417831
Draft Genome Sequence of a Hypermucoviscous Extended-Spectrum-β-Lactamase-Producing Klebsiella quasipneumoniae subsp. similipneumoniae Clinical Isolate. PMID:27389261
Systematic identification and analysis of frequent gene fusion events in metabolic pathways. PMID:27342196
Genomic Rearrangements and Functional Diversification of lecA and lecB Lectin-Coding Regions Impacting the Efficacy of Glycomimetics Directed against Pseudomonas aeruginosa. PMID:27303392
Genome Sequences of Multiresistant Staphylococcus capitis Pulsotype NRCS-A and Methicillin-Susceptible S. capitis Pulsotype NRCS-C. PMID:27284154
In vivo gene expression in a Staphylococcus aureus prosthetic joint infection characterized by RNA sequencing and metabolomics: a pilot study. PMID:27150914
Single-Cell Genome and Group-Specific dsrAB Sequencing Implicate Marine Members of the Class Dehalococcoidia (Phylum Chloroflexi) in Sulfur Cycling. PMID:27143384
Contrasting effects of historical contingency on phenotypic and genomic trajectories during a two-step evolution experiment with bacteria. PMID:27108090
Genomics of a phototrophic nitrite oxidizer: insights into the evolution of photosynthesis and nitrification. PMID:27093047
SuperPhy: predictive genomics for the bacterial pathogen Escherichia coli. PMID:27067409
Genomic insights into members of the candidate phylum Hyd24-12 common in mesophilic anaerobic digesters. PMID:27058503
Draft Genome Sequence of Campylobacter jejuni Bf, an Atypical Strain Able To Grow under Aerobiosis. PMID:27056213
Genomic and physiological analysis reveals versatile metabolic capacity of deep-sea Photobacterium phosphoreum ANT-2200. PMID:27039108
Complete Genome Sequence of Bacillus methylotrophicus Strain B25, a Potential Plant Growth-Promoting Rhizobacterium. PMID:26966215
Draft Genome Sequence of the Butyric Acid Producer Clostridium tyrobutyricum Strain CIP I-776 (IFP923). PMID:26941139
News in livestock research - use of Omics-technologies to study the microbiota in the gastrointestinal tract of farm animals. PMID:26900430
Pulsed (13)C2-Acetate Protein-SIP Unveils Epsilonproteobacteria as Dominant Acetate Utilizers in a Sulfate-Reducing Microbial Community Mineralizing Benzene. PMID:26846217
Draft Genome Sequences of Nine Strains of Ralstonia solanacearum Differing in Virulence to Eggplant (Solanum melongena). PMID:26823572
Comparative Genomics between Two Xenorhabdus bovienii Strains Highlights Differential Evolutionary Scenarios within an Entomopathogenic Bacterial Species. PMID:26769959
Complete Genome Sequence of the Hyperthermophilic and Piezophilic Archaeon Thermococcus barophilus Ch5, Capable of Growth at the Expense of Hydrogenogenesis from Carbon Monoxide and Formate. PMID:26769929
RNase J depletion leads to massive changes in mRNA abundance in Helicobacter pylori. PMID:26726773
Development of a Taqman real-time PCR assay for rapid detection and quantification of Vibrio tapetis in extrapallial fluids of clams. PMID:26713238
Escherichia coli Population Structure and Antibiotic Resistance at a Buffalo/Cattle Interface in Southern Africa. PMID:26712551
A Comprehensive tRNA Genomic Survey Unravels the Evolutionary History of tRNA Arrays in Prokaryotes. PMID:26710853
Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges. PMID:26699528
Metagenome-Based Metabolic Reconstruction Reveals the Ecophysiological Function of Epsilonproteobacteria in a Hydrocarbon-Contaminated Sulfidic Aquifer. PMID:26696999
Complete nitrification by a single microorganism. PMID:26610025
Complete nitrification by Nitrospira bacteria. PMID:26610024
Genome Sequences of Three Strains of the Pseudomonas aeruginosa PA7 Clade. PMID:26586898
Genome Analysis of Kingella kingae Strain KWG1 Reveals How a β-Lactamase Gene Inserted in the Chromosome of This Species. PMID:26574009
Genome Sequence of a Clinical Klebsiella pneumoniae Sequence Type 6 Strain. PMID:26564039
Physiological and genomic characterization of two novel marine thaumarchaeal strains indicates niche differentiation. PMID:26528837
Comparison of Xenorhabdus bovienii bacterial strain genomes reveals diversity in symbiotic functions. PMID:26525894
Draft Genome Sequences of Acinetobacter parvus CM11, Acinetobacter radioresistens CM38, and Stenotrophomonas maltophilia BR12, Isolated from Murine Proximal Colonic Tissue. PMID:26472823
Thiomonas sp. CB2 is able to degrade urea and promote toxic metal precipitation in acid mine drainage waters supplemented with urea. PMID:26441922
Functional analysis of an unusual type IV pilus in the Gram-positive Streptococcus sanguinis. PMID:26435398
Adaptation in Toxic Environments: Arsenic Genomic Islands in the Bacterial Genus Thiomonas. PMID:26422469
Draft Genome Sequences of Klebsiella variicola Plant Isolates. PMID:26358599
Control of Gene Expression in Leptospira spp. by Transcription Activator-Like Effectors Demonstrates a Potential Role for LigA and LigB in Leptospira interrogans Virulence. PMID:26341206
Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira. PMID:26305944
Comparative Genomics of Environmental and Clinical Stenotrophomonas maltophilia Strains with Different Antibiotic Resistance Profiles. PMID:26276674
Genome Sequences of Four Staphylococcus capitis NRCS-A Isolates from Geographically Distant Neonatal Intensive Care Units. PMID:26251481
Genome Wide Re-Annotation of Caldicellulosiruptor saccharolyticus with New Insights into Genes Involved in Biomass Degradation and Hydrogen Production. PMID:26196387
Genome Sequence of Rhodococcus sp. Strain RD6.2 DSM 46800, a Methanesulfonate-Degrading Strain. PMID:26184930
Complete Genome Sequence of Endomicrobium proavitum, a Free-Living Relative of the Intracellular Symbionts of Termite Gut Flagellates (Phylum Elusimicrobia). PMID:26184928
AAC(3)-XI, a new aminoglycoside 3-N-acetyltransferase from Corynebacterium striatum. PMID:26149994
Quantitative frame analysis and the annotation of GC-rich (and other) prokaryotic genomes. An application to Anaeromyxobacter dehalogenans. PMID:26048600
Xenorhabdus bovienii Strain Diversity Impacts Coevolution and Symbiotic Maintenance with Steinernema spp. Nematode Hosts. PMID:26045536
Draft genomes of gammaproteobacterial methanotrophs isolated from terrestrial ecosystems. PMID:26044417
Draft Genome Sequences of Three Capnocytophaga cynodegmi Strains Isolated from the Oral Cavity of Healthy Dogs. PMID:26021913
Draft Genome Sequences of Three Capnocytophaga canimorsus Strains Isolated from Healthy Canine Oral Cavities. PMID:26021912
Draft Genome Sequences of Three Capnocytophaga canimorsus Strains Isolated from Septic Patients. PMID:26021910
Databases for Microbiologists. PMID:26013493
Optimal programs of pathway control: dissecting the influence of pathway topology and feedback inhibition on pathway regulation. PMID:25982966
Genomes of sequence type 121 Listeria monocytogenes strains harbor highly conserved plasmids and prophages. PMID:25972859
Mosaic genome of endobacteria in arbuscular mycorrhizal fungi: Transkingdom gene transfer in an ancient mycoplasma-fungus association. PMID:25964335
Complete Genome Sequences of Two Strains of "Candidatus Filomicrobium marinum," a Methanesulfonate-Degrading Species. PMID:25953167
The SwissLipids knowledgebase for lipid biology. PMID:25943471
The ecology of pelagic freshwater methylotrophs assessed by a high-resolution monitoring and isolation campaign. PMID:25942006
Footprints of optimal protein assembly strategies in the operonic structure of prokaryotes. PMID:25927816
Draft Genome Sequence of the First Hypermucoviscous Klebsiella variicola Clinical Isolate. PMID:25858850
RNA chaperones buffer deleterious mutations in E. coli. PMID:25806682
Complete Genome Sequence of the Persistent Listeria monocytogenes Strain R479a. PMID:25792065
In silico analysis of usher encoding genes in Klebsiella pneumoniae and characterization of their role in adhesion and colonization. PMID:25751658
A replicative plasmid vector allows efficient complementation of pathogenic Leptospira strains. PMID:25724960
Two host clades, two bacterial arsenals: evolution through gene losses in facultative endosymbionts. PMID:25714744
Genome Sequence and Annotation of a Human Infection Isolate of Escherichia coli O26:H11 Involved in a Raw Milk Cheese Outbreak. PMID:25700408
Genetic tools for the industrially promising methanotroph Methylomicrobium buryatense. PMID:25548049
Draft Genome Sequence of Propane- and Butane-Oxidizing Actinobacterium Rhodococcus ruber IEGM 231. PMID:25502680
Populations, not clones, are the unit of vibrio pathogenesis in naturally infected oysters. PMID:25489729
Comparative genomic analysis of nine Sphingobium strains: insights into their evolution and hexachlorocyclohexane (HCH) degradation pathways. PMID:25418849
Phylum-wide comparative genomics unravel the diversity of secondary metabolism in Cyanobacteria. PMID:25404466
Novel metabolic features in Acinetobacter baylyi ADP1 revealed by a multiomics approach. PMID:25374488
Comparative analyses of Legionella species identifies genetic features of strains causing Legionnaires' disease. PMID:25370836
Genomic definition of hypervirulent and multidrug-resistant Klebsiella pneumoniae clonal groups. PMID:25341126
Updates in Rhea--a manually curated resource of biochemical reactions. PMID:25332395
Comparison of library preparation methods reveals their impact on interpretation of metatranscriptomic data. PMID:25331572
Complete Genome Sequence of Mycoplasma capricolum subsp. capripneumoniae Strain 9231-Abomsa. PMID:25323727
Draft Genome Sequence of Sphingobacterium sp. Strain PM2-P1-29, a Tetracycline-Degrading TetX-Expressing Aerobic Bacterium Isolated from Agricultural Soil. PMID:25301646
Integration of heterogeneous molecular networks to unravel gene-regulation in Mycobacterium tuberculosis. PMID:25279447
The conserved nhaAR operon is drastically divergent between B2 and non-B2 Escherichia coli and is involved in extra-intestinal virulence. PMID:25268639
Variations in metabolic pathways create challenges for automated metabolic reconstructions: Examples from the tetrahydrofolate synthesis pathway. PMID:25210598
Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli. PMID:25205090
Non-contiguous finished genome sequence of Staphylococcus capitis CR01 (pulsetype NRCS-A). PMID:25197487
Draft Genome Sequences of Ralstonia pickettii Strains SSH4 and CW2, Isolated from Space Equipment. PMID:25189592
Transient hypermutagenesis accelerates the evolution of legume endosymbionts following horizontal gene transfer. PMID:25181317
Genome Sequences of Cupriavidus metallidurans Strains NA1, NA4, and NE12, Isolated from Space Equipment. PMID:25059868
The genome of the fungal-interactive soil bacterium Burkholderia terrae BS001-a plethora of outstanding interactive capabilities unveiled. PMID:24923325
Profiling the orphan enzymes. PMID:24906382
Attenuated virulence and genomic reductive evolution in the entomopathogenic bacterial symbiont species, Xenorhabdus poinarii. PMID:24904010
Genome Sequence of Luminous Piezophile Photobacterium phosphoreum ANT-2200. PMID:24744322
RNA sequencing and proteogenomics reveal the importance of leaderless mRNAs in the radiation-tolerant bacterium Deinococcus deserti. PMID:24723731
SearchDOGS bacteria, software that provides automated identification of potentially missed genes in annotated bacterial genomes. PMID:24659774
Draft Genome Sequence and Annotation of the Entomopathogenic Bacterium Xenorhabdus szentirmaii Strain DSM16338. PMID:24625876
Genomic and transcriptomic analyses of the facultative methanotroph Methylocystis sp. strain SB2 grown on methane or ethanol. PMID:24610846
A proteomic approach of bradyrhizobium/aeschynomene root and stem symbioses reveals the importance of the fixA locus for symbiosis. PMID:24590127
Draft Genome Sequence of the Sulfonamide Antibiotic-Degrading Microbacterium sp. Strain C448. PMID:24526651
Microbial molecular markers and epidemiological surveillance in the era of high throughput sequencing: an update from the IMMEM-10 conference. PMID:24486597
Comparative analysis of the complete genome of KPC-2-producing Klebsiella pneumoniae Kp13 reveals remarkable genome plasticity and a wide repertoire of virulence and resistance mechanisms. PMID:24450656
Laboratory divergence of Methylobacterium extorquens AM1 through unintended domestication and past selection for antibiotic resistance. PMID:24384040
Genome Sequence of Cupriavidus metallidurans Strain H1130, Isolated from an Invasive Human Infection. PMID:24336383
INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles. PMID:24324765
Structural and gene expression analyses of uptake hydrogenases and other proteins involved in nitrogenase protection in Frankia. PMID:24287649
Biochemical and functional characterization of SpdA, a 2', 3'cyclic nucleotide phosphodiesterase from Sinorhizobium meliloti. PMID:24279347
Complete Genome Sequence of the Sesbania Symbiont and Rice Growth-Promoting Endophyte Rhizobium sp. Strain IRBG74. PMID:24265489
FliZ is a global regulatory protein affecting the expression of flagellar and virulence genes in individual Xenorhabdus nematophila bacterial cells. PMID:24204316
Organization and regulation of the arsenite oxidase operon of the moderately acidophilic and facultative chemoautotrophic Thiomonas arsenitoxydans. PMID:23974983
Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum Chloroflexi. PMID:23966099
Complete Genome Sequence of a Variant of the Methicillin-Resistant Staphylococcus aureus ST239 Lineage, Strain BMB9393, Displaying Superior Ability To Accumulate ica-Independent Biofilm. PMID:23929475
Draft Genome Sequence and Annotation of the Entomopathogenic Bacterium Xenorhabdus nematophila Strain F1. PMID:23788541
Next-generation annotation of prokaryotic genomes with EuGene-P: application to Sinorhizobium meliloti 2011. PMID:23599422
http://dx.doi.org/10.1093/nar/gks1194

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More detailed information about this field from each metasource.

annotation
metasource: Fairsharing.org
version: FAIRsharing.org: MicroScope; Microbial Genome Annotation & Analysis Platform; DOI: https://doi.org/10.25504/FAIRsharing.3t5qc3; Last edited: Jan. 8, 2019, 1:23 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

gene functional annotation
metasource: Fairsharing.org
version: FAIRsharing.org: MicroScope; Microbial Genome Annotation & Analysis Platform; DOI: https://doi.org/10.25504/FAIRsharing.3t5qc3; Last edited: Jan. 8, 2019, 1:23 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

genome annotation
metasource: Fairsharing.org
version: FAIRsharing.org: MicroScope; Microbial Genome Annotation & Analysis Platform; DOI: https://doi.org/10.25504/FAIRsharing.3t5qc3; Last edited: Jan. 8, 2019, 1:23 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

molecular interaction
metasource: Fairsharing.org
version: FAIRsharing.org: MicroScope; Microbial Genome Annotation & Analysis Platform; DOI: https://doi.org/10.25504/FAIRsharing.3t5qc3; Last edited: Jan. 8, 2019, 1:23 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

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

microcyc
metasource: re3data.org
version: re3data.org: MicroScope; editing status 2020-07-29; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMGW last accessed: 2022-11-04

pkgdb, prokaryotic genome database
metasource: re3data.org
version: re3data.org: MicroScope; editing status 2020-07-29; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMGW last accessed: 2022-11-04

bioinformatics
metasource: re3data.org
version: re3data.org: MicroScope; editing status 2020-07-29; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMGW last accessed: 2022-11-04

comperative genomics
metasource: re3data.org
version: re3data.org: MicroScope; editing status 2020-07-29; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMGW last accessed: 2022-11-04

expression analysis
metasource: re3data.org
version: re3data.org: MicroScope; editing status 2020-07-29; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMGW last accessed: 2022-11-04

microbiology
metasource: re3data.org
version: re3data.org: MicroScope; editing status 2020-07-29; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMGW last accessed: 2022-11-04

nucleid sequences
metasource: re3data.org
version: re3data.org: MicroScope; editing status 2020-07-29; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMGW last accessed: 2022-11-04

protein -coding genes
metasource: re3data.org
version: re3data.org: MicroScope; editing status 2020-07-29; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMGW last accessed: 2022-11-04

systems biology
metasource: re3data.org
version: re3data.org: MicroScope; editing status 2020-07-29; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R31NJMGW last accessed: 2022-11-04

gene functional annotation genome annotation molecular interaction genomics prokaryotic genome microcyc pkgdb, prokaryotic genome database bioinformatics comperative genomics expression analysis microbiology nucleid sequences protein -coding genes systems biology

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Integrated Microbial Genomes And Microbiomes

GenoList Genome Browser

ParameciumDB

MBGD - Microbial Genome Database

Genome Properties

Ensembl Genomes

MGAN

Pseudomonas Genome DB

Strepto_DB

The Vertebrate Genome Annotation Database

Functional ANnoTation Of the Mammalian genome Database

An INtegrated Data warehouse of mIcrobial GenOmes

MANTA_DB

Genome Annotation File version 2

ASAP - A Systematic Annotation Package

HPMCD

GadFly

Genome Annotation File version 1

DESM

Colibri