R35W56 last accessed: 2022-11-04

Other names: PATRIC, Pathosystems Resource Integration Center

PATRIC is part of the Bacterial Bioinformatics Resource Center, and is an information system designed to support the biomedical research community’s work on bacterial infectious diseases via integration of vital pathogen information with rich data and analysis tools. PATRIC provides an interface for biologists to discover data and information and conduct comprehensive comparative genomics and other analyses. PATRIC includes over 250 000 publicly available microbial genomes and tools for comparative analysis.

Webpage:

https://www.patricbrc.org/

Licence:

Name: other
URL: http://www.niaid.nih.gov/LabsAndResources/resources/dmid/Pages/data.aspx

Publications:

Publications
More detailed information about this field from each metasource.

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center
PMID: 27899627
metasource: Fairsharing.org
version: FAIRsharing.org: PATRIC; PathosSystems Resource Integration Center Repository; DOI: https://doi.org/10.25504/FAIRsharing.oaLCAI; Last edited: July 31, 2020, 2:04 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities
PMID: 31667520
metasource: Fairsharing.org
version: FAIRsharing.org: PATRIC; PathosSystems Resource Integration Center Repository; DOI: https://doi.org/10.25504/FAIRsharing.oaLCAI; Last edited: July 31, 2020, 2:04 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center PubMed citations: 589.

589 articles citing: Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center

Comparative and functional analyses of fecal microbiome in Asian elephants. PMID:35902439
Actinospica acidithermotolerans sp. nov., a novel actinomycete isolated from sediment from an Indonesian hot spring. PMID:35871242
A convolutional neural network highlights mutations relevant to antimicrobial resistance in Mycobacterium tuberculosis. PMID:35780211
Prosthecate aerobic anoxygenic phototrophs Photocaulis sulfatitolerans gen. nov. sp. nov. and Photocaulis rubescens sp. nov. isolated from alpine meromictic lakes in British Columbia, Canada. PMID:35776224
Genome-based reclassification of Anoxybacillus karvacharensis Panosyan et al. as a later heterotypic synonym of Anoxybacillus kestanbolensis Dulger et al. 2004; A. flavithermus subsp. yunnanensis CCTCC AB2010187T Dai et al. 2011 as a later heterotypic synonym of A. tengchongensis DSM 23211T Zhang et al. 2011. PMID:35768663
Novel Bacteriophage Specific against Staphylococcus epidermidis and with Antibiofilm Activity. PMID:35746811
Genome Sequence and Characterization of a Xanthorhodopsin-Containing, Aerobic Anoxygenic Phototrophic Rhodobacter Species, Isolated from Mesophilic Conditions at Yellowstone National Park. PMID:35744687
Host control and the evolution of cooperation in host microbiomes. PMID:35732630
Characterization of antibiotic-resistant, coagulase-negative staphylococci from fresh produce and description of Staphylococcus shinii sp. nov. isolated from chives. PMID:35731349
A 16th century Escherichia coli draft genome associated with an opportunistic bile infection. PMID:35710940
A genome-wide atlas of antibiotic susceptibility targets and pathways to tolerance. PMID:35672367
Saccharopolyspora soli sp. nov., isolated from Northern Cyprus soil. PMID:35670849
Characterization of Three Novel Virulent Aeromonas Phages Provides Insights into the Diversity of the Autographiviridae Family. PMID:35632757
Phylogeny and Metabolic Potential of the Methanotrophic Lineage MO3 in Beijerinckiaceae from the Paddy Soil through Metagenome-Assembled Genome Reconstruction. PMID:35630399
Draft Genome Sequence of Nereida sp. Strain MMG025, Isolated from Giant Kelp. PMID:35532230
In-Human Multiyear Evolution of Carbapenem-Resistant Klebsiella pneumoniae Causing Chronic Colonization and Intermittent Urinary Tract Infections: A Case Study. PMID:35531657
Data on complete genome sequence and annotation of two multidrug resistant atypical enteropathogenic Escherichia coli O177 serotype isolated from cattle faeces. PMID:35510268
The predictive potential of different molecular markers linked to amikacin susceptibility phenotypes in Pseudomonas aeruginosa. PMID:35468158
Genomics-Based Reconstruction and Predictive Profiling of Amino Acid Biosynthesis in the Human Gut Microbiome. PMID:35456791
Imipenem/Relebactam Resistance in Clinical Isolates of Extensively Drug Resistant Pseudomonas aeruginosa: Inhibitor-Resistant β-Lactamases and Their Increasing Importance. PMID:35435707
Wild Boars as an Indicator of Environmental Spread of ESβL-Producing Escherichia coli. PMID:35432265
Complete Genome Sequence of Bacillus toyonensis Strain HA0190, Isolated from a Commercial Hydroxyapatite Product Extensively Used as a Synthetic Bone Graft Substitute. PMID:35377175
Comparative Genome Analysis of the Photosynthetic Betaproteobacteria of the Genus Rhodocyclus: Heterogeneity within Strains Assigned to Rhodocyclus tenuis and Description of Rhodocyclus gracilis sp. nov. as a New Species. PMID:35336224
Whole-Genome Sequencing and Comparative Genomic Analysis of Antimicrobial Producing Streptococcus lutetiensis from the Rumen. PMID:35336126
Application of Psychrotolerant Antarctic Bacteria and Their Metabolites as Efficient Plant Growth Promoting Agents. PMID:35284420
Limosilactobacillus fermentum ING8, a Potential Multifunctional Non-Starter Strain with Relevant Technological Properties and Antimicrobial Activity. PMID:35267336
The CIAMIB: a Large and Metabolically Diverse Collection of Inflammation-Associated Bacteria from the Murine Gut. PMID:35266814
Genome Sequences of Marichromatium gracile HOL-1 and Its Purple Photosynthetic Coisolate, Afifella sp. H1R. PMID:35258324
Draft Genomic Sequences of Four Pseudomonas spp. and a Xanthomonas sp. from Cranberry Stem Galls. PMID:35230127
A high-quality reference genome for the fish pathogen Streptococcus iniae. PMID:35229712
Gut Commensal Bacteroidetes Encode a Novel Class of Vitamin B12-Binding Proteins. PMID:35227073
Shallow-Water Hydrothermal Vents as Natural Accelerators of Bacterial Antibiotic Resistance in Marine Coastal Areas. PMID:35208933
Genomic Comparison, Phylogeny and Taxonomic Reevaluation of the Ectothiorhodospiraceae and Description of Halorhodospiraceae fam. nov. and Halochlorospira gen. nov. PMID:35208750
Genome Sequence and Assessment of Safety and Potential Probiotic Traits of Lactobacillus johnsonii CNCM I-4884. PMID:35208728
Illumina Short-Read Sequencing of the Mitogenomes of Novel Scarites subterraneus Isolates Allows for Taxonomic Refinement of the Genus Scarites Fabricius 1775, within the Carabidae Family. PMID:35206763
Antimicrobial Susceptibility, Virulence, and Genomic Features of a Hypervirulent Serotype K2, ST65 Klebsiella pneumoniae Causing Meningitis in Italy. PMID:35203864
Similarities in Virulence and Extended Spectrum Beta-Lactamase Gene Profiles among Cefotaxime-Resistant Escherichia coli Wastewater and Clinical Isolates. PMID:35203862
Aged related human skin microbiome and mycobiome in Korean women. PMID:35149745
Bacteroides thetaiotaomicron uses a widespread extracellular DNase to promote bile-dependent biofilm formation. PMID:35145026
Isolation, characterization and comparative genomics of potentially probiotic Lactiplantibacillus plantarum strains from Indian foods. PMID:35121802
Genomic Features and Pervasive Negative Selection in Rhodanobacter Strains Isolated from Nitrate and Heavy Metal Contaminated Aquifer. PMID:35107332
Turicibacter bilis sp. nov., a novel bacterium isolated from the chicken eggshell and swine ileum. PMID:35084297
Draft Genome Sequence of Ralstonia pickettii Strain NCTR106, Isolated from Milk Carton Paperboard. PMID:35084218
The potential of bacteriophages to control Xanthomonas campestris pv. campestris at different stages of disease development. PMID:35084112
Combination of pre-adapted bacteriophage therapy and antibiotics for treatment of fracture-related infection due to pandrug-resistant Klebsiella pneumoniae. PMID:35042848
Gut dysbiosis is associated with acceleration of lupus nephritis. PMID:34996983
Natronococcus pandeyae sp. nov., a Novel Haloarchaeon from Sambhar Salt Lake. PMID:34982242
A catalogue of 1,167 genomes from the human gut archaeome. PMID:34969981
Mining the Genome of Bacillus velezensis VB7 (CP047587) for MAMP Genes and Non-Ribosomal Peptide Synthetase Gene Clusters Conferring Antiviral and Antifungal Activity. PMID:34946111
The Integrative and Conjugative Element ICECspPOL2 Contributes to the Outbreak of Multi-Antibiotic-Resistant Bacteria for Chryseobacterium Spp. and Elizabethkingia Spp. PMID:34937181
The de novo Purine Biosynthesis Pathway Is the Only Commonly Regulated Cellular Pathway during Biofilm Formation in TSB-Based Medium in Staphylococcus aureus and Enterococcus faecalis. PMID:34935415
Draft Genome Sequence of Bacillus pacificus KVCMST-8A-12, Isolated from a Marine Sediment Sample from the Kanyakumari Coast, India. PMID:34913714
Prediction and Analysis in silico of Genomic Islands in Aeromonas hydrophila. PMID:34912316
Multilocus Sequence Typing of Aggregatibacter actinomycetemcomitans Competently Depicts the Population Structure of the Species. PMID:34908433
Helicobacter pylori virulence factors: relationship between genetic variability and phylogeographic origin. PMID:34900406
Genome-Wide Mutation Scoring for Machine-Learning-Based Antimicrobial Resistance Prediction. PMID:34884852
Looking through the FOG: microbiome characterization and lipolytic bacteria isolation from a fatberg site. PMID:34870579
The Acquisition of the scr Gene Cluster Encoding Sucrose Metabolization Enzymes Enables Strains of Vibrio parahaemolyticus and Vibrio vulnificus to Utilize Sucrose as Carbon Source. PMID:34867877
Manganese transport by Streptococcus sanguinis in acidic conditions and its impact on growth in vitro and in vivo. PMID:34862691
Identification of antibiotic collateral sensitivity and resistance interactions in population surveillance data. PMID:34859221
Polyphenol Utilization Proteins in the Human Gut Microbiome. PMID:34851722
RFPlasmid: predicting plasmid sequences from short-read assembly data using machine learning. PMID:34846288
Draft genome sequence of Stenotrophomonas maltophilia strain P13 gives insight into its protease production and assessment of sulfur and nitrogen metabolism. PMID:34841305
Mycobacterium intracellulare subsp. chimaera from Cardio Surgery Heating-Cooling Units and from Clinical Samples in Israel Are Genetically Unrelated. PMID:34832548
The Effect of Feeding Restriction on the Microbiota and Metabolome Response in Late-Phase Laying Hens. PMID:34827776
High prevalence of multiple antibiotic resistance in clinical E. coli isolates from Bangladesh and prediction of molecular resistance determinants using WGS of an XDR isolate. PMID:34819576
Whole genome sequence data of Chromobacterium violaceum WCH4, a human pathogenic strain from Sabah, Malaysia. PMID:34805463
Transcriptomic Analysis Reveals That Municipal Wastewater Effluent Enhances Vibrio vulnificus Growth and Virulence Potential. PMID:34759904
PangenomeNet: a pan-genome-based network reveals functional modules on antimicrobial resistome for Escherichia coli strains. PMID:34758735
Genomics and simulated laboratory studies reveal Thermococcus sp. 101C5 as a novel hyperthermophilic archaeon possessing a specialized metabolic arsenal for enhanced oil recovery. PMID:34734348
Citrullination Was Introduced into Animals by Horizontal Gene Transfer from Cyanobacteria. PMID:34730808
Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO). PMID:34710081
Draft Genome Sequence of the Multidrug-Resistant Strain Stenotrophomonas maltophilia N0320, Isolated from a Commercial Nanoparticle Product. PMID:34709057
Multidrug Resistance Dynamics in Salmonella in Food Animals in the United States: An Analysis of Genomes from Public Databases. PMID:34704804
Molecular Characterization and Taxonomic Assignment of Three Phage Isolates from a Collection Infecting Pseudomonas syringae pv. actinidiae and P. syringae pv. phaseolicola from Northern Italy. PMID:34696512
Phage Therapy Related Microbial Succession Associated with Successful Clinical Outcome for a Recurrent Urinary Tract Infection. PMID:34696479
Genome Study of a Novel Virulent Phage vB_SspS_KASIA and Mu-like Prophages of Shewanella sp. M16 Provides Insights into the Genetic Diversity of the Shewanella Virome. PMID:34681734
Population structure, biogeography and transmissibility of Mycobacterium tuberculosis. PMID:34671035
Utilization Efficiency of Human Milk Oligosaccharides by Human-Associated Akkermansia Is Strain Dependent. PMID:34669436
Active virus-host interactions at sub-freezing temperatures in Arctic peat soil. PMID:34663463
Whole-Genome Assessment of Clinical Acinetobacter baumannii Isolates Uncovers Potentially Novel Factors Influencing Carbapenem Resistance. PMID:34659144
Complete Genome Sequence of SMBL-WEM22, a Halotolerant Strain of Kosakonia cowanii Isolated from Hong Kong Seawater. PMID:34647797
Plasmidome of Listeria spp.-The repA-Family Business. PMID:34638661
In vivo commensal control of Clostridioides difficile virulence. PMID:34637781
An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism. PMID:34625561
Whole-genome sequencing reveals high genetic diversity of Streptococcus uberis isolated from cows with mastitis. PMID:34620161
Novel Drivers of Virulence in Clostridioides difficile Identified via Context-Specific Metabolic Network Analysis. PMID:34609164
Global Expansion of Linezolid-Resistant Coagulase-Negative Staphylococci. PMID:34589061
Comparative Genome Analysis and Spore Heat Resistance Assay Reveal a New Component to Population Structure and Genome Epidemiology Within Clostridium perfringens Enterotoxin-Carrying Isolates. PMID:34566921
Draft Genome Sequences of Four Different Strains Belonging to Leptospira interrogans Serovar Pomona Isolated from Mammals in the Island of Sardinia, Italy. PMID:34553992
Citrate Synthase and OGDH as Potential Biomarkers of Atherosclerosis under Chronic Stress. PMID:34539976
Draft genome sequencing and functional annotation and characterization of biofilm-producing bacterium Bacillus novalis PD1 isolated from rhizospheric soil. PMID:34537868
Comprehensive genome analysis of a novel actinobacterium with high potential for biotechnological applications, Nonomuraea aridisoli sp. nov., isolated from desert soil. PMID:34529164
Draft Genome Sequences of Staphylococcus sp. Strain CWZ226, of Unknown Origin, and Pseudomonas sp. Strain CVAP#3, Antagonistic to Strain CWZ226. PMID:34528827
PathFams: statistical detection of pathogen-associated protein domains. PMID:34521345
Flavobacterium erciyesense sp. nov., a putative non-pathogenic fish symbiont. PMID:34515811
Certain Listeria monocytogenes plasmids contribute to increased UVC ultraviolet light stress. PMID:34498664
Adlercreutzia rubneri sp. nov., a resveratrol-metabolizing bacterium isolated from human faeces and emended description of the genus Adlercreutzia. PMID:34495823
Molecular Characterization of Microbiota in Cerebrospinal Fluid From Patients With CSF Shunt Infections Using Whole Genome Amplification Followed by Shotgun Sequencing. PMID:34490140
Transcriptomics reveal different metabolic strategies for acid resistance and gamma-aminobutyric acid (GABA) production in select Levilactobacillus brevis strains. PMID:34488774
GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning. PMID:34461978
Genomic and Phenotypic Biology of Novel Strains of Dickeya zeae Isolated From Pineapple and Taro in Hawaii: Insights Into Genome Plasticity, Pathogenicity, and Virulence Determinants. PMID:34456933
Identification and Characterization of Pleiotropic High-Persistence Mutations in the Beta Subunit of the Bacterial RNA Polymerase. PMID:34424038
A multi-omics study on quantifying antimicrobial resistance in European freshwater lakes. PMID:34403881
A genomic perspective on the potential of termite-associated Cellulosimicrobium cellulans MP1 as producer of plant biomass-acting enzymes and exopolysaccharides. PMID:34395081
Characterization of Anti-Bacterial Effect of the Two New Phages against Uropathogenic Escherichia coli. PMID:34372554
Genomic Landscape and Phenotypic Assessment of Cronobacter sakazakii Isolated From Raw Material, Environment, and Production Facilities in Powdered Infant Formula Factories in China. PMID:34354686
Analysis of Virulence and Antimicrobial Resistance Gene Carriage in Staphylococcus aureus Infections in Equids Using Whole-Genome Sequencing. PMID:34346711
Genotoxic Agents Produce Stressor-Specific Spectra of Spectinomycin Resistance Mutations Based on Mechanism of Action and Selection in Bacillus subtilis. PMID:34339280
First Molecular Characterization of Siphoviridae-Like Bacteriophages Infecting Staphylococcus hyicus in a Case of Exudative Epidermitis. PMID:34305825
Whole genome sequence of colistin-resistant Escherichia coli from western India. PMID:34305283
Antifungal Activity and Biosynthetic Potential of New Streptomyces sp. MW-W600-10 Strain Isolated from Coal Mine Water. PMID:34299061
Genome Annotation of Poly(lactic acid) Degrading Pseudomonas aeruginosa, Sphingobacterium sp. and Geobacillus sp. PMID:34299026
Genomic characterization of Achromobacter species isolates from chronic and occasional lung infection in cystic fibrosis patients. PMID:34292148
Genome-scale metabolic modeling reveals key features of a minimal gene set. PMID:34288418
Risk Factors for and Mechanisms of COlistin Resistance Among Enterobacterales: Getting at the CORE of the Issue. PMID:34285928
Genome Sequences of Two Pseudomonas aeruginosa Isolates with Defects in Type III Secretion System Gene Expression from a Chronic Ankle Wound Infection. PMID:34259549
Draft Genome Sequences of Pseudomonas spp. Isolated from Berry Surfaces in Commercial Cranberry Bogs in Massachusetts, USA. PMID:34236228
Identification and Characterization of Mycobacterial Species Using Whole-Genome Sequences. PMID:34235665
Phenotypic and Genotypic Properties of Fluoroquinolone-Resistant, qnr-Carrying Escherichia coli Isolated from the German Food Chain in 2017. PMID:34208509
Whole-Genome Sequencing Investigation of a Large Nosocomial Outbreak Caused by ST131 H30Rx KPC-Producing Escherichia coli in Italy. PMID:34203731
Genomic Analysis of Pasteurella atlantica Provides Insight on Its Virulence Factors and Phylogeny and Highlights the Potential of Reverse Vaccinology in Aquaculture. PMID:34199775
Strain diversity of plant-associated Lactiplantibacillus plantarum. PMID:34171185
Subtypes, resistance and virulence platforms in extended-drug resistant Acinetobacter baumannii Romanian isolates. PMID:34168184
Caloric restriction disrupts the microbiota and colonization resistance. PMID:34163067
Genomic analysis of halophilic bacterium, Lentibacillus sp. CBA3610, derived from human feces. PMID:34162403
Untargeted Metabolomics Reveals Species-Specific Metabolite Production and Shared Nutrient Consumption by Pseudomonas aeruginosa and Staphylococcus aureus. PMID:34156287
Corynebacterium phoceense - a rare Corynebacterium species isolated from a urine sample. PMID:34151147
Investigation of Plasmids Among Clinical Staphylococcus aureus and Staphylococcus haemolyticus Isolates From Egypt. PMID:34149648
Reactive Oxygen Species-Dependent Innate Immune Mechanisms Control Methicillin-Resistant Staphylococcus aureus Virulence in the Drosophila Larval Model. PMID:34126772
Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain. PMID:34121661
Degradation of biological macromolecules supports uncultured microbial populations in Guaymas Basin hydrothermal sediments. PMID:34112968
Draft Genome Sequence of Rhodococcus qingshengii Strain PN_19, Isolated from a Moribund Individual of Pinna nobilis in Sardinia, Italy. PMID:34110242
Colonisation dynamics of Listeria monocytogenes strains isolated from food production environments. PMID:34108547
Whole-Genome Sequencing and Machine Learning Analysis of Staphylococcus aureus from Multiple Heterogeneous Sources in China Reveals Common Genetic Traits of Antimicrobial Resistance. PMID:34100643
A deep-sea bacterium related to coastal marine pathogens. PMID:34097814
Unveiling the Virulent Genotype and Unusual Biochemical Behavior of Escherichia coli ST59. PMID:34085857
RNA atlas of human bacterial pathogens uncovers stress dynamics linked to infection. PMID:34078900
Identifying genomic islands with deep neural networks. PMID:34078279
Proteome-wide analysis of Coxiella burnetii for conserved T-cell epitopes with presentation across multiple host species. PMID:34078271
Identification of an Attenuated Substrain of Francisella tularensis SCHU S4 by Phenotypic and Genotypic Analyses. PMID:34067337
The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment. PMID:34063450
Phage Biocontrol of Bacterial Leaf Blight Disease on Welsh Onion Caused by Xanthomonas axonopodis pv. allii. PMID:34062921
Complete Genome Sequence of Bacillus cereus Sensu Stricto VKM B-370, Isolated from the Silkworm Bombyx mori. PMID:34016682
Metagenomic analysis reveals the shared and distinct features of the soil resistome across tundra, temperate prairie, and tropical ecosystems. PMID:33990222
Genome Sequences of 17 Diverse Pseudomonas aeruginosa Phages. PMID:33986073
Draft genome sequencing of Sporolactobacillus terrae SBT-1, an efficient bacterium to ferment concentrated sugar to D-lactic acid. PMID:33961074
Experimental evolution in morbidostat reveals converging genomic trajectories on the path to triclosan resistance. PMID:33945454
A plasmid locus associated with Klebsiella clinical infections encodes a microbiome-dependent gut fitness factor. PMID:33930099
Biotechnological and Ecological Potential of Micromonospora provocatoris sp. nov., a Gifted Strain Isolated from the Challenger Deep of the Mariana Trench. PMID:33923039
Hybrid Atypical Enteropathogenic and Extraintestinal Escherichia coli (aEPEC/ExPEC) BA1250 Strain: A Draft Genome. PMID:33919948
Genome and Pangenome Analysis of Lactobacillus hilgardii FLUB-A New Strain Isolated from Mead. PMID:33917427
Globally diverse Mycobacterium tuberculosis resistance acquisition: a retrospective geographical and temporal analysis of whole genome sequences. PMID:33912853
Prediction of host-pathogen protein interactions by extended network model. PMID:33907496
Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom. PMID:33902727
Malonate utilization by Pseudomonas aeruginosa affects quorum-sensing and virulence and leads to formation of mineralized biofilm-like structures. PMID:33892520
Dissecting industrial fermentations of fine flavour cocoa through metagenomic analysis. PMID:33883642
High-Resolution Genomic Comparisons within Salmonella enterica Serotypes Derived from Beef Feedlot Cattle: Parsing the Roles of Cattle Source, Pen, Animal, Sample Type, and Production Period. PMID:33863705
Draft Genome Sequence of Enterococcus faecalis 1351, Isolated from a Mastitis-Affected Camel in Isiolo County, Kenya. PMID:33858924
Typing methods based on whole genome sequencing data. PMID:33829127
Genetic Characterization of Clostridium botulinum Isolated from the First Case of Infant Botulism in Korea. PMID:33824238
Genome-based classification of the Streptomyces violaceusniger clade and description of Streptomyces sabulosicollis sp. nov. from an Indonesian sand dune. PMID:33797685
Analysis of Yersinia pseudotuberculosis Isolates Recovered from Deceased Mammals of a German Zoo Animal Collection. PMID:33789956
Surveillance of antimicrobial resistance in low- and middle-income countries: a scattered picture. PMID:33789754
Streptococcus pyogenes upregulates arginine catabolism to exert its pathogenesis on the skin surface. PMID:33789094
Hidden Markov Model: a shortest unique representative approach to detect the protein toxins, virulence factors and antibiotic resistance genes. PMID:33785071
Scarcity of scale-free topology is universal across biochemical networks. PMID:33753807
Draft Genome Sequence of a Burkholderia cepacia Complex Strain Isolated from a Human Intra-abdominal Abscess. PMID:33737360
Genomic diversity of Mycobacterium avium subsp. paratuberculosis: pangenomic approach for highlighting unique genomic features with newly constructed complete genomes. PMID:33736686
The extent of carbapenemase-encoding genes in public genome sequences. PMID:33732552
Patient and Microbial Genomic Factors Associated with Carbapenem-Resistant Klebsiella pneumoniae Extraintestinal Colonization and Infection. PMID:33727393
Nonomuraea cypriaca sp. nov., isolated from soil. PMID:33710377
Lactobacillus paracasei DTA81, a cholesterol-lowering strain having immunomodulatory activity, reveals gut microbiota regulation capability in BALB/c mice receiving high-fat diet. PMID:33709536
Complete Genome Sequence of Brucella abortus 68, Isolated from Aborted Fetal Sheep in Ukraine. PMID:33707337
Helicobacter pylori Antimicrobial Resistance and Gene Variants in High- and Low-Gastric-Cancer-Risk Populations. PMID:33692136
Genome sequence analysis and bioactivity profiling of marine-derived actinobacteria, Brevibacterium luteolum, and Cellulosimicrobium funkei. PMID:33677635
Comparative Genomic Analysis of Three Pseudomonas Species Isolated from the Eastern Oyster (Crassostrea virginica) Tissues, Mantle Fluid, and the Overlying Estuarine Water Column. PMID:33673397
Cohnella pontilimi sp. nov., isolated from tidal-flat mud. PMID:33666688
Pseudomonas allokribbensis sp. nov. and Pseudomonas gozinkensis sp. nov., Two New Species Isolated from a Volcanic Island, Izu Oshima, Japan. PMID:33660045
Learning From Limited Data: Towards Best Practice Techniques for Antimicrobial Resistance Prediction From Whole Genome Sequencing Data. PMID:33659219
Distribution and preservation of the components of the engulfment. What is beyond representative genomes? PMID:33651833
Genome announcement of Steinernema khuongi and its associated symbiont from Florida. PMID:33624756
Megasphaera lornae sp. nov., Megasphaera hutchinsoni sp. nov., and Megasphaera vaginalis sp. nov.: novel bacteria isolated from the female genital tract. PMID:33616513
Lifestyle of sponge symbiont phages by host prediction and correlative microscopy. PMID:33603147
Genomic Characterization of Multidrug-Resistant Escherichia coli BH100 Sub-strains. PMID:33584554
Crateriforma spongiae sp. nov., isolated from a marine sponge and emended description of the genus "Crateriforma". PMID:33582885
Draft Genome Sequences of Pseudomonas sp. Isolates Recovered from Ghanaian Fish Food Samples in 2018. PMID:33574108
Complete Genome Sequence of Sphingomonas paucimobilis Strain Kira, Isolated from Human Neuroblastoma SH-SY5Y Cell Cultures Supplemented with Retinoic Acid. PMID:33574107
Whole-Genome Sequencing for Investigating a Health Care-Associated Outbreak of Carbapenem-Resistant Acinetobacter baumannii. PMID:33573077
Rapid transcriptional and metabolic adaptation of intestinal microbes to host immune activation. PMID:33539766
A Sarcina bacterium linked to lethal disease in sanctuary chimpanzees in Sierra Leone. PMID:33536429
Taxonomic Evaluation of the Heyndrickxia (Basonym Bacillus) sporothermodurans Group (H. sporothermodurans, H. vini, H. oleronia) Based on Whole Genome Sequences. PMID:33530338
Variable Release of Lipoteichoic Acid From Staphylococcus aureus Bloodstream Isolates Relates to Distinct Clinical Phenotypes, Strain Background, and Antibiotic Exposure. PMID:33519759
Resistome of a carbapenemase-producing novel ST232 Klebsiella michiganensis isolate from urban hospital effluent in South Africa. PMID:33508483
Cytotoxic Escherichia coli strains encoding colibactin, cytotoxic necrotizing factor, and cytolethal distending toxin colonize laboratory common marmosets (Callithrix jacchus). PMID:33504843
Mash-based analyses of Escherichia coli genomes reveal 14 distinct phylogroups. PMID:33500552
Pangenome Analytics Reveal Two-Component Systems as Conserved Targets in ESKAPEE Pathogens. PMID:33500331
Monoassociation with bacterial isolates reveals the role of colonization, community complexity and abundance on locomotor behavior in larval zebrafish. PMID:33499997
Genome Analysis of a Historical Shigella dysenteriae Serotype 1 Strain Carrying a Conserved Stx Prophage Region. PMID:33488558
Detecting operons in bacterial genomes via visual representation learning. PMID:33483546
Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types. PMID:33465077
Freshwater monitoring by nanopore sequencing. PMID:33461660
Genomic insight into a novel actinobacterium, Actinomadura rubrisoli sp. nov., reveals high potential for bioactive metabolites. PMID:33449222
Whole-Genome Sequencing Analysis of Salmonella Enterica Serotype Enteritidis Isolated from Poultry Sources in South Korea, 2010-2017. PMID:33430364
Comparative Genomics Provides Insights into the Taxonomy of Azoarcus and Reveals Separate Origins of Nif Genes in the Proposed Azoarcus and Aromatoleum Genera. PMID:33430351
Identifying novel β-lactamase substrate activity through in silico prediction of antimicrobial resistance. PMID:33416461
Staphylococcus aureus Tolerance and Genomic Response to Photodynamic Inactivation. PMID:33408223
MetGEMs Toolbox: Metagenome-scale models as integrative toolbox for uncovering metabolic functions and routes of human gut microbiome. PMID:33406089
Novel Molecular Markers Linked to Pseudomonas aeruginosa Epidemic High-Risk Clones. PMID:33401446
Characterization of bacteriophage T7-Ah reveals its lytic activity against a subset of both mesophilic and psychrophilic Aeromonas salmonicida strains. PMID:33394168
Swine Conjunctivitis Associated with a Novel Mycoplasma Species Closely Related to Mycoplasma hyorhinis. PMID:33375690
Taxonomic classification of strain PO100/5 shows a broader geographic distribution and genetic markers of the recently described Corynebacterium silvaticum. PMID:33347470
Distribution of Important Probiotic Genes and Identification of the Biogenic Amines Produced by Lactobacillus acidophilus PNW3. PMID:33321968
Characterization of Salmonella Isolates from Various Geographical Regions of the Caucasus and Their Susceptibility to Bacteriophages. PMID:33321823
Draft Genome Sequence of Lactobacillus salivarius KZ-NCB, Isolated from Chicken Cecum. PMID:33303665
Simultaneous Genome Sequencing of Prosthecochloris ethylica and Desulfuromonas acetoxidans within a Syntrophic Mixture Reveals Unique Pili and Protein Interactions. PMID:33297414
Phenotypic and Genomic Comparison of the Two Most Common ExoU-Positive Pseudomonas aeruginosa Clones, PA14 and ST235. PMID:33293405
Pandemic Vibrio cholerae shuts down site-specific recombination to retain an interbacterial defence mechanism. PMID:33288753
Non-adaptive Evolution of Trimeric Autotransporters in Brucellaceae. PMID:33281759
Molecular and phenotypic characterization of Salmonella Typhimurium monophasic variant (1,4,[5],12:i:-) from Colombian clinical isolates. PMID:33275350
Genome Sequence of the Unusual Purple Photosynthetic Bacterium Phaeovibrio sulfidiphilus, Only Distantly Related to Rhodospirillaceae, Reveals Unique Genes for Respiratory Nitrate Reduction and Glycerol Metabolism. PMID:33273003
Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Kottbus Strain Kharkiv, Isolated from a Commercial Pork Production Facility in Ukraine. PMID:33273001
Virulence characterization and comparative genomics of Listeria monocytogenes sequence type 155 strains. PMID:33256601
Manganese Depletion Leads to Multisystem Changes in the Transcriptome of the Opportunistic Pathogen Streptococcus sanguinis. PMID:33250881
Fusobacteriumnucleatum Adheres to Clostridioides difficile via the RadD Adhesin to Enhance Biofilm Formation in Intestinal Mucus. PMID:33227279
Prophages are associated with extensive CRISPR-Cas auto-immunity. PMID:33219687
Genetic Carriers and Genomic Distribution of cadA6-A Novel Variant of a Cadmium Resistance Determinant Identified in Listeria spp. PMID:33218089
Characterization of Clinical and Carrier Streptococcus agalactiae and Prophage Contribution to the Strain Variability. PMID:33217933
BRENDA, the ELIXIR core data resource in 2021: new developments and updates. PMID:33211880
Genetic Variation in Toll-Like Receptor 5 and Colonization with Flagellated Bacterial Vaginosis-Associated Bacteria. PMID:33199356
Genomic analysis of Bacillus cereus NWUAB01 and its heavy metal removal from polluted soil. PMID:33184305
Expansion segments in bacterial and archaeal 5S ribosomal RNAs. PMID:33184227
Draft Genome Sequences of Vibrio cholerae Non-O1, Non-O139 Isolates from Common Tern Chicks (Sterna hirundo) following a Mass Mortality Event. PMID:33184162
First Report of Filamentous Phages Isolated from Tunisian Orchards to Control Erwinia amylovora. PMID:33182526
Navigating the Human Gut Microbiome: Pathway to Success from Lessons Learned. PMID:33181127
Long inverted repeats around the chromosome replication terminus in the model strain Bacillus thuringiensis serovar israelensis BGSC 4Q7. PMID:33180015
Complete Genomic Analysis of VRE From a Cattle Feedlot: Focus on 2 Antibiotic Resistance. PMID:33178155
Reclassification of Chromobacterium violaceum ATCC 31532 and its quorum biosensor mutant CV026 to Chromobacterium subtsugae. PMID:33159606
PhANNs, a fast and accurate tool and web server to classify phage structural proteins. PMID:33137102
Genetic and Virulence Characteristics of a Hybrid Atypical Enteropathogenic and Uropathogenic Escherichia coli (aEPEC/UPEC) Strain. PMID:33134184
Quantitative analysis and virulence phenotypes of atypical enteropathogenic Escherichia coli (EPEC) acquired from diarrheal stool samples from a Midwest US hospital. PMID:33131419
Amino Acid k-mer Feature Extraction for Quantitative Antimicrobial Resistance (AMR) Prediction by Machine Learning and Model Interpretation for Biological Insights. PMID:33126516
Draft Genome Sequences of Cronobacter muytjensii Cr150, Cronobacter turicensis Cr170, and Cronobacter sakazakii Cr611. PMID:33122419
Phenotypic Characterization and Whole Genome Analysis of a Strong Biofilm-Forming Staphylococcus aureus Strain Associated With Subclinical Bovine Mastitis in Colombia. PMID:33102540
Analysis of the Molecular Diversity Among Cronobacter Species Isolated From Filth Flies Using Targeted PCR, Pan Genomic DNA Microarray, and Whole Genome Sequencing Analyses. PMID:33101235
Rapid growth inhibitory activity of a YafQ-family endonuclease toxin of the Helicobacter pylori tfs4 integrative and conjugative element. PMID:33097748
IurV, Encoded by ORF VCA0231, Is Involved in the Regulation of Iron Uptake Genes in Vibrio cholerae. PMID:33053678
Nonredundant functions of Mycobacterium tuberculosis chaperones promote survival under stress. PMID:32996193
Virulence of the Pathogen Porphyromonas gingivalis Is Controlled by the CRISPR-Cas Protein Cas3. PMID:32994292
Translocation of Viable Gut Microbiota to Mesenteric Adipose Drives Formation of Creeping Fat in Humans. PMID:32991841
Minimizing the number of optimizations for efficient community dynamic flux balance analysis. PMID:32991583
CsrA Supports both Environmental Persistence and Host-Associated Growth of Acinetobacter baumannii. PMID:32989034
Strain-specific strategies of 2'-fucosyllactose, 3-fucosyllactose, and difucosyllactose assimilation by Bifidobacterium longum subsp. infantis Bi-26 and ATCC 15697. PMID:32985563
Genome-Based Insights into the Production of Carotenoids by Antarctic Bacteria, Planococcus sp. ANT_H30 and Rhodococcus sp. ANT_H53B. PMID:32977394
Is Long-Term Heavy Metal Exposure Driving Carriage of Antibiotic Resistance in Environmental Opportunistic Pathogens: A Comprehensive Phenomic and Genomic Assessment Using Serratia sp. SRS-8-S-2018. PMID:32973703
Complete Genome Sequence of Enterococcus faecium FS86, Used for Propagation of Bacteriophages with Therapeutic Potential. PMID:32972936
Streptococcus equi Subspecies zooepidemicus and Sudden Deaths in Swine, Canada. PMID:32946731
Paludisphaera soli sp. nov., a new member of the family Isosphaeraceae isolated from high altitude soil in the Western Himalaya. PMID:32936355
Identification, Characterization, and Genomic Analysis of Novel Serratia Temperate Phages from a Gold Mine. PMID:32933193
Bridging the membrane lipid divide: bacteria of the FCB group superphylum have the potential to synthesize archaeal ether lipids. PMID:32929208
Streptomyces boncukensis sp. nov., isolated from saltern soil. PMID:32915250
Growth rate alterations of human colorectal cancer cells by 157 gut bacteria. PMID:32915102
Integrated Metabolic Modeling, Culturing, and Transcriptomics Explain Enhanced Virulence of Vibrio cholerae during Coinfection with Enterotoxigenic Escherichia coli. PMID:32900868
DrpB (YedR) Is a Nonessential Cell Division Protein in Escherichia coli. PMID:32900831
Redefining the H-NS protein family: a diversity of specialized core and accessory forms exhibit hierarchical transcriptional network integration. PMID:32894292
Whole-genome sequence of multi-drug resistant Pseudomonas aeruginosa strains UY1PSABAL and UY1PSABAL2 isolated from human broncho-alveolar lavage, Yaoundé, Cameroon. PMID:32886694
Interbacterial competition and anti-predatory behaviour of environmental Vibrio cholerae strains. PMID:32885535
Characterization of methicillin-resistant Staphylococcus aureus through genomics approach. PMID:32864286
The Three Flagellar Loci of Brucella ovis PA Are Dispensable for Virulence in Cellular Models and Mice. PMID:32851024
Genome Sequences of Allochromatium palmeri and Allochromatium humboldtianum Expand the Allochromatium Family Tree of Purple Sulfur Photosynthetic Bacteria within the Gammaproteobacteria and Further Refine the Genus. PMID:32817156
Draft Genome Sequences of Six Strains Isolated from the Rhizosphere of Wheat Grown in Cadmium-Contaminated Soil. PMID:32816975
First insight into the whole-genome sequence variations in Mycobacterium bovis BCG-1 (Russia) vaccine seed lots and their progeny clinical isolates from children with BCG-induced adverse events. PMID:32811436
Cellular and Extracellular Proteome of the Animal Pathogen Corynebacterium silvaticum, a Close Relative of Zoonotic Corynebacterium ulcerans and Corynebacterium pseudotuberculosis. PMID:32806579
Strains of Bradyrhizobium cosmicum sp. nov., isolated from contrasting habitats in Japan and Canada possess photosynthesis gene clusters with the hallmark of genomic islands. PMID:32804606
Criteria to Qualify Microorganisms as "Probiotic" in Foods and Dietary Supplements. PMID:32793153
Genomic Analysis of Three Cheese-Borne Pseudomonas lactis with Biofilm and Spoilage-Associated Behavior. PMID:32784363
Comparative Genome Analysis of Bacillus sporothermodurans with Its Closest Phylogenetic Neighbor, Bacillus oleronius, and Bacillus cereus and Bacillus subtilis Groups. PMID:32759699
Genomic epidemiology of animal-derived tigecycline-resistant Escherichia coli across China reveals recent endemic plasmid-encoded tet(X4) gene. PMID:32737421
Functions of Bacterial tRNA Modifications: From Ubiquity to Diversity. PMID:32718697
Phenotypic and Genotypic Properties of Vibrio cholerae non-O1, non-O139 Isolates Recovered from Domestic Ducks in Germany. PMID:32717968
Selection of Exopolysaccharide-Producing Lactobacillus Plantarum (Lactiplantibacillus Plantarum) Isolated from Algerian Fermented Foods for the Manufacture of Skim-Milk Fermented Products. PMID:32717902
Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity. PMID:32711472
Standardized bacteriophage purification for personalized phage therapy. PMID:32709990
A unified catalog of 204,938 reference genomes from the human gut microbiome. PMID:32690973
Complete Genome Sequences of 10 Phages Lytic against Multidrug-Resistant Pseudomonas aeruginosa. PMID:32675185
Experimental approaches to tracking mobile genetic elements in microbial communities. PMID:32672812
Dataset of complete genome assembly and analysis of mycobacterium tuberculosis strain SIT745/EAI1-MYS. PMID:32671154
From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes. PMID:32670511
Biofilm and Pathogenesis-Related Proteins in the Foodborne P. fluorescens ITEM 17298 With Distinctive Phenotypes During Cold Storage. PMID:32670211
Antimicrobial Susceptibility and Characterization of Resistance Mechanisms of Corynebacterium urealyticum Clinical Isolates. PMID:32668585
Vitamin Biosynthesis by Human Gut Butyrate-Producing Bacteria and Cross-Feeding in Synthetic Microbial Communities. PMID:32665271
Large-scale assessment of antimicrobial resistance marker databases for genetic phenotype prediction: a systematic review. PMID:32658975
Genomic Analysis of Staphylococcus aureus Strains Originating from Hungarian Rabbit Farms Reinforce the Clonal Origin of Various Virulence Types. PMID:32630808
Survey and Validation of tRNA Modifications and Their Corresponding Genes in Bacillus subtilis sp Subtilis Strain 168. PMID:32629984
Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food-borne microorganisms. PMID:32626197
PARGT: a software tool for predicting antimicrobial resistance in bacteria. PMID:32620856
Draft Genome Sequence of a New Oscillospiraceae Bacterium Isolated from Anaerobic Digestion of Biomass. PMID:32616639
Tetracenomycin X inhibits translation by binding within the ribosomal exit tunnel. PMID:32601485
DeepVF: a deep learning-based hybrid framework for identifying virulence factors using the stacking strategy. PMID:32599617
Metabolism of Soy Isoflavones by Intestinal Bacteria: Genome Analysis of an Adlercreutzia Equolifaciens Strain That Does Not Produce Equol. PMID:32586036
Rapid diversification of wild social groups driven by toxin-immunity loci on mobile genetic elements. PMID:32565537
Draft Genome Sequences of Xylella fastidiosa subsp. fastidiosa Strains OK3, VB11, and NOB1, Isolated from Bunch and Muscadine Grapes Grown in Southern Mississippi. PMID:32554794
Complete Genome Sequences of Seven Strains of Pseudomonas spp. Isolated from Boreal Forest Soil in Interior Alaska. PMID:32554792
Modeling of nitrogen fixation and polymer production in the heterotrophic diazotroph Azotobacter vinelandii DJ. PMID:32551229
Clostridioides difficile Senses and Hijacks Host Heme for Incorporation into an Oxidative Stress Defense System. PMID:32526159
BacEffluxPred: A two-tier system to predict and categorize bacterial efflux mediated antibiotic resistance proteins. PMID:32518231
A synthesis of bacterial and archaeal phenotypic trait data. PMID:32503990
Draft Genome Sequence of Escherichia coli UMB9246, Isolated from the Bladder of a Woman with Recurrent Urinary Tract Infection. PMID:32499352
Draft Genome Sequence of Staphylococcus epidermidis UMB8493, Isolated from the Female Urinary Tract. PMID:32499349
Draft Genome Sequence of Escherichia coli UMB1353, Isolated from the Female Urinary Tract. PMID:32499348
Case Report: Successful Rescue Therapy of Extensively Drug-Resistant Acinetobacter baumannii Osteomyelitis With Cefiderocol. PMID:32494581
Virulence Potential of a Multidrug-Resistant Escherichia coli Strain Belonging to the Emerging Clonal Group ST101-B1 Isolated from Bloodstream Infection. PMID:32486334
An evolutionary path to altered cofactor specificity in a metalloenzyme. PMID:32483131
Draft Genome Sequence of Shewanella sp. Strain ISO12, a Candidate Probiotic Isolated from the Intestine of Fundulus heteroclitus. PMID:32467277
Parallel Evolution of Tobramycin Resistance across Species and Environments. PMID:32457248
Predicting Phenotypic Polymyxin Resistance in Klebsiella pneumoniae through Machine Learning Analysis of Genomic Data. PMID:32457240
Extracellular vesicles produced by human and animal Staphylococcus aureus strains share a highly conserved core proteome. PMID:32439871
Draft Genome Sequence of Proteus mirabilis Strain UMB0038, Isolated from the Female Bladder. PMID:32439674
Phenotypic and Genotypic Characterization of Veterinary Vibrio cincinnatiensis Isolates. PMID:32429107
Draft Genome Sequence of Antibiotic-Resistant Enterococcus faecalis Strain UMB0843, Isolated from the Female Urinary Tract. PMID:32409554
Draft Genome Sequence of Klebsiella pneumoniae UMB7779, Isolated from the Female Urinary Tract. PMID:32409552
Draft Genome Sequence of Corynebacterium coyleae UMB8490, Isolated from the Female Urinary Tract. PMID:32409550
Draft Genome Sequence of Lactobacillus jensenii Strain UMB7766, Isolated from the Female Bladder. PMID:32409549
Draft Genome Sequence of Proteus mirabilis UMB1310, Isolated from the Female Urinary Tract. PMID:32409548
Whole genome sequence analysis of Cupriavidus campinensis S14E4C, a heavy metal resistant bacterium. PMID:32406019
The Serratia marcescens Siderophore Serratiochelin Is Necessary for Full Virulence during Bloodstream Infection. PMID:32393508
Whole genome sequencing and antibiotic diffusion assays, provide new insight on drug resistance in the genus Pedobacter. PMID:32386210
Phage biocontrol to combat Pseudomonas syringae pathogens causing disease in cherry. PMID:32383813
Draft Genome Sequence of Klebsiella pneumoniae UMB7783, Isolated from the Female Bladder. PMID:32381623
Genome Sequence of the Alphaproteobacterium Blastochloris sulfoviridis DSM 729, Which Requires Reduced Sulfur as a Growth Supplement and Contains Bacteriochlorophyll b. PMID:32354981
Acetaldehyde production by Rothia mucilaginosa isolates from patients with oral leukoplakia. PMID:32341761
Preparing for the KIL: Receptor Analysis of Pseudomonas syringae pv. porri Phages and Their Impact on Bacterial Virulence. PMID:32331264
Comparative Genomics Reveals Pathogenicity-Related Loci in Shewanella algae. PMID:32318128
Novel Mobilizable Genomic Island GEI-D18A Mediates Conjugational Transfer of Antibiotic Resistance Genes in the Multidrug-Resistant Strain Rheinheimera sp. D18. PMID:32318052
Salmonella Pathogenicity Island 1 (SPI-1): The Evolution and Stabilization of a Core Genomic Type Three Secretion System. PMID:32316180
Unveiling salinity effects on photo-bioelectrocatalysis through combination of bioinformatics and electrochemistry. PMID:32308212
Draft Genome Sequences of Novel Campylobacter Species Isolated from Nonhuman Primates. PMID:32273357
Virulence Factors and Phylogeny of Staphylococcus aureus Associated With Bovine Mastitis in Russia Based on Genome Sequences. PMID:32270001
Improving the usability and comprehensiveness of microbial databases. PMID:32264902
Draft Genome Sequence of Streptomyces sp. Strain C8S0, Isolated from a Highly Oligotrophic Sediment. PMID:32241863
Draft Genome Sequences of Thiorhodococcus mannitoliphagus and Thiorhodococcus minor, Purple Sulfur Photosynthetic Bacteria in the Gammaproteobacterial Family Chromatiaceae. PMID:32241858
Nonomuraea basaltis sp. nov., a siderophore-producing actinobacteria isolated from surface soil of basaltic parent material. PMID:32236722
Lactobacillus garii sp. nov., isolated from a fermented cassava product. PMID:32228805
Draft genome sequence of Kocuria indica DP-K7, a methyl red degrading actinobacterium. PMID:32226704
Natural Transmission of Helicobacter saguini Causes Multigenerational Inflammatory Bowel Disease in C57/129 IL-10-/- Mice. PMID:32213619
Metatranscriptomics Reveals Antibiotic-Induced Resistance Gene Expression in the Murine Gut Microbiota. PMID:32210932
Meta-analysis Reveals Potential Influence of Oxidative Stress on the Airway Microbiomes of Cystic Fibrosis Patients. PMID:32171662
Draft Genome Sequence of a Mycobacterium porcinum Strain Isolated from a Pet Cat with Atypical Mycobacterial Panniculitis. PMID:32165379
Data on genome sequencing, assembly, annotation and genomic analysis of Rhodococcus rhodochrous strain SPC17 isolated from Lonar Lake. PMID:32154356
Comparison of core-genome MLST, coreSNP and PFGE methods for Klebsiella pneumoniae cluster analysis. PMID:32149598
ASA3P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates. PMID:32134915
Escherichia coli ST302: Genomic Analysis of Virulence Potential and Antimicrobial Resistance Mediated by Mobile Genetic Elements. PMID:32063891
Integrated Genome-Wide Analysis of an Isogenic Pair of Pseudomonas aeruginosa Clinical Isolates with Differential Antimicrobial Resistance to Ceftolozane/Tazobactam, Ceftazidime/Avibactam, and Piperacillin/Tazobactam. PMID:32033143
Characterization of the First mecA-Positive Multidrug-Resistant Staphylococcus pseudintermedius Isolated from an Argentinian Patient. PMID:32031908
Genome Sequence of the Acidophilic Nonsulfur Purple Photosynthetic Alphaproteobacterium Rhodovastum atsumiense, a Divergent Member of the Acetobacteraceae Family. PMID:32029562
Genomic Characterization of a Mercury Resistant Arthrobacter sp. H-02-3 Reveals the Presence of Heavy Metal and Antibiotic Resistance Determinants. PMID:32010097
The Identification and Conservation of Tunicaminyluracil-Related Biosynthetic Gene Clusters in Several Rathayibacter Species Collected From Australia, Africa, Eurasia, and North America. PMID:31998251
Genomic Analysis of Mycobacterium tuberculosis Isolates and Construction of a Beijing Lineage Reference Genome. PMID:31971587
Complete Genome Sequence of a New Clostridium sp. Isolated from Anaerobic Digestion and Biomethanation. PMID:31948972
PRAP: Pan Resistome analysis pipeline. PMID:31941435
Guiding the Refinement of Biochemical Knowledgebases with Ensembles of Metabolic Networks and Machine Learning. PMID:31926940
Genome-Scale Metabolic Reconstruction of Acetobacter pasteurianus 386B, a Candidate Functional Starter Culture for Cocoa Bean Fermentation. PMID:31921009
Draft Genome Sequence of Pseudomonas sp. Strain MWU12-2323, Isolated from a Wild Cranberry Bog in Truro, Massachusetts. PMID:31919180
Draft Genome Sequence of a Serratia marcescens Strain Isolated from the Pitcher Fluids of a Sarracenia Pitcher Plant. PMID:31919167
Complete Genome Sequence of Lactobacillus plantarum Strain JDARSH, Isolated from Sheep Milk. PMID:31919166
Whole Genome Sequencing and Comparative Genomics of Two Nematicidal Bacillus Strains Reveals a Wide Range of Possible Virulence Factors. PMID:31919110
Role of FAD-I in Fusobacterial Interspecies Interaction and Biofilm Formation. PMID:31906541
Intestinal colonization of genotoxic Escherichia coli strains encoding colibactin and cytotoxic necrotizing factor in small mammal pets. PMID:31902483
Draft Genome Sequence of Megaplasmid-Bearing Staphylococcus sciuri Strain B9-58B, Isolated from Retail Pork. PMID:31896659
Draft Genome Sequences of Lactobacillus helveticus, Lactobacillus fermentum, and Lactobacillus delbrueckii Strains from African Fermented Nono. PMID:31896647
Draft Genome Sequence of an Escherichia coli Strain Harboring bla CTX-M-115, bla CMY-2, Aminoglycoside, Tetracycline, and Sulfonamide Resistance Genes, Isolated from a Costa Rican Wastewater Treatment Plant. PMID:31896625
Genome-Wide Profiling of Enterotoxigenic Staphylococcus aureus Strains Used for the Production of Naturally Contaminated Cheeses. PMID:31892220
Genome sequencing of Mycobacterium pinnipedii strains: genetic characterization and evidence of superinfection in a South American sea lion (Otaria flavescens). PMID:31888476
One evolutionarily selected amino acid variation is sufficient to provide functional specificity in the cold shock protein paralogs of Staphylococcus aureus. PMID:31876031
Genetic determinants of genus-level glycan diversity in a bacterial protein glycosylation system. PMID:31869330
Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection. PMID:31860667
Multiple Klebsiella pneumoniae KPC Clones Contribute to an Extended Hospital Outbreak. PMID:31849904
Potentiated In Vitro Probiotic Activities of Lactobacillus fermentum LfQi6 Biofilm Biomass Versus Planktonic Culture. PMID:31828607
The enemy from within: a prophage of Roseburia intestinalis systematically turns lytic in the mouse gut, driving bacterial adaptation by CRISPR spacer acquisition. PMID:31827247
Manually curated genome-scale reconstruction of the metabolic network of Bacillus megaterium DSM319. PMID:31822710
Draft Genome Sequence of a Wohlfahrtiimonas chitiniclastica Strain Isolated from Frozen Chicken in Rio De Janeiro, Brazil. PMID:31806738
Helicobacter pylori Infections in the Bronx, New York: Surveying Antibiotic Susceptibility and Strain Lineage by Whole-Genome Sequencing. PMID:31801839
Constructing and Characterizing Bacteriophage Libraries for Phage Therapy of Human Infections. PMID:31781060
A Mesophilic Aeromonas salmonicida Strain Isolated from an Unsuspected Host, the Migratory Bird Pied Avocet. PMID:31757113
Genome-Wide Analyses Revealed Remarkable Heterogeneity in Pathogenicity Determinants, Antimicrobial Compounds, and CRISPR-Cas Systems of Complex Phytopathogenic Genus Pectobacterium. PMID:31756888
Systematic Identification and Analysis of Acinetobacter baumannii Type VI Secretion System Effector and Immunity Components. PMID:31736890
Analysis of the Complete Genome Sequence of the Widely Studied Strain Bradyrhizobium betae PL7HG1T Reveals the Presence of Photosynthesis Genes and a Putative Plasmid. PMID:31727720
Complete Genome Sequence of a New Bacteroidaceae Bacterium Isolated from Anaerobic Biomass Digestion. PMID:31727715
Draft Genome Sequence of Cronobacter sakazakii Cr268, Isolated from Infant Powder Formula. PMID:31727706
Antibiotics resistance and toxin profiles of Bacillus cereus-group isolates from fresh vegetables from German retail markets. PMID:31706266
Exfoliative toxin E, a new Staphylococcus aureus virulence factor with host-specific activity. PMID:31704997
The Whole-Genome Sequence of Plasmid-Bearing Staphylococcus argenteus Strain B3-25B from Retail Beef Liver Encodes the Type VII Secretion System and Several Virulence Factors. PMID:31699758
Isolation and Characterization of a Novel Pathogenic Strain of Ehrlichia minasensis. PMID:31694172
Genetic Features of mcr-1 Mediated Colistin Resistance in CMY-2-Producing Escherichia coli From Romanian Poultry. PMID:31681191
Cyanuric Acid Biodegradation via Biuret: Physiology, Taxonomy, and Geospatial Distribution. PMID:31676480
Whole-Genome Sequence of a Unique Elioraea Species Strain Isolated from a Yellowstone National Park Hot Spring. PMID:31672742
Genome Sequence of the Plant Growth-Promoting Rhizobacterium Pantoea agglomerans C1. PMID:31672740
The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities. PMID:31667520
ChlamDB: a comparative genomics database of the phylum Chlamydiae and other members of the Planctomycetes-Verrucomicrobiae-Chlamydiae superphylum. PMID:31665454
OxyR Is a Convergent Target for Mutations Acquired during Adaptation to Oxidative Stress-Prone Metabolic States. PMID:31651953
MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis. PMID:31647104
proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes. PMID:31647096
Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT. PMID:31640809
Molecular Phenotyping and Genomic Characterization of a Novel Neuroactive Bacterium Strain, Lactobacillus murinus HU-1. PMID:31636567
Description and complete genome sequences of Bradyrhizobium symbiodeficiens sp. nov., a non-symbiotic bacterium associated with legumes native to Canada. PMID:31626586
Draft Genome Sequences of Klebsiella pneumoniae Strains Isolated from Immunocompromised NOD-scid Gamma Research Mice. PMID:31624163
The recombination-cold region as an epidemiological marker of recombinogenic opportunistic pathogen Mycobacterium avium. PMID:31623552
Draft Whole-Genome Sequence of a Novel Chryseobacterium viscerum Strain Isolated from Fresh Water at Dripping Springs, New Mexico. PMID:31601674
Draft Genome Sequences of Bacteroides pyogenes Strains Isolated from the Uterus of Holstein Dairy Cows with Metritis. PMID:31601669
Antimicrobial Resistance Prediction for Gram-Negative Bacteria via Game Theory-Based Feature Evaluation. PMID:31597945
A machine learning-based service for estimating quality of genomes using PATRIC. PMID:31581946
Comparative Genomics Reveals a Well-Conserved Intrinsic Resistome in the Emerging Multidrug-Resistant Pathogen Cupriavidus gilardii. PMID:31578249
Genome Mining and Comparative Pathogenomic Analysis of An Endemic Methicillin-Resistant Staphylococcus Aureus (MRSA) Clone, ST612-CC8-t1257-SCCmec_IVd(2B), Isolated in South Africa. PMID:31569754
Evaluation of Incompatibility Group I1 (IncI1) Plasmid-Containing Salmonella enterica and Assessment of the Plasmids in Bacteriocin Production and Biofilm Development. PMID:31552285
Using Genomics to Track Global Antimicrobial Resistance. PMID:31552211
Deciphering the interplay between the genotoxic and probiotic activities of Escherichia coli Nissle 1917. PMID:31545853
Population Dynamics of Salmonella enterica within Beef Cattle Cohorts Followed from Single-Dose Metaphylactic Antibiotic Treatment until Slaughter. PMID:31519659
Gene Tags Assessment by Comparative Genomics (GTACG): A User-Friendly Framework for Bacterial Comparative Genomics. PMID:31507629
The Role of Iron in the P-Acquisition Mechanisms of the Unicellular N2-Fixing Cyanobacteria Halothece sp., Found in Association With the Mediterranean Seagrass Posidonia oceanica. PMID:31507547
Whole genome sequence analysis reveals high genetic variation of newly isolated Acidithiobacillus ferrooxidans IO-2C. PMID:31506467
Detection of a novel mcr-5.4 gene variant in hospital tap water by shotgun metagenomic sequencing. PMID:31504580
RetSynth: determining all optimal and sub-optimal synthetic pathways that facilitate synthesis of target compounds in chassis organisms. PMID:31500573
Identification and characterization of OmpT-like proteases in uropathogenic Escherichia coli clinical isolates. PMID:31496120
Discovery of novel bacterial queuine salvage enzymes and pathways in human pathogens. PMID:31481610
A Carbonic Anhydrase Pseudogene Sensitizes Select Brucella Lineages to Low CO2 Tension. PMID:31481543
Streptococcus pyogenes Transcriptome Changes in the Inflammatory Environment of Necrotizing Fasciitis. PMID:31471300
Draft Genome Sequence of a Chryseobacterium indologenes Strain Isolated from a Blood Culture of a Hospitalized Child in Antananarivo, Madagascar. PMID:31467100
Draft Genome Sequence of a Chitinimonas Species from Hudson Valley Waterways That Expresses Violacein Pigment. PMID:31467098
Systems Biology and Pangenome of Salmonella O-Antigens. PMID:31455646
Draft Genome Sequences of Three Sponge-Associated Actinomycetes Exhibiting Antimycobacterial Activity. PMID:31439704
Insights into the Phylogeny and Evolution of Cold Shock Proteins: From Enteropathogenic Yersinia and Escherichia coli to Eubacteria. PMID:31434224
Draft Genome Sequence of Duganella sp. Strain DN04, Isolated from Cultivated Soil. PMID:31395651
Draft Genome Sequence of Massilia sp. Strain MC02, Isolated from a Sandy Loam Maize Soil. PMID:31395629
Draft Genome Sequence of Massilia sp. Strain ONC3, a Novel Bacterial Species of the Oxalobacteraceae Family Isolated from Garden Soil. PMID:31395627
The increasing threat of silver-resistance in clinical isolates from wounds and burns. PMID:31372006
Metagenome-Assembled Genome Sequence of Sulfuricurvum sp. Strain IAE1, Isolated from a 4-Chlorophenol-Degrading Consortium. PMID:31371533
Identification and molecular epidemiology of methicillin resistant Staphylococcus pseudintermedius strains isolated from canine clinical samples in Argentina. PMID:31351494
Plantibacter flavus, Curtobacterium herbarum, Paenibacillus taichungensis, and Rhizobium selenitireducens Endophytes Provide Host-Specific Growth Promotion of Arabidopsis thaliana, Basil, Lettuce, and Bok Choy Plants. PMID:31350315
Molecular variability of Streptococcus uberis isolates from intramammary infections in Canadian dairy farms from the Maritime region. PMID:31308588
GeneHunt for rapid domain-specific annotation of glycoside hydrolases. PMID:31300677
Genome Sequence of Lipopeptide- and Antioxidant-Producing Strain Bacillus velezensis NWUMFkBS10.5. PMID:31296686
Multiple origins of reverse transcriptases linked to CRISPR-Cas systems. PMID:31276437
Micronutrient Requirements and Sharing Capabilities of the Human Gut Microbiome. PMID:31275260
Generation of a Prophage-Free Variant of the Fast-Growing Bacterium Vibrio natriegens. PMID:31253674
Genome Sequences of Escherichia Bacteriophages Isolated from Raw Wastewater. PMID:31248997
Comparative Genomics of Wild Bee and Flower Isolated Lactobacillus Reveals Potential Adaptation to the Bee Host. PMID:31243442
Genomewide Assessment of Mycobacterium tuberculosis Conditionally Essential Metabolic Pathways. PMID:31239393
Shotgun Metagenomics Reveals the Benthic Microbial Community Response to Plastic and Bioplastic in a Coastal Marine Environment. PMID:31231339
Pathogenic Autoreactive T and B Cells Cross-React with Mimotopes Expressed by a Common Human Gut Commensal to Trigger Autoimmunity. PMID:31227334
Prediction of bacterial E3 ubiquitin ligase effectors using reduced amino acid peptide fingerprinting. PMID:31211016
Complete Genome Sequence of Bacillus mycoides TH26, Isolated from a Permafrost Thaw Gradient. PMID:31196927
Two intracellular and cell type-specific bacterial symbionts in the placozoan Trichoplax H2. PMID:31182796
In-Depth Genomic and Phenotypic Characterization of the Antarctic Psychrotolerant Strain Pseudomonas sp. MPC6 Reveals Unique Metabolic Features, Plasticity, and Biotechnological Potential. PMID:31178851
Filling the gap between collection, transport and storage of the human gut microbiota. PMID:31171823
Cyberbiosecurity Challenges of Pathogen Genome Databases. PMID:31157218
Draft Genome Sequences of Helcococcus ovis Strains Isolated at Time of Metritis Diagnosis from the Uterus of Holstein Dairy Cows. PMID:31147432
Whole Genome Sequencing and Metabolomic Study of Cave Streptomyces Isolates ICC1 and ICC4. PMID:31134037
Genomic Characterization Provides New Insights for Detailed Phage- Resistant Mechanism for Brucella abortus. PMID:31130926
Immunoinformatics Approach to Design a Novel Epitope-Based Oral Vaccine Against Helicobacter pylori. PMID:31120321
Stenotrophomonas maltophilia Differential Gene Expression in Synthetic Cystic Fibrosis Sputum Reveals Shared and Cystic Fibrosis Strain-Specific Responses to the Sputum Environment. PMID:31109991
The Placental Atlas Tool (PAT): A collaborative research and discovery platform for the placental research community. PMID:31103066
Integrating Culture-based Antibiotic Resistance Profiles with Whole-genome Sequencing Data for 11,087 Clinical Isolates. PMID:31100356
Draft Genome Sequences of Pseudomonas sp. Strains Isolated from Wheat in Germany. PMID:31072895
First Report of Integrative Conjugative Elements in Riemerella anatipestifer Isolates From Ducks in China. PMID:31069241
Genomic Comparison Reveals Natural Occurrence of Clinically Relevant Multidrug-Resistant Extended-Spectrum-β-Lactamase-Producing Escherichia coli Strains. PMID:31053578
The MACADAM database: a MetAboliC pAthways DAtabase for Microbial taxonomic groups for mining potential metabolic capacities of archaeal and bacterial taxonomic groups. PMID:31032842
Environmental and Clinical Strains of Vibrio cholerae Non-O1, Non-O139 From Germany Possess Similar Virulence Gene Profiles. PMID:31031724
Draft Genome Sequence of Multidrug-Resistant Enterococcus faecium Strain E1298, with a Sequence Type 1274 Profile, Recovered from the Cloacal Microbiome of a Tropical Screech Owl (Megascops choliba) in Rio de Janeiro, Brazil. PMID:31000546
Genome Sequence of Bordetella pertussis Vaccine Strain BP 165. PMID:31000545
Greedy de novo motif discovery to construct motif repositories for bacterial proteomes. PMID:30999854
Brevibacterium from Austrian hard cheese harbor a putative histamine catabolism pathway and a plasmid for adaptation to the cheese environment. PMID:30992535
Cystic Fibrosis Rapid Response: Translating Multi-omics Data into Clinically Relevant Information. PMID:30992350
Genome Sequence of "Candidatus Rickettsia colombianensi," a Novel Tick-Associated Bacterium Distributed in Colombia. PMID:30948469
Characterization of agr Groups of Staphylococcus pseudintermedius Isolates from Dogs in Texas. PMID:30918056
Genotoxic Escherichia coli Strains Encoding Colibactin, Cytolethal Distending Toxin, and Cytotoxic Necrotizing Factor in Laboratory Rats. PMID:30902120
Genome-Wide Screening for Enteric Colonization Factors in Carbapenem-Resistant ST258 Klebsiella pneumoniae. PMID:30862751
Interpretable genotype-to-phenotype classifiers with performance guarantees. PMID:30858411
Genomic Analysis of Shewanella sp. O23S-The Natural Host of the pSheB Plasmid Carrying Genes for Arsenic Resistance and Dissimilatory Reduction. PMID:30813619
High contiguity genome sequence of a multidrug-resistant hospital isolate of Enterobacter hormaechei. PMID:30805030
Draft Genome Sequences of Four Metallo-Beta-Lactamase-Producing Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates, Including Two Colistin-Resistant Strains, from Cairo, Egypt. PMID:30801061
Draft genome sequence of Enterococcus faecium SP15, a potential probiotic strain isolated from spring water. PMID:30795795
Predictable Molecular Adaptation of Coevolving Enterococcus faecium and Lytic Phage EfV12-phi1. PMID:30766528
VraSR and Virulence Trait Modulation during Daptomycin Resistance in Methicillin-Resistant Staphylococcus aureus Infection. PMID:30760612
Extensive transmission of microbes along the gastrointestinal tract. PMID:30747106
Oxidative Pathways of Deoxyribose and Deoxyribonate Catabolism. PMID:30746495
Universal scaling across biochemical networks on Earth. PMID:30746442
Characterization of Hypermutator Pseudomonas aeruginosa Isolates from Patients with Cystic Fibrosis in Australia. PMID:30745381
Genomic prediction of tuberculosis drug-resistance: benchmarking existing databases and prediction algorithms. PMID:30736750
Separating host and microbiome contributions to drug pharmacokinetics and toxicity. PMID:30733391
Mining the Core Gut Microbiome from a Sample Indian Population. PMID:30728635
Bioinformatics Analysis of Metabolism Pathways of Archaeal Energy Reserves. PMID:30705313
Virulence Characteristics and an Action Mode of Antibiotic Resistance in Multidrug-Resistant Pseudomonas aeruginosa. PMID:30679735
OMeta: an ontology-based, data-driven metadata tracking system. PMID:30612540
Mycobacterium tuberculosis SatS is a chaperone for the SecA2 protein export pathway. PMID:30604681
Genotypic differences between strains of the opportunistic pathogen Corynebacterium bovis isolated from humans, cows, and rodents. PMID:30586440
The dilemma of bacterial expansins evolution. The unusual case of Streptomyces acidiscabies and Kutzneria sp. 744. PMID:30574264
Genomic characterization of Listeria monocytogenes isolates reveals that their persistence in a pig slaughterhouse is linked to the presence of benzalkonium chloride resistance genes. PMID:30572836
Polyphyly in 16S rRNA-based LVTree Versus Monophyly in Whole-genome-based CVTree. PMID:30550857
Characterization of Campylobacter jejuni, Campylobacter upsaliensis, and a novel Campylobacter sp. in a captive non-human primate zoological collection. PMID:30536921
Draft Genome Sequence of Aquitalea sp. Strain MWU14-2217, Isolated from a Wild Cranberry Bog in Provincetown, Massachusetts. PMID:30533844
Complete Genome Sequence of Bradyrhizobium ottawaense OO99T, an Efficient Nitrogen-Fixing Symbiont of Soybean. PMID:30533842
Draft Genome Sequence of Enterococcus faecium CL-6729, a Clinical Isolate Showing Constitutive Vancomycin Resistance. PMID:30533817
Genomic Alterations of Staphylococcus aureus ATCC 25923 after Prolonged Passage in the Laboratory. PMID:30533771
Draft Genome Sequence of Marine Bacillus sp. Strain ISO11, a Candidate Finfish and Shellfish Probiotic. PMID:30533731
Draft Genome Sequence of Pseudomonas sp. Strain MWU12-2534b, Isolated from a Wild Cranberry Bog in Truro, Massachusetts. PMID:30533697
Draft Genome Sequence of Pseudomonas sp. Strain MWU13-2860, Isolated from a Wild Cranberry Bog in Truro, Massachusetts. PMID:30533681
Draft Genome Sequences of Violacein-Producing Duganella sp. Isolates from a Waterway in Eastern Pennsylvania. PMID:30533678
Draft Genome Sequences of Pseudomonas MWU13-2625 and MWU12-2115, Isolated from a Wild Cranberry Bog at the Cape Cod National Seashore. PMID:30533670
Draft Genome Sequence of the Type Strain Streptomyces armeniacus ATCC 15676. PMID:30533638
GABA-modulating bacteria of the human gut microbiota. PMID:30531975
The afc antifungal activity cluster, which is under tight regulatory control of ShvR, is essential for transition from intracellular persistence of Burkholderia cenocepacia to acute pro-inflammatory infection. PMID:30513124
Comparative genomics analysis to differentiate metabolic and virulence gene potential in gastric versus enterohepatic Helicobacter species. PMID:30458713
Rapidly evolving changes and gene loss associated with host switching in Corynebacterium pseudotuberculosis. PMID:30419061
A fast and agnostic method for bacterial genome-wide association studies: Bridging the gap between k-mers and genetic events. PMID:30419019
Genome Structure of the Opportunistic Pathogen Paracoccus yeei (Alphaproteobacteria) and Identification of Putative Virulence Factors. PMID:30410477
VFDB 2019: a comparative pathogenomic platform with an interactive web interface. PMID:30395255
The extreme C terminus of the Pseudomonas aeruginosa effector ExoY is crucial for binding to its eukaryotic activator, F-actin. PMID:30377256
Victors: a web-based knowledge base of virulence factors in human and animal pathogens. PMID:30365026
Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes. PMID:30364992
Selecting lipopeptide-producing, Fusarium-suppressing Bacillus spp.: Metabolomic and genomic probing of Bacillus velezensis NWUMFkBS10.5. PMID:30358165
BacCapSeq: a Platform for Diagnosis and Characterization of Bacterial Infections. PMID:30352937
Determination of virulence and fitness genes associated with the pheU, pheV and selC integration sites of LEE-negative food-borne Shiga toxin-producing Escherichia coli strains. PMID:30337962
Using Machine Learning To Predict Antimicrobial MICs and Associated Genomic Features for Nontyphoidal Salmonella. PMID:30333126
Desiccation tolerance in Acinetobacter baumannii is mediated by the two-component response regulator BfmR. PMID:30308034
Environmentally-driven gene content convergence and the Bacillus phylogeny. PMID:30285626
MultiTwin: A Software Suite to Analyze Evolution at Multiple Levels of Organization Using Multipartite Graphs. PMID:30247672
Revisiting the Taxonomy of the Genus Arcobacter: Getting Order From the Chaos. PMID:30233547
Spfy: an integrated graph database for real-time prediction of bacterial phenotypes and downstream comparative analyses. PMID:30212910
Inferring Metabolic Mechanisms of Interaction within a Defined Gut Microbiota. PMID:30195437
Gut Microbiota and Clinical Features Distinguish Colonization With Klebsiella pneumoniae Carbapenemase-Producing Klebsiella pneumoniae at the Time of Admission to a Long-term Acute Care Hospital. PMID:30151415
Whole-genome sequencing and comparative analysis of two plant-associated strains of Rhodopseudomonas palustris (PS3 and YSC3). PMID:30143697
Deep genome annotation of the opportunistic human pathogen Streptococcus pneumoniae D39. PMID:30107613
Citrobacter freundii fitness during bloodstream infection. PMID:30087402
Bartonella rochalimae Detection by a Sensitive and Specific PCR Platform. PMID:30084343
MrpJ Directly Regulates Proteus mirabilis Virulence Factors, Including Fimbriae and Type VI Secretion, during Urinary Tract Infection. PMID:30082479
The Helicobacter pylori cell shape promoting protein Csd5 interacts with the cell wall, MurF, and the bacterial cytoskeleton. PMID:30039535
Genome-Guided Characterization of Ochrobactrum sp. POC9 Enhancing Sewage Sludge Utilization-Biotechnological Potential and Biosafety Considerations. PMID:30013002
The Stringent Response Determines the Ability of a Commensal Bacterium to Survive Starvation and to Persist in the Gut. PMID:30008292
Streptococcal inhibitor of complement (SIC) modulates fibrinolysis and enhances bacterial survival within fibrin clots. PMID:30002122
Understanding the Representative Gut Microbiota Dysbiosis in Metformin-Treated Type 2 Diabetes Patients Using Genome-Scale Metabolic Modeling. PMID:29988585
A pan-genome-based machine learning approach for predicting antimicrobial resistance activities of the Escherichia coli strains. PMID:29949970
Organic micropollutants paracetamol and ibuprofen-toxicity, biodegradation, and genetic background of their utilization by bacteria. PMID:29923050
Glucocorticoids Impair Phagocytosis and Inflammatory Response Against Crohn's Disease-Associated Adherent-Invasive Escherichia coli. PMID:29867993
A Polyphasic and Taxogenomic Evaluation Uncovers Arcobacter cryaerophilus as a Species Complex That Embraces Four Genomovars. PMID:29755434
Distribution Patterns of Polyphosphate Metabolism Pathway and Its Relationships With Bacterial Durability and Virulence. PMID:29755430
Searching whole genome sequences for biochemical identification features of emerging and reemerging pathogenic Corynebacterium species. PMID:29752561
Comparative Genomics Reveals the Regulatory Complexity of Bifidobacterial Arabinose and Arabino-Oligosaccharide Utilization. PMID:29740413
MetaCompare: a computational pipeline for prioritizing environmental resistome risk. PMID:29718191
Pulmonary Surfactant Promotes Virulence Gene Expression and Biofilm Formation in Klebsiella pneumoniae. PMID:29712730
Plasmids carrying DHA-1 β-lactamases. PMID:29663096
Draft Genomic Sequences of Chromobacterium sp. nov. Strains MWU13-2610 and MWU14-2602, Isolated from Wild Cranberry Bogs in Massachusetts. PMID:29650585
Two-Component Flavin-Dependent Riboflavin Monooxygenase Degrades Riboflavin in Devosia riboflavina. PMID:29610214
Plasmid-Mediated Quinolone Resistance in Shigella flexneri Isolated From Macaques. PMID:29556221
Complete Genome Sequence of Listeria monocytogenes Strain MR310, Isolated from a Pastured-Flock Poultry Farm System. PMID:29519846
A Metagenome-Wide Association Study and Arrayed Mutant Library Confirm Acetobacter Lipopolysaccharide Genes Are Necessary for Association with Drosophila melanogaster. PMID:29487183
New Aspects on Listeria monocytogenes ST5-ECVI Predominance in a Heavily Contaminated Cheese Processing Environment. PMID:29472901
Draft Genome Sequence of Bacillus sp. Strain UFRGS-B20, a Hydrocarbon Degrader. PMID:29472329
Pathogenesis of Proteus mirabilis Infection. PMID:29424333
Phylogeographic diversity and mosaicism of the Helicobacter pylori tfs integrative and conjugative elements. PMID:29416569
Complete Genome Sequence of a blaCTX-M-1-Harboring Escherichia coli Isolate Recovered from Cattle in Germany. PMID:29371351
Draft Genome Sequences of Phenotypically Distinct Janthinobacterium sp. Isolates Cultured from the Hudson Valley Watershed. PMID:29348334
Draft Genome Sequences of Two Vibrio parahaemolyticus Strains Associated with Gastroenteritis after Raw Seafood Ingestion in Colorado. PMID:29348331
Genomics of Corynebacterium striatum, an emerging multidrug-resistant pathogen of immunocompromised patients. PMID:29326010
Developing an in silico minimum inhibitory concentration panel test for Klebsiella pneumoniae. PMID:29323230
Deciphering the unexplored Leptospira diversity from soils uncovers genomic evolution to virulence. PMID:29310748
The regulon of the RNA chaperone CspA and its auto-regulation in Staphylococcus aureus. PMID:29309682
Draft Genome Sequence of a Red-Pigmented Janthinobacterium sp. Native to the Hudson Valley Watershed. PMID:29301893
Draft Genome Sequence of a Violacein-Producing Iodobacter sp. from the Hudson Valley Watershed. PMID:29301892
Daptomycin Resistance in Clinical MRSA Strains Is Associated with a High Biological Fitness Cost. PMID:29259579
Gene Graphics: a genomic neighborhood data visualization web application. PMID:29228171
Cytotoxic Escherichia coli strains encoding colibactin and cytotoxic necrotizing factor (CNF) colonize laboratory macaques. PMID:29225701
Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes. PMID:29183281
Mutations in Gene fusA1 as a Novel Mechanism of Aminoglycoside Resistance in Clinical Strains of Pseudomonas aeruginosa. PMID:29133559
Bacterial colonization stimulates a complex physiological response in the immature human intestinal epithelium. PMID:29110754
MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments. PMID:29106667
The MAR databases: development and implementation of databases specific for marine metagenomics. PMID:29106641
Insight of Genus Corynebacterium: Ascertaining the Role of Pathogenic and Non-pathogenic Species. PMID:29075239
MicroScope-an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data. PMID:28968784
PATRIC as a unique resource for studying antimicrobial resistance. PMID:28968762
Population Structure and Local Adaptation of MAC Lung Disease Agent Mycobacterium avium subsp. hominissuis. PMID:28957464
Real-Time PCR Targeting the penA Mosaic XXXIV Type for Prediction of Extended-Spectrum-Cephalosporin Susceptibility in Clinical Neisseria gonorrhoeae Isolates. PMID:28848021
Genome Sequence of an Australian Monophasic Salmonella enterica subsp. enterica Typhimurium Isolate (TW-Stm6) Carrying a Large Plasmid with Multiple Antimicrobial Resistance Genes. PMID:28818900
Whole-Genome Shotgun Sequences of Salmonella enterica Serovar Typhimurium Lilleengen Type Strains LT1, LT18, LT19, LT20, LT21, and LT22. PMID:28751402
The t6A modification acts as a positive determinant for the anticodon nuclease PrrC, and is distinctively nonessential in Streptococcus mutans. PMID:28726545
Whole-Genome Sequence Analysis of Antimicrobial Resistance Genes in Streptococcus uberis and Streptococcus dysgalactiae Isolates from Canadian Dairy Herds. PMID:28589129
MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data. PMID:28449106
Brucella spp. of amphibians comprise genomically diverse motile strains competent for replication in macrophages and survival in mammalian hosts. PMID:28300153
Genome Sequences of Two Brucella suis Strains Isolated from the Same Patient, 8 Years Apart. PMID:28254974
Genome Sequences of Three Brucella canis Strains Isolated from Humans and a Dog. PMID:28232424
The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities PubMed citations: 210.

210 articles citing: The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities

FastANI, Mash and Dashing equally differentiate between Klebsiella species. PMID:35891643
Actinospica acidithermotolerans sp. nov., a novel actinomycete isolated from sediment from an Indonesian hot spring. PMID:35871242
Non-random genetic alterations in the cyanobacterium Nostoc sp. exposed to space conditions. PMID:35869252
Genome Analysis of Enterobacter asburiae and Lelliottia spp. Proliferating in Oligotrophic Drinking Water Reservoirs and Lakes. PMID:35862664
Sala cibi gen. nov., sp. nov., an extremely halophilic archaeon isolated from solar salt. PMID:35835956
Identification of the new prenyltransferase Ubi-297 from marine bacteria and elucidation of its substrate specificity. PMID:35821696
Discovery of archaeal fusexins homologous to eukaryotic HAP2/GCS1 gamete fusion proteins. PMID:35794124
Genomic insights of beta-lactamase producing Klebsiella quasipneumoniae subsp. similipneumoniae belonging to sequence type 1699 from retail market fish, India. PMID:35781844
A convolutional neural network highlights mutations relevant to antimicrobial resistance in Mycobacterium tuberculosis. PMID:35780211
Draft Genome Sequence of Serratia marcescens SSA1, Isolated from Dioxin-Polluted Soil. PMID:35758755
Spontaneous Riboflavin-Overproducing Limosilactobacillus reuteri for Biofortification of Fermented Foods. PMID:35757245
Predicting the pathogenicity of bacterial genomes using widely spread protein families. PMID:35751023
Genomic Analysis Reveals That Isolation Temperature on Selective Media Introduces Genetic Variation in Campylobacter jejuni from Bovine Feces. PMID:35745532
Genomic and Biological Profile of a Novel Bacteriophage, Vibrio phage Virtus, Which Improves Survival of Sparus aurata Larvae Challenged with Vibrio harveyi. PMID:35745484
Complete Genome Sequence of Klebsiella quasipneumoniae subsp. similipneumoniae Strain IF3SW-P1, Isolated from the International Space Station. PMID:35735981
Draft Genome Sequences of Erysipelothrix sp. Strains Isolated from Stranded Septic Bottlenose Dolphins in Alabama, USA. PMID:35730954
SeqScreen: accurate and sensitive functional screening of pathogenic sequences via ensemble learning. PMID:35725628
Genome-scale metabolic modelling enables deciphering ethanol metabolism via the acrylate pathway in the propionate-producer Anaerotignum neopropionicum. PMID:35710409
Mining therapeutic targets from the antibiotic-resistant Campylobacter coli and virtual screening of natural product inhibitors against its riboflavin synthase. PMID:35699868
Multilocus Sequence Typing and Virulence Potential of Vibrio parahaemolyticus Strains Isolated from Aquatic Bird Feces. PMID:35695558
Hymenobacter cyanobacteriorum sp. nov., isolated from a freshwater reservoir during the cyanobacterial bloom period. PMID:35668215
Isolation and Whole-Genome Sequencing of Four Antibiotic-Producing Pseudomonas Strains. PMID:35658559
Evolutionarily stable gene clusters shed light on the common grounds of pathogenicity in the Acinetobacter calcoaceticus-baumannii complex. PMID:35653398
5NosoAE: a web server for nosocomial bacterial antibiogram investigation and epidemiology survey. PMID:35639518
Diversity of the culturable lichen-derived actinobacteria and the taxonomy of Streptomyces parmotrematis sp. nov. PMID:35637321
The Notable Achievements and the Prospects of Bacterial Pathogen Genomics. PMID:35630482
Unusual Lipid Components of Legionella gormanii Membranes. PMID:35629922
PhyloM: A Computer Program for Phylogenetic Inference from Measurement or Binary Data, with Bootstrapping. PMID:35629386
Biomarker Characterization and Prediction of Virulence and Antibiotic Resistance from Helicobacter pylori Next Generation Sequencing Data. PMID:35625618
Antimicrobial Resistance and Comparative Genomic Analysis of Elizabethkingia anophelis subsp. endophytica Isolated from Raw Milk. PMID:35625292
Genomic Analysis of Multidrug-Resistant Hypervirulent (Hypermucoviscous) Klebsiella pneumoniae Strain Lacking the Hypermucoviscous Regulators (rmpA/rmpA2). PMID:35625240
Immunosuppression broadens evolutionary pathways to drug resistance and treatment failure during Acinetobacter baumannii pneumonia in mice. PMID:35618774
Dynamic character displacement among a pair of bacterial phyllosphere commensals in situ. PMID:35595740
Genomic, morphological, and biochemical analyses of a multi-metal resistant but multi-drug susceptible strain of Bordetella petrii from hospital soil. PMID:35589928
Streptomyces sp. AC04842: Genomic Insights and Functional Expression of Its Latex Clearing Protein Genes (lcp1 and lcp2) When Cultivated With Natural and Vulcanized Rubber as the Sole Carbon Source. PMID:35586859
A compilation of fecal microbiome shotgun metagenomics from hematopoietic cell transplantation patients. PMID:35585088
AMR-meta: a k-mer and metafeature approach to classify antimicrobial resistance from high-throughput short-read metagenomics data. PMID:35583675
Insights from the comparative genome analysis of natural rubber degrading Nocardia species. PMID:35574501
Whole genome sequencing of cyanobacterium Nostoc sp. CCCryo 231-06 using microfluidic single cell technology. PMID:35573199
Ferric Citrate Uptake Is a Virulence Factor in Uropathogenic Escherichia coli. PMID:35546538
Black Soldier Fly Larvae Influence Internal and Substrate Bacterial Community Composition Depending on Substrate Type and Larval Density. PMID:35532232
Draft Genome Sequence of Nereida sp. Strain MMG025, Isolated from Giant Kelp. PMID:35532230
Evolutionary Genome Mining for the Discovery and Engineering of Natural Product Biosynthesis. PMID:35524049
Streptococcus oriscaviae sp. nov. Infection Associated with Guinea Pigs. PMID:35510851
Analysis of host-pathogen gene association networks reveals patient-specific response to streptococcal and polymicrobial necrotising soft tissue infections. PMID:35505341
Panacibacter microcysteis sp. nov., isolated from a eutrophic reservoir during the Microcystis bloom period. PMID:35503579
Genomic Characterization of a Uropathogenic Escherichia coli ST405 Isolate Harboring bla CTX-M-15-Encoding IncFIA-FIB Plasmid, bla CTX-M-24-Encoding IncI1 Plasmid, and Phage-Like Plasmid. PMID:35479623
Probe design for simultaneous, targeted capture of diverse metagenomic targets. PMID:35474894
DEPhT: a novel approach for efficient prophage discovery and precise extraction. PMID:35451479
Imipenem/Relebactam Resistance in Clinical Isolates of Extensively Drug Resistant Pseudomonas aeruginosa: Inhibitor-Resistant β-Lactamases and Their Increasing Importance. PMID:35435707
Enhancing predictions of antimicrobial resistance of pathogens by expanding the potential resistance gene repertoire using a pan-genome-based feature selection approach. PMID:35428201
Zooplankton as a Transitional Host for Escherichia coli in Freshwater. PMID:35416683
Genome Sequences for Levilactobacillus brevis Autochthonous to Commercial Cucumber Fermentations. PMID:35412360
Sensing the Messenger: Potential Roles of Cyclic-di-GMP in Rickettsial Pathogenesis. PMID:35409212
A Phage Foundry Framework to Systematically Develop Viral Countermeasures to Combat Antibiotic-Resistant Bacterial Pathogens. PMID:35402883
Contribution of genome-scale metabolic modelling to niche theory. PMID:35384214
PlasmidHostFinder: Prediction of Plasmid Hosts Using Random Forest. PMID:35382558
Glby, Encoded by MAB_3167c, Is Required for In Vivo Growth of Mycobacteroides abscessus and Exhibits Mild β-Lactamase Activity. PMID:35380462
Draft genome sequence data of Gordonia hongkongensis strain EUFUS-Z928 isolated from the octocoral Eunicea fusca. PMID:35372653
Horizontal Gene Transfer of Fluoroquinolone Resistance-Conferring Genes From Commensal Neisseria to Neisseria gonorrhoeae: A Global Phylogenetic Analysis of 20,047 Isolates. PMID:35369513
Growth promotion and antibiotic induced metabolic shifts in the chicken gut microbiome. PMID:35365748
Characterization of Escherichia coli harboring colibactin genes (clb) isolated from beef production and processing systems. PMID:35351927
Unamplified, Long-Read Metagenomic Sequencing Approach to Close Endosymbiont Genomes of Low-Biomass Insect Populations. PMID:35336091
Escherichia coli and Pseudomonas aeruginosa Isolated From Urine of Healthy Bovine Have Potential as Emerging Human and Bovine Pathogens. PMID:35330764
An In Vivo Model of Separate M. tuberculosis Phagocytosis by Neutrophils and Macrophages: Gene Expression Profiles in the Parasite and Disease Development in the Mouse Host. PMID:35328388
Screening Repurposed Antiviral Small Molecules as Antimycobacterial Compounds by a Lux-Based phoP Promoter-Reporter Platform. PMID:35326832
Review and Comparison of Antimicrobial Resistance Gene Databases. PMID:35326803
Computational Tools for the Analysis of Uncultivated Phage Genomes. PMID:35311574
First-line drug resistance profiling of Mycobacterium tuberculosis: a machine learning approach. PMID:35309001
Regulator of Actin-Based Motility (RoaM) Downregulates Actin Tail Formation by Rickettsia rickettsii and Is Negatively Selected in Mammalian Cell Culture. PMID:35285700
A Comparative Genomic and Safety Assessment of Six Lactiplantibacillus plantarum subsp. argentoratensis Strains Isolated from Spontaneously Fermented Greek Wheat Sourdoughs for Potential Biotechnological Application. PMID:35269627
Acids produced by lactobacilli inhibit the growth of commensal Lachnospiraceae and S24-7 bacteria. PMID:35266847
Case Report: Vibrio fluvialis isolated from a wound infection after a piercing trauma in the Baltic Sea. PMID:35252751
Changes of Intestinal Microflora in Colorectal Cancer Patients after Surgical Resection and Chemotherapy. PMID:35251295
Draft genome sequence of Psychrobacter nivimaris LAMA 639 and its biotechnological potential. PMID:35242911
Draft Genome Sequences of Buttiauxella spp. Isolates from Water and Gastropods with Putative β-d-Glucuronidase Activity. PMID:35234507
Towards routine employment of computational tools for antimicrobial resistance determination via high-throughput sequencing. PMID:35212354
Shallow-Water Hydrothermal Vents as Natural Accelerators of Bacterial Antibiotic Resistance in Marine Coastal Areas. PMID:35208933
Wolbachia in Aedes koreicus: Rare Detections and Possible Implications. PMID:35206789
Diversity of Pseudomonas aeruginosa Temperate Phages. PMID:35196122
Evidence of episodic positive selection in Corynebacterium diphtheriae complex of species and its implementations in identification of drug and vaccine targets. PMID:35190783
Glucosyltransferase-dependent and independent effects of Clostridioides difficile toxins during infection. PMID:35176123
Detection of SARS-CoV-2 Omicron variant (B.1.1.529) infection of white-tailed deer. PMID:35169802
Bacteroides thetaiotaomicron uses a widespread extracellular DNase to promote bile-dependent biofilm formation. PMID:35145026
Hospital sink traps as a potential source of the emerging multidrug-resistant pathogen Cupriavidus pauculus: characterization and draft genome sequence of strain MF1. PMID:35113779
Draft Genome Sequence of Oceanobacillus jordanicus Strain GSFE11, a Halotolerant Plant Growth-Promoting Bacterial Endophyte Isolated From the Jordan Valley. PMID:35095268
Turicibacter bilis sp. nov., a novel bacterium isolated from the chicken eggshell and swine ileum. PMID:35084297
Phage Annotation Guide: Guidelines for Assembly and High-Quality Annotation. PMID:35083439
Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer. PMID:35078920
Experimental Confirmation that an Uncommon rrs Gene Mutation (g878a) of Mycobacterium tuberculosis Confers Resistance to Streptomycin. PMID:35072512
Genome Sequences of Soft Rot-Causing Pectobacterium Isolates from Different Vegetables. PMID:35049346
Mining for novel cyclomaltodextrin glucanotransferases unravels the carbohydrate metabolism pathway via cyclodextrins in Thermoanaerobacterales. PMID:35031648
Unique mobile elements and scalable gene flow at the prokaryote-eukaryote boundary revealed by circularized Asgard archaea genomes. PMID:35027677
Draft Whole-Genome Sequences of Two Multidrug-Resistant Salmonella enterica Serovar Senftenberg Sequence Type 14 Strains Resistant to Ciprofloxacin, Ceftriaxone, and/or Azithromycin, Isolated from Kolkata, India. PMID:35023782
Differences in the Accessory Genomes and Methylomes of Strains of Streptococcus equi subsp. equi and of Streptococcus equi subsp. zooepidemicus Obtained from the Respiratory Tract of Horses from Texas. PMID:35019696
Analysis of the Genome of the Heavy Metal Resistant and Hydrocarbon-Degrading Rhizospheric Pseudomonas qingdaonensis ZCR6 Strain and Assessment of Its Plant-Growth-Promoting Traits. PMID:35008639
Acquisition of the arginine deiminase system benefits epiparasitic Saccharibacteria and their host bacteria in a mammalian niche environment. PMID:34992141
Myxopyronin B inhibits growth of a Fidaxomicin-resistant Clostridioides difficile isolate and interferes with toxin synthesis. PMID:34991700
Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reveals personalized growth rates. PMID:34987055
Development of a Genomics-Based Approach To Identify Putative Hypervirulent Nontyphoidal Salmonella Isolates: Salmonella enterica Serovar Saintpaul as a Model. PMID:34986312
Comparative pangenomics: analysis of 12 microbial pathogen pangenomes reveals conserved global structures of genetic and functional diversity. PMID:34983386
Transcriptomic analysis of Streptococcus agalactiae periprosthetic joint infection. PMID:34964296
Chronic pancreatitis in a caerulein-induced mouse model is associated with an altered gut microbiome. PMID:34949545
Hybrid Assembly Provides Improved Resolution of Plasmids, Antimicrobial Resistance Genes, and Virulence Factors in Escherichia coli and Klebsiella pneumoniae Clinical Isolates. PMID:34946161
Genome-Based Characterization of a Plasmid-Associated Micrococcin P1 Biosynthetic Gene Cluster and Virulence Factors in Mammaliicoccus sciuri IMDO-S72. PMID:34936836
Plant-growth-promoting Caulobacter strains isolated from distinct plant hosts share conserved genetic factors involved in beneficial plant-bacteria interactions. PMID:34932160
Structural systems pharmacology: A framework for integrating metabolic network and structure-based virtual screening for drug discovery against bacteria. PMID:34905555
Loss of an Intimin-Like Protein Encoded on a Uropathogenic E. coli Pathogenicity Island Reduces Inflammation and Affects Interactions with the Urothelium. PMID:34871042
Acinetobacter baumannii Regulates Its Stress Responses via the BfmRS Two-Component Regulatory System. PMID:34871031
Looking through the FOG: microbiome characterization and lipolytic bacteria isolation from a fatberg site. PMID:34870579
Host life-history traits influence the distribution of prophages and the genes they carry. PMID:34839698
Genomic Analysis of Prophages from Klebsiella pneumoniae Clinical Isolates. PMID:34835377
Complete genome sequence of Lactobacillus amylovorus 1394N20, a potential probiotic strain, isolated from a Hanwoo calf. PMID:34796359
A comparative study of pan-genome methods for microbial organisms: Acinetobacter baumannii pan-genome reveals structural variation in antimicrobial resistance-carrying plasmids. PMID:34761737
Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences. PMID:34752446
BacDive in 2022: the knowledge base for standardized bacterial and archaeal data. PMID:34718743
Whole-Genome Sequencing and Annotation of Selected Lactobacillales Isolated from Commercial Cucumber Fermentation. PMID:34709055
Rubber Degrading Strains: Microtetraspora and Dactylosporangium. PMID:34685283
Complete Genome Sequence of Myxococcus Phage Mx4. PMID:34672703
Molecular signatures of Janthinobacterium lividum from Trinidad support high potential for crude oil metabolism. PMID:34670489
Comparative Genomics of Mycobacterium avium Complex Reveals Signatures of Environment-Specific Adaptation and Community Acquisition. PMID:34665012
Genome analysis of alginate synthesizing Pseudomonas aeruginosa strain SW1 isolated from degraded seaweeds. PMID:34661815
Draft Genome Sequence of NDM-Encoding Klebsiella pneumoniae Isolated from Feral Swine. PMID:34647798
In vivo commensal control of Clostridioides difficile virulence. PMID:34637781
Genome-Resolved Meta-Analysis of the Microbiome in Oil Reservoirs Worldwide. PMID:34576708
Colistin and Carbapenem-Resistant Acinetobacter baumannii Aci46 in Thailand: Genome Analysis and Antibiotic Resistance Profiling. PMID:34572636
Comparative Efficacy of the Novel Diarylquinoline TBAJ-876 and Bedaquiline against a Resistant Rv0678 Mutant in a Mouse Model of Tuberculosis. PMID:34570644
Draft genome sequence of a prodigiosin-hyperproducing Serratia marcescens strain isolated from Cairo, Egypt. PMID:34568929
Draft Genome Sequences of Three Shewanella sp. Strains Isolated from Urban Freshwaters in the Ohio River Valley, USA. PMID:34528821
Characterization and engineering of Streptomyces griseofuscus DSM 40191 as a potential host for heterologous expression of biosynthetic gene clusters. PMID:34526549
Genome-resolved metagenome and metatranscriptome analyses of thermophilic composting reveal key bacterial players and their metabolic interactions. PMID:34507539
Accelerating antibiotic discovery through artificial intelligence. PMID:34504303
Draft Genome Sequence of Salegentibacter sp. Strain BDJ18, a Plankton-Associated Bacterium in the Northeast Atlantic Ocean. PMID:34498925
Nitric Oxide Inhibition of Rickettsia rickettsii. PMID:34491789
Transcriptomics reveal different metabolic strategies for acid resistance and gamma-aminobutyric acid (GABA) production in select Levilactobacillus brevis strains. PMID:34488774
A Common Pathway for Activation of Host-Targeting and Bacteria-Targeting Toxins in Human Intestinal Bacteria. PMID:34465018
KARGA: Multi-platform Toolkit for k-mer-based Antibiotic Resistance Gene Analysis of High-throughput Sequencing Data. PMID:34447942
Virulence Pattern Analysis of Three Listeria monocytogenes Lineage I Epidemic Strains with Distinct Outbreak Histories. PMID:34442824
Isolation, Phylogenetic and Gephyromycin Metabolites Characterization of New Exopolysaccharides-Bearing Antarctic Actinobacterium from Feces of Emperor Penguin. PMID:34436297
Draft Genome Sequence and Annotation of the Synthetic Textile Dye-Decolorizing Strain Bacillus amyloliquefaciens AD20, Isolated from a Dye Waste Pond. PMID:34435869
Core Genome Multilocus Sequence Typing and Prediction of Antimicrobial Susceptibility Using Whole-Genome Sequences of Escherichia coli Bloodstream Infection Isolates. PMID:34424049
Bacterial translation machinery for deliberate mistranslation of the genetic code. PMID:34413202
Draft Genome Sequences of 10 Bacteria from the Marine Pseudoalteromonas Group. PMID:34382833
Draft Genome Sequences of Enterobacter spp., Lelliottia spp., and Serratia spp., Coliform Bacteria from Drinking Water Reservoirs and Lakes. PMID:34382825
Novel PhoH-encoding vibriophages with lytic activity against environmental Vibrio strains. PMID:34379161
A genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes. PMID:34379107
Draft Genome Sequences of Two Bacteria from the Roseobacter Group. PMID:34323605
Draft Genome Sequences of the Three Massilia Strains AB1, ST3, and ZL223. PMID:34323604
Genome-wide gene expression tuning reveals diverse vulnerabilities of M. tuberculosis. PMID:34297925
Identification and Characterization of Mycobacterial Species Using Whole-Genome Sequences. PMID:34235665
Whole genome sequence data of Bacillus australimaris strain B28A, isolated from Marine Water in India. PMID:34235237
Parabacteroides distasonis: intriguing aerotolerant gut anaerobe with emerging antimicrobial resistance and pathogenic and probiotic roles in human health. PMID:34196581
Curating and comparing 114 strain-specific genome-scale metabolic models of Staphylococcus aureus. PMID:34188046
Shared and Unique Evolutionary Trajectories to Ciprofloxacin Resistance in Gram-Negative Bacterial Pathogens. PMID:34154405
High-quality draft genome sequence data of six Lactiplantibacillus plantarum subsp. argentoratensis strains isolated from various Greek wheat sourdoughs. PMID:34150961
Predicting Antimicrobial Resistance Using Partial Genome Alignments. PMID:34128695
Differences in the genome, methylome, and transcriptome do not differentiate isolates of Streptococcus equi subsp. equi from horses with acute clinical signs from isolates of inapparent carriers. PMID:34125848
Analysis of genomes of bacterial isolates from lameness outbreaks in broilers. PMID:34077848
Complete Genome Sequence of the Plant-Growth-Promoting Bacterium Caulobacter segnis CBR1. PMID:34047832
A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at pathogenwatch. PMID:34001879
Regional Spread of blaNDM-1-Containing Klebsiella pneumoniae ST147 in Post-Acute Care Facilities. PMID:33999991
Draft Genome Sequences of Four Bacterial Strains of Heterotrophic Alteromonas macleodii and Marinobacter, Isolated from a Nonaxenic Culture of Two Marine Synechococcus Strains. PMID:33986074
Effect of Gut Microbiota Biotransformation on Dietary Tannins and Human Health Implications. PMID:33947064
Comparative Pathogenomics of Escherichia coli: Polyvalent Vaccine Target Identification through Virulome Analysis. PMID:33941580
A plasmid locus associated with Klebsiella clinical infections encodes a microbiome-dependent gut fitness factor. PMID:33930099
Metagenome-Assembled Genome Sequences of Novel Prokaryotic Species from the Mercury-Contaminated East Fork Poplar Creek, Oak Ridge, Tennessee, USA. PMID:33927032
Unraveling the Metabolic Potential of Asgardarchaeota in a Sediment from the Mediterranean Hydrocarbon-Contaminated Water Basin Mar Piccolo (Taranto, Italy). PMID:33923677
Luminescent Phage-Based Detection of Klebsiella pneumoniae: From Engineering to Diagnostics. PMID:33918942
Genetic analysis of electroactive biofilms. PMID:33907940
Antiviral Resistance and Phage Counter Adaptation to Antibiotic-Resistant Extraintestinal Pathogenic Escherichia coli. PMID:33906920
Supervised extraction of near-complete genomes from metagenomic samples: A new service in PATRIC. PMID:33857229
Characterization of the first vaginal Lactobacillus crispatus genomes isolated in Brazil. PMID:33854845
Computational characterizations of GDP-mannose 4,6-dehydratase (NoeL) Rhizobial proteins. PMID:33837815
Molecular Analysis of Polymyxin Resistance among Carbapenemase-Producing Klebsiella pneumoniae in Colombia. PMID:33801833
The Prophage and Plasmid Mobilome as a Likely Driver of Mycobacterium abscessus Diversity. PMID:33785627
Emergence of Resistance to Ceftazidime-Avibactam in a Pseudomonas aeruginosa Isolate Producing Derepressed bla PDC in a Hollow-Fiber Infection Model. PMID:33782013
A Large-Scale Sequencing-Based Survey of Plasmids in Listeria monocytogenes Reveals Global Dissemination of Plasmids. PMID:33776982
Draft Genome Sequences of Blastococcus sp. Clones TML/M2B and TML/C7B, with Different Motilities, Isolated in a Laboratory. PMID:33766900
Sequence Analysis of 20,453 Severe Acute Respiratory Syndrome Coronavirus 2 Genomes from the Houston Metropolitan Area Identifies the Emergence and Widespread Distribution of Multiple Isolates of All Major Variants of Concern. PMID:33741335
MultiPhATE2: code for functional annotation and comparison of phage genomes. PMID:33734357
Description and genomic insights into a multidrug resistant novel bacterium Savagea serpentis sp. nov., isolated from the scats of a vine snake (Ahaetulla nasuta). PMID:33715106
Dihydrouridine synthesis in tRNAs is under reductive evolution in Mollicutes. PMID:33685366
Safety Assessment of Bacillus subtilis MB40 for Use in Foods and Dietary Supplements. PMID:33668992
Whole Genome Sequence Analysis of Phage-Resistant Listeria monocytogenes Serotype 1/2a Strains from Turkey Processing Plants. PMID:33668492
Paenibacillus glycinis sp. nov., an Endophytic Bacterium Isolated from the Nodules of Soybean (Glycine max (L.) Merr). PMID:33666748
Validation strategy of a bioinformatics whole genome sequencing workflow for Shiga toxin-producing Escherichia coli using a reference collection extensively characterized with conventional methods. PMID:33656437
Genome-Driven Discovery of Enzymes with Industrial Implications from the Genus Aneurinibacillus. PMID:33652876
Genome announcement of Steinernema khuongi and its associated symbiont from Florida. PMID:33624756
Carbohydrates great and small, from dietary fiber to sialic acids: How glycans influence the gut microbiome and affect human health. PMID:33615984
Genomic Investigation of Virulence Potential in Shiga Toxin Escherichia coli (STEC) Strains From a Semi-Hard Raw Milk Cheese. PMID:33597935
Genomic and Phenotypic Characterization of Campylobacter fetus subsp. venerealis Strains. PMID:33572216
Vagococcus fluvialis isolation and sequencing from urine of healthy cattle. PMID:33561240
Exploring Prediction of Antimicrobial Resistance Based on Protein Solvent Accessibility Variation. PMID:33552147
Metabolic Versatility of Mycobacterium tuberculosis during Infection and Dormancy. PMID:33540752
Taxonomic Evaluation of the Heyndrickxia (Basonym Bacillus) sporothermodurans Group (H. sporothermodurans, H. vini, H. oleronia) Based on Whole Genome Sequences. PMID:33530338
The genomic characterisation and comparison of Bacillus cereus strains isolated from indoor air. PMID:33516253
Systematic Analysis of the Stress-Induced Genomic Instability of Type Three Secretion System in Aeromonas salmonicida subsp. salmonicida. PMID:33396556
Characterization of the Biodiesel Degrading Acinetobacter oleivorans Strain PT8 Isolated from the Fecal Material of a Painted Turtle (Chrysemys picta). PMID:33392672
Oral Microbiome Signatures in Hematological Cancers Reveal Predominance of Actinomyces and Rothia Species. PMID:33348567
Elucidating Essential Genes in Plant-Associated Pseudomonas protegens Pf-5 Using Transposon Insertion Sequencing. PMID:33257523
Amino Acid k-mer Feature Extraction for Quantitative Antimicrobial Resistance (AMR) Prediction by Machine Learning and Model Interpretation for Biological Insights. PMID:33126516
Whole-Genome Sequence of Aeromonas hydrophila CVM861 Isolated from Diarrhetic Neonatal Swine. PMID:33114362
Two Nearly Complete Nosocomial Pathogen Genome Sequences Reconstructed from Early-Middle 20th-Century Dental Calculus. PMID:33093055
Genomic Characterization of Methicillin-Resistant Staphylococcus aureus (MRSA) by High-Throughput Sequencing in a Tertiary Care Hospital. PMID:33080885
Predicting antimicrobial resistance using conserved genes. PMID:33075053
Searching for putative virulence factors in the genomes of Shewanella indica and Shewanella algae. PMID:33040180
Reconstructing organisms in silico: genome-scale models and their emerging applications. PMID:32958892
Comprehensive genome analysis and comparisons of the swine pathogen, Chlamydia suis reveals unique ORFs and candidate host-specificity factors. PMID:32639528
Novel Target Exploration from Hypothetical Proteins of Klebsiella pneumoniae MGH 78578 Reveals a Protein Involved in Host-Pathogen Interaction. PMID:32318354
The 27th annual Nucleic Acids Research database issue and molecular biology database collection. PMID:31906604

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genome
metasource: Fairsharing.org
version: FAIRsharing.org: PATRIC; PathosSystems Resource Integration Center Repository; DOI: https://doi.org/10.25504/FAIRsharing.oaLCAI; Last edited: July 31, 2020, 2:04 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

genome annotation
metasource: Fairsharing.org
version: FAIRsharing.org: PATRIC; PathosSystems Resource Integration Center Repository; DOI: https://doi.org/10.25504/FAIRsharing.oaLCAI; Last edited: July 31, 2020, 2:04 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

pathogen
metasource: Fairsharing.org
version: FAIRsharing.org: PATRIC; PathosSystems Resource Integration Center Repository; DOI: https://doi.org/10.25504/FAIRsharing.oaLCAI; Last edited: July 31, 2020, 2:04 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

bacteria
metasource: re3data.org
version: re3data.org: PATRIC; editing status 2017-12-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R35W56 last accessed: 2022-11-04

bacterial species
metasource: re3data.org
version: re3data.org: PATRIC; editing status 2017-12-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R35W56 last accessed: 2022-11-04

bioinformatics
metasource: re3data.org
version: re3data.org: PATRIC; editing status 2017-12-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R35W56 last accessed: 2022-11-04

biology
metasource: re3data.org
version: re3data.org: PATRIC; editing status 2017-12-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R35W56 last accessed: 2022-11-04

genomes
metasource: re3data.org
version: re3data.org: PATRIC; editing status 2017-12-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R35W56 last accessed: 2022-11-04

genomics
metasource: re3data.org
version: re3data.org: PATRIC; editing status 2017-12-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R35W56 last accessed: 2022-11-04

infectious disease
metasource: re3data.org
version: re3data.org: PATRIC; editing status 2017-12-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R35W56 last accessed: 2022-11-04

procaryotics
metasource: re3data.org
version: re3data.org: PATRIC; editing status 2017-12-06; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R35W56 last accessed: 2022-11-04

genome genome annotation pathogen bacteria bacterial species bioinformatics genomes genomics infectious disease procaryotics

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