RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

Brettin, Thomas; Davis, James J.; Disz, Terry; Edwards, Robert A.; Gerdes, Svetlana; Olsen, Gary J.; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D.; Shukla, Maulik; Thomason, III, James A.; Stevens, Rick; Vonstein, Veronika; Wattam, Alice R.; Xia, Fangfang

doi:10.1038/srep08365

Title: RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

Journal Article · Tue Feb 10 00:00:00 EST 2015 · Scientific Reports

DOI:https://doi.org/10.1038/srep08365· OSTI ID:1194128

Brettin, Thomas ^[1]; Davis, James J. ^[1]; Disz, Terry ^[2]; Edwards, Robert A. ^[3]; Gerdes, Svetlana ^[4]; Olsen, Gary J. ^[5]; Olson, Robert ^[6]; Overbeek, Ross ^[4]; Parrello, Bruce ^[4]; Pusch, Gordon D. ^[4]; Shukla, Maulik ^[7]; Thomason, III, James A. ^[8]; Stevens, Rick ^[1]; Vonstein, Veronika ^[4]; Wattam, Alice R. ^[7]; Xia, Fangfang ^[6]

Argonne National Lab. (ANL), Argonne, IL (United States); Univ. of Chicago, Chicago, IL (United States)
Fellowship for Interpretation of Genomes, Burr Ridge, IL (United States)
Argonne National Lab. (ANL), Argonne, IL (United States); San Diego State Univ., San Diego, CA (United States)
Argonne National Lab. (ANL), Argonne, IL (United States); Fellowship for Interpretation of Genomes, Burr Ridge, IL (United States)
University of Illinois at Urbana-Champaign, Urbana, IL (US)
Univ. of Chicago, Chicago, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States)
Virginia Tech Univ., Blacksburg, VA (United States)
USDA-ARS Lab. at Cold Spring Harbor Lab., NY (United States)

The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1194128

Journal Information:: Scientific Reports, Vol. 5, Issue 1; ISSN 2045-2322

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 1279 works

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A novel prophage identified in strains from Salmonella enterica serovar Enteritidis is a phylogenetic signature of the lineage ST-1974 D'Alessandro, Bruno; Pérez Escanda, Victoria; Balestrazzi, Lucía Microbial Genomics, Vol. 4, Issue 3 https://doi.org/10.1099/mgen.0.000161	journal	March 2018
Complete genome of Enterobacter sichuanensis strain SGAir0282 isolated from air in Singapore Uchida, Akira; Kim, Hie Lim; Purbojati, Rikky W. Gut Pathogens, Vol. 12, Issue 1 https://doi.org/10.1186/s13099-020-00350-z	journal	February 2020
Molecular characterisation of the NDM-1-encoding plasmid p2189-NDM in an Escherichia coli ST410 clinical isolate from Ghana Ayibieke, Alafate; Sato, Wakana; Mahazu, Samiratu PLOS ONE, Vol. 13, Issue 12 https://doi.org/10.1371/journal.pone.0209623	journal	December 2018
Paenibacillus ottowii sp. nov. isolated from a fermentation system processing bovine manure Velazquez, Luis F.; Rajbanshi, Shashi; Guan, Shaohua International Journal of Systematic and Evolutionary Microbiology, Vol. 70, Issue 3 https://doi.org/10.1099/ijsem.0.003672	journal	March 2020
Complete Genome Sequence of Acinetobacter indicus Type Strain SGAir0564 Isolated from Tropical Air Collected in Singapore Vettath, Vineeth Kodengil; Junqueira, Ana Carolina M.; Uchida, Akira Genome Announcements, Vol. 6, Issue 18 https://doi.org/10.1128/genomea.00230-18	journal	May 2018
Draft Genome Sequence of Sideroxydans sp. Strain CL21, an Fe(II)-Oxidizing Bacterium Cooper, Rebecca E.; Wegner, Carl-Eric; McAllister, Sean M. Microbiology Resource Announcements, Vol. 9, Issue 2 https://doi.org/10.1128/mra.01444-19	journal	January 2020
Complete Genome Sequence of Leuconostoc kimchii Strain NKJ218, Isolated from Homemade Kimchi Jung, Ji Young; Jeong, Jin-Woo; Lee, Seung-Young Microbiology Resource Announcements, Vol. 8, Issue 27 https://doi.org/10.1128/mra.00367-19	journal	July 2019
Draft Whole-Genome Sequences of Haemophilus influenzae Biogroup aegyptius Strains Isolated from Five Brazilian Purpuric Fever Cases and One Conjunctivitis Case Pereira, Rafaella F. C.; Mofatto, Luciana S.; Silva, Ana C. A. Microbiology Resource Announcements, Vol. 8, Issue 30 https://doi.org/10.1128/mra.00642-19	journal	July 2019
Genomic insights on heterogeneous resistance to vancomycin and teicoplanin in Methicillin-resistant Staphylococcus aureus: A first report from South India Bakthavatchalam, Yamuna Devi; Babu, Priyanka; Munusamy, Elakkiya PLOS ONE, Vol. 14, Issue 12 https://doi.org/10.1371/journal.pone.0227009	journal	December 2019
Biochemical and genetic characterization of a novel metallo-β-lactamase from marine bacterium Erythrobacter litoralis HTCC 2594 Jiang, Xia-Wei; Cheng, Hong; Huo, Ying-Yi Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-19279-0	journal	January 2018
Molecular characterization of carbapenem-resistant Klebsiella pneumoniae isolates with focus on antimicrobial resistance Yu, Xiaoling; Zhang, Wen; Zhao, Zhiping BMC Genomics, Vol. 20, Issue 1 https://doi.org/10.1186/s12864-019-6225-9	journal	November 2019
Complete Genome Sequence of Microbacterium sp. Strain SGAir0570, Isolated from Tropical Air Collected in Singapore Kalsi, Namrata; Drautz-Moses, Daniela I.; Uchida, Akira Microbiology Resource Announcements, Vol. 8, Issue 34 https://doi.org/10.1128/mra.00613-19	journal	August 2019
SMRT sequencing of the Campylobacter coli BfR-CA-9557 genome sequence reveals unique methylation motifs Zautner, Andreas E.; Goldschmidt, Anne-Marie; Thürmer, Andrea BMC Genomics, Vol. 16, Issue 1 https://doi.org/10.1186/s12864-015-2317-3	journal	December 2015
Limnoglobus roseus gen. nov., sp. nov., a novel freshwater planctomycete with a giant genome from the family Gemmataceae Kulichevskaya, Irina S.; Naumoff, Daniil G.; Miroshnikov, Kirill K. International Journal of Systematic and Evolutionary Microbiology, Vol. 70, Issue 2 https://doi.org/10.1099/ijsem.0.003904	journal	February 2020
Moab Desert Crust - Sample 4E Chivian, Dylan; Jungbluth, Sean; Dehal, Paramvir U.S. Department of Energy Systems Biology Knowledgebase https://doi.org/10.25982/62384.253/1831503	dataset	January 2021
Draft Genome Sequence of Freshwater-Derived Streptomyces Microbiology Resource Announcements, Vol. 8, Issue 43 https://doi.org/10.1128/mra.00874-19	journal	October 2019
KBase Silver Case Study: Determining Media Formulation Requirements for Isolation of Microbiome Constituents Whitham, Jason North Carolina State University https://doi.org/10.25982/68579.143/1766297	dataset	January 2021
L -cysteine transporter-PCR to detect hydrogen sulfide-producing Campylobacter fetus Farace, Pablo D.; Morsella, Claudia G.; Cravero, Silvio L. PeerJ, Vol. 7 https://doi.org/10.7717/peerj.7820	journal	January 2019
Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome Bernstein, David B.; Dewhirst, Floyd E.; Segrè, Daniel eLife, Vol. 8 https://doi.org/10.7554/elife.39733	journal	June 2019
A conjugative plasmid that augments virulence in Klebsiella pneumoniae Yang, Xuemei; Wai-Chi Chan, Edward; Zhang, Rong Nature Microbiology, Vol. 4, Issue 12 https://doi.org/10.1038/s41564-019-0566-7	journal	September 2019
Novel Genes and Metabolite Trends in Bifidobacterium longum subsp. infantis Bi-26 Metabolism of Human Milk Oligosaccharide 2′-fucosyllactose Zabel, Bryan; Yde, Christian Clement; Roos, Paige Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-43780-9	journal	May 2019
Identification of a novel transposon-associated phosphoethanolamine transferase gene, mcr-5, conferring colistin resistance in d-tartrate fermenting Salmonella enterica subsp. enterica serovar Paratyphi B Borowiak, Maria; Fischer, Jennie; Hammerl, Jens A. Journal of Antimicrobial Chemotherapy, Vol. 72, Issue 12 https://doi.org/10.1093/jac/dkx327	journal	September 2017
Genome Organization and Adaptive Potential of Archetypal Organophosphate Degrading Sphingobium fuliginis ATCC 27551 Azam, Sarwar; Parthasarathy, Sunil; Singh, Chhaya Genome Biology and Evolution, Vol. 11, Issue 9 https://doi.org/10.1093/gbe/evz189	journal	August 2019
Complete Genome Sequence of Staphylococcus haemolyticus Type Strain SGAir0252 Premkrishnan, Balakrishnan N. V.; Junqueira, Ana Carolina M.; Uchida, Akira Genome Announcements, Vol. 6, Issue 19 https://doi.org/10.1128/genomea.00229-18	journal	May 2018
Impact of BBDuk metagenomic read trimming and decontamination Whitham, Jason North Carolina State Univ., Raleigh, NC (United States) https://doi.org/10.25982/77705.1341/1779218	dataset	January 2021
Genome mining of Streptomyces xinghaiensis NRRL B-24674T for the discovery of the gene cluster involved in anticomplement activities and detection of novel xiamycin analogs Chen, Liang-Yu; Wang, Xiao-Qing; Wang, Yu-Mei Applied Microbiology and Biotechnology, Vol. 102, Issue 22 https://doi.org/10.1007/s00253-018-9337-2	journal	September 2018
Domestication of previously uncultivated Candidatus Desulforudis audaxviator from a deep aquifer in Siberia sheds light on its physiology and evolution Karnachuk, Olga V.; Frank, Yulia A.; Lukina, Anastasia P. The ISME Journal, Vol. 13, Issue 8 https://doi.org/10.1038/s41396-019-0402-3	journal	March 2019
Comparative genome analysis reveals important genetic differences among serotype O1 and serotype O2 strains of Y. ruckeri and provides insights into host adaptation and virulence Cascales, Desirée; Guijarro, José A.; García-Torrico, Ana I. MicrobiologyOpen, Vol. 6, Issue 4 https://doi.org/10.1002/mbo3.460	journal	March 2017
Complete Genome of ORR Isolate Bacillus cereus CPT56D-587-MTF Goff, Jennifer Univ. of Georgia, Athens, GA (United States) https://doi.org/10.25982/105874.55/1844990	dataset	January 2022
Tracking a serial killer: Integrating phylogenetic relationships, epidemiology, and geography for two invasive meningococcal disease outbreaks Ezeoke, Ifeoma; Galac, Madeline R.; Lin, Ying PLOS ONE, Vol. 13, Issue 11 https://doi.org/10.1371/journal.pone.0202615	journal	November 2018
Complete Genome Sequence of Brachybacterium sp. Strain SGAir0954, Isolated from Singapore Air Hlaing, Phu Pwint Thin; Junqueira, Ana Carolina M.; Uchida, Akira Microbiology Resource Announcements, Vol. 8, Issue 32 https://doi.org/10.1128/mra.00619-19	journal	August 2019
Comparative Genomics of Four Isosphaeraceae Planctomycetes: A Common Pool of Plasmids and Glycoside Hydrolase Genes Shared by Paludisphaera borealis PX4T, Isosphaera pallida IS1BT, Singulisphaera acidiphila DSM 18658T, and Strain SH-PL62 Ivanova, Anastasia A.; Naumoff, Daniil G.; Miroshnikov, Kirill K. Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.00412	journal	March 2017
High contiguity genome sequence of a multidrug-resistant hospital isolate of Enterobacter hormaechei Monahan, Leigh G.; DeMaere, Matthew Z.; Cummins, Max L. Gut Pathogens, Vol. 11, Issue 1 https://doi.org/10.1186/s13099-019-0288-7	journal	February 2019
Genomic and evolutionary features of two AHPND positive Vibrio parahaemolyticus strains isolated from shrimp (Penaeus monodon) of south-west Bangladesh Ahmmed, Shawon; Khan, Md. Abdullah-Al-Kamran; Eshik, Md. Mostavi Enan BMC Microbiology, Vol. 19, Issue 1 https://doi.org/10.1186/s12866-019-1655-8	journal	December 2019
Enhanced bacterial mutualism through an evolved biofilm phenotype Røder, Henriette L.; Herschend, Jakob; Russel, Jakob The ISME Journal, Vol. 12, Issue 11 https://doi.org/10.1038/s41396-018-0165-2	journal	July 2018
Complete Genome Sequence of Enterococcus faecalis Strain SGAir0397, Isolated from a Tropical Air Sample Collected in Singapore Purbojati, Rikky W.; Drautz-Moses, Daniela I.; Uchida, Akira Microbiology Resource Announcements, Vol. 8, Issue 33 https://doi.org/10.1128/mra.00593-19	journal	August 2019
Genome Sequence of Bacillus velezensis SGAir0473, Isolated from Tropical Air Collected in Singapore Lim, Serene B. Y.; Junqueira, Ana Carolina M.; Uchida, Akira Genome Announcements, Vol. 6, Issue 27 https://doi.org/10.1128/genomea.00642-18	journal	July 2018
CRISPRDetect: A flexible algorithm to define CRISPR arrays Biswas, Ambarish; Staals, Raymond H. J.; Morales, Sergio E. BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-2627-0	journal	May 2016
Complete genome sequencing and analysis of endophytic Sphingomonas sp. LK11 and its potential in plant growth Asaf, Sajjad; Khan, Abdul Latif; Khan, Muhammad Aaqil 3 Biotech, Vol. 8, Issue 9 https://doi.org/10.1007/s13205-018-1403-z	journal	August 2018
Phenazines in plant-beneficial Pseudomonas spp.: biosynthesis, regulation, function and genomics: Phenazines in plant-beneficial Pseudomonas spp . Biessy, Adrien; Filion, Martin Environmental Microbiology, Vol. 20, Issue 11 https://doi.org/10.1111/1462-2920.14395	journal	October 2018
Characterization and overproduction of cell-associated cholesterol oxidase ChoD from Streptomyces lavendulae YAKB-15 Yamada, Keith; Koroleva, Arina; Laughlin, Mitchell Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-48132-1	journal	August 2019
A comparative genomics approach for identifying host-range determinants in Streptococcus thermophilus bacteriophages Szymczak, Paula; Rau, Martin Holm; Monteiro, João M. Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-44481-z	journal	May 2019
Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential Carro, Lorena; Nouioui, Imen; Sangal, Vartul Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-017-17392-0	journal	January 2018
Multiscale analysis of autotroph-heterotroph interactions in a high-temperature microbial community Hunt, Kristopher A.; Jennings, Ryan M.; Inskeep, William P. PLOS Computational Biology, Vol. 14, Issue 9 https://doi.org/10.1371/journal.pcbi.1006431	journal	September 2018
Draft Genome Sequence of the Marine Pathogen Vibrio coralliilyticus RE22 Spinard, Edward; Kessner, Linda; Gomez-Chiarri, Marta Genome Announcements, Vol. 3, Issue 6 https://doi.org/10.1128/genomea.01432-15	journal	December 2015
Complete Genome Sequence of Nissabacter sp. Strain SGAir0207, Isolated from an Air Sample Collected in Singapore Gaultier, Nicolas E.; Junqueira, Ana Carolina M.; Uchida, Akira Microbiology Resource Announcements, Vol. 8, Issue 32 https://doi.org/10.1128/mra.00559-19	journal	August 2019
Comparative Genomics Revealed Multiple Helicobacter pylori Genes Associated with Biofilm Formation In Vitro Wong, Eric Hong Jian; Ng, Chow Goon; Chua, Eng Guan PLOS ONE, Vol. 11, Issue 11 https://doi.org/10.1371/journal.pone.0166835	journal	November 2016
Complete Genome Sequence of the Novel Roseimicrobium sp. Strain ORNL1, a Verrucomicrobium Isolated from the Populus deltoides Rhizosphere Podar, Mircea; Crockett, Zachary Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States) U.S. Department of Energy Systems Biology Knowledgebase https://doi.org/10.25982/56021.26/1637512	dataset	January 2020
Draft Genome Sequence of Pseudarthrobacter phenanthrenivorans Strain MHSD1, a Bacterial Endophyte Isolated From the Medicinal Plant Pellaea calomelanos Tshishonga, Khuthadzo; Serepa-Dlamini, Mahloro Hope Evolutionary Bioinformatics, Vol. 16 https://doi.org/10.1177/1176934320913257	journal	January 2020
Ecogenomics reveals community interactions in a long-term methanogenic bioreactor and a rapid switch to sulfate-reducing conditions St. James, Andrew; Crockett, Zachary Cornell Univ., Ithaca, NY (United States);Department of Energy Systems Biology Knowledgebase; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States) https://doi.org/10.25982/51077.6/1637903	dataset	January 2020
Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains Acuña-Amador, Luis; Primot, Aline; Cadieu, Edouard BMC Genomics, Vol. 19, Issue 1 https://doi.org/10.1186/s12864-017-4429-4	journal	January 2018
Draft Genome Sequence of Pseudomonas sp. Strain MWU13-2860, Isolated from a Wild Cranberry Bog in Truro, Massachusetts Ebadzadsahrai, Ghazal; Thomson, Jonathon; Soby, Scott Microbiology Resource Announcements, Vol. 7, Issue 13 https://doi.org/10.1128/mra.01007-18	journal	October 2018
Origin of Chemical Diversity in Prochloron-Tunicate Symbiosis Lin, Zhenjian; Torres, Joshua P.; Tianero, M. Diarey Applied and Environmental Microbiology, Vol. 82, Issue 12 https://doi.org/10.1128/aem.00860-16	journal	April 2016
Newly Isolated Bacteriophages from the Podoviridae, Siphoviridae, and Myoviridae Families Have Variable Effects on Putative Novel Dickeya spp. Alič, Špela; Naglič, Tina; Tušek-Žnidarič, Magda Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.01870	journal	September 2017
JGI QC impact on assembly, binning, phylogenomics, and functional analysis Whitham, Jason North Carolina State Univ., Raleigh, NC (United States) https://doi.org/10.25982/62657.1515/1779219	dataset	January 2021
Draft Genome Sequence of Geotoga petraea Strain HO-Geo1, Isolated from a Petroleum Reservoir in Russia Grouzdev, Denis S.; Semenova, Ekaterina M.; Sokolova, Diyana S. Microbiology Resource Announcements, Vol. 8, Issue 29 https://doi.org/10.1128/MRA.00706-19	journal	July 2019
A jumbo phage that forms a nucleus-like structure evades CRISPR–Cas DNA targeting but is vulnerable to type III RNA-based immunity Malone, Lucia M.; Warring, Suzanne L.; Jackson, Simon A. Nature Microbiology, Vol. 5, Issue 1 https://doi.org/10.1038/s41564-019-0612-5	journal	December 2019
Scytodecamide from the Cultured Scytonema sp. UIC 10036 Expands the Chemical and Genetic Diversity of Cyanobactins Crnkovic, Camila M.; Braesel, Jana; Krunic, Aleksej ChemBioChem, Vol. 21, Issue 6 https://doi.org/10.1002/cbic.201900511	journal	November 2019
Capturing One of the Human Gut Microbiome’s Most Wanted: Reconstructing the Genome of a Novel Butyrate-Producing, Clostridial Scavenger from Metagenomic Sequence Data Jeraldo, Patricio; Hernandez, Alvaro; Nielsen, Henrik B. Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00783	journal	May 2016
Genome sequence and comparative genomic analysis of a clinically important strain CD11-4 of Janibacter melonis isolated from celiac disease patient Chander, Atul Munish; Kochhar, Rakesh; Dhawan, Devinder Kumar Gut Pathogens, Vol. 10, Issue 1 https://doi.org/10.1186/s13099-018-0229-x	journal	January 2018
Osur_paper Kiefer, Julian Johannes Gutenberg Universität Mainz, Mainz, Rheinland-Pfalz, DE https://doi.org/10.25982/58799.728/1798340	dataset	January 2021
Characterization of Two Pseudomonas aeruginosa Viruses vB_PaeM_SCUT-S1 and vB_PaeM_SCUT-S2 Guo, Yangyijun; Chen, Ping; Lin, Zhanglin Viruses, Vol. 11, Issue 4 https://doi.org/10.3390/v11040318	journal	April 2019
Distribution and diversity of enzymes for polysaccharide degradation in fungi Berlemont, Renaud Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-00258-w	journal	March 2017
A Coxiella mutualist symbiont is essential to the development of Rhipicephalus microplus Guizzo, Melina Garcia; Parizi, Luís Fernando; Nunes, Rodrigo Dutra Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-17309-x	journal	December 2017
May the Phage be With You? Prophage-Like Elements in the Genomes of Soft Rot Pectobacteriaceae: Pectobacterium spp. and Dickeya spp. Czajkowski, Robert Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00138	journal	February 2019
Adaptation of metal and antibiotic resistant traits in novel β-Proteobacterium Achromobacter xylosoxidans BHW-15 Istiaq, Arif; Shuvo, Md. Sadikur Rahman; Rahman, Khondaker Md. Jaminur PeerJ, Vol. 7 https://doi.org/10.7717/peerj.6537	journal	January 2019
Metagenomic Insights into the Phylogenetic and Metabolic Diversity of the Prokaryotic Community Dwelling in Hypersaline Soils from the Odiel Saltmarshes (SW Spain) Vera-Gargallo, Blanca; Ventosa, Antonio Genes, Vol. 9, Issue 3 https://doi.org/10.3390/genes9030152	journal	March 2018
Production of multiple bacteriocins, including the novel bacteriocin gassericin M, by Lactobacillus gasseri LM19, a strain isolated from human milk Garcia-Gutierrez, Enriqueta; O’Connor, Paula M.; Colquhoun, Ian J. Applied Microbiology and Biotechnology, Vol. 104, Issue 9 https://doi.org/10.1007/s00253-020-10493-3	journal	March 2020
New insights on Pseudoalteromonas haloplanktis TAC125 genome organization and benchmarks of genome assembly applications using next and third generation sequencing technologies Qi, Weihong; Colarusso, Andrea; Olombrada, Miriam ETH Zurich https://doi.org/10.3929/ethz-b-000380001	text	January 2019
Complete Genome Sequence of Terriglobus albidus Strain ORNL, an Acidobacterium Isolated from the Populus deltoides Rhizosphere Podar, Mircea; Crockett, Zachary Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); U.S. Department of Energy Systems Biology Knowledgebase https://doi.org/10.25982/44746.21/1635640	dataset	January 2020
First Genome Sequence of Pasteurella multocida Type B Strain BAUTB2, a Major Pathogen Responsible for Mortality of Bovines in Bangladesh Sarker, M. Shahjahan Ali; Rahman, M. Tanvir; Mahmud, M. Muket Microbiology Resource Announcements, Vol. 7, Issue 9 https://doi.org/10.1128/mra.00901-18	journal	September 2018
Essential Steps in Characterizing Bacteriophages: Biology, Taxonomy, and Genome Analysis Aziz, Ramy Karam; Ackermann, Hans-Wolfgang; Petty, Nicola K. Methods in Molecular Biology https://doi.org/10.1007/978-1-4939-7343-9_15	book	November 2017
Draft Genome Sequence of an Enterococcus faecalis Strain (24FS) That Was Isolated from Healthy Infant Feces and Exhibits High Antibacterial Activity, Multiple-Antibiotic Resistance, and Multiple Virulence Factors El Halfawy, Nancy M.; El-Naggar, Moustafa Y.; Andrews, Simon C. Microbiology Resource Announcements, Vol. 8, Issue 13 https://doi.org/10.1128/mra.00047-19	journal	March 2019
Genome of the candidate phylum Aminicenantes bacterium from a deep subsurface thermal aquifer revealed its fermentative saccharolytic lifestyle Kadnikov, Vitaly V.; Mardanov, Andrey V.; Beletsky, Alexey V. Extremophiles, Vol. 23, Issue 2 https://doi.org/10.1007/s00792-018-01073-5	journal	January 2019
Genomic analysis of methanogenic archaea reveals a shift towards energy conservation Gilmore, Sean P.; Henske, John K.; Sexton, Jessica A. BMC Genomics, Vol. 18, Issue 1 https://doi.org/10.1186/s12864-017-4036-4	journal	August 2017
Lactose drives Enterococcus expansion to promote graft-versus-host disease Stein-Thoeringer, C. K.; Nichols, K. B.; Lazrak, A. Science, Vol. 366, Issue 6469 https://doi.org/10.1126/science.aax3760	journal	November 2019
Brucella spp. of amphibians comprise genomically diverse motile strains competent for replication in macrophages and survival in mammalian hosts Al Dahouk, Sascha; Köhler, Stephan; Occhialini, Alessandra Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/srep44420	journal	March 2017
Draft Genome Sequences of Four Metallo-Beta-Lactamase-Producing Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates, Including Two Colistin-Resistant Strains, from Cairo, Egypt Attia, Heba; Szubin, Richard; Yassin, Aymen S. Microbiology Resource Announcements, Vol. 8, Issue 7 https://doi.org/10.1128/mra.01418-18	journal	February 2019
May the phage be with you? Prophage-like elements in the genomes of Soft Rot Pectobacteriaceae ( Pectobacterium spp. and Dickeya spp.) Czajkowski, Robert Frontiers in Microbiology https://doi.org/10.1101/399675	journal	August 2018
Novel Multidrug-Resistant Enterococcal Mobile Linear Plasmid pELF1 Encoding vanA and vanM Gene Clusters From a Japanese Vancomycin-Resistant Enterococci Isolate Hashimoto, Yusuke; Taniguchi, Makoto; Uesaka, Kazuma Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.02568	journal	November 2019
Draft Genome Sequence of Rhodococcus sp. Strain NCIMB 12038, a Naphthalene-Degrading Bacterium Dandare, Shamsudeen U.; Skvortsov, Timofey; Arkhipova, Ksenia Genome Announcements, Vol. 6, Issue 1 https://doi.org/10.1128/genomea.01420-17	journal	January 2018
Draft Genome Sequence of Streptomyces thermocarboxydus BPSAC147, a Potentially Plant Growth-Promoting Endophytic Bacterium Passari, Ajit Kumar; Rajput, Vinay Microbiology Resource Announcements, Vol. 8, Issue 23 https://doi.org/10.1128/mra.00363-19	journal	June 2019
Uncovering the potential of novel micromonosporae isolated from an extreme hyper-arid Atacama Desert soil Carro, Lorena; Castro, Jean Franco; Razmilic, Valeria Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-38789-z	journal	March 2019
Comparative genomics reveals a novel genetic organization of the sad cluster in the sulfonamide-degrader ‘Candidatus Leucobacter sulfamidivorax’ strain GP Reis, Ana C.; Kolvenbach, Boris A.; Chami, Mohamed BMC Genomics, Vol. 20, Issue 1 https://doi.org/10.1186/s12864-019-6206-z	journal	November 2019
Characterization of the first double-stranded RNA bacteriophage infecting Pseudomonas aeruginosa Yang, Yuhui; Lu, Shuguang; Shen, Wei Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep38795	journal	December 2016
Granulicella sibirica sp. nov., a psychrotolerant acidobacterium isolated from an organic soil layer in forested tundra, West Siberia Oshkin, Igor Y.; Kulichevskaya, Irina S.; Rijpstra, W. Irene C. International Journal of Systematic and Evolutionary Microbiology, Vol. 69, Issue 4 https://doi.org/10.1099/ijsem.0.003290	journal	April 2019
KBase Narrative - kb_DRAM E. coli annotation Shaffer, Michael U.S. Department of Energy Systems Biology Knowledgebase https://doi.org/10.25982/103341.23/1893106	dataset	January 2022
Isolation and characterisation of carbapenem-resistant Xanthomonas citri pv. mangiferaeindicae-like strain gir from the faecal material of giraffes McFarland, Renee; Anacker, Melissa; Snippes Vagnone, Paula M. Antonie van Leeuwenhoek, Vol. 113, Issue 1 https://doi.org/10.1007/s10482-019-01323-2	journal	September 2019
A Specific Sugar Moiety in the Lactococcus lactis Cell Wall Pellicle Is Required for Infection by CHPC971, a Member of the Rare 1706 Phage Species Marcelli, Barbara; de Jong, Anne; Karsens, Harma Applied and Environmental Microbiology, Vol. 85, Issue 19 https://doi.org/10.1128/aem.01224-19	journal	July 2019
Genomic analysis of a novel Rhodococcus (Prescottella) equi isolate from a bovine host Paterson, Megan L.; Ranasinghe, Diyanath; Blom, Jochen Archives of Microbiology, Vol. 201, Issue 9 https://doi.org/10.1007/s00203-019-01695-z	journal	July 2019
Draft Genome Sequence of Bacillus thuringiensis DPC6431, Producer of the Bacteriocin Thuricin CD Arbulu, Sara; Murphy, Kiera; O’Sullivan, Orla Microbiology Resource Announcements, Vol. 8, Issue 33 https://doi.org/10.1128/mra.00398-19	journal	August 2019
Calorimonas adulescens gen. nov., sp. nov., an anaerobic thermophilic bacterium utilizing methoxylated benzoates Khomyakova, M. A.; Merkel, A. Y.; Kopitsyn, D. S. International Journal of Systematic and Evolutionary Microbiology, Vol. 70, Issue 3 https://doi.org/10.1099/ijsem.0.004019	journal	March 2020
Draft Genome Sequence of Pseudomonas sp. Strain MWU12-2534b, Isolated from a Wild Cranberry Bog in Truro, Massachusetts Ebadzadsahrai, Ghazal; Thomson, Jonathon; Soby, Scott Microbiology Resource Announcements, Vol. 7, Issue 13 https://doi.org/10.1128/mra.01005-18	journal	October 2018
Diversity of phytobeneficial traits revealed by whole-genome analysis of worldwide-isolated phenazine-producing Pseudomonas spp.: Genomic diversity of Phz+ Pseudomonas spp. Biessy, Adrien; Novinscak, Amy; Blom, Jochen Environmental Microbiology https://doi.org/10.1111/1462-2920.14476	journal	December 2018
Complete Genome Sequence of the Bacterium Serratia marcescens SGAir0764, Isolated from Singapore Air Gaultier, Nicolas E.; Junqueira, Ana Carolina M.; Uchida, Akira Genome Announcements, Vol. 6, Issue 27 https://doi.org/10.1128/genomea.00637-18	journal	July 2018
Complete Genome Sequences of Endophytic Bacilli Isolated from Grapevine Plants Mardanov, Andrey V.; Chizhevskaya, Elena P.; Lazarev, Alexander M. Microbiology Resource Announcements, Vol. 8, Issue 48 https://doi.org/10.1128/mra.01265-19	journal	November 2019
Whole-Genome Sequence of Lactobacillus acidophilus PNW3, Isolated from Weaned Piglets of the Indigenous South African Windsnyer Pig Breed Alayande, Kazeem A.; Aiyegoro, Olayinka A.; Ateba, Collins N. Microbiology Resource Announcements, Vol. 8, Issue 25 https://doi.org/10.1128/mra.00362-19	journal	June 2019
Prey Range and Genome Evolution of Halobacteriovorax marinus Predatory Bacteria from an Estuary Enos, Brett G.; Anthony, Molly K.; DeGiorgis, Joseph A. mSphere, Vol. 3, Issue 1 https://doi.org/10.1128/msphere.00508-17	journal	January 2018
A Novel Cyanobacterium Synechococcus elongatus PCC 11802 has Distinct Genomic and Metabolomic Characteristics Compared to its Neighbor PCC 11801 Jaiswal, Damini; Sengupta, Annesha; Sengupta, Shinjinee Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-019-57051-0	journal	January 2020
Complete genome of Staphylococcus aureus Tager 104 provides evidence of its relation to modern systemic hospital-acquired strains Davis, Richard W.; Brannen, Andrew D.; Hossain, Mohammad J. BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-2433-8	journal	March 2016
Draft Genome Sequence of Larkinella sp. Strain BK230, Isolated from Populus deltoides Roots Pelletier, Dale; Crockett, Zachary Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); U.S. Department of Energy Systems Biology Knowledgebase https://doi.org/10.25982/54100.27/1635639	dataset	January 2020
Polaribacter aquimarinus sp. nov., isolated from the surface of a marine red alga Xu, Wei; Chen, Xu-Yang; Wei, Xiang-Tao Antonie van Leeuwenhoek, Vol. 113, Issue 3 https://doi.org/10.1007/s10482-019-01350-z	journal	October 2019
Draft Genome Sequence of Lactobacillus helveticus Strain Lh 12 Isolated from Natural Whey Starter Bertani, Gaia; Bassi, Daniela; Gatti, Monica Genome Announcements, Vol. 6, Issue 10 https://doi.org/10.1128/genomea.00139-18	journal	March 2018
Draft Genome Sequences of Endophytic Pseudomonas spp. Isolated from Grapevine Tissue and Antagonistic to Grapevine Trunk Disease Pathogens Niem, Jennifer; Billones-Baaijens, Regina; Savocchia, Sandra Microbiology Resource Announcements, Vol. 8, Issue 26 https://doi.org/10.1128/mra.00345-19	journal	June 2019
Complete Genome Sequences of Two Listeria Phages of the Genus Pecentumvirus Peters, Tracey L.; Hudson, Lauren K.; Song, Yaxiong Microbiology Resource Announcements, Vol. 8, Issue 46 https://doi.org/10.1128/mra.01229-19	journal	November 2019
Plasmid and chromosomal integration of four novel blaIMP-carrying transposons from Pseudomonas aeruginosa, Klebsiella pneumoniae and an Enterobacter sp. Zhan, Zhe; Hu, Lingfei; Jiang, Xiaoyuan Journal of Antimicrobial Chemotherapy, Vol. 73, Issue 11 https://doi.org/10.1093/jac/dky288	journal	July 2018
Complete Genome Sequence of Agrobacterium fabrum Strain 1D159 Huo, Naxin; Gu, Yong; McCue, Kent F. Microbiology Resource Announcements, Vol. 8, Issue 19 https://doi.org/10.1128/mra.00207-19	journal	May 2019
Genomic analysis of two drug‐resistant clinical Morganella morganii strains isolated from UTI patients in Pretoria, South Africa Mbelle, N.; Osei Sekyere, J.; Feldman, C. Letters in Applied Microbiology, Vol. 70, Issue 1 https://doi.org/10.1111/lam.13237	journal	November 2019
Description of Erysipelothrix piscisicarius sp. nov., an emergent fish pathogen, and assessment of virulence using a tiger barb (Puntigrus tetrazona) infection model Pomaranski, Eric K.; Griffin, Matt J.; Camus, Alvin C. International Journal of Systematic and Evolutionary Microbiology, Vol. 70, Issue 2 https://doi.org/10.1099/ijsem.0.003838	journal	February 2020
Complete hybrid genome assembly of clinical multidrug-resistant Bacteroides fragilis isolates enables comprehensive identification of antimicrobial-resistance genes and plasmids Sydenham, Thomas V.; Overballe-Petersen, Søren; Hasman, Henrik Microbial Genomics, Vol. 5, Issue 11 https://doi.org/10.1099/mgen.0.000312	journal	November 2019
Draft Genome Sequences of Pseudomonas putida UV4 and UV4/95, Toluene Dioxygenase-Expressing Producers of cis -1,2-Dihydrodiols Skvortsov, Timofey; Hoering, Patrick; Arkhipova, Ksenia Genome Announcements, Vol. 6, Issue 1 https://doi.org/10.1128/genomea.01419-17	journal	January 2018
Whole Genome Sequencing and Comparative Genomics of Two Nematicidal Bacillus Strains Reveals a Wide Range of Possible Virulence Factors Susič, Nik; Janežič, Sandra; Rupnik, Maja G3: Genes\|Genomes\|Genetics, Vol. 10, Issue 3 https://doi.org/10.1534/g3.119.400716	journal	January 2020
Prey range and genome evolution of Halobacteriovorax marinus predatory bacteria from an estuary Enos, Brett G.; Anthony, Molly K.; DeGiorgis, Joseph A. mSphere https://doi.org/10.1101/180265	journal	August 2017
Metatranscriptomic and comparative genomic insights into resuscitation mechanisms during enrichment culturing Mu, Da-Shuai; Liang, Qi-Yun; Wang, Xiao-Man Microbiome, Vol. 6, Issue 1 https://doi.org/10.1186/s40168-018-0613-2	journal	December 2018
Evidence for Multidrug Resistance in Nonpathogenic Mycoplasma Species Isolated from South African Poultry Beylefeld, Amanda; Wambulawaye, Pamela; Bwala, Dauda Garba Applied and Environmental Microbiology, Vol. 84, Issue 21 https://doi.org/10.1128/aem.01660-18	journal	November 2018
Genetic characterization of blaNDM-harboring plasmids in carbapenem-resistant Escherichia coli from Myanmar Sugawara, Yo; Akeda, Yukihiro; Sakamoto, Noriko PLOS ONE, Vol. 12, Issue 9 https://doi.org/10.1371/journal.pone.0184720	journal	September 2017
New insights on Pseudoalteromonas haloplanktis TAC125 genome organization and benchmarks of genome assembly applications using next and third generation sequencing technologies Qi, Weihong; Colarusso, Andrea; Olombrada, Miriam Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-52832-z	journal	November 2019
The flagellin of candidate live biotherapeutic Enterococcus gallinarum MRx0518 is a potent immunostimulant Lauté-Caly, Delphine L.; Raftis, Emma J.; Cowie, Philip Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-018-36926-8	journal	January 2019
Tracking a Serial Killer: Integrating Phylogenetic Relationships, Epidemiology, and Geography for Two Invasive Meningococcal Disease Outbreaks Ezeoke, Ifeoma; Galac, Madeline R.; Lin, Ying PLOS ONE https://doi.org/10.1101/387597	journal	August 2018
Isolation, Genomic and Metabolomic Characterization of Streptomyces tendae VITAKN with Quorum Sensing Inhibitory Activity from Southern India Ishaque, Nabila Mohammed; Burgsdorf, Ilia; Limlingan Malit, Jessie James Microorganisms, Vol. 8, Issue 1 https://doi.org/10.3390/microorganisms8010121	journal	January 2020
Homburgvirus LP-018 Has a Unique Ability to Infect Phage-Resistant Listeria monocytogenes Song, Yaxiong; Peters, Tracey L.; Bryan, Daniel W. Viruses, Vol. 11, Issue 12 https://doi.org/10.3390/v11121166	journal	December 2019
Genome Analysis of Vallitalea guaymasensis Strain L81 Isolated from a Deep-Sea Hydrothermal Vent System Schouw, Anders; Vulcano, Francesca; Roalkvam, Irene Microorganisms, Vol. 6, Issue 3 https://doi.org/10.3390/microorganisms6030063	journal	July 2018
Genome Sequence of the Tropical Atmosphere Bacterium Pontibacter sp. Strain SGAir0037 Lim, Serene B. Y.; Junqueira, Ana Carolina M.; Uchida, Akira Microbiology Resource Announcements, Vol. 8, Issue 37 https://doi.org/10.1128/mra.00610-19	journal	September 2019
Complete Genome Sequences and Transmission Electron Micrographs of Listeria Phages of the Genus Homburgvirus Hudson, Lauren K.; Peters, Tracey L.; Song, Yaxiong Microbiology Resource Announcements, Vol. 8, Issue 41 https://doi.org/10.1128/mra.00825-19	journal	October 2019
Host Resistance, Genomics and Population Dynamics in a Salmonella Enteritidis and Phage System Holguín, Angela; Cárdenas, Pablo; Prada-Peñaranda, Catalina Viruses, Vol. 11, Issue 2 https://doi.org/10.3390/v11020188	journal	February 2019
Functional Annotations of Paralogs: A Blessing and a Curse Zallot, Rémi; Harrison, Katherine; Kolaczkowski, Bryan Life, Vol. 6, Issue 3 https://doi.org/10.3390/life6030039	journal	September 2016
PATRIC as a unique resource for studying antimicrobial resistance Antonopoulos, Dionysios A.; Assaf, Rida; Aziz, Ramy Karam Briefings in Bioinformatics, Vol. 20, Issue 4 https://doi.org/10.1093/bib/bbx083	journal	July 2017
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 Saile, Nadja; Schuh, Elisabeth; Semmler, Torsten Gut Pathogens, Vol. 10, Issue 1 https://doi.org/10.1186/s13099-018-0271-8	journal	October 2018
Heterogeneous and Flexible Transmission of mcr-1 in Hospital-Associated Escherichia coli Shen, Yingbo; Wu, Zuowei; Wang, Yang mBio, Vol. 9, Issue 4 https://doi.org/10.1128/mbio.00943-18	journal	September 2018
KBase Narrative - Mse_Genome_Assembly Rastegar, Kiarash U.S. Department of Energy Systems Biology Knowledgebase https://doi.org/10.25982/116829.47/1887425	dataset	January 2022
Alterations of c-di-GMP turnover proteins modulate semi-constitutive rdar biofilm formation in commensal and uropathogenic Escherichia coli Cimdins, Annika; Simm, Roger; Li, Fengyang MicrobiologyOpen, Vol. 6, Issue 5 https://doi.org/10.1002/mbo3.508	journal	September 2017
The genomes of three Bradyrhizobium sp. isolated from root nodules of Lupinus albescens grown in extremely poor soils display important genes for resistance to environmental stress Granada, Camille E.; Vargas, Luciano K.; Sant’Anna, Fernando Hayashi Genetics and Molecular Biology, Vol. 41, Issue 2 https://doi.org/10.1590/1678-4685-gmb-2017-0098	journal	May 2018
A genomic analysis of Mycobacterium immunogenum strain CD11_6 and its potential role in the activation of T cells against Mycobacterium tuberculosis Kaur, Gurpreet; Chander, Atul Munish; Kaur, Gurwinder BMC Microbiology, Vol. 19, Issue 1 https://doi.org/10.1186/s12866-019-1421-y	journal	March 2019
Surveillance and Genomics of Toxigenic Vibrio cholerae O1 From Fish, Phytoplankton and Water in Lake Victoria, Tanzania Hounmanou, Yaovi M. Gildas; Leekitcharoenphon, Pimlapas; Hendriksen, Rene S. Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00901	journal	April 2019
Characterization of C-nucleoside Antimicrobials from Streptomyces albus DSM 40763: Strepturidin is Pseudouridimycin Rosenqvist, Petja; Palmu, Kaisa; Prajapati, Ranjit Kumar Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-45375-w	journal	June 2019
Complete Genome Sequences of Two Klebsiella pneumoniae Phages Isolated as Part of an International Effort Yerushalmy, Ortal; Coppenhagen-Glazer, Shunit; Nir-Paz, Ran Microbiology Resource Announcements, Vol. 8, Issue 38 https://doi.org/10.1128/mra.00843-19	journal	September 2019
Bacillus Phage vB_BtS_B83 Previously Designated as a Plasmid May Represent a New Siphoviridae Genus Piligrimova, Emma G.; Kazantseva, Olesya A.; Nikulin, Nikita A. Viruses, Vol. 11, Issue 7 https://doi.org/10.3390/v11070624	journal	July 2019
Comparative Genomics and CAZyme Genome Repertoires of Marine Zobellia amurskyensis KMM 3526T and Zobellia laminariae KMM 3676T Chernysheva, Nadezhda; Bystritskaya, Evgeniya; Stenkova, Anna Marine Drugs, Vol. 17, Issue 12 https://doi.org/10.3390/md17120661	journal	November 2019
Complete Genome Sequence of Lysinibacillus sp. Strain SGAir0095, Isolated from Tropical Air Samples Collected in Singapore Wong, Anthony; Junqueira, Ana Carolina M.; Uchida, Akira Microbiology Resource Announcements, Vol. 8, Issue 38 https://doi.org/10.1128/mra.00604-19	journal	September 2019
Draft Genome Sequence of Bowmanella denitrificans JL63, a Bacterium Isolated from Whiteleg Shrimp (Litopenaeus vannamei) That Can Inhibit the Growth of Vibrio parahaemolyticus LaPorte, Jason P.; Spinard, Edward J.; Gomez-Chiarri, Marta Genome Announcements, Vol. 6, Issue 14 https://doi.org/10.1128/genomea.00215-18	journal	April 2018
Comparative Genomics Reveals a Well-Conserved Intrinsic Resistome in the Emerging Multidrug-Resistant Pathogen Cupriavidus gilardii Ruiz, Cristian; McCarley, Ashley; Espejo, Manuel Luis mSphere, Vol. 4, Issue 5 https://doi.org/10.1128/msphere.00631-19	journal	October 2019
Paraburkholderia tropica as a plant-growth–promoting bacterium in barley: characterization of tissues colonization by culture-dependent and -independent techniques for use as an agronomic bioinput García, Sabrina Soledad; Bernabeu, Pamela Romina; Vio, Santiago Adolfo Plant and Soil, Vol. 451, Issue 1-2 https://doi.org/10.1007/s11104-019-04174-y	journal	June 2019
Hydrolytic Capabilities as a Key to Environmental Success: Chitinolytic and Cellulolytic Acidobacteria From Acidic Sub-arctic Soils and Boreal Peatlands Belova, Svetlana E.; Ravin, Nikolai V.; Pankratov, Timofey A. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.02775	journal	November 2018
Production of hemolysin BL by Bacillus cereus group isolates of dairy origin is associated with whole-genome phylogenetic clade Kovac, Jasna; Miller, Rachel A.; Carroll, Laura M. BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-2883-z	journal	August 2016
Draft Genome Sequences of Four Antibiotic-Resistant Salmonella Strains Isolated from Australian Red Meat Animal Species Sarjit, Amreeta; Ravensdale, Joshua T.; Coorey, Ranil Microbiology Resource Announcements, Vol. 8, Issue 35 https://doi.org/10.1128/mra.00925-19	journal	August 2019
Interrogation of a live-attenuated enterotoxigenic Escherichia coli vaccine highlights features unique to wild-type infection Chakraborty, Subhra; Randall, Arlo; Vickers, Tim J. npj Vaccines, Vol. 4, Issue 1 https://doi.org/10.1038/s41541-019-0131-7	journal	August 2019
Complete Genome Sequence of “Candidatus Syntrophocurvum alkaliphilum” Strain B(2M), Obtained from the Metagenome of a Salt-Tolerant Alkaliphilic Anaerobic Syntrophic Butyrate-Degrading Consortium Mardanov, Andrey V.; Sorokin, Dmitry Y.; Beletsky, Alexey V. Microbiology Resource Announcements, Vol. 9, Issue 6 https://doi.org/10.1128/mra.01511-19	journal	February 2020
Transcriptomic profiling of Streptococcus pyogenes M1T1 strain in a mouse model of necrotizing fasciitis Hirose, Yujiro; Yamaguchi, Masaya; Okuzaki, Daisuke BioRxiv https://doi.org/10.1101/610139	posted_content	April 2019
A machine learning-based service for estimating quality of genomes using PATRIC Parrello, Bruce; Butler, Rory; Chlenski, Philippe BMC Bioinformatics, Vol. 20, Issue 1 https://doi.org/10.1186/s12859-019-3068-y	journal	October 2019
Resilience of small intestinal beneficial bacteria to the toxicity of soybean oil fatty acids Di Rienzi, Sara C.; Jacobson, Juliet; Kennedy, Elizabeth A. eLife https://doi.org/10.1101/164715	journal	March 2018
New Genus Fibralongavirus in Siphoviridae Phages of Staphylococcus pseudintermedius Zeman, Michal; Bárdy, Pavol; Vrbovská, Veronika Viruses, Vol. 11, Issue 12 https://doi.org/10.3390/v11121143	journal	December 2019
Pan-Genomic and Polymorphic Driven Prediction of Antibiotic Resistance in Elizabethkingia Naidenov, Bryan; Lim, Alexander; Willyerd, Karyn Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01446	journal	July 2019
Complete Genome Sequences of Two Escherichia Phages Isolated from Wastewater in Finland Kiljunen, Saija; Wicklund, Anu; Skurnik, Mikael Genome Announcements, Vol. 6, Issue 22 https://doi.org/10.1128/genomea.00401-18	journal	May 2018
Complete Genome Sequence of Lelliottia nimipressuralis Type Strain SGAir0187, Isolated from Tropical Air Collected in Singapore Heinle, Cassie E.; Junqueira, Ana Carolina M.; Uchida, Akira Genome Announcements, Vol. 6, Issue 18 https://doi.org/10.1128/genomea.00231-18	journal	May 2018
Production of multiple bacteriocins, including the novel bacteriocin gassericin M, by Lactobacillus gasseri LM19, a strain isolated from human milk Garcia-Gutierrez, Enriqueta; O’Connor, Paula M.; Colquhoun, Ian J. Applied Microbiology and Biotechnology https://doi.org/10.1101/841254	journal	November 2019
A metagenomic window into the 2-km-deep terrestrial subsurface aquifer revealed multiple pathways of organic matter decomposition Kadnikov, Vitaly V.; Mardanov, Andrey V.; Beletsky, Alexey V. FEMS Microbiology Ecology, Vol. 94, Issue 10 https://doi.org/10.1093/femsec/fiy152	journal	August 2018
Mobilizable antibiotic resistance genes are present in dust microbial communities Ben Maamar, Sarah; Glawe, Adam J.; Brown, Taylor K. PLOS Pathogens, Vol. 16, Issue 1 https://doi.org/10.1371/journal.ppat.1008211	journal	January 2020
Draft Genome Sequence of Plant Growth-Promoting Endophytic Microbacterium hydrothermale BPSAC84, Isolated from the Medicinal Plant Mirabilis jalapa Passari, Ajit Kumar; Rajput, Vinay Microbiology Resource Announcements, Vol. 8, Issue 22 https://doi.org/10.1128/mra.00406-19	journal	May 2019
Strain typing and characterization of virulence genes in clinical Staphylococcus aureus isolates from Kenya Kyany’a, Cecilia; Nyasinga, Justin; Matano, Daniel BioRxiv https://doi.org/10.1101/390955	posted_content	August 2018
Complete Genome Sequence of Agrococcus sp. Strain SGAir0287, Isolated from Tropical Air Collected in Singapore Lau, Kenny J. X.; Junqueira, Ana Carolina M.; Uchida, Akira Microbiology Resource Announcements, Vol. 8, Issue 32 https://doi.org/10.1128/mra.00616-19	journal	August 2019
Comprehensive analysis of draft genomes of two closely related pseudomonas syringae phylogroup 2b strains infecting mono- and dicotyledon host plants Sultanov, Rinat I.; Arapidi, Georgij P.; Vinogradova, Svetlana V. BMC Genomics, Vol. 17, Issue S14 https://doi.org/10.1186/s12864-016-3358-y	journal	December 2016
The draft genomes of Elizabethkingia anophelis of equine origin are genetically similar to three isolates from human clinical specimens Johnson, William L.; Ramachandran, Akhilesh; Torres, Nathanial J. PLOS ONE, Vol. 13, Issue 7 https://doi.org/10.1371/journal.pone.0200731	journal	July 2018
Litorilituus lipolyticus sp. nov., isolated from intertidal sand of the Yellow Sea in China, and emended description of Colwellia asteriadis Liu, Ang; Zhang, Yan-Jiao; Xue, Qing-Jie Antonie van Leeuwenhoek, Vol. 113, Issue 4 https://doi.org/10.1007/s10482-019-01355-8	journal	November 2019
SXT/R391 integrative and conjugative elements in Proteus species reveal abundant genetic diversity and multidrug resistance Li, Xinyue; Du, Yu; Du, Pengcheng Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep37372	journal	November 2016
Extended-spectrum beta-lactamases and plasmid diversity in urinary isolates of Escherichia coli in Croatia: a nation-wide, multicentric, retrospective study Krilanović, Marija; Tomić-Paradžik, Maja; Meštrović, Tomislav Folia Microbiologica, Vol. 65, Issue 4 https://doi.org/10.1007/s12223-019-00769-1	journal	January 2020
Complete Genome Sequence of Pseudomonas stutzeri Type Strain SGAir0442, Isolated from Singapore Air Samples Kee, Carmon; Junqueira, Ana Carolina M.; Uchida, Akira Genome Announcements, Vol. 6, Issue 22 https://doi.org/10.1128/genomea.00424-18	journal	May 2018
Molecular characterization of carbapenem-resistant Klebsiella pneumoniae isolates with focus on antimicrobial resistance Yu, Xiaoling; Zhang, Wen; Zhao, Zhipomg BMC Genomics https://doi.org/10.1101/778795	journal	September 2019
Characterization of Salmonella Dublin isolated from bovine and human hosts Paudyal, Narayan; Pan, Hang; Elbediwi, Mohammed BMC Microbiology, Vol. 19, Issue 1 https://doi.org/10.1186/s12866-019-1598-0	journal	October 2019
Multi-omics reveal various potential antimonate reductases from phylogenetically diverse microorganisms Shi, Ling-Dong; Wang, Min; Han, Yu-Lin Applied Microbiology and Biotechnology, Vol. 103, Issue 21-22 https://doi.org/10.1007/s00253-019-10111-x	journal	September 2019
Genomics of Aerobic Photoheterotrophs in Wheat Phyllosphere Reveals Divergent Evolutionary Patterns of Photosynthetic Genes in Methylobacterium spp. Zervas, Athanasios; Zeng, Yonghui; Madsen, Anne Mette Genome Biology and Evolution, Vol. 11, Issue 10 https://doi.org/10.1093/gbe/evz204	journal	September 2019
Data on draft genome sequence of Bacillus sp. strain VKPM B-3276 isolated from Culex pipiens larvae Zinina, V. V.; Korzhenkov, A. A.; Tepliuk, A. V. Data in Brief, Vol. 24 https://doi.org/10.1016/j.dib.2019.103757	journal	June 2019
Complete genome sequence of a natural compounds producer, Streptomyces violaceus S21 Fu, Jiafang; Zhong, Chuanqing; Zhao, Zhilong Genomics Data, Vol. 12 https://doi.org/10.1016/j.gdata.2017.04.002	journal	June 2017
Comparative genomics of Salmonella enterica serovar Enteritidis ST-11 isolated in Uruguay reveals lineages associated with particular epidemiological traits D’Alessandro, Bruno; Pérez Escanda, Victoria; Balestrazzi, Lucía Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-60502-8	journal	February 2020
Complete Genome Sequence of the Biocontrol Agent Bacillus velezensis UFLA258 and Its Comparison with Related Species: Diversity within the Commons Silva, Fabíola de Jesus; Ferreira, Larissa Carvalho; Campos, Vicente Paulo Genome Biology and Evolution, Vol. 11, Issue 10 https://doi.org/10.1093/gbe/evz208	journal	October 2019
Isolation and characterisation of novel phages infecting Lactobacillus plantarum and proposal of a new genus, “Silenusvirus” Kyrkou, Ifigeneia; Carstens, Alexander Byth; Eilegaard-Jensen, Lea Scientific Reports https://doi.org/10.1101/728261	journal	August 2019
Genome Sequence of Elizabethkingia anophelis Strain EaAs1, Isolated from the Asian Malaria Mosquito Anopheles stephensi Raygoza Garay, Juan Antonio; Hughes, Grant L.; Koundal, Vikas Genome Announcements, Vol. 4, Issue 2 https://doi.org/10.1128/genomea.00084-16	journal	April 2016
Draft Genome Sequences of Four Pseudomonas aeruginosa Isolates Obtained from Patients with Chronic Obstructive Pulmonary Disease Lira, Felipe; García-León, Guillermo; Oliver, Antonio Genome Announcements, Vol. 5, Issue 24 https://doi.org/10.1128/genomea.00147-17	journal	June 2017
Draft Genome Sequence of Aliiroseovarius crassostreae CV919-312, the Causative Agent of Roseovarius Oyster Disease (Formerly Juvenile Oyster Disease) Kessner, Linda; Spinard, Edward; Gomez-Chiarri, Marta Genome Announcements, Vol. 4, Issue 2 https://doi.org/10.1128/genomea.00148-16	journal	April 2016
Draft Genome Sequence of the Tacrolimus-Producing Bacterium Streptomyces tsukubaensis F601 Zong, Gongli; Zhong, Chuanqing; Fu, Jiafang Genome Announcements, Vol. 5, Issue 20 https://doi.org/10.1128/genomea.00385-17	journal	May 2017
Complete Genome Sequence of Melissococcus plutonius DAT561, a Strain That Shows an Unusual Growth Profile, Obtained by PacBio Sequencing Okumura, Kayo; Takamatsu, Daisuke; Okura, Masatoshi Genome Announcements, Vol. 6, Issue 23 https://doi.org/10.1128/genomea.00431-18	journal	June 2018
Draft Genome Sequence of the Emerging Bivalve Pathogen Vibrio tubiashii subsp. europaeus Spinard, Edward J.; Dubert, Javier; Nelson, David R. Genome Announcements, Vol. 4, Issue 4 https://doi.org/10.1128/genomea.00625-16	journal	August 2016
Genome Sequences of Klebsiella variicola Isolates from Dairy Animals with Bovine Mastitis from Newfoundland, Canada Davidson, Fraser W.; Whitney, Hugh G.; Tahlan, Kapil Genome Announcements, Vol. 3, Issue 5 https://doi.org/10.1128/genomea.00938-15	journal	October 2015
Draft Genome Sequence of Lactobacillus plantarum Strain SNU.Lp177 from Pig Feces in South Korea Kim, Eun Bae; Jin, Gwi-Deuk; Lee, Jun-Yeong Genome Announcements, Vol. 3, Issue 5 https://doi.org/10.1128/genomea.01184-15	journal	October 2015
Draft Genome Sequence of Hypervirulent and Vaccine Candidate Streptococcus suis Strain SC19 Teng, Lin; Dong, Xingxing; Zhou, Yang Genome Announcements, Vol. 5, Issue 3 https://doi.org/10.1128/genomea.01484-16	journal	January 2017
Complete Genome Sequence of the Triclosan- and Multidrug-Resistant Pseudomonas aeruginosa Strain B10W Isolated from Municipal Wastewater Zhong, Chuanqing; Nelson, Matthew; Cao, Guangxiang Genome Announcements, Vol. 5, Issue 3 https://doi.org/10.1128/genomea.01489-16	journal	January 2017
Genome Sequence of Megasphaera cerevisiae NSB1, a Bacterium Isolated from a Canning Line and Able To Grow in Beer with High Alcohol Content Bergsveinson, Jordyn; Thomson, Euan; Jacoby, Derek Genome Announcements, Vol. 5, Issue 8 https://doi.org/10.1128/genomea.01686-16	journal	February 2017
Draft Genome Sequences of Two Vibrio splendidus Strains, Isolated from Seagrass Sediment Lee, Ruth D.; Jospin, Guillaume; Lang, Jenna M. Genome Announcements, Vol. 4, Issue 1 https://doi.org/10.1128/genomea.01769-15	journal	February 2016
Draft Genome Sequence of Bacillus subtilis TLO3, Isolated from Olive Tree Rhizosphere Soil Choubane, Slimane; Gabed, Noujoud; Khelil, Omar Microbiology Resource Announcements, Vol. 7, Issue 11 https://doi.org/10.1128/mra.00852-18	journal	September 2018
Genomic Alterations of Staphylococcus aureus ATCC 25923 after Prolonged Passage in the Laboratory Chin, Pei-Ju; Liao, Hsiao-Mei; Li, Bingjie Microbiology Resource Announcements, Vol. 7, Issue 18 https://doi.org/10.1128/mra.01108-18	journal	November 2018
Draft Genome Sequence of Serratia sp. 1D1416 Alabed, Diaa; Huo, Naxin; Gu, Yong Microbiology Resource Announcements, Vol. 8, Issue 3 https://doi.org/10.1128/mra.01354-18	journal	January 2019
Genome Sequence of Paracoccus sp. JM45, a Bacterial Strain Isolated from a Marine Sponge with a Dual Quorum Sensing Inhibition Activity Gutiérrez-Barranquero, José A.; Parages, María L.; Dobson, Alan D. W. Microbiology Resource Announcements, Vol. 8, Issue 2 https://doi.org/10.1128/mra.01496-18	journal	January 2019
Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI Hamilton, Joshua J.; Garcia, Sarahi L.; Brown, Brittany S. mSystems, Vol. 2, Issue 4 https://doi.org/10.1128/msystems.00091-17	journal	August 2017
The isolation and characterization of Stenotrophomonas maltophilia T4-like bacteriophage DLP6 Peters, Danielle L.; Stothard, Paul; Dennis, Jonathan J. PLOS ONE, Vol. 12, Issue 3 https://doi.org/10.1371/journal.pone.0173341	journal	March 2017
Evolution of Antibiotic Synthesis Gene Clusters in the Streptomyces globisporus TFH56, Isolated from Tomato Flower Cho, Gyeongjun; Kwak, Youn-Sig G3 Genes\|Genomes\|Genetics, Vol. 9, Issue 6 https://doi.org/10.1534/g3.119.400037	journal	June 2019
Why Close a Bacterial Genome? The Plasmid of Alteromonas Macleodii HOT1A3 is a Vector for Inter-Specific Transfer of a Flexible Genomic Island Fadeev, Eduard; De Pascale, Fabio; Vezzi, Alessandro Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00248	journal	March 2016
Respiratory Ammonification of Nitrate Coupled to Anaerobic Oxidation of Elemental Sulfur in Deep-Sea Autotrophic Thermophilic Bacteria Slobodkina, Galina B.; Mardanov, Andrey V.; Ravin, Nikolai V. Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.00087	journal	January 2017
Replicon-Based Typing of IncI-Complex Plasmids, and Comparative Genomics Analysis of IncIγ/K1 Plasmids Zhang, Defu; Zhao, Yuzong; Feng, Jiao Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00048	journal	January 2019
Microevolution and Adaptive Strategy of Psychrophilic Species Flavobacterium bomense sp. nov. Isolated From Glaciers Liu, Qing; Liu, Hong-Can; Zhou, Yu-Guang Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01069	journal	May 2019
Genome of a Novel Bacterium “Candidatus Jettenia ecosi” Reconstructed From the Metagenome of an Anammox Bioreactor Mardanov, Andrey V.; Beletsky, Alexey V.; Ravin, Nikolai V. Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.02442	journal	October 2019
Escherichia coli ST302: Genomic Analysis of Virulence Potential and Antimicrobial Resistance Mediated by Mobile Genetic Elements Jarocki, Veronica M.; Reid, Cameron J.; Chapman, Toni A. Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.03098	journal	January 2020
Capsular Switching and ICE Transformation Occurred in Human Streptococcus agalactiae ST19 With High Pathogenicity to Fish Wang, Rui; Li, Liping; Huang, Ting Frontiers in Veterinary Science, Vol. 5 https://doi.org/10.3389/fvets.2018.00281	journal	November 2018
Sequencing and Analysis of the Genome of Propionibacterium freudenreichii T82 Strain: Importance for Industry Piwowarek, Kamil; Lipińska, Edyta; Hać-Szymańczuk, Elżbieta Biomolecules, Vol. 10, Issue 2 https://doi.org/10.3390/biom10020348	journal	February 2020
Biotechnological Potential of Cold Adapted Pseudoalteromonas spp. Isolated from ‘Deep Sea’ Sponges Borchert, Erik; Knobloch, Stephen; Dwyer, Emilie Marine Drugs, Vol. 15, Issue 6 https://doi.org/10.3390/md15060184	journal	June 2017
Genetic Screening and Expression Analysis of Psychrophilic Bacillus spp. Reveal Their Potential to Alleviate Cold Stress and Modulate Phytohormones in Wheat Microorganisms, Vol. 7, Issue 9 https://doi.org/10.3390/microorganisms7090337	journal	September 2019
Genome Sequence and Analysis ofPeptoclostridium difficileStrain ZJCDC-S82 Luo, Yun; Huang, Chen; Ye, Julian Evolutionary Bioinformatics, Vol. 12 https://doi.org/10.4137/ebo.s32476	journal	January 2016

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