The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

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

doi:10.1093/nar/gkt1226

Title: The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

Journal Article · Fri Nov 29 00:00:00 EST 2013 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkt1226· OSTI ID:1625520

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

Fellowship for Interpretation of Genomes, Burr Ridge, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States). Mathematics and Computer Science Division
Argonne National Lab. (ANL), Argonne, IL (United States). Mathematics and Computer Science Division; Univ. of Chicago, IL (United States). Computational Inst.
Fellowship for Interpretation of Genomes, Burr Ridge, IL (United States)
Univ. of Illinois at Urbana-Champaign, IL (United States). Dept. of Microbiology
San Diego State Univ., CA (United States). Dept. of Computer Science
Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States). Virginia Bioinformatics Inst.
Univ. of Chicago, IL (United States). Computation Inst.; Argonne National Lab. (ANL), Argonne, IL (United States). Computing, Environment and Life Sciences; Univ. of Chicago, IL (United States). Dept. of Computer Science

In 2004, the SEED (http://pubseed.theseed.org/) was created to provide consistent and accurate genome annotations across thousands of genomes and as a platform for discovering and developing de novo annotations. The SEED is a constantly updated integration of genomic data with a genome database, web front end, API and server scripts. It is used by many scientists for predicting gene functions and discovering new pathways. In addition to being a powerful database for bioinformatics research, the SEED also houses subsystems (collections of functionally related protein families) and their derived FIGfams (protein families), which represent the core of the RAST annotation engine (http://rast. nmpdr.org/). When a new genome is submitted to RAST, genes are called and their annotations are made by comparison to the FIGfam collection. If the genome is made public, it is then housed within the SEED and its proteins populate the FIGfam collection. This annotation cycle has proven to be a robust and scalable solution to the problem of annotating the exponentially increasing number of genomes. To date, >12 000 users worldwide have annotated >60 000 distinct genomes using RAST. Here we describe the interconnectedness of the SEED database and RAST, the RAST annotation pipeline and updates to both resources.

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

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1625520

Journal Information:: Nucleic Acids Research, Vol. 42, Issue D1; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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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
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Three New Escherichia coli Phages from the Human Gut Show Promising Potential for Phage Therapy Dalmasso, Marion; Strain, Ronan; Neve, Horst PLOS ONE, Vol. 11, Issue 6 https://doi.org/10.1371/journal.pone.0156773	journal	June 2016
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Draft Genome Sequence of Labrenzia sp. Strain EL143, a Coral-Associated Alphaproteobacterium with Versatile Symbiotic Living Capability and Strong Halogen Degradation Potential Rodrigues, Gisele Nunes; Lago-Lestón, Asunción; Costa, Rodrigo Genome Announcements, Vol. 6, Issue 10 https://doi.org/10.1128/genomeA.00132-18	journal	March 2018
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Draft Genome Sequence of a New Vibrio Strain with the Potential To Produce Bacteriocin-Like Inhibitory Substances, Isolated from the Gut Microflora of Scallop (Argopecten purpuratus) Serrano, Wilbert; Tarazona, Ulrike I.; Olaechea, Raul M. Genome Announcements, Vol. 6, Issue 20 https://doi.org/10.1128/genomea.00419-18	journal	May 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
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Complete Genome Sequence of Edwardsiella tarda Isolate FL95-01, Recovered from Channel Catfish Reichley, Stephen R.; Waldbieser, Geoffrey C.; Tekedar, Hasan C. Genome Announcements, Vol. 3, Issue 3 https://doi.org/10.1128/genomeA.00682-15	journal	June 2015
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Draft Genome Sequence of a Novel Luteimonas sp. Strain from Coral Mucus, Hawai‘i Wan, Xuehua; Miller, James M.; Rowley, Sonia J. Genome Announcements, Vol. 4, Issue 6 https://doi.org/10.1128/genomea.01228-16	journal	December 2016
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Complete Genome Sequence of Edwardsiella hoshinae ATCC 35051 Reichley, Stephen R.; Waldbieser, Geoffrey C.; Lawrence, Mark L. Genome Announcements, Vol. 5, Issue 6 https://doi.org/10.1128/genomea.01605-16	journal	February 2017
Bacteriophages of the Urinary Microbiome Miller-Ensminger, Taylor; Garretto, Andrea; Brenner, Jonathon Journal of Bacteriology, Vol. 200, Issue 7 https://doi.org/10.1128/JB.00738-17	journal	April 2018
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Draft Genome Sequence of Mediterraneibacter sp. nov. Strain gm002, Isolated from Human Feces Huang, Chien-Hsun; Liou, Jong-Shian; Wang, Chun-Lin Microbiology Resource Announcements, Vol. 8, Issue 31 https://doi.org/10.1128/mra.00217-19	journal	August 2019
Draft Genome Sequence of Desulfosporosinus fructosivorans Strain 63.6FT, Isolated from Marine Sediment in the Baltic Sea Hausmann, Bela; Vandieken, Verona; Pjevac, Petra Microbiology Resource Announcements, Vol. 8, Issue 31 https://doi.org/10.1128/mra.00427-19	journal	August 2019
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Metagenomic binning reveals versatile nutrient cycling and distinct adaptive features in alphaproteobacterial symbionts of marine sponges Karimi, Elham; Slaby, Beate M.; Soares, André R. FEMS Microbiology Ecology, Vol. 94, Issue 6 https://doi.org/10.1093/femsec/fiy074	journal	April 2018
The spread of KPC-producing Enterobacteriaceae in Spain: WGS analysis of the emerging high-risk clones of Klebsiella pneumoniae ST11/KPC-2, ST101/KPC-2 and ST512/KPC-3 Oteo, Jesús; Pérez-Vázquez, María; Bautista, Verónica Journal of Antimicrobial Chemotherapy, Vol. 71, Issue 12 https://doi.org/10.1093/jac/dkw321	journal	August 2016
Complete genetic analysis of plasmids carrying mcr-1 and other resistance genes in an Escherichia coli isolate of animal origin Li, Ruichao; Xie, Miaomiao; Lv, Jingzhang Journal of Antimicrobial Chemotherapy https://doi.org/10.1093/jac/dkw509	journal	December 2016
Halomonas nigrificans sp. nov., isolated from cheese Oguntoyinbo, Folarin A.; Cnockaert, Margo; Cho, Gyu-Sung International Journal of Systematic and Evolutionary Microbiology, Vol. 68, Issue 1 https://doi.org/10.1099/ijsem.0.002515	journal	January 2018
Genome analysis of clinical multilocus sequence Type 11 Klebsiella pneumoniae from China Dong, Ning; Zhang, Rong; Liu, Lizhang Microbial Genomics, Vol. 4, Issue 2 https://doi.org/10.1099/mgen.0.000149	journal	February 2018
The cell wall of the filamentous anoxygenic phototrophic bacterium Oscillochloris trichoides Keppen, Olga I.; Ivanovsky, Ruslan N.; Streshinskaya, Galina M. Microbiology, Vol. 164, Issue 1 https://doi.org/10.1099/mic.0.000590	journal	January 2018
New archaeal viruses discovered by metagenomic analysis of viral communities in enrichment cultures Liu, Ying; Brandt, David; Ishino, Sonoko Environmental Microbiology, Vol. 21, Issue 6 https://doi.org/10.1111/1462-2920.14479	journal	January 2019
Holocene paleodepositional changes reflected in the sedimentary microbiome of the Black Sea More, Kuldeep D.; Giosan, Liviu; Grice, Kliti Geobiology, Vol. 17, Issue 4 https://doi.org/10.1111/gbi.12338	journal	March 2019
Whole genome mining reveals a diverse repertoire of lanthionine synthetases and lanthipeptides among the genus Paenibacillus Baindara, P.; Nallabelli, N.; Korpole, S. Journal of Applied Microbiology, Vol. 128, Issue 2 https://doi.org/10.1111/jam.14495	journal	November 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
Complete Genome Sequence of a Deletion Mutant of Vibrio parahaemolyticus from Pacific White Shrimp (Penaeus vannamei) Kanrar, Siddhartha; Dhar, Arun K. Genome Announcements, Vol. 6, Issue 25 https://doi.org/10.1128/genomea.00544-18	journal	June 2018
Genome Sequence of “ Candidatus Thioglobus singularis” Strain PS1, a Mixotroph from the SUP05 Clade of Marine Gammaproteobacteria Marshall, Katharine T.; Morris, Robert M. Genome Announcements, Vol. 3, Issue 5 https://doi.org/10.1128/genomea.01155-15	journal	October 2015
Draft Genome Sequences of Acinetobacter and Bacillus Strains Isolated from Spacecraft-Associated Surfaces Seuylemezian, Arman; Vaishampayan, Parag; Cooper, Kerry Genome Announcements, Vol. 6, Issue 6 https://doi.org/10.1128/genomea.01554-17	journal	February 2018
Manganese Detoxification by MntE Is Critical for Resistance to Oxidative Stress and Virulence of Staphylococcus aureus Grunenwald, Caroline M.; Choby, Jacob E.; Juttukonda, Lillian J. mBio, Vol. 10, Issue 1 https://doi.org/10.1128/mbio.02915-18	journal	February 2019
Complete Genome Sequence of Lactobacillus reuteri PNW1, a Promising Probiotic Candidate Alayande, Kazeem A.; Aiyegoro, Olayinka A.; Ateba, Collins N. Microbiology Resource Announcements, Vol. 8, Issue 8 https://doi.org/10.1128/mra.00034-19	journal	February 2019
Draft Genome Sequence of a Fermenting Bacterium, Soehngenia sp. Strain 1933P, Isolated from a Petroleum Reservoir in Azerbaijan Grouzdev, Denis S.; Bidzhieva, Salimat K.; Sokolova, Diyana S. Microbiology Resource Announcements, Vol. 8, Issue 29 https://doi.org/10.1128/mra.00689-19	journal	July 2019
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
Structural and functional organization of the plasmid regulons of Rhizobium leguminosarum symbiotic genes Chirak, E. R.; Kopat’, V. V.; Kimeklis, A. K. Microbiology, Vol. 85, Issue 6 https://doi.org/10.1134/s0026261716060072	journal	November 2016
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Comparative genome and transcriptome analysis reveals distinctive surface characteristics and unique physiological potentials of Pseudomonas aeruginosa ATCC 27853 Cao, Huiluo; Lai, Yong; Bougouffa, Salim BMC Genomics, Vol. 18, Issue 1 https://doi.org/10.1186/s12864-017-3842-z	journal	June 2017
Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures Medvecky, Matej; Cejkova, Darina; Polansky, Ondrej BMC Genomics, Vol. 19, Issue 1 https://doi.org/10.1186/s12864-018-4959-4	journal	July 2018
In vivo competition and horizontal gene transfer among distinct Staphylococcus aureus lineages as major drivers for adaptational changes during long-term persistence in humans Langhanki, Lars; Berger, Petya; Treffon, Janina BMC Microbiology, Vol. 18, Issue 1 https://doi.org/10.1186/s12866-018-1308-3	journal	October 2018
The use of genome-scale metabolic network reconstruction to predict fluxes and equilibrium composition of N-fixing versus C-fixing cells in a diazotrophic cyanobacterium, Trichodesmium erythraeum Gardner, Joseph J.; Boyle, Nanette R. BMC Systems Biology, Vol. 11, Issue 1 https://doi.org/10.1186/s12918-016-0383-z	journal	January 2017
Dissection of exopolysaccharide biosynthesis in Kozakia baliensis Brandt, Julia U.; Jakob, Frank; Behr, Jürgen Microbial Cell Factories, Vol. 15, Issue 1 https://doi.org/10.1186/s12934-016-0572-x	journal	October 2016
Genome architecture of Lactobacillus plantarum PS128, a probiotic strain with potential immunomodulatory activity Liu, Wei-Hsien; Yang, Chih-Hsien; Lin, Ching-Ting Gut Pathogens, Vol. 7, Issue 1 https://doi.org/10.1186/s13099-015-0068-y	journal	August 2015
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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
Draft genome sequence of the strain 16-537536, isolated from a patient with bronchiectasis and its relationship to the Pseudomonas koreensis group of the Pseudomonas fluorescens complex Fluit, Ad. C.; Rogers, Malbert R. C.; Díez-Aguilar, María BMC Research Notes, Vol. 13, Issue 1 https://doi.org/10.1186/s13104-019-4863-2	journal	January 2020
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Draft genome sequence of Cellulomonas carbonis T26T and comparative analysis of six Cellulomonas genomes Zhuang, Weiping; Zhang, Shengzhe; Xia, Xian Standards in Genomic Sciences, Vol. 10, Issue 1 https://doi.org/10.1186/s40793-015-0096-8	journal	November 2015
Insights from the draft genome of the subsection V (Stigonematales) cyanobacterium Hapalosiphon sp. Strain MRB220 associated with 2-MIB production Tan, Boon Fei; Te, Shu Harn; Boo, Chek Yin Standards in Genomic Sciences, Vol. 11, Issue 1 https://doi.org/10.1186/s40793-016-0175-5	journal	September 2016
Complete genome sequence of Pseudomonas citronellolis P3B5, a candidate for microbial phyllo-remediation of hydrocarbon-contaminated sites Remus-Emsermann, Mitja N. P.; Schmid, Michael; Gekenidis, Maria-Theresia Standards in Genomic Sciences, Vol. 11, Issue 1 https://doi.org/10.1186/s40793-016-0190-6	journal	September 2016
New Applications of Synthetic Biology Tools for Cyanobacterial Metabolic Engineering Santos-Merino, María; Singh, Amit K.; Ducat, Daniel C. Frontiers in Bioengineering and Biotechnology, Vol. 7 https://doi.org/10.3389/fbioe.2019.00033	journal	February 2019
QnrS1- and Aac(6′)-Ib-cr-Producing Escherichia coli among Isolates from Animals of Different Sources: Susceptibility and Genomic Characterization Jones-Dias, Daniela; Manageiro, Vera; Graça, Rafael Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00671	journal	May 2016
Comparative Genomics and Transcriptional Analysis of Flavobacterium columnare Strain ATCC 49512 Tekedar, Hasan C.; Karsi, Attila; Reddy, Joseph S. Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.00588	journal	April 2017
Salmonella enterica serovar Infantis from Food and Human Infections, Switzerland, 2010–2015: Poultry-Related Multidrug Resistant Clones and an Emerging ESBL Producing Clonal Lineage Hindermann, Denise; Gopinath, Gopal; Chase, Hannah Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.01322	journal	July 2017
Comparative Genomics of Thalassobius Including the Description of Thalassobius activus sp. nov., and Thalassobius autumnalis sp. nov. Pujalte, María J.; Lucena, Teresa; Rodrigo-Torres, Lidia Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.02645	journal	January 2018
Extended Spectrum Beta-Lactamase-Producing Gram-Negative Bacteria Recovered From an Amazonian Lake Near the City of Belém, Brazil Freitas, Dhara Y.; Araújo, Susana; Folador, Adriana R. C. Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00364	journal	February 2019
Whole Genome Sequencing-Based Comparison of Food Isolates of Cronobacter sakazakii Aly, Mohamed A.; Domig, Konrad J.; Kneifel, Wolfgang Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01464	journal	July 2019
Rhizosphere Metagenomics of Paspalum scrobiculatum L. (Kodo Millet) Reveals Rhizobiome Multifunctionalities Prabha, Ratna; Singh, Dhananjaya P.; Gupta, Shailendra Microorganisms, Vol. 7, Issue 12 https://doi.org/10.3390/microorganisms7120608	journal	November 2019
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Miniphocibacter massiliensis gen. nov., sp. nov., a new species isolated from the human gut and its taxono‐genomics description Bilen, Melhem; Mbogning Fonkou, Maxime D.; Nguyen, Thi T. MicrobiologyOpen, Vol. 8, Issue 5 https://doi.org/10.1002/mbo3.735	journal	October 2018
Aquella oligotrophica gen. nov. sp. nov.: A new member of the family Neisseriaceae isolated from laboratory tap water Chan, Kok‐Gan; See‐Too, Wah‐Seng; Chua, Kah‐Ooi MicrobiologyOpen, Vol. 8, Issue 7 https://doi.org/10.1002/mbo3.793	journal	December 2018
Description of Alteromonas abrolhosensis sp. nov., isolated from sea water of Abrolhos Bank, Brazil Nóbrega, Maria S.; Silva, Bruno S.; Leomil, Luciana Antonie van Leeuwenhoek, Vol. 111, Issue 7 https://doi.org/10.1007/s10482-018-1016-x	journal	January 2018
Draft genome sequence of Bacillus paralicheniformis TRQ65, a biological control agent and plant growth-promoting bacterium isolated from wheat (Triticum turgidum subsp. durum) rhizosphere in the Yaqui Valley, Mexico Valenzuela-Ruiz, Valeria; Robles-Montoya, Rosa Icela; Parra-Cota, Fannie Isela 3 Biotech, Vol. 9, Issue 11 https://doi.org/10.1007/s13205-019-1972-5	journal	November 2019
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The outer mucus layer hosts a distinct intestinal microbial niche Li, Hai; Limenitakis, Julien P.; Fuhrer, Tobias Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms9292	journal	September 2015
Functional annotation of orthologs in metagenomes: a case study of genes for the transformation of oceanic dimethylsulfoniopropionate González, José M.; Hernández, Laura; Manzano, Iris The ISME Journal, Vol. 13, Issue 5 https://doi.org/10.1038/s41396-019-0347-6	journal	January 2019
HqiA, a novel quorum-quenching enzyme which expands the AHL lactonase family Torres, Marta; Uroz, Stéphane; Salto, Rafael Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-01176-7	journal	April 2017
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Novel genomic island modifies DNA with 7-deazaguanine derivatives Thiaville, Jennifer J.; Kellner, Stefanie M.; Yuan, Yifeng Proceedings of the National Academy of Sciences, Vol. 113, Issue 11 https://doi.org/10.1073/pnas.1518570113	journal	February 2016
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Bacillus glycinifermentans sp. nov., isolated from fermented soybean paste Kim, Soo-Jin; Dunlap, Christopher A.; Kwon, Soon-Wo International Journal of Systematic and Evolutionary Microbiology, Vol. 65, Issue Pt_10 https://doi.org/10.1099/ijsem.0.000462	journal	October 2015
Ruegeria lutea sp. nov., isolated from marine sediment, Masan Bay, South Korea Kim, Jinsoo; Kim, Da-Young; Yang, Keun-Hyeok International Journal of Systematic and Evolutionary Microbiology, Vol. 69, Issue 9 https://doi.org/10.1099/ijsem.0.003568	journal	September 2019
Characterization of the first cultured representative of a Bacteroidetes clade specialized on the scavenging of cyanobacteria : Cyanobacteria foraging in hypersaline mats Ben Hania, Wajdi; Joseph, Manon; Bunk, Boyke Environmental Microbiology, Vol. 19, Issue 3 https://doi.org/10.1111/1462-2920.13639	journal	January 2017
A common mechanism for efficient N ₂ O reduction in diverse isolates of nodule‐forming bradyrhizobia Mania, Daniel; Woliy, Kedir; Degefu, Tulu Environmental Microbiology, Vol. 22, Issue 1 https://doi.org/10.1111/1462-2920.14731	journal	July 2019
Thiomicrorhabdus streamers and sulfur cycling in perennial hypersaline cold springs in the Canadian high Arctic Magnuson, Elisse; Mykytczuk, Nadia C. S.; Pellerin, Andre Environmental Microbiology https://doi.org/10.1111/1462-2920.14916	journal	January 2020
Rhizobacteria improve sugarcane growth and photosynthesis under well-watered conditions: Rhizobacteria and sugarcane Rampazzo, P. E.; Marcos, F. C. C.; Cipriano, M. A. P. Annals of Applied Biology, Vol. 172, Issue 3 https://doi.org/10.1111/aab.12421	journal	February 2018
Transcriptional and Functional Analysis of Bifidobacterium animalis subsp. lactis Exposure to Tetracycline Morovic, Wesley; Roos, Paige; Zabel, Bryan Applied and Environmental Microbiology, Vol. 84, Issue 23 https://doi.org/10.1128/aem.01999-18	journal	December 2018
Genome Sequence of “ Candidatus Thioglobus autotrophica” Strain EF1, a Chemoautotroph from the SUP05 Clade of Marine Gammaproteobacteria Shah, Vega; Morris, Robert M. Genome Announcements, Vol. 3, Issue 5 https://doi.org/10.1128/genomea.01156-15	journal	October 2015
Draft Genome Sequence of Streptomyces sp. Strain JV178, a Producer of Clifednamide-Type Polycyclic Tetramate Macrolactams Qi, Yunci; D’Alessandro, John M.; Blodgett, Joshua A. V. Genome Announcements, Vol. 6, Issue 1 https://doi.org/10.1128/genomea.01401-17	journal	January 2018
Genome Sequences of Bacillus sporothermodurans Strains Isolated from Ultra-High-Temperature Milk Owusu-Darko, Rodney; Allam, Mushal; de Oliveira, Sílvia D. Microbiology Resource Announcements, Vol. 8, Issue 22 https://doi.org/10.1128/mra.00145-19	journal	May 2019
Draft Genome Sequence of Blautia sp. Strain BCRC 81119, Isolated from Human Feces Huang, Chien-Hsun; Liou, Jong-Shian; Wang, Chun-Lin Microbiology Resource Announcements, Vol. 7, Issue 4 https://doi.org/10.1128/mra.00812-18	journal	August 2018
Draft Genome Sequence of Ruminococcus sp. nov. B05, Isolated from Human Feces Huang, Chien-Hsun; Liou, Jong-Shian; Wang, Chun-Lin Microbiology Resource Announcements, Vol. 8, Issue 2 https://doi.org/10.1128/mra.01458-18	journal	January 2019
Genome Sequence of Bacillus velezensis 5RB, an Overproducer of 2,3-Butanediol Petrova, Penka; Velikova, Petya; Petrov, Kaloyan Microbiology Resource Announcements, Vol. 8, Issue 1 https://doi.org/10.1128/mra.01475-18	journal	January 2019
The Gut Commensal Microbiome of Drosophila melanogaster Is Modified by the Endosymbiont Wolbachia Simhadri, Rama K.; Fast, Eva M.; Guo, Rong mSphere, Vol. 2, Issue 5 https://doi.org/10.1128/msphere.00287-17	journal	October 2017
Life at Home and on the Roam: Genomic Adaptions Reflect the Dual Lifestyle of an Intracellular, Facultative Symbiont Burgsdorf, Ilia; Handley, Kim M.; Bar-Shalom, Rinat mSystems, Vol. 4, Issue 4 https://doi.org/10.1128/msystems.00057-19	journal	May 2019
Consumption of a Western-Style Diet Modulates the Response of the Murine Gut Microbiome to Ciprofloxacin Cabral, Damien J.; Wurster, Jenna I.; Korry, Benjamin J. mSystems, Vol. 5, Issue 4 https://doi.org/10.1128/msystems.00317-20	journal	August 2020
Prebiotic Potential of Culinary Spices Used to Support Digestion and Bioabsorption Peterson, Christine T.; Rodionov, Dmitry A.; Iablokov, Stanislav N. Evidence-Based Complementary and Alternative Medicine, Vol. 2019 https://doi.org/10.1155/2019/8973704	journal	June 2019
Comparative genomics of Pseudomonas fluorescens subclade III strains from human lungs Scales, Brittan S.; Erb-Downward, John R.; Huffnagle, Ian M. BMC Genomics, Vol. 16, Issue 1 https://doi.org/10.1186/s12864-015-2261-2	journal	December 2015
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
Plasmid composition in Aeromonas salmonicida subsp. salmonicida 01-B526 unravels unsuspected type three secretion system loss patterns Tanaka, Katherine H.; Vincent, Antony T.; Emond-Rheault, Jean-Guillaume BMC Genomics, Vol. 18, Issue 1 https://doi.org/10.1186/s12864-017-3921-1	journal	July 2017
Wound infection with Vibrio harveyi following a traumatic leg amputation after a motorboat propeller injury in Mallorca, Spain: a case report and review of literature Brehm, Thomas Theo; Berneking, Laura; Rohde, Holger BMC Infectious Diseases, Vol. 20, Issue 1 https://doi.org/10.1186/s12879-020-4789-2	journal	February 2020
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Identification and molecular epidemiology of methicillin resistant Staphylococcus pseudintermedius strains isolated from canine clinical samples in Argentina Gagetti, Paula; Wattam, Alice R.; Giacoboni, Gabriela BMC Veterinary Research, Vol. 15, Issue 1 https://doi.org/10.1186/s12917-019-1990-x	journal	July 2019
Comparative proteome analysis in an Escherichia coli CyDisCo strain identifies stress responses related to protein production, oxidative stress and accumulation of misfolded protein Guerrero Montero, Isabel; Dolata, Katarzyna Magdalena; Schlüter, Rabea Microbial Cell Factories, Vol. 18, Issue 1 https://doi.org/10.1186/s12934-019-1071-7	journal	January 2019
Whole-genome sequencing and comparative genomic analysis of Escherichia coli O91 strains isolated from symptomatic and asymptomatic human carriers Kwon, Taesoo; Bak, Young-Seok; Jung, Young-Hee Gut Pathogens, Vol. 8, Issue 1 https://doi.org/10.1186/s13099-016-0138-9	journal	November 2016
The dynamics of the piglet gut microbiome during the weaning transition in association with health and nutrition Guevarra, Robin B.; Hong, Sang Hyun; Cho, Jin Ho Journal of Animal Science and Biotechnology, Vol. 9, Issue 1 https://doi.org/10.1186/s40104-018-0269-6	journal	July 2018
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Complete genome of Rhizobium leguminosarum Norway, an ineffective Lotus micro-symbiont Liang, Juan; Hoffrichter, Anne; Brachmann, Andreas Standards in Genomic Sciences, Vol. 13, Issue 1 https://doi.org/10.1186/s40793-018-0336-9	journal	December 2018
Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome Steinway, Steven N.; Biggs, Matthew B.; Loughran, Thomas P. PLOS Computational Biology, Vol. 11, Issue 6 https://doi.org/10.1371/journal.pcbi.1004338	journal	June 2015
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Genome-Guided Insights into the Plant Growth Promotion Capabilities of the Physiologically Versatile Bacillus aryabhattai Strain AB211 Bhattacharyya, Chandrima; Bakshi, Utpal; Mallick, Ivy Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.00411	journal	March 2017
Genome Sequencing of Extended-Spectrum β-Lactamase (ESBL)-Producing Klebsiella pneumoniae Isolated from Pigs and Abattoir Workers in Cameroon Founou, Luria L.; Founou, Raspail C.; Allam, Mushal Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00188	journal	February 2018
Comparative Metatranscriptomics of Wheat Rhizosphere Microbiomes in Disease Suppressive and Non-suppressive Soils for Rhizoctonia solani AG8 Hayden, Helen L.; Savin, Keith W.; Wadeson, Jenny Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00859	journal	May 2018
Metagenomic and Resistome Analysis of a Full-Scale Municipal Wastewater Treatment Plant in Singapore Containing Membrane Bioreactors Ng, Charmaine; Tan, Boonfei; Jiang, Xiao-Tao Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00172	journal	February 2019
Genomic Features, Comparative Genomic Analysis, and Antimicrobial Susceptibility Patterns of Chryseobacterium arthrosphaerae Strain ED882-96 Isolated in Taiwan Liang, Chih-Yu; Yang, Chih-Hui; Lai, Chung-Hsu Genes, Vol. 10, Issue 4 https://doi.org/10.3390/genes10040309	journal	April 2019
Comparative Genomic Insights into Secondary Metabolism Biosynthetic Gene Cluster Distributions of Marine Streptomyces Xu, Lin; Ye, Kai-Xiong; Dai, Wen-Hua Marine Drugs, Vol. 17, Issue 9 https://doi.org/10.3390/md17090498	journal	August 2019
Comparative Analysis of Listeria monocytogenes Plasmids and Expression Levels of Plasmid-Encoded Genes during Growth under Salt and Acid Stress Conditions Hingston, Patricia; Brenner, Thomas; Truelstrup Hansen, Lisbeth Toxins, Vol. 11, Issue 7 https://doi.org/10.3390/toxins11070426	journal	July 2019
Galleria mellonella as an infection model to investigate virulence of Vibrio parahaemolyticus Wagley, Sariqa; Borne, Richard; Harrison, Jamie Taylor & Francis https://doi.org/10.6084/m9.figshare.7492112.v1	text	January 2018
Sequencing at sea: Challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition Lim, Yan Wei; Cuevas, Daniel A.; Silva, Genivaldo Gueiros Z. https://doi.org/10.7287/peerj.preprints.433v1	preprint	July 2014
A KBase Case Study on Genome-wide Transcriptomics and Plant Primary Metabolism in Sorghum Kumari, Sunita Cold Spring Harbor Laboratory Cold Spring Harbor, NY (United States) https://doi.org/10.25982/101788.79/1828290	dataset	January 2021
Genome Extraction from Shotgun Metagenome Sequence Data Chivian, Dylan; Jungbluth, Sean; Dehal, Paramvir U.S. Department of Energy Systems Biology Knowledgebase https://doi.org/10.25982/33233.606/1831502	dataset	January 2021
Osur_paper Kiefer, Julian Johannes Gutenberg Universität Mainz, Mainz, Rheinland-Pfalz, DE https://doi.org/10.25982/58799.728/1798340	dataset	January 2021
Genomic insights of Pannonibacter phragmitetus strain 31801 isolated from a patient with a liver abscess Zhou, Yajun; Jiang, Tao; Hu, Shaohua MicrobiologyOpen, Vol. 6, Issue 6 https://doi.org/10.1002/mbo3.515	journal	August 2017
Nitrogen assimilation in denitrifier Bacillus azotoformans LMG 9581T Sun, Yihua; De Vos, Paul; Willems, Anne Antonie van Leeuwenhoek, Vol. 110, Issue 12 https://doi.org/10.1007/s10482-017-0911-x	journal	July 2017
Man-made microbial resistances in built environments Mahnert, Alexander; Moissl-Eichinger, Christine; Zojer, Markus Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-08864-0	journal	February 2019
Impact of Module-X2 and Carbohydrate Binding Module-3 on the catalytic activity of associated glycoside hydrolases towards plant biomass Pasari, Nandita; Adlakha, Nidhi; Gupta, Mayank Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-03927-y	journal	June 2017
Microbial bioinformatics for food safety and production Alkema, Wynand; Boekhorst, Jos; Wels, Michiel Briefings in Bioinformatics, Vol. 17, Issue 2 https://doi.org/10.1093/bib/bbv034	journal	June 2015
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
Curation, integration and visualization of bacterial virulence factors in PATRIC Mao, Chunhong; Abraham, David; Wattam, Alice R. Bioinformatics, Vol. 31, Issue 2 https://doi.org/10.1093/bioinformatics/btu631	journal	September 2014
Pedobacter chinensis sp. nov., a cellulose-decomposing bacterium from Arctic tundra soil Zhou, Liu-Yan; Chen, Xu-Yang; Du, Zong-Jun International Journal of Systematic and Evolutionary Microbiology, Vol. 69, Issue 7 https://doi.org/10.1099/ijsem.0.003403	journal	July 2019
Algoriphagus aquimaris sp. nov., isolated from seashore sand Kim, Jinsoo; Yoon, Sung-Ho; Yang, Keun-Hyeok International Journal of Systematic and Evolutionary Microbiology, Vol. 70, Issue 2 https://doi.org/10.1099/ijsem.0.003793	journal	February 2020
In Silico Identification of Three Types of Integrative and Conjugative Elements (ICEs) in Elizabethkingia anophelis Strains Isolated from Around the World Xu, Jiannong; Pei, Dong; Nicholson, Ainsley mSphere https://doi.org/10.1101/402107	posted_content	August 2018
Identifying the Biosynthetic Gene Cluster for Triacsins with an N-hydroxytriazene Moiety Twigg, Frederick F.; Cai, Wenlong; Huang, Wei ChemBioChem https://doi.org/10.1101/495424	posted_content	December 2018
New Methyloceanibacter diversity from North Sea sediments includes methanotroph containing solely the soluble methane monooxygenase: New Methyloceanibacter Diversity from North Sea Sediments Vekeman, Bram; Kerckhof, Frederiek-Maarten; Cremers, Geert Environmental Microbiology, Vol. 18, Issue 12 https://doi.org/10.1111/1462-2920.13485	journal	September 2016
Phylogeny and genomics of SAUL, an enigmatic bacterial lineage frequently associated with marine sponges: Phylogeny and genomics of SAUL Astudillo-García, Carmen; Slaby, Beate M.; Waite, David W. Environmental Microbiology, Vol. 20, Issue 2 https://doi.org/10.1111/1462-2920.13965	journal	November 2017
Insights into microbial community structure and function from a shallow, simulated CO ₂ ‐leakage aquifer demonstrate microbial selection and adaptation Gulliver, Djuna; Lipus, Daniel; Ross, Daniel Environmental Microbiology Reports, Vol. 11, Issue 3 https://doi.org/10.1111/1758-2229.12675	journal	August 2018
Iron acquisition and siderophore production in the fish pathogen Renibacterium salmoninarum Bethke, J.; Poblete-Morales, M.; Irgang, R. Journal of Fish Diseases, Vol. 39, Issue 11 https://doi.org/10.1111/jfd.12456	journal	January 2016
A novel streptococcal cell–cell communication peptide promotes pneumococcal virulence and biofilm formation Cuevas, Rolando A.; Eutsey, Rory; Kadam, Anagha Molecular Microbiology, Vol. 105, Issue 4 https://doi.org/10.1111/mmi.13721	journal	June 2017
Three Draft Genome Sequences of Vibrio coralliilyticus Strains Isolated from Bivalve Hatcheries Kehlet-Delgado, Hanna; Richards, Gary P.; Häse, Claudia Genome Announcements, Vol. 5, Issue 41 https://doi.org/10.1128/genomea.01162-17	journal	October 2017
Databases for Microbiologists: TABLE 1 Zhulin, Igor B. Journal of Bacteriology, Vol. 197, Issue 15 https://doi.org/10.1128/jb.00330-15	journal	May 2015
The Complete Genome Sequence of the Emerging Pathogen Mycobacterium haemophilum Explains Its Unique Culture Requirements Tufariello, JoAnn M.; Kerantzas, Christopher A.; Vilchèze, Catherine mBio, Vol. 6, Issue 6 https://doi.org/10.1128/mbio.01313-15	journal	November 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
Draft Genome Sequence of the Non-Microcystin-Producing Microcystis aeruginosa Strain KLA2, Isolated from a Freshwater Reservoir in Northern California, USA Moisander, Pia H.; Ochiai, Mari Microbiology Resource Announcements, Vol. 9, Issue 3 https://doi.org/10.1128/mra.01086-19	journal	January 2020
Complete Genome Sequence of Aeromonas Phage ZPAH7 with Halo Zones, Isolated in China Islam, Mohammad Sharifull; Raz, Assaf; Liu, Yang Microbiology Resource Announcements, Vol. 8, Issue 10 https://doi.org/10.1128/mra.01678-18	journal	March 2019
Comparative Genome Analyses of Vibrio anguillarum Strains Reveal a Link with Pathogenicity Traits Castillo, Daniel; Alvise, Paul D.; Xu, Ruiqi mSystems, Vol. 2, Issue 1 https://doi.org/10.1128/msystems.00001-17	journal	February 2017
Environmentally-driven gene content convergence and the Bacillus phylogeny Hernández-González, Ismael L.; Moreno-Hagelsieb, Gabriel; Olmedo-Álvarez, Gabriela BMC Evolutionary Biology, Vol. 18, Issue 1 https://doi.org/10.1186/s12862-018-1261-7	journal	October 2018
Genomic characterization of Ensifer aridi, a proposed new species of nitrogen-fixing rhizobium recovered from Asian, African and American deserts Le Quéré, Antoine; Tak, Nisha; Gehlot, Hukam Singh BMC Genomics, Vol. 18, Issue 1 https://doi.org/10.1186/s12864-016-3447-y	journal	January 2017
Comparative genome analysis reveals key genetic factors associated with probiotic property in Enterococcus faecium strains Ghattargi, Vikas C.; Gaikwad, Meghana A.; Meti, Bharati S. BMC Genomics, Vol. 19, Issue 1 https://doi.org/10.1186/s12864-018-5043-9	journal	September 2018
Genome and proteome of the chlorophyll f-producing cyanobacterium Halomicronema hongdechloris: adaptative proteomic shifts under different light conditions Chen, Min; Hernandez-Prieto, Miguel A.; Loughlin, Patrick C. BMC Genomics, Vol. 20, Issue 1 https://doi.org/10.1186/s12864-019-5587-3	journal	March 2019
Regional outbreak of community-associated methicillin-resistant Staphylococcus aureus ST834 in Japanese children Uehara, Yuki; Sasaki, Takashi; Baba, Tadashi BMC Infectious Diseases, Vol. 19, Issue 1 https://doi.org/10.1186/s12879-018-3646-z	journal	January 2019
Decoding the complete arsenal for cellulose and hemicellulose deconstruction in the highly efficient cellulose decomposer Paenibacillus O199 López-Mondéjar, Rubén; Zühlke, Daniela; Větrovský, Tomáš Biotechnology for Biofuels, Vol. 9, Issue 1 https://doi.org/10.1186/s13068-016-0518-x	journal	May 2016
Complete genome sequence of a commensal bacterium, Hafnia alvei CBA7124, isolated from human feces Song, Hye Seon; Kim, Joon Yong; Kim, Yeon Bee Gut Pathogens, Vol. 9, Issue 1 https://doi.org/10.1186/s13099-017-0190-0	journal	July 2017
Draft genome sequences of two opportunistic pathogenic strains of Staphylococcus cohnii isolated from human patients Mendoza-Olazarán, Soraya; Garcia-Mazcorro, José F.; Morfín-Otero, Rayo Standards in Genomic Sciences, Vol. 12, Issue 1 https://doi.org/10.1186/s40793-017-0263-1	journal	August 2017
Draft genome sequence of the type strain of the sulfur-oxidizing acidophile, Acidithiobacillus albertensis (DSM 14366) Castro, Matías; Moya-Beltrán, Ana; Covarrubias, Paulo C. Standards in Genomic Sciences, Vol. 12, Issue 1 https://doi.org/10.1186/s40793-017-0282-y	journal	December 2017
Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes Xavier, Joana C.; Patil, Kiran Raosaheb; Rocha, Isabel PLOS Computational Biology, Vol. 14, Issue 11 https://doi.org/10.1371/journal.pcbi.1006556	journal	November 2018
Community-intrinsic properties enhance keratin degradation from bacterial consortia Nasipuri, Poonam; Herschend, Jakob; Brejnrod, Asker D. PLOS ONE, Vol. 15, Issue 1 https://doi.org/10.1371/journal.pone.0228108	journal	January 2020
Genomic Characterization of Lactobacillus delbrueckii TUA4408L and Evaluation of the Antiviral Activities of its Extracellular Polysaccharides in Porcine Intestinal Epithelial Cells Kanmani, Paulraj; Albarracin, Leonardo; Kobayashi, Hisakazu Frontiers in Immunology, Vol. 9 https://doi.org/10.3389/fimmu.2018.02178	journal	September 2018
Conjugative Transfer of a Novel Staphylococcal Plasmid Encoding the Biocide Resistance Gene, qacA LaBreck, Patrick T.; Rice, Gregory K.; Paskey, Adrian C. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.02664	journal	November 2018
Biological Potential of Chitinolytic Marine Bacteria Paulsen, Sara; Andersen, Birgitte; Gram, Lone Marine Drugs, Vol. 14, Issue 12 https://doi.org/10.3390/md14120230	journal	December 2016
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
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
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
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
KBase Narrative - kb_DRAM P. normanii annotation with model Flynn, Rory; Faria, José U.S. Department of Energy Systems Biology Knowledgebase https://doi.org/10.25982/128174.5/1893104	dataset	January 2022
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
Complete Genome Sequence of Starkeya sp. Strain ORNL1, a Soil Alphaproteobacterium Isolated from the Rhizosphere of Populus deltoides 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/10.25982/55377.22/1637507	dataset	January 2020
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
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
Case Study: Can you find Delftia? Krebs, Rose; Goller, Carlos C. https://doi.org/10.25982/67335.259/1773074		August 2020
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
Omics-to-Reactive-Transport (ORT): A workflow linking genome-scale metabolic models with reactive transport codes Rubinstein, Rebecca; Borton, Mikayla; Zhou, Haiyan U.S. Department of Energy Systems Biology Knowledgebase https://doi.org/10.25982/71260.262/1827108	dataset	January 2021
Genome sequence of Methylocystis hirsuta CSC1, a polyhydroxyalkanoate producing methanotroph Bordel, Sergio; Rodríguez, Elisa; Muñoz, Raúl MicrobiologyOpen, Vol. 8, Issue 6 https://doi.org/10.1002/mbo3.771	journal	December 2018
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
Data on genome sequencing, assembly, annotation and genomic analysis of Rhodococcus rhodochrous strain SPC17 isolated from Lonar Lake Kumar, Satish; Paul, Dhiraj; Shouche, Yogesh Data in Brief, Vol. 29 https://doi.org/10.1016/j.dib.2020.105336	journal	April 2020
Noncontiguous finished genome sequence and description of Paenibacillus ihumii sp. nov. strain AT5 Togo, A. H.; Khelaifia, S.; Lagier, J. -C. New Microbes and New Infections, Vol. 10 https://doi.org/10.1016/j.nmni.2016.01.013	journal	March 2016
Author Correction: Searching for signatures across microbial communities: Metagenomic analysis of soil samples from mangrove and other ecosystems Imchen, Madangchanok; Kumavath, Ranjith; Barh, Debmalya Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-017-18550-0	journal	January 2018
Citrobacter freundii fitness during bloodstream infection Anderson, Mark T.; Mitchell, Lindsay A.; Zhao, Lili Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-30196-0	journal	August 2018
Comparative Genomics of 86 Whole-Genome Sequences in the Six Species of the Elizabethkingia Genus Reveals Intraspecific and Interspecific Divergence Liang, Chih-Yu; Yang, Chih-Hui; Lai, Chung-Hsu Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-55795-3	journal	December 2019
Genomic Epidemiology of Vancomycin-Resistant Enterococcus faecium (VREfm) in Latin America: Revisiting The Global VRE Population Structure Rios, Rafael; Reyes, Jinnethe; Carvajal, Lina P. Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-62371-7	journal	March 2020
Diversity of antibiotic-resistance genes in Canadian isolates of Aeromonas salmonicida subsp. salmonicida: dominance of pSN254b and discovery of pAsa8 Trudel, Mélanie V.; Vincent, Antony T.; Attéré, Sabrina A. Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep35617	journal	October 2016
Transcriptomic analysis of the highly efficient oil-degrading bacteriumAcinetobacter venetianusRAG-1 reveals genes important in dodecane uptake and utilization Kothari, Ankita; Charrier, Marimikel; Wu, Yu-Wei FEMS Microbiology Letters, Vol. 363, Issue 20 https://doi.org/10.1093/femsle/fnw224	journal	September 2016
The Variable Regions ofLactobacillus rhamnosusGenomes Reveal the Dynamic Evolution of Metabolic and Host-Adaptation Repertoires Ceapa, Corina; Davids, Mark; Ritari, Jarmo Genome Biology and Evolution, Vol. 8, Issue 6 https://doi.org/10.1093/gbe/evw123	journal	June 2016
Whole-Genome Sequence of the Anaerobic Isosaccharinic Acid Degrading Isolate, Macellibacteroides fermentans Strain HH-ZS Rout, Simon P.; Salah, Zohier B.; Charles, Christopher J. Genome Biology and Evolution, Vol. 9, Issue 8 https://doi.org/10.1093/gbe/evx151	journal	August 2017
A novel bifunctional transcriptional regulator of riboflavin metabolism in Archaea Rodionova, Irina A.; Vetting, Matthew W.; Li, Xiaoqing Nucleic Acids Research https://doi.org/10.1093/nar/gkw1331	journal	January 2017
Effects of microbiota-directed foods in gnotobiotic animals and undernourished children Gehrig, Jeanette L.; Venkatesh, Siddarth; Chang, Hao-Wei Science, Vol. 365, Issue 6449 https://doi.org/10.1126/science.aau4732	journal	July 2019
Complete Genome Sequence of a Staphylococcus epidermidis Strain with Exceptional Antimicrobial Activity Lassen, Simon B.; Lomholt, Hans B.; Brüggemann, Holger Genome Announcements, Vol. 5, Issue 10 https://doi.org/10.1128/genomea.00004-17	journal	March 2017
Draft Genome Sequence of Plant Growth-Promoting and Drought-Tolerant Bacillus altitudinis FD48, Isolated from Rice Phylloplane Kumaravel, Sowmya; Thankappan, Sugitha; Raghupathi, Sridar Genome Announcements, Vol. 6, Issue 9 https://doi.org/10.1128/genomea.00019-18	journal	March 2018
Draft Genome Sequence of Bacillus licheniformis VSD4, a Diesel Fuel–Degrading and Plant Growth–Promoting Phyllospheric Bacterium Stevens, Vincent; Thijs, Sofie; McAmmond, Breanne Genome Announcements, Vol. 5, Issue 11 https://doi.org/10.1128/genomea.00027-17	journal	March 2017
Draft Genome Sequences of Two Kocuria Isolates, K. salsicia G1 and K. rhizophila G2, Isolated from a Slaughterhouse in Denmark Herschend, Jakob; Raghupathi, Prem K.; Røder, Henriette L. Genome Announcements, Vol. 4, Issue 2 https://doi.org/10.1128/genomea.00075-16	journal	April 2016
Complete Genome Sequences of Two Phage-Like Plasmids Carrying the CTX-M-15 Extended-Spectrum β-Lactamase Gene Colavecchio, Anna; Jeukens, Julie; Freschi, Luca Genome Announcements, Vol. 5, Issue 19 https://doi.org/10.1128/genomea.00102-17	journal	May 2017
Draft Genome Sequence of Sphingorhabdus sp. Strain EL138, a Metabolically Versatile Alphaproteobacterium Isolated from the Gorgonian Coral Eunicella labiata Silva, Sandra Godinho; Lago-Lestón, Asunción; Costa, Rodrigo Genome Announcements, Vol. 6, Issue 9 https://doi.org/10.1128/genomea.00142-18	journal	March 2018
Complete Genome Sequence of Multiple-Antibiotic-Resistant Streptococcus parauberis Strain SPOF3K, Isolated from Diseased Olive Flounder (Paralichthys olivaceus) Lee, Yoonhang; Nguyen, Thanh Luan; Kim, Ahran Genome Announcements, Vol. 6, Issue 17 https://doi.org/10.1128/genomea.00248-18	journal	April 2018
Draft Genome Sequence and Assembly of a Lysobacter enzymogenes Strain with Biological Control Activity against Root Knot Nematodes Hernández, Iker; Fernàndez, Carolina Genome Announcements, Vol. 5, Issue 18 https://doi.org/10.1128/genomea.00271-17	journal	May 2017
Genome Sequences of Four Staphylococcus aureus Strains Isolated from Bovine Mastitis Kant, Ravi; Taponen, Suvi; Koort, Joanna Genome Announcements, Vol. 3, Issue 2 https://doi.org/10.1128/genomea.00334-15	journal	April 2015
Complete Genome Sequence of a Mosaic Bacteriophage, Waukesha92 Sauder, A. Brooke; Carter, Brandon; Langouet Astrie, Christophe Genome Announcements, Vol. 2, Issue 4 https://doi.org/10.1128/genomea.00339-14	journal	August 2014
Complete Genome Sequence of Erwinia amylovora Bacteriophage vB_EamM_Ea35-70 Yagubi, Abdelbaset I.; Castle, Alan J.; Kropinski, Andrew M. Genome Announcements, Vol. 2, Issue 4 https://doi.org/10.1128/genomea.00413-14	journal	August 2014
Draft Genome Sequence of the Obligately Alkaliphilic Sulfate-Reducing Bacterium Desulfonatronum thiodismutans Strain MLF1 Trubitsyn, Denis; Geurink, Corey; Pikuta, Elena Genome Announcements, Vol. 2, Issue 4 https://doi.org/10.1128/genomea.00741-14	journal	August 2014
Complete Genome Sequence of an Edwardsiella piscicida -Like Species Isolated from Diseased Grouper in Israel Reichley, Stephen R.; Waldbieser, Geoffrey C.; Ucko, Michal Genome Announcements, Vol. 3, Issue 4 https://doi.org/10.1128/genomea.00829-15	journal	August 2015
Draft Genome Sequence of Desulfocarbo indianensis SCBM, a New Genus of Sulfate-Reducing Bacteria, Isolated from Water Extracted from an Active Coalbed Methane Gas Well An, Thuy T.; Picardal, Flynn W. Genome Announcements, Vol. 3, Issue 5 https://doi.org/10.1128/genomea.00970-15	journal	October 2015
Draft Genome Sequences of the Fish Pathogen Vibrio harveyi Strains VH2 and VH5 Castillo, Daniel; D’Alvise, Paul; Middelboe, Mathias Genome Announcements, Vol. 3, Issue 5 https://doi.org/10.1128/genomea.01062-15	journal	October 2015
Whole-Genome Sequence of Pseudomonas xanthomarina Strain UASWS0955, a Potential Biological Agent for Agricultural and Environmental Uses Crovadore, Julien; Cochard, Bastien; Calmin, Gautier Genome Announcements, Vol. 4, Issue 5 https://doi.org/10.1128/genomea.01136-16	journal	October 2016
Complete Genome Sequences of Four Escherichia coli ST95 Isolates from Bloodstream Infections Stephens, Craig M.; Skerker, Jeffrey M.; Sekhon, Manraj S. Genome Announcements, Vol. 3, Issue 6 https://doi.org/10.1128/genomea.01241-15	journal	December 2015
Draft Genome Sequence of the Moderately Heat-Tolerant Lactococcus lactis subsp. lactis bv. diacetylactis Strain GL2 from Algerian Dromedary Milk Gabed, Noujoud; Yang, Manli; Bey Baba Hamed, Mohamed Genome Announcements, Vol. 3, Issue 6 https://doi.org/10.1128/genomea.01334-15	journal	December 2015
Draft Genome Sequence of Violacein-Producing Marine Bacterium Pseudoalteromonas sp. 520P1 Dang, Hoang Tran; Yotsumoto, Kentarou; Enomoto, Keiichi Genome Announcements, Vol. 2, Issue 6 https://doi.org/10.1128/genomea.01346-14	journal	December 2014
Complete Genome Sequence of Bacillus altitudinis P-10, a Potential Bioprotectant against Xanthomonas oryzae pv. oryzae, Isolated from Rice Rhizosphere in Java, Indonesia Budiharjo, Anto; Jeong, Haeyoung; Wulandari, Dyah Genome Announcements, Vol. 5, Issue 48 https://doi.org/10.1128/genomea.01388-17	journal	November 2017
Draft Genome Sequence of Streptomyces sp. Strain 150FB, a Mushroom Mycoparasite Antagonist Tarkka, M. T.; Feldhahn, L.; Krüger, D. Genome Announcements, Vol. 3, Issue 2 https://doi.org/10.1128/genomea.01441-14	journal	April 2015
Draft Genome Sequence of a Virulent Pectobacterium carotovorum subsp. brasiliense Isolate Causing Soft Rot of Cucumber Onkendi, Edward M.; Ramesh, Aadi Moolam; Kwenda, Stanford Genome Announcements, Vol. 4, Issue 1 https://doi.org/10.1128/genomea.01530-15	journal	February 2016
Draft Genome Sequence of Thalassospira xiamenensis Strain MCCC 1A03042 ^T Li, Meiqing; Yang, Shuo; Lai, Qiliang Genome Announcements, Vol. 5, Issue 9 https://doi.org/10.1128/genomea.01702-16	journal	March 2017
Metabolism of Toxic Sugars by Strains of the Bee Gut Symbiont Gilliamella apicola Zheng, Hao; Nishida, Alex; Kwong, Waldan K. mBio, Vol. 7, Issue 6 https://doi.org/10.1128/mbio.01326-16	journal	November 2016
Draft Genome Sequences of Five Methicillin-Sensitive Staphylococcus aureus Isolates from Skin Lesions in Patients with Atopic Dermatitis in the Russian Federation Dmitrenko, Olga; Alkhovsky, Sergey; Balbutskaya, Anna Microbiology Resource Announcements, Vol. 7, Issue 13 https://doi.org/10.1128/mra.00879-18	journal	October 2018
Genome Sequence of a Potentially New Buttiauxella Species, Strain B2, Isolated from Rhizosphere of Olivillo Trees ( Aextoxicon punctatum ) Almasia, Romina; Henríquez, Marlene; Levican, Arturo Microbiology Resource Announcements, Vol. 9, Issue 9 https://doi.org/10.1128/mra.01351-19	journal	February 2020
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
Draft Genome Sequence of Bradyrhizobium elkanii BR 2003, an Efficient Rhizobium Strain for Cajanus, Canavalia , Crotalaria , and Indigofera Zilli, Jerri Édson; Simoes-Araujo, Jean Luiz; Rouws, Luc Felicianus Marie Microbiology Resource Announcements, Vol. 9, Issue 11 https://doi.org/10.1128/mra.01565-19	journal	March 2020
Draft Genome Sequence of a Marine Photoferrotrophic Bacterium, Rhodovulum robiginosum DSM 12329T Gupta, Dinesh; Guzman, Michael S.; Bose, Arpita Microbiology Resource Announcements, Vol. 8, Issue 8 https://doi.org/10.1128/mra.01684-18	journal	February 2019
Draft genome sequences of strains Salinicola socius SMB35T, Salinicola sp. MH3R3–1 and Chromohalobacter sp. SMB17 from the Verkhnekamsk potash mining region of Russia Olsson, Björn E.; Korsakova, Ekaterina S.; Anan’ina, Lyudmila N. Standards in Genomic Sciences, Vol. 12, Issue 1 https://doi.org/10.1186/s40793-017-0251-5	journal	July 2017
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Identification of the Genes Required for the Culture of Liberibacter crescens, the Closest Cultured Relative of the Liberibacter Plant Pathogens Lai, Kin-Kwan; Davis-Richardson, Austin G.; Dias, Raquel Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00547	journal	April 2016
Comparative Analysis of Genomics and Proteomics in the New Isolated Bacillus thuringiensis X022 Revealed the Metabolic Regulation Mechanism of Carbon Flux Following Cu2+ Treatment Quan, Meifang; Xie, Junyan; Liu, Xuemei Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00792	journal	May 2016
The Complete Sequences and Ecological Roles of Two IncP-1β Plasmids, pHB44 and pBS64, Isolated from the Mycosphere of Laccaria proxima Zhang, Miaozhi; Brons, Jolanda K.; van Elsas, Jan Dirk Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00909	journal	June 2016
CRISPR-Cas Defense System and Potential Prophages in Cyanobacteria Associated with the Coral Black Band Disease Buerger, Patrick; Wood-Charlson, Elisha M.; Weynberg, Karen D. Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.02077	journal	December 2016
Comparative Genomic Characterization of the Highly Persistent and Potentially Virulent Cronobacter sakazakii ST83, CC65 Strain H322 and Other ST83 Strains Chase, Hannah R.; Gopinath, Gopal R.; Eshwar, Athmanya K. Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.01136	journal	June 2017
Isolation, Development, and Genomic Analysis of Bacillus megaterium SR7 for Growth and Metabolite Production Under Supercritical Carbon Dioxide Freedman, Adam J. E.; Peet, Kyle C.; Boock, Jason T. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.02152	journal	September 2018
Co-culture of a Novel Fermentative Bacterium, Lucifera butyrica gen. nov. sp. nov., With the Sulfur Reducer Desulfurella amilsii for Enhanced Sulfidogenesis Sánchez-Andrea, Irene; Florentino, Anna Patrícya; Semerel, Jeltzlin Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.03108	journal	December 2018
A Comparison of Microbial Genome Web Portals Karp, Peter D.; Ivanova, Natalia; Krummenacker, Markus Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00208	journal	February 2019
Two Broad Host Range Rhizobial Strains Isolated From Relict Legumes Have Various Complementary Effects on Symbiotic Parameters of Co-inoculated Plants Safronova, Vera; Belimov, Andrey; Sazanova, Anna Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00514	journal	March 2019
Comparative Genomics and Metabolomics Analyses of Clavulanic Acid-Producing Streptomyces Species Provides Insight Into Specialized Metabolism AbuSara, Nader F.; Piercey, Brandon M.; Moore, Marcus A. Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.02550	journal	November 2019
Metatranscriptomic Insights Into the Response of River Biofilm Communities to Ionic and Nano-Zinc Oxide Exposures Bergsveinson, Jordyn; Roy, Julie; Maynard, Christine Frontiers in Microbiology, Vol. 11 https://doi.org/10.3389/fmicb.2020.00267	journal	February 2020
Two Novel Myoviruses from the North of Iraq Reveal Insights into Clostridium difficile Phage Diversity and Biology Rashid, Srwa; Barylski, Jakub; Hargreaves, Katherine Viruses, Vol. 8, Issue 11 https://doi.org/10.3390/v8110310	journal	November 2016
proGenomes: A resource for consistent functional and taxonomic annotations of prokaryotic genomes R., Mende, Daniel; Ivica, Letunic,; Jaime, Huerta-Cepas, ETH Zurich https://doi.org/10.3929/ethz-b-000122266	text	January 2017
Essential metabolism for a minimal cell Breuer, Marian; Earnest, Tyler M.; Merryman, Chuck eLife, Vol. 8 https://doi.org/10.7554/elife.36842	journal	January 2019

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