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

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.

View Accepted Manuscript (DOE)

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

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1194128

Alternate ID(s):: OSTI ID: 1391665

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

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

References (45)

Identifying bacterial genes and endosymbiont DNA with Glimmer Delcher, Arthur L.; Bratke, Kirsten A.; Powers, Edwin C. Bioinformatics, Vol. 23, Issue 6 https://doi.org/10.1093/bioinformatics/btm009	journal	January 2007
Real Time Metagenomics: Using k-mers to annotate metagenomes Edwards, Robert A.; Olson, Robert; Disz, Terry Bioinformatics, Vol. 28, Issue 24 https://doi.org/10.1093/bioinformatics/bts599	journal	October 2012
The integrated microbial genomes (IMG) system Markowitz, V. M. Nucleic Acids Research, Vol. 34, Issue 90001 https://doi.org/10.1093/nar/gkj024	journal	January 2006
DrugBank 4.0: shedding new light on drug metabolism Law, Vivian; Knox, Craig; Djoumbou, Yannick Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1068	journal	November 2013
Therapeutic target database update 2014: a resource for targeted therapeutics Qin, Chu; Zhang, Cheng; Zhu, Feng Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1129	journal	November 2013
Modernizing Reference Genome Assemblies Church, Deanna M.; Schneider, Valerie A.; Graves, Tina PLoS Biology, Vol. 9, Issue 7 https://doi.org/10.1371/journal.pbio.1001091	journal	July 2011
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
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
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
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
Gene Identification in Prokaryotic Genomes, Phages, Metagenomes, and EST Sequences with GeneMarkS Suite Borodovsky, Mark; Lomsadze, Alex Current Protocols in Bioinformatics, Vol. 35, Issue 1 https://doi.org/10.1002/0471250953.bi0405s35	journal	September 2011
Translational recoding in archaea Cobucci-Ponzano, Beatrice; Rossi, Mosè; Moracci, Marco Extremophiles, Vol. 16, Issue 6 https://doi.org/10.1007/s00792-012-0482-8	journal	September 2012
In search of genome annotation consistency: solid gene clusters and how to use them Davis, James J.; Olsen, Gary J.; Overbeek, Ross 3 Biotech, Vol. 4, Issue 3 https://doi.org/10.1007/s13205-013-0152-2	journal	July 2013
Technology: The $1,000 genome Check Hayden, Erika Nature, Vol. 507, Issue 7492 https://doi.org/10.1038/507294a	journal	March 2014
High-throughput generation, optimization and analysis of genome-scale metabolic models Henry, Christopher S.; DeJongh, Matthew; Best, Aaron A. Nature Biotechnology, Vol. 28, Issue 9 https://doi.org/10.1038/nbt.1672	journal	August 2010
Next-generation DNA sequencing Shendure, Jay; Ji, Hanlee Nature Biotechnology, Vol. 26, Issue 10 https://doi.org/10.1038/nbt1486	journal	October 2008
CRISPR — a widespread system that provides acquired resistance against phages in bacteria and archaea Sorek, Rotem; Kunin, Victor; Hugenholtz, Philip Nature Reviews Microbiology, Vol. 6, Issue 3 https://doi.org/10.1038/nrmicro1793	journal	March 2008
A System for Automated Bacterial (genome) Integrated Annotation--SABIA Almeida, L. G. P.; Paixao, R.; Souza, R. C. Bioinformatics, Vol. 20, Issue 16 https://doi.org/10.1093/bioinformatics/bth273	journal	April 2004
Prokka: rapid prokaryotic genome annotation Seemann, T. Bioinformatics, Vol. 30, Issue 14 https://doi.org/10.1093/bioinformatics/btu153	journal	March 2014
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
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence Lowe, Todd M.; Eddy, Sean R. Nucleic Acids Research, Vol. 25, Issue 5 https://doi.org/10.1093/nar/25.5.0955	journal	March 1997
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence Lowe, Todd M.; Eddy, Sean R. Nucleic Acids Research, Vol. 25, Issue 5 https://doi.org/10.1093/nar/25.5.955	journal	March 1997
The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes Overbeek, R. Nucleic Acids Research, Vol. 33, Issue 17 https://doi.org/10.1093/nar/gki866	journal	September 2005
ISfinder: the reference centre for bacterial insertion sequences Siguier, P. Nucleic Acids Research, Vol. 34, Issue 90001 https://doi.org/10.1093/nar/gkj014	journal	January 2006
RNAmmer: consistent and rapid annotation of ribosomal RNA genes Lagesen, Karin; Hallin, Peter; Rødland, Einar Andreas Nucleic Acids Research, Vol. 35, Issue 9 https://doi.org/10.1093/nar/gkm160	journal	April 2007
ARDB--Antibiotic Resistance Genes Database Liu, B.; Pop, M. Nucleic Acids Research, Vol. 37, Issue Database https://doi.org/10.1093/nar/gkn656	journal	January 2009
FIGfams: yet another set of protein families Meyer, Folker; Overbeek, Ross; Rodriguez, Alex Nucleic Acids Research, Vol. 37, Issue 20 https://doi.org/10.1093/nar/gkp698	journal	September 2009
VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors Chen, L.; Xiong, Z.; Sun, L. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr989	journal	November 2011
PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies Akhter, Sajia; Aziz, Ramy K.; Edwards, Robert A. Nucleic Acids Research, Vol. 40, Issue 16 https://doi.org/10.1093/nar/gks406	journal	May 2012
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST) Overbeek, Ross; Olson, Robert; Pusch, Gordon D. Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1226	journal	November 2013
BLAT---The BLAST-Like Alignment Tool Kent, W. J. Genome Research, Vol. 12, Issue 4 https://doi.org/10.1101/gr.229202	journal	March 2002
RNA-Guided Human Genome Engineering via Cas9 Mali, P.; Yang, L.; Esvelt, K. M. Science, Vol. 339, Issue 6121, p. 823-826 https://doi.org/10.1126/science.1232033	journal	January 2013
The Comprehensive Antibiotic Resistance Database McArthur, Andrew G.; Waglechner, Nicholas; Nizam, Fazmin Antimicrobial Agents and Chemotherapy, Vol. 57, Issue 7 https://doi.org/10.1128/AAC.00419-13	journal	May 2013
PATRIC: the Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species Gillespie, Joseph J.; Wattam, Alice R.; Cammer, Stephen A. Infection and Immunity, Vol. 79, Issue 11 https://doi.org/10.1128/IAI.00207-11	journal	September 2011
Novel BOX repeat PCR assay for high-resolution typing of Streptococcus pneumoniae strains. van Belkum, A.; Sluijuter, M.; de Groot, R. Journal of clinical microbiology, Vol. 34, Issue 5 https://doi.org/10.1128/JCM.34.5.1176-1179.1996	journal	January 1996
Novel BOX repeat PCR assay for high-resolution typing of Streptococcus pneumoniae strains. van Belkum, A.; Sluijuter, M.; de Groot, R. Journal of clinical microbiology, Vol. 34, Issue 5 https://doi.org/10.1128/jcm.34.5.1176-1179.1996	journal	January 1996
Draft Genome Sequence of Comamonas aquatilis Strain LK (= CSUR P6418 = CECT 9772), Isolated from the Planarian Schmidtea mediterranea Kangale, Luis Johnson; Levasseur, Anthony; Raoult, Didier Microbiology Resource Announcements, Vol. 10, Issue 5 https://doi.org/10.1128/mra.00297-20	journal	February 2021
BLAST+: architecture and applications Camacho, Christiam; Coulouris, George; Avagyan, Vahram BMC Bioinformatics, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2105-10-421	journal	January 2009
Prodigal: prokaryotic gene recognition and translation initiation site identification Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-119	journal	March 2010
Identification, variation and transcription of pneumococcal repeat sequences Croucher, Nicholas J.; Vernikos, Georgios S.; Parkhill, Julian BMC Genomics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2164-12-120	journal	February 2011
The RAST Server: Rapid Annotations using Subsystems Technology Aziz, Ramy K.; Bartels, Daniela; Best, Aaron A. BMC Genomics, Vol. 9, Issue 1, Article No. 75 https://doi.org/10.1186/1471-2164-9-75	journal	January 2008
PHIDIAS: a pathogen-host interaction data integration and analysis system Xiang, Zuoshuang; Tian, Yuying; He, Yongqun Genome Biology, Vol. 8, Issue 7 https://doi.org/10.1186/gb-2007-8-7-r150	journal	January 2007
Identification, variation and transcription of pneumococcal repeat sequences. Croucher, Nicholas J.; Vernikos, Georgios S.; Parkhill, Julian Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.43566	text	January 2011
The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes Mavromatis, Konstantinos; Ivanova, Natalia N.; Chen, I-Min A. Standards in Genomic Sciences, Vol. 1, Issue 1 https://doi.org/10.4056/sigs.632	journal	July 2009
Identification, variation and transcription of pneumococcal repeat sequences Croucher, Nicholas J.; Vernikos, Georgios S.; Parkhill, Julian figshare https://doi.org/10.6084/m9.figshare.c.4845843.v1	collection	January 2020

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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
KBase Narrative - BIT 295 MRA Isolate 106- Final Chadha, Aditya; Goller, Carlos; Sjogren, Carly U.S. Department of Energy Systems Biology Knowledgebase https://doi.org/10.25982/133260.12/1901826	dataset	January 2022
KBase Narrative - SOMATA - Motivating Example Cashman, Mikaela; Marsh, Alexis; Cottingham, Bob U.S. Department of Energy Systems Biology Knowledgebase https://doi.org/10.25982/135473.103/1960315	dataset	January 2023
KBase Narrative - Timberlake Metagenomes De Mesquita, Clifton; Ciapina, Wyatt; Ardón, Marcelo U.S. Department of Energy Systems Biology Knowledgebase https://doi.org/10.25982/138721.208/2336591	dataset	January 2024
KBase Narrative - MRA Genome Announcement Bradyrhizobium NP1 Morrow, Maureen; DeAngelis, Kristen; Fisher, Trevor U.S. Department of Energy Systems Biology Knowledgebase https://doi.org/10.25982/147325.113/1987691	dataset	January 2023
Five draft genome assemblies from Bacillaceae isolated from a degraded wetland environment McLoon, Anna; Asante, Prince; Anderson, Thomas Sienna College, Loudonville, New York, USA https://doi.org/10.25982/152701.14/1996997	dataset	January 2023
KBase Narrative - Complete Genome Sequence of Acidovorax temperans strain LMJ Mitra, Mautusi; Stanescu, Ana U.S. Department of Energy Systems Biology Knowledgebase https://doi.org/10.25982/161632.357/2228677	dataset	January 2023
Metabacillus indicus EGFCL74 Lopez, Christopher; Garcia-Fuentes, Eileen California State University, Sacramento, California, USA https://doi.org/10.25982/163445.15/2223098	dataset	January 2023
KBase Narrative - Methylobacterium fujisawaense Strain C14 Genomic Sequence Kiledal, E.; Moxley, Iz; Shevchenko, Olga U.S. Department of Energy Systems Biology Knowledgebase https://doi.org/10.25982/169030.42/2345706	dataset	January 2024
KBase Narrative - Porphyromonadaceae sp. W3.11 genome Hackmann, Timothy; Zhang, Bo U.S. Department of Energy Systems Biology Knowledgebase https://doi.org/10.25982/171029.13/2309718	dataset	January 2024
KBase Narrative - Lachnospiraceae sp. C1.1 genome Hackmann, Timothy; Zhang, Bo U.S. Department of Energy Systems Biology Knowledgebase https://doi.org/10.25982/171033.8/2309719	dataset	January 2024
KBase Narrative - Metabolically diverse Miscanthus x giganteus microbiome isolates with tremendous growth-promoting potential - Copy Schirmer, Aaron; Whitham, Jason U.S. Department of Energy Systems Biology Knowledgebase https://doi.org/10.25982/175568.4/2329277	dataset	January 2024
KBase Narrative - Genome sequences of four bacterial strains isolated from organofluorine enrichment cultures Goff, Jennifer; Hahn, Chris; Ingrassia, Rebecca U.S. Department of Energy Systems Biology Knowledgebase https://doi.org/10.25982/179975.10/2345704	dataset	January 2024
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
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
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
Grant_Staphylococcus_succinus Nickolson, Grant; Marshall, Christopher; Balasjin, Nasim Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, USA https://doi.org/10.25982/51640.53/1808273	dataset	January 2021
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
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
Osur_paper Kiefer, Julian Johannes Gutenberg Universität Mainz, Mainz, Rheinland-Pfalz, DE https://doi.org/10.25982/58799.728/1798340	dataset	January 2021
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
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
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
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
KBase Narrative - Atacama Trench & Sn Clemente 2018 cruise Metagenomes -Sequence quality filtration & Assembly- Plominsky, Alvaro U.S. Department of Energy Systems Biology Knowledgebase https://doi.org/10.25982/90888.1452/2327015	dataset	January 2024
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
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
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 No authors listed 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
Additional file 1 of The diversity of unique 1,4,5,6-Tetrahydro-2-methyl-4-pyrimidinecarboxylic acid coding common genes and Universal stress protein in Ectoine TRAP cluster (UspA) in 32 Halomonas species Rekadwad, Bhagwan Narayan; Li, Wen-Jun; Rekha, P. D. figshare https://doi.org/10.6084/m9.figshare.15102811	image	January 2021
Additional file 2 of The diversity of unique 1,4,5,6-Tetrahydro-2-methyl-4-pyrimidinecarboxylic acid coding common genes and Universal stress protein in Ectoine TRAP cluster (UspA) in 32 Halomonas species Rekadwad, Bhagwan Narayan; Li, Wen-Jun; Rekha, P. D. figshare https://doi.org/10.6084/m9.figshare.15102814.v1	image	January 2021
Additional file 3 of The diversity of unique 1,4,5,6-Tetrahydro-2-methyl-4-pyrimidinecarboxylic acid coding common genes and Universal stress protein in Ectoine TRAP cluster (UspA) in 32 Halomonas species Rekadwad, Bhagwan Narayan; Li, Wen-Jun; Rekha, P. D. figshare https://doi.org/10.6084/m9.figshare.15102817	image	January 2021
Additional file 4 of The diversity of unique 1,4,5,6-Tetrahydro-2-methyl-4-pyrimidinecarboxylic acid coding common genes and Universal stress protein in Ectoine TRAP cluster (UspA) in 32 Halomonas species Rekadwad, Bhagwan Narayan; Li, Wen-Jun; Rekha, P. D. figshare https://doi.org/10.6084/m9.figshare.15102820.v1	image	January 2021
Additional file 5 of The diversity of unique 1,4,5,6-Tetrahydro-2-methyl-4-pyrimidinecarboxylic acid coding common genes and Universal stress protein in Ectoine TRAP cluster (UspA) in 32 Halomonas species Rekadwad, Bhagwan Narayan; Li, Wen-Jun; Rekha, P. D. figshare https://doi.org/10.6084/m9.figshare.15102823	image	January 2021
Additional file 6 of The diversity of unique 1,4,5,6-Tetrahydro-2-methyl-4-pyrimidinecarboxylic acid coding common genes and Universal stress protein in Ectoine TRAP cluster (UspA) in 32 Halomonas species Rekadwad, Bhagwan Narayan; Li, Wen-Jun; Rekha, P. D. figshare https://doi.org/10.6084/m9.figshare.15102826	dataset	January 2021
Additional file 2 of Whole genome sequencing of Enterobacter mori, an emerging pathogen of kiwifruit and the potential genetic adaptation to pathogenic lifestyle Zhang, Mingyang; Zhang, Yilin; Han, Xue figshare https://doi.org/10.6084/m9.figshare.16639849	dataset	January 2021
Additional file 3 of Whole genome sequencing of Enterobacter mori, an emerging pathogen of kiwifruit and the potential genetic adaptation to pathogenic lifestyle Zhang, Mingyang; Zhang, Yilin; Han, Xue figshare https://doi.org/10.6084/m9.figshare.16639852.v1	dataset	January 2021
Additional file 4 of Whole genome sequencing of Enterobacter mori, an emerging pathogen of kiwifruit and the potential genetic adaptation to pathogenic lifestyle Zhang, Mingyang; Zhang, Yilin; Han, Xue figshare https://doi.org/10.6084/m9.figshare.16639855.v1	dataset	January 2021
Additional file 5 of Whole genome sequencing and comparative genomic analyses of Planococcus alpniumensis MSAK28401T, a new species isolated from Antarctic krill Wang, Yuanyuan; Ma, Lingbo; He, Jian figshare https://doi.org/10.6084/m9.figshare.16862785	dataset	January 2021
Additional file 1 of Genome characterization and taxonomy of Actinomyces acetigenes sp. nov., and Actinomyces stomatis sp. nov., previously isolated from the human oral cavity Tian, Xuechen; Teo, Wee Fei Aaron; Wee, Wei Yee figshare https://doi.org/10.6084/m9.figshare.24741751	dataset	January 2023
Additional file 1 of Horizontal gene transfer of the Mer operon is associated with large effects on the transcriptome and increased tolerance to mercury in nitrogen-fixing bacteria Bhat, Aditi; Sharma, Reena; Desigan, Kumaran figshare https://doi.org/10.6084/m9.figshare.26197448	dataset	January 2024
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
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
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
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
Lipopeptide biodiversity in antifungal Bacillus strains isolated from Algeria Abdellaziz, Lamia; Chollet, Marlène; Abderrahmani, Ahmed Archives of Microbiology, Vol. 200, Issue 8 https://doi.org/10.1007/s00203-018-1537-8	journal	June 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
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
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
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
Horizontal Transfer of Antimicrobial Resistance Determinants Among Enteric Pathogens Through Bacterial Conjugation Devanga Ragupathi, Naveen Kumar; Muthuirulandi Sethuvel, Dhiviya Prabaa; Gajendran, Revathi Current Microbiology, Vol. 76, Issue 6 https://doi.org/10.1007/s00284-019-01676-x	journal	April 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
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
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
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
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
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 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
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
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
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
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
Functional diversity enables multiple symbiont strains to coexist in deep-sea mussels Ansorge, Rebecca; Romano, Stefano; Sayavedra, Lizbeth Nature Microbiology, Vol. 4, Issue 12 https://doi.org/10.1038/s41564-019-0572-9	journal	October 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
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
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
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
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
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
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
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
In vitro evolution of Pseudomonas aeruginosa AA2 biofilms in the presence of cystic fibrosis lung microbiome members Vandeplassche, Eva; Sass, Andrea; Lemarcq, Astrid Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-49371-y	journal	September 2019
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
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
Antimicrobial Resistance Prediction in PATRIC and RAST Davis, James J.; Boisvert, Sébastien; Brettin, Thomas Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep27930	journal	June 2016
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
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
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
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
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
Toxin and Genome Evolution in a Drosophila Defensive Symbiosis Ballinger, Matthew J.; Gawryluk, Ryan M. R.; Perlman, Steve J. Genome Biology and Evolution, Vol. 11, Issue 1 https://doi.org/10.1093/gbe/evy272	journal	December 2018
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
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
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
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
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center Wattam, Alice R.; Davis, James J.; Assaf, Rida Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw1017	journal	November 2016
The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities Davis, James J.; Wattam, Alice R.; Aziz, Ramy K. Nucleic Acids Research https://doi.org/10.1093/nar/gkz943	journal	October 2019
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
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
Sulfurimonas crateris sp. nov., a facultative anaerobic sulfur-oxidizing chemolithoautotrophic bacterium isolated from a terrestrial mud volcano Ratnikova, N. M.; Slobodkin, A. I.; Merkel, A. Y. International Journal of Systematic and Evolutionary Microbiology, Vol. 70, Issue 1 https://doi.org/10.1099/ijsem.0.003779	journal	January 2020
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
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
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
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
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
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
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
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
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
Complete 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 https://doi.org/10.1101/633602	journal	July 2019
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
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
Surfactin variants mediate species-specific biofilm formation and root colonization in Bacillus: Surfactins Mediate species-Specific Signaling Aleti, Gajender; Lehner, Sylvia; Bacher, Markus Environmental Microbiology, Vol. 18, Issue 8 https://doi.org/10.1111/1462-2920.13405	journal	July 2016
Comparative genomics of Mortierella elongata and its bacterial endosymbiont Mycoavidus cysteinexigens Uehling, J.; Gryganskyi, A.; Hameed, K. Environmental Microbiology, Vol. 19, Issue 8 https://doi.org/10.1111/1462-2920.13669	journal	February 2017
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
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
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
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
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
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
In Silico Serotyping Based on Whole-Genome Sequencing Improves the Accuracy of Shigella Identification Wu, Yun; Lau, Henry K.; Lee, Teresa Applied and Environmental Microbiology, Vol. 85, Issue 7 https://doi.org/10.1128/aem.00165-19	journal	February 2019
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
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
Streptococcus pyogenes Transcriptome Changes in the Inflammatory Environment of Necrotizing Fasciitis Hirose, Yujiro; Yamaguchi, Masaya; Okuzaki, Daisuke Applied and Environmental Microbiology, Vol. 85, Issue 21 https://doi.org/10.1128/aem.01428-19	journal	November 2019
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
Genome Analysis of Fimbriiglobus ruber SP5 ^T , a Planctomycete with Confirmed Chitinolytic Capability Ravin, Nikolai V.; Rakitin, Andrey L.; Ivanova, Anastasia A. Applied and Environmental Microbiology, Vol. 84, Issue 7 https://doi.org/10.1128/aem.02645-17	journal	January 2018
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 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 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
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
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
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 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
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
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
Draft Genome Sequences of Semiconstitutive Red, Dry, and Rough Biofilm-Forming Commensal and Uropathogenic Escherichia coli Isolates Cimdins, Annika; Lüthje, Petra; Li, Fengyang Genome Announcements, Vol. 5, Issue 4 https://doi.org/10.1128/genomea.01249-16	journal	January 2017
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
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 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
Using Machine Learning To Predict Antimicrobial MICs and Associated Genomic Features for Nontyphoidal Salmonella Nguyen, Marcus; Long, S. Wesley; McDermott, Patrick F. Journal of Clinical Microbiology, Vol. 57, Issue 2 https://doi.org/10.1128/jcm.01260-18	journal	October 2018
Novel Sulfolobus Fuselloviruses with Extensive Genomic Variations Zhang, Junxia; Zheng, Xiaowei; Wang, Haina Journal of Virology, Vol. 94, Issue 4 https://doi.org/10.1128/jvi.01624-19	journal	November 2019
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
Genome Sequence of Marine-Derived Streptomyces sp. Strain F001, a Producer of Akashin A and Diazaquinomycins Braesel, Jana; Clark, Chase M.; Kunstman, Kevin J. Microbiology Resource Announcements, Vol. 8, Issue 19 https://doi.org/10.1128/mra.00165-19	journal	May 2019
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
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
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
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
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 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
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
Complete Genome Sequence of Brevundimonas sp. Strain SGAir0440, Isolated from Indoor Air in Singapore Purbojati, Rikky W.; Drautz-Moses, Daniela I.; Uchida, Akira Microbiology Resource Announcements, Vol. 8, Issue 31 https://doi.org/10.1128/mra.00594-19	journal	August 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
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 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
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
Complete Genome Sequence of Pseudomonas sp. Strain SGAir0191, Isolated from Tropical Air Collected in Singapore Wong, Anthony; Junqueira, Ana Carolina M.; Chaturvedi, Ankur Microbiology Resource Announcements, Vol. 8, Issue 34 https://doi.org/10.1128/mra.00617-19	journal	August 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
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
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
Draft Genome Sequence of Freshwater-Derived Streptomyces No authors listed Microbiology Resource Announcements, Vol. 8, Issue 43 https://doi.org/10.1128/mra.00874-19	journal	October 2019
Complete Genome Sequence of Streptomyces sp. Strain SGAir0924, an Actinobacterium Isolated from Outdoor Air in Singapore Gupta, Anjali Bansal; Uchida, Akira; Purbojati, Rikky W. Microbiology Resource Announcements, Vol. 8, Issue 35 https://doi.org/10.1128/mra.00899-19	journal	August 2019
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
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
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
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
Draft Genome Sequence of Cronobacter sakazakii Cr268, Isolated from Infant Powder Formula Zizelski Valenci, Gal; Rubinstein, Mor; Afriat, Reuven Microbiology Resource Announcements, Vol. 8, Issue 46 https://doi.org/10.1128/mra.01067-19	journal	November 2019
Draft Genome Sequence of Agrobacterium tumefaciens Strain 1D1526 Huo, Naxin; Gu, Yong; McCue, Kent F. Microbiology Resource Announcements, Vol. 8, Issue 45 https://doi.org/10.1128/mra.01084-19	journal	November 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
Draft Genome Sequence of Enterobacter hormaechei Strain MHSD6, a Plant Endophyte Isolated from Medicinal Plant Pellaea calomelanos Tshishonga, Khuthadzo; Serepa-Dlamini, Mahloro H. Microbiology Resource Announcements, Vol. 8, Issue 48 https://doi.org/10.1128/mra.01251-19	journal	November 2019
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
Draft Genome Sequence of the Caffeine-Degrading Methylotroph Methylorubrum populi Pinkel Parales, Rebecca E.; Sharma, Gaurav; Zhang, Xiangsheng Microbiology Resource Announcements, Vol. 8, Issue 47 https://doi.org/10.1128/mra.01300-19	journal	November 2019
Draft Genome Sequence of Pseudomonas sp. Strain MWU12-2323, Isolated from a Wild Cranberry Bog in Truro, Massachusetts Ebadzadsahrai, Ghazal; Soby, Scott Microbiology Resource Announcements, Vol. 9, Issue 2 https://doi.org/10.1128/mra.01387-19	journal	January 2020
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
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
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
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
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
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
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
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
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
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
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
Comparative genomic analysis reveals the evolution and environmental adaptation strategies of vibrios Lin, Heyu; Yu, Min; Wang, Xiaolei BMC Genomics, Vol. 19, Issue 1 https://doi.org/10.1186/s12864-018-4531-2	journal	February 2018
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
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
The complete genome sequence of the nitrile biocatalyst Rhodococcus rhodochrous ATCC BAA-870 Frederick, Joni; Hennessy, Fritha; Horn, Uli BMC Genomics, Vol. 21, Issue 1 https://doi.org/10.1186/s12864-019-6405-7	journal	January 2020
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
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
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
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
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
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
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
In silico genome analysis reveals the metabolic versatility and biotechnology potential of a halotorelant phthalic acid esters degrading Gordonia alkanivorans strain YC-RL2 Nahurira, Ruth; Wang, Junhuan; Yan, Yanchun AMB Express, Vol. 9, Issue 1 https://doi.org/10.1186/s13568-019-0733-5	journal	February 2019
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
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
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
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
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
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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
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
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 Multidisciplinary Digital Publishing Institute https://doi.org/10.14288/1.0380211	text	January 2019
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
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
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 RWTH Aachen University https://doi.org/10.18154/rwth-conv-221967	text	January 2017
Genetic and molecular characterization of multicomponent resistance of Pseudomonas against allicin Borlinghaus, Jan; Bolger, Anthony; Schier, Christina Life Science Alliance, Vol. 3, Issue 5 https://doi.org/10.26508/lsa.202000670	journal	March 2020
PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database Davis, James J.; Gerdes, Svetlana; Olsen, Gary J. Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00118	journal	February 2016
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
New Genomic Insights into “Entotheonella” Symbionts in Theonella swinhoei: Mixotrophy, Anaerobic Adaptation, Resilience, and Interaction Liu, Fang; Li, Jinlong; Feng, Guofang Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.01333	journal	August 2016
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
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
Genome Mining of the Marine Actinomycete Streptomyces sp. DUT11 and Discovery of Tunicamycins as Anti-complement Agents Xu, Xiao-Na; Chen, Liang-Yu; Chen, Chao Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.01318	journal	June 2018
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
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
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
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
Comparative Genomics and Phenotypic Investigations Into Antibiotic, Heavy Metal, and Disinfectant Susceptibilities of Salmonella enterica Strains Isolated in Australia Wilson, Annaleise; Fox, Edward M.; Fegan, Narelle Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01620	journal	July 2019
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
First Report of Integrative Conjugative Elements in Riemerella anatipestifer Isolates From Ducks in China Zhu, Dekang; Wan, Jianbang; Yang, Zhishuang Frontiers in Veterinary Science, Vol. 6 https://doi.org/10.3389/fvets.2019.00128	journal	April 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
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
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
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
Pseudomonas sp. COW3 Produces New Bananamide-Type Cyclic Lipopeptides with Antimicrobial Activity against Pythium myriotylum and Pyricularia oryzae Omoboye, Olumide Owolabi; Geudens, Niels; Duban, Matthieu Molecules, Vol. 24, Issue 22 https://doi.org/10.3390/molecules24224170	journal	November 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
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
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
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
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
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
Resilience of small intestinal beneficial bacteria to the toxicity of soybean oil fatty acids Di Rienzi, Sara C.; Jacobson, Juliet; Kennedy, Elizabeth A. eLife, Vol. 7 https://doi.org/10.7554/elife.32581	journal	March 2018
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
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
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

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