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

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; DOE/OSTI
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.

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Lab. (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, Journal Name: Nucleic Acids Research Journal Issue: D1 Vol. 42; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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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
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
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
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
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
DFAST and DAGA: web-based integrated genome annotation tools and resources Tanizawa, Yasuhiro; Fujisawa, Takatomo; Kaminuma, Eli Bioscience of Microbiota, Food and Health, Vol. 35, Issue 4 https://doi.org/10.12938/bmfh.16-003	journal	January 2016
Coordinated regulation of core and accessory genes in the multipartite genome of Sinorhizobium fredii Jiao, Jian; Ni, Meng; Zhang, Biliang PLOS Genetics, Vol. 14, Issue 5 https://doi.org/10.1371/journal.pgen.1007428	journal	May 2018
Mutation-Driven Divergence and Convergence Indicate Adaptive Evolution of the Intracellular Human-Restricted Pathogen, Bartonella bacilliformis Paul, Sandip; Minnick, Michael F.; Chattopadhyay, Sujay PLOS Neglected Tropical Diseases, Vol. 10, Issue 5 https://doi.org/10.1371/journal.pntd.0004712	journal	May 2016
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
Microbial Potential for Ecosystem N Loss Is Increased by Experimental N Deposition Freedman, Zachary B.; Upchurch, Rima A.; Zak, Donald R. PLOS ONE, Vol. 11, Issue 10 https://doi.org/10.1371/journal.pone.0164531	journal	October 2016
A genome-scale metabolic reconstruction of Lysinibacillus sphaericus unveils unexploited biotechnological potentials Gómez-Garzón, Camilo; Hernández-Santana, Alejandra; Dussán, Jenny PLOS ONE, Vol. 12, Issue 6 https://doi.org/10.1371/journal.pone.0179666	journal	June 2017
Microbial catabolic pathways for complex aromatics Palamuru, Shannu The Australian National University https://doi.org/10.25911/5d66657d9aee3	other	January 2015
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
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 - natrialba Rodge, Seema U.S. Department of Energy Systems Biology Knowledgebase https://doi.org/10.25982/106247.14/1924621	dataset	January 2023
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 - Metabolic_reconstruction_ETDI_mangrove Laux, Marcele; Ciapina, Luciane; Carvalho, Fabiola U.S. Department of Energy Systems Biology Knowledgebase https://doi.org/10.25982/157568.747/2335480	dataset	January 2024
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
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
DRAM example narrative Shaffer, Michael Colorado State Univ., Fort Collins, CO (United States) https://doi.org/10.25982/88325.84/1855758	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
The molecular dimension of microbial species: 3. Comparative genomics of Synechococcus strains with different light responses and in situ diel transcription patterns of associated putative ecotypes in the Mushroom Spring microbial mat Olsen, Millie T.; Nowack, Shane; Wood, Jason M. Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.00604	journal	June 2015
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 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
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
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
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
FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies Garber, Arkadiy I.; Nealson, Kenneth H.; Okamoto, Akihiro Frontiers in Microbiology, Vol. 11 https://doi.org/10.3389/fmicb.2020.00037	journal	January 2020
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
Additional file 2 of Linking genomic and physiological characteristics of psychrophilic Arthrobacter to metagenomic data to explain global environmental distribution Shen, Liang; Liu, Yongqin; Allen, Michelle A. figshare https://doi.org/10.6084/m9.figshare.14775424.v1	dataset	January 2021
Additional file 3 of Linking genomic and physiological characteristics of psychrophilic Arthrobacter to metagenomic data to explain global environmental distribution Shen, Liang; Liu, Yongqin; Allen, Michelle A. figshare https://doi.org/10.6084/m9.figshare.14775427.v1	dataset	January 2021
Additional file 4 of Linking genomic and physiological characteristics of psychrophilic Arthrobacter to metagenomic data to explain global environmental distribution Shen, Liang; Liu, Yongqin; Allen, Michelle A. figshare https://doi.org/10.6084/m9.figshare.14775430.v1	dataset	January 2021
Additional file 5 of Linking genomic and physiological characteristics of psychrophilic Arthrobacter to metagenomic data to explain global environmental distribution Shen, Liang; Liu, Yongqin; Allen, Michelle A. figshare https://doi.org/10.6084/m9.figshare.14775433	dataset	January 2021
Additional file 6 of Linking genomic and physiological characteristics of psychrophilic Arthrobacter to metagenomic data to explain global environmental distribution Shen, Liang; Liu, Yongqin; Allen, Michelle A. figshare https://doi.org/10.6084/m9.figshare.14775436	dataset	January 2021
Additional file 7 of Linking genomic and physiological characteristics of psychrophilic Arthrobacter to metagenomic data to explain global environmental distribution Shen, Liang; Liu, Yongqin; Allen, Michelle A. figshare https://doi.org/10.6084/m9.figshare.14775439.v1	dataset	January 2021
Additional file 8 of Linking genomic and physiological characteristics of psychrophilic Arthrobacter to metagenomic data to explain global environmental distribution Shen, Liang; Liu, Yongqin; Allen, Michelle A. figshare https://doi.org/10.6084/m9.figshare.14775442	dataset	January 2021
Additional file 1 of Genome of the pincer wasp Gonatopus flavifemur reveals unique venom evolution and a dual adaptation to parasitism and predation Yang, Yi; Ye, Xinhai; Dang, Cong figshare https://doi.org/10.6084/m9.figshare.15063553	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 Insertion sequence contributes to the evolution and environmental adaptation of Acidithiobacillus Huang, Shanshan; Li, Huiying; Ma, Liyuan figshare https://doi.org/10.6084/m9.figshare.23207893.v1	dataset	January 2023
Additional file 1 of PoMeLo: a systematic computational approach to predicting metabolic loss in pathogen genomes Glascock, Abigail; Waltari, Eric; Dudas, Gytis figshare https://doi.org/10.6084/m9.figshare.25115962.v1	dataset	January 2024
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
Insights into temperature adaptation in the Thermotogae gained through transcriptomics and comparative genomics - Appendices Pollo, Stephen M. J. University of Alberta Libraries https://doi.org/10.7939/r34s1d	other	January 2014
Using KBase to Assemble and Annotate Prokaryotic Genomes Allen, Benjamin; Drake, Meghan; Harris, Nomi Current Protocols in Microbiology, Vol. 46, Issue 1 https://doi.org/10.1002/cpmc.37	journal	August 2017
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
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
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
Computational Methods in Microbial Population Genomics Didelot, Xavier Population Genomics: Microorganisms https://doi.org/10.1007/13836_2017_3	book	November 2017
From RNA-seq to Biological Inference: Using Compositional Data Analysis in Meta-Transcriptomics Macklaim, Jean M.; Gloor, Gregory B. Methods in Molecular Biology https://doi.org/10.1007/978-1-4939-8728-3_13	book	October 2018
Microbial taxonomy in the post-genomic era: Rebuilding from scratch? Thompson, Cristiane C.; Amaral, Gilda R.; Campeão, Mariana Archives of Microbiology, Vol. 197, Issue 3 https://doi.org/10.1007/s00203-014-1071-2	journal	December 2014
New insights into the metabolic potential of the phototrophic purple bacterium Rhodopila globiformis DSM 161T from its draft genome sequence and evidence for a vanadium-dependent nitrogenase Imhoff, Johannes F.; Rahn, Tanja; Künzel, Sven Archives of Microbiology, Vol. 200, Issue 6 https://doi.org/10.1007/s00203-018-1489-z	journal	February 2018
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
Draft genome sequence of Lactobacillus plantarum C4 (CECT 9567), a potential probiotic strain isolated from kefir De Montijo-Prieto, Soumi; Castro, David J.; Reina, Jose C. Archives of Microbiology, Vol. 201, Issue 3 https://doi.org/10.1007/s00203-019-01629-9	journal	February 2019
Comparative genome analysis reveals the evolution of chloroacetanilide herbicide mineralization in Sphingomonas wittichii DC-6 Cheng, Minggen; Yan, Xin; He, Jian Archives of Microbiology, Vol. 201, Issue 7 https://doi.org/10.1007/s00203-019-01660-w	journal	April 2019
Amniculibacterium aquaticum gen. nov., sp. nov., a new member of the family Flavobacteriaceae isolated from a stream Chen, Wen-Ming; Guo, Ya-Ping; Sheu, Ceshing Archives of Microbiology, Vol. 201, Issue 8 https://doi.org/10.1007/s00203-019-01688-y	journal	June 2019
Genome analysis of the marine bacterium Kiloniella laminariae and first insights into comparative genomics with related Kiloniella species Wiese, Jutta; Imhoff, Johannes F.; Horn, Hannes Archives of Microbiology, Vol. 202, Issue 4 https://doi.org/10.1007/s00203-019-01791-0	journal	December 2019
Comparative Genomics, Siderophore Production, and Iron Scavenging Potential of Root Zone Soil Bacteria Isolated from ‘Concord’ Grape Vineyards Lewis, Ricky W.; Islam, Anjuman; Opdahl, Lee Microbial Ecology, Vol. 78, Issue 3 https://doi.org/10.1007/s00248-019-01324-8	journal	February 2019
Screening, identification, and characterization of a novel saccharide-stimulated β-glycosidase from a soil metagenomic library Matsuzawa, Tomohiko; Yaoi, Katsuro Applied Microbiology and Biotechnology, Vol. 101, Issue 2 https://doi.org/10.1007/s00253-016-7803-2	journal	August 2016
Pervasiveness of UVC254-resistant Geobacillus strains in extreme environments Carlson, Courtney; Singh, Nitin K.; Bibra, Mohit Applied Microbiology and Biotechnology, Vol. 102, Issue 4 https://doi.org/10.1007/s00253-017-8712-8	journal	January 2018
Genomic and functional characterisation of two Enterococcus strains isolated from Cotija cheese and their potential role in ripening Olvera-García, Myrna; Sanchez-Flores, Alejandro; Quirasco Baruch, Maricarmen Applied Microbiology and Biotechnology, Vol. 102, Issue 5 https://doi.org/10.1007/s00253-018-8765-3	journal	January 2018
Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants Hassa, Julia; Maus, Irena; Off, Sandra Applied Microbiology and Biotechnology, Vol. 102, Issue 12 https://doi.org/10.1007/s00253-018-8976-7	journal	April 2018
2,3-Butanediol production by the non-pathogenic bacterium Paenibacillus brasilensis Dias, Beatriz do Carmo; Lima, Maria Eduarda do Nascimento Vitorin; Vollú, Renata Estebanez Applied Microbiology and Biotechnology, Vol. 102, Issue 20 https://doi.org/10.1007/s00253-018-9312-y	journal	August 2018
Development of a Rapid Identification Method for the Differentiation of Enterococcus Species Using a Species-Specific Multiplex PCR Based on Comparative Genomics Park, Jongbin; Jin, Gwi-Deuk; Pak, Jae In Current Microbiology, Vol. 74, Issue 4 https://doi.org/10.1007/s00284-017-1210-5	journal	February 2017
Achieving Accurate Sequence and Annotation Data for Caulobacter vibrioides CB13 Berrios, Louis; Ely, Bert Current Microbiology, Vol. 75, Issue 12 https://doi.org/10.1007/s00284-018-1572-3	journal	September 2018
Degradation Mechanism of 4-Chlorobiphenyl by Consortium of Pseudomonas sp. Strain CB-3 and Comamonas sp. Strain CD-2 Xing, Ziyu; Hu, Ting; Xiang, Yun Current Microbiology, Vol. 77, Issue 1 https://doi.org/10.1007/s00284-019-01791-9	journal	October 2019
Whole genome sequencing as a tool for phylogenetic analysis of clinical strains of Mitis group streptococci Rasmussen, L. H.; Dargis, R.; Højholt, K. European Journal of Clinical Microbiology & Infectious Diseases, Vol. 35, Issue 10 https://doi.org/10.1007/s10096-016-2700-2	journal	June 2016
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
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
Anaerophilus nitritogenes gen. nov., sp. nov., isolated from salt lake sediment in Xinjiang Province, China Zhang, Ran; Zeng, Yan; Wang, Tian-Qi Antonie van Leeuwenhoek, Vol. 113, Issue 3 https://doi.org/10.1007/s10482-019-01351-y	journal	November 2019
An RND transporter in the monoterpene metabolism of Castellaniella defragrans Puentes-Cala, Edinson; Harder, Jens Biodegradation, Vol. 30, Issue 1 https://doi.org/10.1007/s10532-018-9857-6	journal	October 2018
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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
Ruegeria denitrificans sp. nov., a marine bacterium in the family Rhodobacteraceae with the potential ability for cyanophycin synthesis Arahal, David R.; Lucena, Teresa; Rodrigo-Torres, Lidia International Journal of Systematic and Evolutionary Microbiology, Vol. 68, Issue 8 https://doi.org/10.1099/ijsem.0.002867	journal	August 2018
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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
Indiicoccus explosivorum gen. nov., sp. nov., isolated from an explosives waste contaminated site Pal, Yash; Mayilraj, Shanmugam; Paul, Mohit International Journal of Systematic and Evolutionary Microbiology, Vol. 69, Issue 8 https://doi.org/10.1099/ijsem.0.003541	journal	August 2019
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
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
Halorientalis pallida sp. nov., an extremely halophilic archaeon isolated from a marine saltern Durán-Viseras, Ana; Sánchez-Porro, Cristina; Ventosa, Antonio International Journal of Systematic and Evolutionary Microbiology, Vol. 69, Issue 11 https://doi.org/10.1099/ijsem.0.003675	journal	November 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
Serinibacter arcticus sp. nov., isolated from a thawing ancient ice wedge Filippova, Svetlana N.; Surgucheva, Natalya A.; Detkova, Ekaterina N. International Journal of Systematic and Evolutionary Microbiology, Vol. 70, Issue 2 https://doi.org/10.1099/ijsem.0.003848	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
Thalassocella blandensis gen. nov., sp. nov., a novel member of the family Cellvibrionaceae Lucena, Teresa; Arahal, David R.; Sanz-Sáez, Isabel International Journal of Systematic and Evolutionary Microbiology, Vol. 70, Issue 2 https://doi.org/10.1099/ijsem.0.003906	journal	February 2020
Senegalimassilia faecalis sp. nov., an anaerobic actinobacterium isolated from human faeces, and emended description of the genus Senegalimassilia Han, Kook-Il; Kim, Ji-Sun; Lee, Keun Chul International Journal of Systematic and Evolutionary Microbiology, Vol. 70, Issue 3 https://doi.org/10.1099/ijsem.0.003958	journal	March 2020
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Novel insights into the taxonomic diversity and molecular mechanisms of bacterial Mn(III) reduction Szeinbaum, Nadia; Nunn, Brook L.; Cavazos, Amanda R. https://doi.org/10.1101/695007	posted_content	June 2020
Human gut mobileome during antibiotic therapy. A trajectory-based approach to analysis of the metagenomic time-series datasets Górska, Anna; Schlaberg, Robert; Willmann, Matthias https://doi.org/10.1101/793737	preprint	October 2019
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
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
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
Genome biology of a novel lineage of planctomycetes widespread in anoxic aquatic environments Spring, Stefan; Bunk, Boyke; Spröer, Cathrin Environmental Microbiology, Vol. 20, Issue 7 https://doi.org/10.1111/1462-2920.14253	journal	July 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
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
Geomicrobiology of the carbon, nitrogen and sulphur cycles in Powell Lake: a permanently stratified water column containing ancient seawater Haas, Sebastian; Desai, Dhwani K.; LaRoche, Julie Environmental Microbiology, Vol. 21, Issue 10 https://doi.org/10.1111/1462-2920.14743	journal	July 2019
Comparative genomics reveals complex natural product biosynthesis capacities and carbon metabolism across host‐associated and free‐living Aquimarina ( Bacteroidetes, Flavobacteriaceae ) species Silva, Sandra G.; Blom, Jochen; Keller‐Costa, Tina Environmental Microbiology, Vol. 21, Issue 11 https://doi.org/10.1111/1462-2920.14747	journal	August 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
Direct effects of organic pollutants on the growth and gene expression of the Baltic Sea model bacterium Rheinheimera sp. BAL 341 Karlsson, Christofer M. G.; Cerro‐Gálvez, Elena; Lundin, Daniel Microbial Biotechnology, Vol. 12, Issue 5 https://doi.org/10.1111/1751-7915.13441	journal	July 2019
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
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
Identifying the causal agent of necrotizing hepatopancreatitis in shrimp: Multilocus sequence analysis approach Leyva, Juan Manuel; Martínez-Porchas, Marcel; Hernández-López, Jorge Aquaculture Research, Vol. 49, Issue 5 https://doi.org/10.1111/are.13633	journal	February 2018
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
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
Lineage-specific plasmid acquisition and the evolution of specialized pathogens in Bacillus thuringiensis and the Bacillus cereus group Méric, Guillaume; Mageiros, Leonardos; Pascoe, Ben Molecular Ecology, Vol. 27, Issue 7 https://doi.org/10.1111/mec.14546	journal	April 2018
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
Diversity within the novel Dickeya fangzhongdai sp., isolated from infected orchids, water and pears Alič, Š.; Van Gijsegem, F.; Pédron, J. Plant Pathology, Vol. 67, Issue 7 https://doi.org/10.1111/ppa.12866	journal	May 2018
Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay Marbouty, Martial; Baudry, Lyam; Cournac, Axel Science Advances, Vol. 3, Issue 2 https://doi.org/10.1126/sciadv.1602105	journal	February 2017
A sparse covarying unit that describes healthy and impaired human gut microbiota development Raman, Arjun S.; Gehrig, Jeanette L.; Venkatesh, Siddarth Science, Vol. 365, Issue 6449 https://doi.org/10.1126/science.aau4735	journal	July 2019
The effects of micronutrient deficiencies on bacterial species from the human gut microbiota Hibberd, Matthew C.; Wu, Meng; Rodionov, Dmitry A. Science Translational Medicine, Vol. 9, Issue 390 https://doi.org/10.1126/scitranslmed.aal4069	journal	May 2017
Quantification of Azospirillum brasilense FP2 Bacteria in Wheat Roots by Strain-Specific Quantitative PCR Stets, Maria Isabel; Alqueres, Sylvia Maria Campbell; Souza, Emanuel Maltempi Applied and Environmental Microbiology, Vol. 81, Issue 19 https://doi.org/10.1128/AEM.01351-15	journal	October 2015
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
Complete Sequence of the IncA/C ₁ Plasmid pCf587 Carrying bla _PER-2 from Citrobacter freundii Ruggiero, Melina; Girlich, Delphine; Dabos, Laura Antimicrobial Agents and Chemotherapy, Vol. 62, Issue 5 https://doi.org/10.1128/aac.00006-18	journal	May 2018
Genetic and Functional Characterization of blaCTX-M-199, a Novel Tazobactam and Sulbactam Resistance-Encoding Gene Located in a Conjugative mcr-1-Bearing IncI2 Plasmid Cai, Jiachang; Cheng, Qipeng; Shen, Yingbo Antimicrobial Agents and Chemotherapy, Vol. 61, Issue 7 https://doi.org/10.1128/aac.00562-17	journal	May 2017
A Prospective Cohort Multicenter Study of Molecular Epidemiology and Phylogenomics of Staphylococcus aureus Bacteremia in Nine Latin American Countries Arias, Cesar A.; Reyes, Jinnethe; Carvajal, Lina Paola Antimicrobial Agents and Chemotherapy, Vol. 61, Issue 10 https://doi.org/10.1128/aac.00816-17	journal	July 2017
Molecular Epidemiology and Genome Dynamics of New Delhi Metallo-β-Lactamase-Producing Extraintestinal Pathogenic Escherichia coli Strains from India Ranjan, Amit; Shaik, Sabiha; Mondal, Agnismita Antimicrobial Agents and Chemotherapy, Vol. 60, Issue 11 https://doi.org/10.1128/aac.01345-16	journal	November 2016
Cooccurrence of Two tet (X) Variants in an Empedobacter brevis Strain of Shrimp Origin Li, Ruichao; Liu, Ziyi; Peng, Kai Antimicrobial Agents and Chemotherapy, Vol. 63, Issue 12 https://doi.org/10.1128/aac.01636-19	journal	December 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
Spatial Distribution and Diverse Metabolic Functions of Lignocellulose-Degrading Uncultured Bacteria as Revealed by Genome-Centric Metagenomics Kougias, Panagiotis G.; Campanaro, Stefano; Treu, Laura Applied and Environmental Microbiology, Vol. 84, Issue 18 https://doi.org/10.1128/aem.01244-18	journal	July 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
Population Genetics and Characterization of Campylobacter jejuni Isolates from Western Jackdaws and Game Birds in Finland Kovanen, Sara; Rossi, Mirko; Pohja-Mykrä, Mari Applied and Environmental Microbiology, Vol. 85, Issue 4 https://doi.org/10.1128/aem.02365-18	journal	February 2019
Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis Quainoo, Scott; Coolen, Jordy P. M.; van Hijum, Sacha A. F. T. Clinical Microbiology Reviews, Vol. 30, Issue 4 https://doi.org/10.1128/cmr.00016-17	journal	August 2017
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
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
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
Draft Genome Sequences of Three Virulent Streptococcus thermophilus Bacteriophages Isolated from the Dairy Environment in the Veneto Region of Italy da Silva Duarte, Vinícius; Giaretta, Sabrina; Treu, Laura Genome Announcements, Vol. 6, Issue 10 https://doi.org/10.1128/genomea.00045-18	journal	March 2018
Draft Genome Sequence of Clostridium sp. Strain chh4-2 Isolated from Human Feces Huang, Chien-Hsun; Liou, Jong-Shian; Wang, Chun-Lin Genome Announcements, Vol. 6, Issue 8 https://doi.org/10.1128/genomea.00070-18	journal	February 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 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
Draft Genome Sequences of Five Staphylococcus aureus Strains Isolated from Clinically Healthy Cows in the Russian Federation Fursova, Ksenia K.; Artem’eva, Olga A.; Nikanova, Daria A. Genome Announcements, Vol. 6, Issue 16 https://doi.org/10.1128/genomea.00275-18	journal	April 2018
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 Oyster Isolate Vibrio vulnificus Env1 Noorian, Parisa; Sun, Shuyang; McDougald, Diane Genome Announcements, Vol. 6, Issue 20 https://doi.org/10.1128/genomea.00421-18	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
Draft Genome Sequences of Three Salmonella enterica Serovar 4,[5],12:i:− Strains and One S. enterica Serovar Typhimurium Strain, Isolated in Brazil Sales, Ana Isabela Lopes; Milanez, Guilherme Paier; Nascimento, Leandro C. Genome Announcements, Vol. 6, Issue 27 https://doi.org/10.1128/genomea.00488-18	journal	July 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 Geobacillus thermoleovorans SGAir0734, 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.00636-18	journal	July 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 Pantoea ananatis SGAir0210, Isolated from Outdoor Air in Singapore Luhung, Irvan; Junqueira, Ana Carolina M.; Uchida, Akira Genome Announcements, Vol. 6, Issue 27 https://doi.org/10.1128/genomea.00643-18	journal	July 2018
Draft Genome Sequences of Vibrio alginolyticus Strains V1 and V2, Opportunistic Marine Pathogens Castillo, Daniel; D’Alvise, Paul; Kalatzis, Panos G. Genome Announcements, Vol. 3, Issue 4 https://doi.org/10.1128/genomea.00729-15	journal	August 2015
Complete Genome Sequence of an Edwardsiella piscicida -Like Species, Recovered from Tilapia in the United States Reichley, Stephen R.; Waldbieser, Geoffrey C.; Lawrence, Mark L. Genome Announcements, Vol. 3, Issue 5 https://doi.org/10.1128/genomea.01004-15	journal	October 2015
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
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
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
Draft Genome Sequences of Nonclinical and Clinical Enterobacter cloacae Isolates Exhibiting Multiple Antibiotic Resistance and Virulence Factors Mishra, Mitali; Patole, Shashank; Mohapatra, Harapriya Genome Announcements, Vol. 5, Issue 45 https://doi.org/10.1128/genomea.01218-17	journal	November 2017
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
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
Draft Genome Sequences of Strains TRE 1, TRE D, TRE H, and TRI 7, Isolated from Tamarins and Belonging to Four Putative Novel Bifidobacterium Species Puglisi, Edoardo; Mattarelli, Paola; Modesto, Monica Genome Announcements, Vol. 6, Issue 3 https://doi.org/10.1128/genomea.01449-17	journal	January 2018
Genome Sequence of Acinetobacter baumannii Strain D36, an Antibiotic-Resistant Isolate from Lineage 2 of Global Clone 1 Hamidian, Mohammad; Hawkey, Jane; Holt, Kathryn E. Genome Announcements, Vol. 3, Issue 6 https://doi.org/10.1128/genomea.01478-15	journal	December 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
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
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
Comparative Genomics Study of Staphylococcus epidermidis Isolates from Orthopedic-Device-Related Infections Correlated with Patient Outcome Post, Virginia; Harris, Llinos G.; Morgenstern, Mario Journal of Clinical Microbiology, Vol. 55, Issue 10 https://doi.org/10.1128/jcm.00881-17	journal	October 2017
Molecular Prediction of the O157:H-Negative Phenotype Prevalent in Australian Shiga Toxin-Producing Escherichia coli Cases Improves Concordance of In Silico Serotyping with Phenotypic Motility Pintara, Alexander P.; Guglielmino, Christine J. D.; Rathnayake, Irani U. Journal of Clinical Microbiology, Vol. 56, Issue 4 https://doi.org/10.1128/jcm.01906-17	journal	April 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
A Bacterial Symbiont Protects Honey Bees from Fungal Disease Miller, Delaney L.; Smith, Eric A.; Newton, Irene L. G. mBio, Vol. 12, Issue 3 https://doi.org/10.1128/mBio.00503-21	journal	June 2021
Lifestyle Evolution in Cyanobacterial Symbionts of Sponges Burgsdorf, Ilia; Slaby, Beate M.; Handley, Kim M. mBio, Vol. 6, Issue 3 https://doi.org/10.1128/mbio.00391-15	journal	June 2015
Genomically Informed Surveillance for Carbapenem-Resistant Enterobacteriaceae in a Health Care System Pecora, Nicole D.; Li, Ning; Allard, Marc mBio, Vol. 6, Issue 4 https://doi.org/10.1128/mbio.01030-15	journal	July 2015
Ongoing Transposon-Mediated Genome Reduction in the Luminous Bacterial Symbionts of Deep-Sea Ceratioid Anglerfishes Hendry, Tory A.; Freed, Lindsay L.; Fader, Dana mBio, Vol. 9, Issue 3 https://doi.org/10.1128/mbio.01033-18	journal	July 2018
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
Promiscuous and Adaptable Enzymes Fill “Holes” in the Tetrahydrofolate Pathway in Chlamydia Species Adams, Nancy E.; Thiaville, Jennifer J.; Proestos, James mBio, Vol. 5, Issue 4 https://doi.org/10.1128/mbio.01378-14	journal	July 2014
Bioinformatic Genome Comparisons for Taxonomic and Phylogenetic Assignments Using Aeromonas as a Test Case Colston, Sophie M.; Fullmer, Matthew S.; Beka, Lidia mBio, Vol. 5, Issue 6 https://doi.org/10.1128/mbio.02136-14	journal	November 2014
Staphylococcus aureus HemX Modulates Glutamyl-tRNA Reductase Abundance To Regulate Heme Biosynthesis Choby, Jacob E.; Grunenwald, Caroline M.; Celis, Arianna I. mBio, Vol. 9, Issue 1 https://doi.org/10.1128/mbio.02287-17	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 Halotolerant Bacterium Chromohalobacter salexigens ANJ207, Isolated from Salt Crystal Deposits in Pipelines Srivastava, Alok Kumar; Sharma, Anjney; Srivastava, Ruchi Microbiology Resource Announcements, Vol. 8, Issue 15 https://doi.org/10.1128/mra.00049-19	journal	April 2019
Genome Sequence of Streptomyces cavourensis 1AS2a, a Rhizobacterium Isolated from the Brazilian Cerrado Biome Vargas Hoyos, Harold Alexander; Santos, Suikinai Nobre; Padilla, Gabriel Microbiology Resource Announcements, Vol. 8, Issue 18 https://doi.org/10.1128/mra.00065-19	journal	May 2019
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 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
Genome Sequence of a Jumbo Bacteriophage That Infects the Kiwifruit Phytopathogen Pseudomonas syringae pv. actinidiae Wojtus, Joanna K.; Frampton, Rebekah A.; Warring, Suzanne Microbiology Resource Announcements, Vol. 8, Issue 22 https://doi.org/10.1128/mra.00224-19	journal	May 2019
Draft Genome Sequence of Bacillus thuringiensis DPC6431, Producer of the Bacteriocin Thuricin CD Arbulu, Sara; Murphy, Kiera; O’Sullivan, Orla Microbiology Resource Announcements, Vol. 8, Issue 33 https://doi.org/10.1128/mra.00398-19	journal	August 2019
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
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
Genome Sequence of Lipopeptide- and Antioxidant-Producing Strain Bacillus velezensis NWUMFkBS10.5 Adeniji, Adetomiwa A.; Babalola, Olubukola O. Microbiology Resource Announcements, Vol. 8, Issue 28 https://doi.org/10.1128/mra.00595-19	journal	July 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
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
Complete Genome Sequence of Brachybacterium sp. Strain SGAir0954, Isolated from Singapore Air Hlaing, Phu Pwint Thin; Junqueira, Ana Carolina M.; Uchida, Akira Microbiology Resource Announcements, Vol. 8, Issue 32 https://doi.org/10.1128/mra.00619-19	journal	August 2019
Complete Genome Sequence of Rhodococcus sp. Strain SGAir0479, Isolated from Indoor Air Collected in Singapore Oliveira, Elaine L.; Drautz-Moses, Daniela I.; Uchida, Akira Microbiology Resource Announcements, Vol. 8, Issue 40 https://doi.org/10.1128/mra.00622-19	journal	October 2019
Complete Genome Sequence of Micrococcus luteus Strain SGAir0127, Isolated from Indoor Air Samples from Singapore Kutmutia, Shruti Ketan; Drautz-Moses, Daniela I.; Uchida, Akira Microbiology Resource Announcements, Vol. 8, Issue 41 https://doi.org/10.1128/mra.00646-19	journal	October 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
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 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
Draft Genome Sequence of the Type Strain Streptomyces armeniacus ATCC 15676 Labana, Puneet; Gosse, Jessica T.; Boddy, Christopher N. Microbiology Resource Announcements, Vol. 7, Issue 11 https://doi.org/10.1128/mra.01107-18	journal	September 2018
Draft Genome Sequence of Vibrio cyclitrophicus NCT10V, Cultivated from the Microbiome of a Marine Copepod Nuttall, Ryan; Sharma, Gaurav; Moisander, Pia H. Microbiology Resource Announcements, Vol. 8, Issue 44 https://doi.org/10.1128/mra.01208-19	journal	October 2019
Escherichia coli NGF-1, a Genetically Tractable, Efficiently Colonizing Murine Gut Isolate Ziesack, Marika; Karrenbelt, Michiel A. P.; Bues, Johannes Microbiology Resource Announcements, Vol. 7, Issue 22 https://doi.org/10.1128/mra.01416-18	journal	December 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
Complete Genome Sequence of Microbacterium sp. Strain 10M-3C3, Isolated from an Extremely Phosphorus-Poor Lake Hempel, Priscilla; Keffer, Jessica L.; Shevchenko, Olga Microbiology Resource Announcements, Vol. 8, Issue 4 https://doi.org/10.1128/mra.01649-18	journal	January 2019
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
In Silico Identification of Three Types of Integrative and Conjugative Elements in Elizabethkingia anophelis Strains Isolated from around the World Xu, Jiannong; Pei, Dong; Nicholson, Ainsley mSphere, Vol. 4, Issue 2 https://doi.org/10.1128/msphere.00040-19	journal	April 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
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
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
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
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
Metabolic Responses to Polymyxin Treatment in Acinetobacter baumannii ATCC 19606: Integrating Transcriptomics and Metabolomics with Genome-Scale Metabolic Modeling Zhu, Yan; Zhao, Jinxin; Maifiah, Mohd Hafidz Mahamad mSystems, Vol. 4, Issue 1 https://doi.org/10.1128/msystems.00157-18	journal	February 2019
Identification of Primary Antimicrobial Resistance Drivers in Agricultural Nontyphoidal Salmonella enterica Serovars by Using Machine Learning Maguire, Finlay; Rehman, Muhammad Attiq; Carrillo, Catherine mSystems, Vol. 4, Issue 4 https://doi.org/10.1128/msystems.00211-19	journal	August 2019
Linking Nitrogen Load to the Structure and Function of Wetland Soil and Rhizosphere Microbial Communities Hester, Eric R.; Harpenslager, Sarah F.; van Diggelen, Josepha M. H. mSystems, Vol. 3, Issue 1 https://doi.org/10.1128/msystems.00214-17	journal	January 2018
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
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
Evolution of fixNOQP genes encoding cytochrome oxidase with high affinity to oxygen in rhizobia and related bacteria Kopat, V. V.; Chirak, E. R.; Kimeklis, A. K. Russian Journal of Genetics, Vol. 53, Issue 7 https://doi.org/10.1134/s1022795417070067	journal	July 2017
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
High-throughput DNA sequencing technologies for water and wastewater analysis Chan, Alexander WY; Naphtali, James; Schellhorn, Herb E. Science Progress, Vol. 102, Issue 4 https://doi.org/10.1177/0036850419881855	journal	October 2019
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
Function of BriC peptide in the pneumococcal competence and virulence portfolio Aggarwal, Surya; Eutsey, Rory; West-Roberts, Jacob Carnegie Mellon University https://doi.org/10.1184/r1/7264151.v1	text	January 2018
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
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
High correlation between genotypes and phenotypes of environmental bacteria Comamonas testosteroni strains Liu, Lin; Zhu, Wentao; Cao, Zhan BMC Genomics, Vol. 16, Issue 1 https://doi.org/10.1186/s12864-015-1314-x	journal	February 2015
Comparative genome analysis of Mycoplasma pneumoniae Xiao, Li; Ptacek, Travis; Osborne, John D. BMC Genomics, Vol. 16, Issue 1 https://doi.org/10.1186/s12864-015-1801-0	journal	August 2015
Escherichia coli O157:H7 strains harbor at least three distinct sequence types of Shiga toxin 2a-converting phages Yin, Shuang; Rusconi, Brigida; Sanjar, Fatemeh BMC Genomics, Vol. 16, Issue 1 https://doi.org/10.1186/s12864-015-1934-1	journal	September 2015
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
SMRT sequencing of the Campylobacter coli BfR-CA-9557 genome sequence reveals unique methylation motifs Zautner, Andreas E.; Goldschmidt, Anne-Marie; Thürmer, Andrea BMC Genomics, Vol. 16, Issue 1 https://doi.org/10.1186/s12864-015-2317-3	journal	December 2015
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
Systematic identification and analysis of frequent gene fusion events in metabolic pathways Henry, Christopher S.; Lerma-Ortiz, Claudia; Gerdes, Svetlana Y. BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-2782-3	journal	June 2016
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 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
Development and validation of an updated computational model of Streptomyces coelicolor primary and secondary metabolism Amara, Adam; Takano, Eriko; Breitling, Rainer BMC Genomics, Vol. 19, Issue 1 https://doi.org/10.1186/s12864-018-4905-5	journal	July 2018
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
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
Combining multiple functional annotation tools increases coverage of metabolic annotation Griesemer, Marc; Kimbrel, Jeffrey A.; Zhou, Carol E. BMC Genomics, Vol. 19, Issue 1 https://doi.org/10.1186/s12864-018-5221-9	journal	December 2018
Comparative genomic analysis of Parageobacillus thermoglucosidasius strains with distinct hydrogenogenic capacities Mohr, Teresa; Aliyu, Habibu; Küchlin, Raphael BMC Genomics, Vol. 19, Issue 1 https://doi.org/10.1186/s12864-018-5302-9	journal	December 2018
Comparative genomics of Mycoplasma pneumoniae isolated from children with pneumonia: South Korea, 2010–2016 Lee, Joon Kee; Seong, Moon-Woo; Shin, Dongjin BMC Genomics, Vol. 20, Issue 1 https://doi.org/10.1186/s12864-019-6306-9	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
The anaerobic linalool metabolism in Thauera linaloolentis 47 Lol Marmulla, Robert; Cala, Edinson Puentes; Markert, Stephanie BMC Microbiology, Vol. 16, Issue 1 https://doi.org/10.1186/s12866-016-0693-8	journal	April 2016
Disrupting ROS-protection mechanism allows hydrogen peroxide to accumulate and oxidize Sb(III) to Sb(V) in Pseudomonas stutzeri TS44 Wang, Dan; Zhu, Fengqiu; Wang, Qian BMC Microbiology, Vol. 16, Issue 1 https://doi.org/10.1186/s12866-016-0902-5	journal	November 2016
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
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
Burkholderia thailandensis strain E555 is a surrogate for the investigation of Burkholderia pseudomallei replication and survival in macrophages Kovacs-Simon, A.; Hemsley, C. M.; Scott, A. E. BMC Microbiology, Vol. 19, Issue 1 https://doi.org/10.1186/s12866-019-1469-8	journal	May 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
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
MetAnnotate: function-specific taxonomic profiling and comparison of metagenomes Petrenko, Pavel; Lobb, Briallen; Kurtz, Daniel A. BMC Biology, Vol. 13, Issue 1 https://doi.org/10.1186/s12915-015-0195-4	journal	November 2015
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
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
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
Identification and engineering of 32 membered antifungal macrolactone notonesomycins Goh, Falicia; Zhang, Mingzi M.; Lim, Tian Ru Microbial Cell Factories, Vol. 19, Issue 1 https://doi.org/10.1186/s12934-020-01328-x	journal	March 2020
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
Genomic and proteomic analysis of lignin degrading and polyhydroxyalkanoate accumulating β-proteobacterium Pandoraea sp. ISTKB Kumar, Madan; Verma, Sandhya; Gazara, Rajesh Kumar Biotechnology for Biofuels, Vol. 11, Issue 1 https://doi.org/10.1186/s13068-018-1148-2	journal	June 2018
Characterization and genome analysis of a butanol–isopropanol-producing Clostridium beijerinckii strain BGS1 Zhang, Chen; Li, Tinggang; He, Jianzhong Biotechnology for Biofuels, Vol. 11, Issue 1 https://doi.org/10.1186/s13068-018-1274-x	journal	October 2018
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
Draft genome sequence of non-shiga toxin-producing Escherichia coli O157 NCCP15738 Kwon, Taesoo; Kim, Jung-Beom; Bak, Young-Seok Gut Pathogens, Vol. 8, Issue 1 https://doi.org/10.1186/s13099-016-0096-2	journal	April 2016
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
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
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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Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediments Dombrowski, Nina; Seitz, Kiley W.; Teske, Andreas P. Microbiome, Vol. 5, Issue 1 https://doi.org/10.1186/s40168-017-0322-2	journal	August 2017
Metatranscriptomic and comparative genomic insights into resuscitation mechanisms during enrichment culturing Mu, Da-Shuai; Liang, Qi-Yun; Wang, Xiao-Man Microbiome, Vol. 6, Issue 1 https://doi.org/10.1186/s40168-018-0613-2	journal	December 2018
Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization Westreich, Samuel T.; Ardeshir, Amir; Alkan, Zeynep Microbiome, Vol. 7, Issue 1 https://doi.org/10.1186/s40168-019-0664-z	journal	March 2019
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
Draft genome sequence of chloride-tolerant Leptospirillum ferriphilum Sp-Cl from industrial bioleaching operations in northern Chile Issotta, Francisco; Galleguillos, Pedro A.; Moya-Beltrán, Ana Standards in Genomic Sciences, Vol. 11, Issue 1 https://doi.org/10.1186/s40793-016-0142-1	journal	February 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
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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
Insights from the draft genome into the pathogenicity of a clinical isolate of Elizabethkingia meningoseptica Em3 Chen, Shicheng; Soehnlen, Marty; Downes, Frances P. Standards in Genomic Sciences, Vol. 12, Issue 1 https://doi.org/10.1186/s40793-017-0269-8	journal	September 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
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
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
OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling Shen, Fangzhou; Sun, Renliang; Yao, Jie PLOS Computational Biology, Vol. 15, Issue 3 https://doi.org/10.1371/journal.pcbi.1006835	journal	March 2019
Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics Price, Morgan N.; Zane, Grant M.; Kuehl, Jennifer V. PLOS Genetics, Vol. 14, Issue 1 https://doi.org/10.1371/journal.pgen.1007147	journal	January 2018
Perilipin-2 Modulates Lipid Absorption and Microbiome Responses in the Mouse Intestine Frank, Daniel N.; Bales, Elise S.; Monks, Jenifer PLOS ONE, Vol. 10, Issue 7 https://doi.org/10.1371/journal.pone.0131944	journal	July 2015
Plasmid Characterization and Chromosome Analysis of Two netF+ Clostridium perfringens Isolates Associated with Foal and Canine Necrotizing Enteritis Mehdizadeh Gohari, Iman; Kropinski, Andrew M.; Weese, Scott J. PLOS ONE, Vol. 11, Issue 2 https://doi.org/10.1371/journal.pone.0148344	journal	February 2016
The Identification of Novel Diagnostic Marker Genes for the Detection of Beer Spoiling Pediococcus damnosus Strains Using the BlAst Diagnostic Gene findEr Behr, Jürgen; Geissler, Andreas J.; Schmid, Jonas PLOS ONE, Vol. 11, Issue 3 https://doi.org/10.1371/journal.pone.0152747	journal	March 2016
Analysis of the complete genome sequence of Nocardia seriolae UTF1, the causative agent of fish nocardiosis: The first reference genome sequence of the fish pathogenic Nocardia species Yasuike, Motoshige; Nishiki, Issei; Iwasaki, Yuki PLOS ONE, Vol. 12, Issue 3 https://doi.org/10.1371/journal.pone.0173198	journal	March 2017
Prohibition of antibiotic growth promoters has affected the genomic profiles of Lactobacillus salivarius inhabiting the swine intestine Lee, Jun-Yeong; Han, Geon Goo; Lee, Ho-Bin PLOS ONE, Vol. 12, Issue 10 https://doi.org/10.1371/journal.pone.0186671	journal	October 2017
Isolation and characterization of a N4-like lytic bacteriophage infecting Vibrio splendidus, a pathogen of fish and bivalves Katharios, Pantelis; Kalatzis, Panos G.; Kokkari, Constantina PLOS ONE, Vol. 12, Issue 12 https://doi.org/10.1371/journal.pone.0190083	journal	December 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
Characterization of novel glycosyl hydrolases discovered by cell wall glycan directed monoclonal antibody screening and metagenome analysis of maize aerial root mucilage Pozzo, Tania; Higdon, Shawn M.; Pattathil, Sivakumar PLOS ONE, Vol. 13, Issue 9 https://doi.org/10.1371/journal.pone.0204525	journal	September 2018
Microbial enrichment and gene functional categories revealed on the walls of a spent fuel pool of a nuclear power plant Silva, Rosane; Almeida, Darcy Muniz de; Cabral, Bianca Catarina Azeredo PLOS ONE, Vol. 13, Issue 10 https://doi.org/10.1371/journal.pone.0205228	journal	October 2018
Functional screening for triclosan resistance in a wastewater metagenome and isolates of Escherichia coli and Enterococcus spp. from a large Canadian healthcare region Cameron, Andrew; Barbieri, Ruth; Read, Ron PLOS ONE, Vol. 14, Issue 1 https://doi.org/10.1371/journal.pone.0211144	journal	January 2019
Identification and characterization of putative Aeromonas spp. T3SS effectors Rangel, Luiz Thiberio; Marden, Jeremiah; Colston, Sophie PLOS ONE, Vol. 14, Issue 6 https://doi.org/10.1371/journal.pone.0214035	journal	June 2019
Accessory genome of the multi-drug resistant ocular isolate of Pseudomonas aeruginosa PA34 Subedi, Dinesh; Kohli, Gurjeet Singh; Vijay, Ajay Kumar PLOS ONE, Vol. 14, Issue 4 https://doi.org/10.1371/journal.pone.0215038	journal	April 2019
Comparative genomic analyses reveal diverse virulence factors and antimicrobial resistance mechanisms in clinical Elizabethkingia meningoseptica strains Chen, Shicheng; Soehnlen, Marty; Blom, Jochen PLOS ONE, Vol. 14, Issue 10 https://doi.org/10.1371/journal.pone.0222648	journal	October 2019
Genomic insights on heterogeneous resistance to vancomycin and teicoplanin in Methicillin-resistant Staphylococcus aureus: A first report from South India Bakthavatchalam, Yamuna Devi; Babu, Priyanka; Munusamy, Elakkiya PLOS ONE, Vol. 14, Issue 12 https://doi.org/10.1371/journal.pone.0227009	journal	December 2019
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Promiscuous signaling by a regulatory system unique to the pandemic PMEN1 pneumococcal lineage Kadam, Anagha; Eutsey, Rory A.; Rosch, Jason PLOS Pathogens, Vol. 13, Issue 5 https://doi.org/10.1371/journal.ppat.1006339	journal	May 2017
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Is there a Function for a Sex Pheromone Precursor?: A Predicted Link between Bacterial Redox Metabolism and Propagation of Antibiotic Resistance Vasieva, O.; Goryanin, I. Journal of Integrative Bioinformatics, Vol. 16, Issue 4 https://doi.org/10.1515/jib-2019-0016	journal	July 2019
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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
Whole-Metagenome-Sequencing-Based Community Profiles of Vitis vinifera L. cv. Corvina Berries Withered in Two Post-harvest Conditions Salvetti, Elisa; Campanaro, Stefano; Campedelli, Ilenia Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00937	journal	June 2016
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Inducible Prophage Mutant of Escherichia coli Can Lyse New Host and the Key Sites of Receptor Recognition Identification Chen, Mianmian; Zhang, Lei; Xin, Sipei Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.00147	journal	February 2017
Insights of Phage-Host Interaction in Hypersaline Ecosystem through Metagenomics Analyses Motlagh, Amir Mohaghegh; Bhattacharjee, Ananda S.; Coutinho, Felipe H. Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.00352	journal	March 2017
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
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
The Physiological Functions and Structural Determinants of Catalytic Bias in the [FeFe]-Hydrogenases CpI and CpII of Clostridium pasteurianum Strain W5 Therien, Jesse B.; Artz, Jacob H.; Poudel, Saroj Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.01305	journal	July 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
PacBio But Not Illumina Technology Can Achieve Fast, Accurate and Complete Closure of the High GC, Complex Burkholderia pseudomallei Two-Chromosome Genome Teng, Jade L. L.; Yeung, Man Lung; Chan, Elaine Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.01448	journal	August 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
Photosynthesis Is Widely Distributed among Proteobacteria as Demonstrated by the Phylogeny of PufLM Reaction Center Proteins Imhoff, Johannes F.; Rahn, Tanja; Künzel, Sven Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.02679	journal	January 2018
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
Taxon-Function Decoupling as an Adaptive Signature of Lake Microbial Metacommunities Under a Chronic Polymetallic Pollution Gradient Cheaib, Bachar; Le Boulch, Malo; Mercier, Pierre-Luc Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00869	journal	May 2018
A Novel Strategy for Detecting Recent Horizontal Gene Transfer and Its Application to Rhizobium Strains Li, Xiangchen; Tong, Wenjun; Wang, Lina Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00973	journal	May 2018
Hydrogen-Fueled Microbial Pathways in Biogas Upgrading Systems Revealed by Genome-Centric Metagenomics Treu, Laura; Campanaro, Stefano; Kougias, Panagiotis G. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.01079	journal	May 2018
Integrative and Conjugative Elements (ICEs) in Pasteurellaceae Species and Their Detection by Multiplex PCR Beker, Michal; Rose, Simon; Lykkebo, Claus A. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.01329	journal	June 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
Colanic Acid Is a Novel Phage Receptor of Pectobacterium carotovorum subsp. carotovorum Phage POP72 Kim, Hyeongsoon; Kim, Minsik; Bai, Jaewoo Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00143	journal	February 2019
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
Comparative Genomics of Thiohalobacter thiocyanaticus HRh1T and Guyparkeria sp. SCN-R1, Halophilic Chemolithoautotrophic Sulfur-Oxidizing Gammaproteobacteria Capable of Using Thiocyanate as Energy Source Tsallagov, Stanislav I.; Sorokin, Dimitry Y.; Tikhonova, Tamara V. Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00898	journal	May 2019
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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
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Stumbling across the Same Phage: Comparative Genomics of Widespread Temperate Phages Infecting the Fish Pathogen Vibrio anguillarum Kalatzis, Panos; Rørbo, Nanna; Castillo, Daniel Viruses, Vol. 9, Issue 5 https://doi.org/10.3390/v9050122	journal	May 2017
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Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks Zhao, Suwen; Sakai, Ayano; Zhang, Xinshuai eLife, Vol. 3 https://doi.org/10.7554/elife.03275	journal	June 2014
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
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