IMG/M: integrated genome and metagenome comparative data analysis system

Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken; Palaniappan, Krishna; Szeto, Ernest; Pillay, Manoj; Ratner, Anna; Huang, Jinghua; Andersen, Evan; Huntemann, Marcel; Varghese, Neha; Hadjithomas, Michalis; Tennessen, Kristin; Nielsen, Torben; Ivanova, Natalia N.; Kyrpides, Nikos C.

doi:10.1093/nar/gkw929

Title: IMG/M: integrated genome and metagenome comparative data analysis system

Journal Article · Thu Oct 13 00:00:00 EDT 2016 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkw929· OSTI ID:1379657

Chen, I-Min A. ^[1]; Markowitz, Victor M. ^[1]; Chu, Ken ^[1]; Palaniappan, Krishna ^[1]; Szeto, Ernest ^[1]; Pillay, Manoj ^[1]; Ratner, Anna ^[1]; Huang, Jinghua ^[1]; Andersen, Evan ^[1]; Huntemann, Marcel ^[2]; Varghese, Neha ^[2]; Hadjithomas, Michalis ^[2]; Tennessen, Kristin ^[2]; Nielsen, Torben ^[2]; Ivanova, Natalia N. ^[2]; Kyrpides, Nikos C. ^[2]

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Computational Science Dept.
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States). Microbial Genome and Metagenome Program

The Integrated Microbial Genomes with Microbiome Samples (IMG/M: https://img.jgi.doe.gov/m/) system contains annotated DNA and RNA sequence data of (i) archaeal, bacterial, eukaryotic and viral genomes from cultured organisms, (ii) single cell genomes (SCG) and genomes from metagenomes (GFM) from uncultured archaea, bacteria and viruses and (iii) metagenomes from environmental, host associated and engineered microbiome samples. Sequence data are generated by DOE's Joint Genome Institute (JGI), submitted by individual scientists, or collected from public sequence data archives. Structural and functional annotation is carried out by JGI's genome and metagenome annotation pipelines. A variety of analytical and visualization tools provide support for examining and comparing IMG/M's datasets. IMG/M allows open access interactive analysis of publicly available datasets, while manual curation, submission and access to private datasets and computationally intensive workspace-based analysis require login/password access to its expert review(ER) companion system (IMG/M ER: https://img.jgi.doe.gov/ mer/). Since the last report published in the 2014 NAR Database Issue, IMG/M's dataset content has tripled in terms of number of datasets and overall protein coding genes, while its analysis tools have been extended to cope with the rapid growth in the number and size of datasets handled by the system.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

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

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1379657

Journal Information:: Nucleic Acids Research, Vol. 45, Issue D1; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 296 works

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Rathayibacter oskolensis sp. nov., a novel actinobacterium from Androsace koso-poljanskii Ovcz. (Primulaceae) endemic to the Central Russian Upland Dorofeeva, Lubov V.; Starodumova, Irina P.; Krauzova, Valentina I. International Journal of Systematic and Evolutionary Microbiology, Vol. 68, Issue 5 https://doi.org/10.1099/ijsem.0.002681	journal	May 2018
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Polynucleobacter paneuropaeus sp. nov., characterized by six strains isolated from freshwater lakes located along a 3000 km north–south cross-section across Europe Hoetzinger, Matthias; Schmidt, Johanna; Pitt, Alexandra International Journal of Systematic and Evolutionary Microbiology, Vol. 69, Issue 1 https://doi.org/10.1099/ijsem.0.003130	journal	January 2019
Emergence of trait variability through the lens of nitrogen assimilation in Prochlorococcus Berube, Paul M.; Rasmussen, Anna; Braakman, Rogier eLife https://doi.org/10.1101/383927	journal	November 2018
Swimming motility and chemotaxis control the spatial organization, persistence, and inflammatory activity of a model intestinal pathobiont Wiles, Travis J.; Schlomann, Brandon H.; Wall, Elena S. BioRxiv https://doi.org/10.1101/779983	posted_content	September 2019
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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
Comparison of sulfide‐oxidizing Sulfurimonas strains reveals a new mode of thiosulfate formation in subsurface environments Lahme, Sven; Callbeck, Cameron M.; Eland, Lucy E. Environmental Microbiology, Vol. 22, Issue 5 https://doi.org/10.1111/1462-2920.14894	journal	January 2020
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Giant viruses with an expanded complement of translation system components Schulz, Frederik; Yutin, Natalya; Ivanova, Natalia N. Science, Vol. 356, Issue 6333 https://doi.org/10.1126/science.aal4657	journal	April 2017
Programmed DNA destruction by miniature CRISPR-Cas14 enzymes Harrington, Lucas B.; Burstein, David; Chen, Janice S. Science, Vol. 362, Issue 6416 https://doi.org/10.1126/science.aav4294	journal	October 2018
Unveiling Concealed Functions of Endosymbiotic Bacteria Harbored in the Ascomycete Stachylidium bicolor Almeida, Celso; Silva Pereira, Cristina; Gonzalez-Menendez, Victor Applied and Environmental Microbiology, Vol. 84, Issue 15 https://doi.org/10.1128/aem.00660-18	journal	June 2018
Engineered Root Bacteria Release Plant-Available Phosphate from Phytate Shulse, Christine N.; Chovatia, Mansi; Agosto, Carolyn Applied and Environmental Microbiology, Vol. 85, Issue 18 https://doi.org/10.1128/aem.01210-19	journal	July 2019
Species Deletions from Microbiome Consortia Reveal Key Metabolic Interactions between Gut Microbes Gutiérrez, Natalia; Garrido, Daniel mSystems, Vol. 4, Issue 4 https://doi.org/10.1128/msystems.00185-19	journal	July 2019
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Rational construction of genome-reduced and high-efficient industrial Streptomyces chassis based on multiple comparative genomic approaches Bu, Qing-Ting; Yu, Pin; Wang, Jue Microbial Cell Factories, Vol. 18, Issue 1 https://doi.org/10.1186/s12934-019-1055-7	journal	January 2019
Genomic variation and biogeography of Antarctic haloarchaea Tschitschko, Bernhard; Erdmann, Susanne; DeMaere, Matthew Z. Microbiome, Vol. 6, Issue 1 https://doi.org/10.1186/s40168-018-0495-3	journal	June 2018
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Diversity, evolution, and classification of virophages uncovered through global metagenomics Paez-Espino, David; Zhou, Jinglie; Roux, Simon Microbiome, Vol. 7, Issue 1 https://doi.org/10.1186/s40168-019-0768-5	journal	December 2019
A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes Podell, Sheila; Blanton, Jessica M.; Oliver, Aaron Microbiome, Vol. 8, Issue 1 https://doi.org/10.1186/s40168-020-00877-y	journal	June 2020
Deciphering intra-species bacterial diversity of meat and seafood spoilage microbiota using gyrB amplicon sequencing: A comparative analysis with 16S rDNA V3-V4 amplicon sequencing Poirier, Simon; Rué, Olivier; Peguilhan, Raphaëlle PLOS ONE, Vol. 13, Issue 9 https://doi.org/10.1371/journal.pone.0204629	journal	September 2018
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Comparative Metagenomics Analysis of palm oil mill Effluent (Pome) Using Three Different Bioinformatics Pipelines Parmen, Adibah; Mat Isa, Mohd Noor; Benbelgacem, Farah Fadwa IIUM Engineering Journal, Vol. 20, Issue 1 https://doi.org/10.31436/iiumej.v20i1.909	journal	June 2019
In Silico Analysis of Putrefaction Pathways in Bacteria and Its Implication in Colorectal Cancer Kaur, Harrisham; Das, Chandrani; Mande, Sharmila S. Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.02166	journal	November 2017
Genome Sequencing and Comparative Analysis of Stenotrophomonas acidaminiphila Reveal Evolutionary Insights Into Sulfamethoxazole Resistance Huang, Yao-Ting; Chen, Jia-Min; Ho, Bing-Ching Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.01013	journal	May 2018
Changes in Carbon Oxidation State of Metagenomes Along Geochemical Redox Gradients Dick, Jeffrey M.; Yu, Miao; Tan, Jingqiang Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00120	journal	February 2019
Bacterial Metabolites Produced Under Iron Limitation Kill Pinewood Nematode and Attract Caenorhabditis elegans Proença, Diogo Neves; Heine, Thomas; Senges, Christoph H. R. Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.02166	journal	September 2019
Applying Genome-Resolved Metagenomics to Deconvolute the Halophilic Microbiome Uritskiy, Gherman; DiRuggiero, Jocelyne Genes, Vol. 10, Issue 3 https://doi.org/10.3390/genes10030220	journal	March 2019
Role of the Extremolytes Ectoine and Hydroxyectoine as Stress Protectants and Nutrients: Genetics, Phylogenomics, Biochemistry, and Structural Analysis Czech, Laura; Hermann, Lucas; Stöveken, Nadine Genes, Vol. 9, Issue 4 https://doi.org/10.3390/genes9040177	journal	March 2018
Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview Sen, Partho; Orešič, Matej Metabolites, Vol. 9, Issue 2 https://doi.org/10.3390/metabo9020022	journal	January 2019
Coupled Biological and Abiotic Mechanisms Driving Carbonyl Sulfide Production in Soils Meredith, Laura K.; Boye, Kristin; Youngerman, Connor Soil Systems, Vol. 2, Issue 3 https://doi.org/10.3390/soilsystems2030037	journal	June 2018
1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life Mukherjee, Supratim; Seshadri, Rekha; Varghese, Neha J. Nature Biotechnology, Vol. 35, Issue 7 https://doi.org/10.1038/nbt.3886	journal	June 2017
Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection Seshadri, Rekha; Leahy, Sinead C.; Attwood, Graeme T. Nature Biotechnology, Vol. 36, Issue 4 https://doi.org/10.1038/nbt.4110	journal	March 2018
Carboxythiazole is a key microbial nutrient currency and critical component of thiamin biosynthesis Paerl, Ryan W.; Bertrand, Erin M.; Rowland, Elden Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-24321-2	journal	April 2018
Genomic, metabolic and phenotypic variability shapes ecological differentiation and intraspecies interactions of Alteromonas macleodii Koch, Hanna; Germscheid, Nora; Freese, Heike M. Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-57526-5	journal	January 2020
Organic sulfur fingerprint indicates continued injection fluid signature 10 months after hydraulic fracturing Luek, Jenna L.; Harir, Mourad; Schmitt-Kopplin, Philippe Environmental Science: Processes & Impacts, Vol. 21, Issue 2 https://doi.org/10.1039/c8em00331a	journal	January 2019
The structure of the Thermococcus gammatolerans McrB N-terminal domain reveals a new mode of substrate recognition and specificity among McrB homologs Hosford, Christopher J.; Bui, Anthony Q.; Chappie, Joshua S. Journal of Biological Chemistry, Vol. 295, Issue 3 https://doi.org/10.1074/jbc.ra119.010188	journal	December 2019
Current challenges and best-practice protocols for microbiome analysis Bharti, Richa; Grimm, Dominik G. Briefings in Bioinformatics https://doi.org/10.1093/bib/bbz155	journal	December 2019
Comparative genomics of the genus Desulfitobacterium Kruse, Thomas; Goris, Tobias; Maillard, Julien FEMS Microbiology Ecology, Vol. 93, Issue 12 https://doi.org/10.1093/femsec/fix135	journal	October 2017
EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies Mitchell, Alex L.; Scheremetjew, Maxim; Denise, Hubert Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx967	journal	October 2017
Elioraea thermophila sp. nov., a thermophilic bacterium from hot spring of the class Alphaproteobacteria, emended description of the genus Elioraea and proposal of Elioraeaceae fam. nov. Habib, Neeli; Khan, Inam Ullah; Xiao, Min International Journal of Systematic and Evolutionary Microbiology, Vol. 70, Issue 2 https://doi.org/10.1099/ijsem.0.003915	journal	February 2020
Metagenomic characterization of the viral community of the South Scotia Ridge Yang, Qingwei; Gao, Chen; Jiang, Yong Viruses https://doi.org/10.1101/451732	journal	October 2018
Genomes of rumen bacteria encode atypical pathways for fermenting hexoses to short-chain fatty acids: Atypical fermentation pathways Hackmann, Timothy J.; Ngugi, David Kamanda; Firkins, Jeffrey L. Environmental Microbiology, Vol. 19, Issue 11 https://doi.org/10.1111/1462-2920.13929	journal	November 2017
Bacterial nanocellulose production from naphthalene Marín, Patricia; Martirani‐Von Abercron, Sophie Marie; Urbina, Leire Microbial Biotechnology https://doi.org/10.1111/1751-7915.13399	journal	May 2019
The Polyextremophilic Bacterium Clostridium paradoxum Attains Piezophilic Traits by Modulating Its Energy Metabolism and Cell Membrane Composition Scoma, Alberto; Garrido-Amador, Paloma; Nielsen, Søren Dollerup Applied and Environmental Microbiology, Vol. 85, Issue 15 https://doi.org/10.1128/AEM.00802-19	journal	August 2019
OpuF, a New Bacillus Compatible Solute ABC Transporter with a Substrate-Binding Protein Fused to the Transmembrane Domain Teichmann, Laura; Kümmel, Henriette; Warmbold, Bianca Applied and Environmental Microbiology, Vol. 84, Issue 20 https://doi.org/10.1128/aem.01728-18	journal	October 2018
Comparative Genomics of Rumen Butyrivibrio spp. Uncovers a Continuum of Polysaccharide-Degrading Capabilities Palevich, Nikola; Kelly, William J.; Leahy, Sinead C. Applied and Environmental Microbiology, Vol. 86, Issue 1 https://doi.org/10.1128/aem.01993-19	journal	October 2019
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Members of Marinobacter and Arcobacter Influence System Biogeochemistry During Early Production of Hydraulically Fractured Natural Gas Wells in the Appalachian Basin Evans, Morgan V.; Panescu, Jenny; Hanson, Andrea J. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.02646	journal	November 2018
Complex general stress response regulation in Sphingomonas melonis Fr1 revealed by transcriptional analyses Gottschlich, Lisa; Geiser, Petra; Bortfeld-Miller, Miriam ETH Zurich https://doi.org/10.3929/ethz-b-000351713	text	January 2019
B ‐factor Guided Proline Substitutions in Chromobacterium violaceum Amine Transaminase: Evaluation of the Proline Rule as a Method for Enzyme Stabilization Land, Henrik; Campillo‐Brocal, Jonatan C.; Svedendahl Humble, Maria ChemBioChem, Vol. 20, Issue 10 https://doi.org/10.1002/cbic.201800749	journal	March 2019
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Murine colitis reveals a disease-associated bacteriophage community Duerkop, Breck A.; Kleiner, Manuel; Paez-Espino, David Nature Microbiology, Vol. 3, Issue 9 https://doi.org/10.1038/s41564-018-0210-y	journal	July 2018
Investigation of recombination-intense viral groups and their genes in the Earth’s virome Meier-Kolthoff, Jan P.; Uchiyama, Jumpei; Yahara, Hiroko Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-29272-2	journal	July 2018
Prevalent reliance of bacterioplankton on exogenous vitamin B1 and precursor availability Paerl, Ryan W.; Sundh, John; Tan, Demeng Proceedings of the National Academy of Sciences, Vol. 115, Issue 44 https://doi.org/10.1073/pnas.1806425115	journal	October 2018
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HipMCL: a high-performance parallel implementation of the Markov clustering algorithm for large-scale networks Azad, Ariful; Pavlopoulos, Georgios A.; Ouzounis, Christos A. Nucleic Acids Research, Vol. 46, Issue 6 https://doi.org/10.1093/nar/gkx1313	journal	January 2018
dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation Huang, Le; Zhang, Han; Wu, Peizhi Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx894	journal	October 2017
gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data Shi, Wenyu; Qi, Heyuan; Sun, Qinglan Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky1008	journal	October 2018
Integration of absolute multi-omics reveals translational and metabolic interplay in mixed-kingdom microbiomes Delogu, F.; Kunath, B. J.; Arntzen, M. Ø. BioRxiv https://doi.org/10.1101/857599	posted_content	November 2019
Shewanella khirikhana sp. nov. – a shrimp pathogen isolated from a cultivation pond exhibiting early mortality syndrome Prachumwat, Anuphap; Wechprasit, Piyanuch; Srisala, Jiraporn Microbial Biotechnology, Vol. 13, Issue 3 https://doi.org/10.1111/1751-7915.13538	journal	May 2020
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Use of a Fluorescent Analog of Glucose (2-NBDG) To Identify Uncultured Rumen Bacteria That Take Up Glucose Tao, Junyi; McCourt, Courtney; Sultana, Halima Applied and Environmental Microbiology, Vol. 85, Issue 7 https://doi.org/10.1128/aem.03018-18	journal	February 2019
Complete Genome Sequence of Thermoanaerobacterium sp. Strain RBIITD, a Butyrate- and Butanol-Producing Thermophile Biswas, Ranjita; Huntemann, Marcel; Clum, Alicia Genome Announcements, Vol. 6, Issue 2 https://doi.org/10.1128/genomea.01411-17	journal	January 2018
Improved Draft Genome Sequence of Pseudomonas poae A2-S9, a Strain with Plant Growth-Promoting Activity Xia, Ye; DeBolt, Seth; Ma, Qin Microbiology Resource Announcements, Vol. 8, Issue 15 https://doi.org/10.1128/mra.00275-19	journal	April 2019
ZetaHunter, a Reproducible Taxonomic Classification Tool for Tracking the Ecology of the Zetaproteobacteria and Other Poorly Resolved Taxa McAllister, Sean M.; Moore, Ryan M.; Chan, Clara S. Microbiology Resource Announcements, Vol. 7, Issue 7 https://doi.org/10.1128/mra.00932-18	journal	August 2018
Complete Genome Sequence of Shewanella sp. Strain TH2012, Isolated from Shrimp in a Cultivation Pond Exhibiting Early Mortality Syndrome Wechprasit, Piyanuch; Panphloi, Muthita; Thitamadee, Siripong Microbiology Resource Announcements, Vol. 8, Issue 13 https://doi.org/10.1128/mra.01703-18	journal	March 2019
Metagenomic Characterization of the Viral Community of the South Scotia Ridge Yang, Qingwei; Gao, Chen; Yong, Jiang Viruses https://doi.org/10.20944/preprints201810.0666.v1	journal	October 2018
A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes Podell, Sheila; Blanton, Jessica M.; Oliver, Aaron Microbiome https://doi.org/10.21203/rs.2.17204/v2	posted_content	June 2020
Co-Option and Detoxification of a Phage Lysin for Housekeeping Function Randich, Amelia M.; Kysela, David T.; Morlot, Cécile SSRN Electronic Journal https://doi.org/10.2139/ssrn.3287789	journal	January 2018
Comparative Pangenomics of the Mammalian Gut Commensal Bifidobacterium longum Albert, Korin; Rani, Asha; Sela, David A. Microorganisms, Vol. 8, Issue 1 https://doi.org/10.3390/microorganisms8010007	journal	December 2019
Snf2 controls pulcherriminic acid biosynthesis and antifungal activity of the biocontrol yeast Metschnikowia pulcherrima Gore‐Lloyd, Deborah; Sumann, Inés; Brachmann, Alexander Oliver ETH Zurich https://doi.org/10.3929/ethz-b-000353927	text	January 2019
A roadmap for global synthesis of the plant tree of life Eiserhardt, Wolf L.; Antonelli, Alexandre; Bennett, Dominic J. American Journal of Botany, Vol. 105, Issue 3 https://doi.org/10.1002/ajb2.1041	journal	March 2018
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Co-option and Detoxification of a Phage Lysin for Housekeeping Function Randich, Amelia M.; Kysela, David T.; Morlot, Cécile Current Biology https://doi.org/10.1101/418723	journal	November 2018
Oral bacteriophages are maintained at high levels for months in individuals but infrequently transmitted between mothers and infants Beall, Clifford J.; Sulyanto, Rosalyn M.; Griffen, Ann L. https://doi.org/10.1101/633727	posted_content	May 2019
Genome‐based evolutionary history of Pseudomonas spp Hesse, Cedar; Schulz, Frederik; Bull, Carolee T. Environmental Microbiology, Vol. 20, Issue 6 https://doi.org/10.1111/1462-2920.14130	journal	June 2018
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Genome-Scale Data Call for a Taxonomic Rearrangement of Geodermatophilaceae Montero-Calasanz, Maria del Carmen; Meier-Kolthoff, Jan P.; Zhang, Dao-Feng Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.02501	journal	December 2017
The trajectory of microbial single-cell sequencing Woyke, Tanja; Doud, Devin F. R.; Schulz, Frederik Nature Methods, Vol. 14, Issue 11 https://doi.org/10.1038/nmeth.4469	journal	October 2017
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From proteins to polysaccharides: lifestyle and genetic evolution of Coprothermobacter proteolyticus Kunath, Benoit J.; Delogu, Francesco; Naas, Adrian E. The ISME Journal, Vol. 13, Issue 3 https://doi.org/10.1038/s41396-018-0290-y	journal	October 2018
Complex general stress response regulation in Sphingomonas melonis Fr1 revealed by transcriptional analyses Gottschlich, Lisa; Geiser, Petra; Bortfeld-Miller, Miriam Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-45788-7	journal	June 2019
The Fe(II)-oxidizing Zetaproteobacteria : historical, ecological and genomic perspectives McAllister, Sean M.; Moore, Ryan M.; Gartman, Amy FEMS Microbiology Ecology, Vol. 95, Issue 4 https://doi.org/10.1093/femsec/fiz015	journal	January 2019
MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data Dhariwal, Achal; Chong, Jasmine; Habib, Salam Nucleic Acids Research, Vol. 45, Issue W1 https://doi.org/10.1093/nar/gkx295	journal	April 2017
Leeuwenhoekiella aestuarii sp. nov., isolated from salt-water sediment and first insights in the genomes of Leeuwenhoekiella species Tahon, Guillaume; Lebbe, Liesbeth; De Troch, Marleen International Journal of Systematic and Evolutionary Microbiology, Vol. 70, Issue 3 https://doi.org/10.1099/ijsem.0.003959	journal	March 2020
ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data Kieser, Silas; Brown, Joseph; Zdobnov, Evgeny M. BMC Bioinformatics, Vol. 21, Issue 1 https://doi.org/10.1186/s12859-020-03585-4	journal	June 2020
Viral and metabolic controls on high rates of microbial sulfur and carbon cycling in wetland ecosystems Dalcin Martins, Paula; Danczak, Robert E.; Roux, Simon Microbiome, Vol. 6, Issue 1 https://doi.org/10.1186/s40168-018-0522-4	journal	August 2018
Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies Tramontano, Melanie; Andrejev, Sergej; Pruteanu, Mihaela Nature Microbiology, Vol. 3, Issue 4 https://doi.org/10.1038/s41564-018-0123-9	journal	March 2018
Unexpected host dependency of Antarctic Nanohaloarchaeota Hamm, Joshua N.; Erdmann, Susanne; Eloe-Fadrosh, Emiley A. Proceedings of the National Academy of Sciences, Vol. 116, Issue 29 https://doi.org/10.1073/pnas.1905179116	journal	June 2019
Cellular life from the three domains and viruses are transcriptionally active in a hypersaline desert community Uritskiy, Gherman; Tisza, Michael J.; Gelsinger, Diego R. Environmental Microbiology, Vol. 23, Issue 7 https://doi.org/10.1111/1462-2920.15023	journal	May 2020
Swimming Motility and Chemotaxis Control the Spatial Organization, Persistence, and Inflammatory Activity of a Model Intestinal Pathobiont Wiles, Travis J.; Schlomann, Brandon H.; Wall, Elena S. SSRN Electronic Journal https://doi.org/10.2139/ssrn.3467155	journal	January 2019
Genome Analysis of Vallitalea guaymasensis Strain L81 Isolated from a Deep-Sea Hydrothermal Vent System Schouw, Anders; Vulcano, Francesca; Roalkvam, Irene Microorganisms, Vol. 6, Issue 3 https://doi.org/10.3390/microorganisms6030063	journal	July 2018
Paenibacillus amylolyticus 27C64 has a diverse set of carbohydrate-active enzymes and complete pectin deconstruction system Keggi, Christian; Doran-Peterson, Joy Journal of Industrial Microbiology and Biotechnology, Vol. 46, Issue 1 https://doi.org/10.1007/s10295-018-2098-1	journal	January 2019
Polyphyly in 16S rRNA-based LVTree Versus Monophyly in Whole-genome-based CVTree Zuo, Guanghong; Qi, Ji; Hao, Bailin Genomics, Proteomics & Bioinformatics, Vol. 16, Issue 5 https://doi.org/10.1016/j.gpb.2018.06.005	journal	October 2018
Author Correction: Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria Matheus Carnevali, Paula B.; Schulz, Frederik; Castelle, Cindy J. Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-09423-3	journal	March 2019
The Thaumarchaeon N. gargensis carries functional bioABD genes and has a promiscuous E. coli ΔbioH-complementing esterase EstN1 Chow, Jennifer; Danso, Dominik; Ferrer, Manuel Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-32059-0	journal	September 2018
Metagenomic insights into diazotrophic communities across Arctic glacier forefields Nash, Maisie V.; Anesio, Alexandre M.; Barker, Gary FEMS Microbiology Ecology, Vol. 94, Issue 9 https://doi.org/10.1093/femsec/fiy114	journal	June 2018
The MAR databases: development and implementation of databases specific for marine metagenomics Klemetsen, Terje; Raknes, Inge A.; Fu, Juan Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx1036	journal	November 2017
Interactive microbial distribution analysis using BioAtlas Lund, Jesper Beltoft; List, Markus; Baumbach, Jan Nucleic Acids Research, Vol. 45, Issue W1 https://doi.org/10.1093/nar/gkx304	journal	April 2017
IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes Paez-Espino, David; Roux, Simon; Chen, I-Min A. Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky1127	journal	November 2018
Polyphosphate-Accumulating Bacteria: Potential Contributors to Mineral Dissolution in the Oral Cavity Breiland, Ashley A.; Flood, Beverly E.; Nikrad, Julia Applied and Environmental Microbiology, Vol. 84, Issue 7 https://doi.org/10.1128/aem.02440-17	journal	April 2018
Draft Genome Sequences of Three Sub-Antarctic Rhodococcus spp., Including Two Novel Psychrophilic Genomospecies Nahar, Akhikun; Baker, Anthony L.; Charleston, Michael A. Genome Announcements, Vol. 5, Issue 36 https://doi.org/10.1128/genomea.00898-17	journal	September 2017
Draft Genome Sequences of Two Novel Sub-Antarctic Williamsia Species Nahar, Akhikun; Baker, Anthony L.; Charleston, Michael A. Genome Announcements, Vol. 5, Issue 41 https://doi.org/10.1128/genomea.01047-17	journal	October 2017
On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires Silas, Sukrit; Makarova, Kira S.; Shmakov, Sergey mBio, Vol. 8, Issue 4 https://doi.org/10.1128/mbio.00897-17	journal	September 2017
Metagenomic mining pectinolytic microbes and enzymes from an apple pomace-adapted compost microbial community Zhou, Man; Guo, Peng; Wang, Tao Biotechnology for Biofuels, Vol. 10, Issue 1 https://doi.org/10.1186/s13068-017-0885-y	journal	August 2017
Flexible metagenome analysis using the MGX framework Jaenicke, Sebastian; Albaum, Stefan P.; Blumenkamp, Patrick Microbiome, Vol. 6, Issue 1 https://doi.org/10.1186/s40168-018-0460-1	journal	April 2018
Genome sequences of lower Great Lakes Microcystis sp. reveal strain-specific genes that are present and expressed in western Lake Erie blooms Meyer, Kevin Anthony; Davis, Timothy W.; Watson, Susan B. PLOS ONE, Vol. 12, Issue 10 https://doi.org/10.1371/journal.pone.0183859	journal	October 2017
Beyond cells – The virome in the human holobiont García-López, Rodrigo; Pérez-Brocal, Vicente; Moya, Andrés Microbial Cell, Vol. 6, Issue 9 https://doi.org/10.15698/mic2019.09.689	journal	September 2019
Cyberbiosecurity Challenges of Pathogen Genome Databases Vinatzer, Boris A.; Heath, Lenwood S.; Almohri, Hussain M. J. Frontiers in Bioengineering and Biotechnology, Vol. 7 https://doi.org/10.3389/fbioe.2019.00106	journal	May 2019
An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs Dong, Xiaoli; Strous, Marc Frontiers in Genetics, Vol. 10 https://doi.org/10.3389/fgene.2019.00999	journal	October 2019
Complete Genome Sequence of Vibrio campbellii LMB 29 Isolated from Red Drum with Four Native Megaplasmids Liu, Jinxin; Zhao, Zhe; Deng, Yiqing Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.02035	journal	October 2017
Chromobacterium violaceum Pathogenicity: Updates and Insights from Genome Sequencing of Novel Chromobacterium Species Batista, Juliana H.; da Silva Neto, José F. Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.02213	journal	November 2017
Substrate Shift Reveals Roles for Members of Bacterial Consortia in Degradation of Plant Cell Wall Polymers Carlos, Camila; Fan, Huan; Currie, Cameron R. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00364	journal	March 2018
Genomic Insights Into Energy Metabolism of Carboxydocella thermautotrophica Coupling Hydrogenogenic CO Oxidation With the Reduction of Fe(III) Minerals Toshchakov, Stepan V.; Lebedinsky, Alexander V.; Sokolova, Tatyana G. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.01759	journal	August 2018
The GbsR Family of Transcriptional Regulators: Functional Characterization of the OpuAR Repressor Ronzheimer, Stefanie; Warmbold, Bianca; Arnhold, Christian Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.02536	journal	October 2018
Phenotypic and Genomic Properties of a Novel Deep-Lineage Haloalkaliphilic Member of the Phylum Balneolaeota From Soda Lakes Possessing Na+-Translocating Proteorhodopsin Sorokin, Dimitry Y.; Muntyan, Maria S.; Toshchakov, Stepan V. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.02672	journal	November 2018
Comparative Genome Analysis of Lactococcus lactis Indicates Niche Adaptation and Resolves Genotype/Phenotype Disparity Wels, Michiel; Siezen, Roland; van Hijum, Sacha Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00004	journal	January 2019
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
Comparative Genomic Analysis of Soil Dwelling Bacteria Utilizing a Combinational Codon Usage and Molecular Phylogenetic Approach Accentuating on Key Housekeeping Genes Saha, Jayanti; Saha, Barnan K.; Pal Sarkar, Monalisha Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.02896	journal	December 2019
The Pseudoalteromonas luteoviolacea L-amino Acid Oxidase with Antimicrobial Activity Is a Flavoenzyme Andreo-Vidal, Andrés; Sanchez-Amat, Antonio; Campillo-Brocal, Jonatan Marine Drugs, Vol. 16, Issue 12 https://doi.org/10.3390/md16120499	journal	December 2018
An Integrated Multi-Disciplinary Perspective for Addressing Challenges of the Human Gut Microbiome Shah, Rohan M.; McKenzie, Elizabeth J.; Rosin, Magda T. Metabolites, Vol. 10, Issue 3 https://doi.org/10.3390/metabo10030094	journal	March 2020

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