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Title: IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes

Abstract

The Integrated Microbial Genomes & Microbiomes system v.5.0 (IMG/M: https://img.jgi.doe.gov/m/) contains annotated datasets categorized into: archaea, bacteria, eukarya, plasmids, viruses, genome fragments, metagenomes, cell enrichments, single particle sorts, and metatranscriptomes. Source datasets include those generated by the DOE's Joint Genome Institute (JGI), submitted by external scientists, or collected from public sequence data archives such as NCBI. All submissions are typically processed through the IMG annotation pipeline and then loaded into the IMG data warehouse. IMG's web user interface provides a variety of analytical and visualization tools for comparative analysis of isolate genomes and metagenomes in IMG. IMG/M allows open access to all public genomes in the IMG data warehouse, while its expert review (ER) system (IMG/MER: https://img.jgi.doe.gov/mer/) enabled registered users to access their private genomes and to store their private datasets in workspace for sharing and for further analysis. IMG/M data content has increased by 60% since the last report published in the 2017 NAR Database Issue. IMG/M v.5.0 has a new and more powerful genome search feature, new statistical tools, and supports metagenome binning.

Authors:
 [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [2];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1]
+ Show Author Affiliations
  1. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  2. Resphera Biosciences, Baltimore, MD (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); National Energy Research Scientific Computing Center (NERSC)
OSTI Identifier:
1542357
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Volume: 47; Journal Issue: D1; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Chen, I-Min A., Chu, Ken, Palaniappan, Krishna, Pillay, Manoj, Ratner, Anna, Huang, Jinghua, Huntemann, Marcel, Varghese, Neha, White, James R., Seshadri, Rekha, Smirnova, Tatyana, Kirton, Edward, Jungbluth, Sean P., Woyke, Tanja, Eloe-Fadrosh, Emiley A., Ivanova, Natalia N., and Kyrpides, Nikos C. IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. United States: N. p., 2018. Web. doi:10.1093/nar/gky901.
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Chen, I-Min A., Chu, Ken, Palaniappan, Krishna, Pillay, Manoj, Ratner, Anna, Huang, Jinghua, Huntemann, Marcel, Varghese, Neha, White, James R., Seshadri, Rekha, Smirnova, Tatyana, Kirton, Edward, Jungbluth, Sean P., Woyke, Tanja, Eloe-Fadrosh, Emiley A., Ivanova, Natalia N., & Kyrpides, Nikos C. IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. United States. https://doi.org/10.1093/nar/gky901
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Chen, I-Min A., Chu, Ken, Palaniappan, Krishna, Pillay, Manoj, Ratner, Anna, Huang, Jinghua, Huntemann, Marcel, Varghese, Neha, White, James R., Seshadri, Rekha, Smirnova, Tatyana, Kirton, Edward, Jungbluth, Sean P., Woyke, Tanja, Eloe-Fadrosh, Emiley A., Ivanova, Natalia N., and Kyrpides, Nikos C. Fri . "IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes". United States. https://doi.org/10.1093/nar/gky901. https://www.osti.gov/servlets/purl/1542357.
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@article{osti_1542357,
title = {IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes},
author = {Chen, I-Min A. and Chu, Ken and Palaniappan, Krishna and Pillay, Manoj and Ratner, Anna and Huang, Jinghua and Huntemann, Marcel and Varghese, Neha and White, James R. and Seshadri, Rekha and Smirnova, Tatyana and Kirton, Edward and Jungbluth, Sean P. and Woyke, Tanja and Eloe-Fadrosh, Emiley A. and Ivanova, Natalia N. and Kyrpides, Nikos C.},
abstractNote = {The Integrated Microbial Genomes & Microbiomes system v.5.0 (IMG/M: https://img.jgi.doe.gov/m/) contains annotated datasets categorized into: archaea, bacteria, eukarya, plasmids, viruses, genome fragments, metagenomes, cell enrichments, single particle sorts, and metatranscriptomes. Source datasets include those generated by the DOE's Joint Genome Institute (JGI), submitted by external scientists, or collected from public sequence data archives such as NCBI. All submissions are typically processed through the IMG annotation pipeline and then loaded into the IMG data warehouse. IMG's web user interface provides a variety of analytical and visualization tools for comparative analysis of isolate genomes and metagenomes in IMG. IMG/M allows open access to all public genomes in the IMG data warehouse, while its expert review (ER) system (IMG/MER: https://img.jgi.doe.gov/mer/) enabled registered users to access their private genomes and to store their private datasets in workspace for sharing and for further analysis. IMG/M data content has increased by 60% since the last report published in the 2017 NAR Database Issue. IMG/M v.5.0 has a new and more powerful genome search feature, new statistical tools, and supports metagenome binning.},
doi = {10.1093/nar/gky901},
journal = {Nucleic Acids Research},
number = D1,
volume = 47,
place = {United States},
year = {Fri Oct 05 00:00:00 EDT 2018},
month = {Fri Oct 05 00:00:00 EDT 2018}
}
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https://doi.org/10.1093/nar/gky901
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    • Duell, Elke R.; D’Agostino, Paul M.; Shapiro, Nicole
    • Microbial Cell Factories, Vol. 18, Issue 1
    • DOI: 10.1186/s12934-019-1080-6

    Fueling ab initio folding with marine metagenomics enables structure and function predictions of new protein families
    journal, November 2019

    Challenges in the construction of knowledge bases for human microbiome-disease associations
    journal, September 2019

    A pipeline for targeted metagenomics of environmental bacteria
    journal, February 2020

    Shotgun metagenomic analysis of microbial communities from the Loxahatchee nature preserve in the Florida Everglades
    journal, January 2020

    • Abraham, Briana S.; Caglayan, Deniz; Carrillo, Natalie V.
    • Environmental Microbiome, Vol. 15, Issue 1
    • DOI: 10.1186/s40793-019-0352-4

    Genome Sequences of a Plant Beneficial Synthetic Bacterial Community Reveal Genetic Features for Successful Plant Colonization
    journal, August 2019

    • de Souza, Rafael Soares Correa; Armanhi, Jaderson Silveira Leite; Damasceno, Natália de Brito
    • Frontiers in Microbiology, Vol. 10
    • DOI: 10.3389/fmicb.2019.01779

    Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes
    journal, September 2019

    • García-López, Marina; Meier-Kolthoff, Jan P.; Tindall, Brian J.
    • Frontiers in Microbiology, Vol. 10
    • DOI: 10.3389/fmicb.2019.02083

    Cytochrome P450 Monooxygenase CYP139 Family Involved in the Synthesis of Secondary Metabolites in 824 Mycobacterial Species
    journal, May 2019

    • Syed, Puleng Rosinah; Chen, Wanping; Nelson, David R.
    • International Journal of Molecular Sciences, Vol. 20, Issue 11
    • DOI: 10.3390/ijms20112690

    Chemotaxis Towards Aromatic Compounds: Insights from Comamonas testosteroni
    journal, June 2019

    • Wang, Yun-Hao; Huang, Zhou; Liu, Shuang-Jiang
    • International Journal of Molecular Sciences, Vol. 20, Issue 11
    • DOI: 10.3390/ijms20112701

    Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives
    journal, October 2019

    • Ambrosino, Luca; Tangherlini, Michael; Colantuono, Chiara
    • Marine Drugs, Vol. 17, Issue 10
    • DOI: 10.3390/md17100576

    Broad Environmental Tolerance for a Salicola Host-Phage Pair Isolated from the Cargill Solar Saltworks, Newark, CA, USA
    journal, April 2019

    Structural elucidation and environmental distributions of butanetriol and pentanetriol dialkyl glycerol tetraethers (BDGTs and PDGTs)
    journal, January 2020

    • Coffinet, Sarah; Meador, Travis B.; Mühlena, Lukas
    • Biogeosciences, Vol. 17, Issue 2
    • DOI: 10.5194/bg-17-317-2020

    Enterococcus faecium secreted antigen A generates muropeptides to enhance host immunity and limit bacterial pathogenesis
    journal, April 2019

    MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies
    journal, January 2019

    Genome analysis of the marine bacterium Kiloniella laminariae and first insights into comparative genomics with related Kiloniella species
    journal, December 2019

    A Division of Labor in the Recruitment and Topological Organization of a Bacterial Morphogenic Complex
    journal, October 2020

    • Caccamo, Paul D.; Jacq, Maxime; VanNieuwenhze, Michael S.
    • Current Biology, Vol. 30, Issue 20
    • DOI: 10.1016/j.cub.2020.07.063

    Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments
    journal, December 2019

    New insights from uncultivated genomes of the global human gut microbiome
    journal, March 2019

    gutMDisorder: a comprehensive database for dysbiosis of the gut microbiota in disorders and interventions
    journal, June 2020

    Rariglobus hedericola gen. nov., sp. nov., belonging to the Verrucomicrobia, isolated from a temperate freshwater habitat
    journal, March 2020

    • Pitt, Alexandra; Schmidt, Johanna; Koll, Ulrike
    • International Journal of Systematic and Evolutionary Microbiology, Vol. 70, Issue 3
    • DOI: 10.1099/ijsem.0.003980

    Comparative Genomics Guides Elucidation of Vitamin B 12 Biosynthesis in Novel Human-Associated Akkermansia Strains
    journal, January 2020

    • Kirmiz, Nina; Galindo, Kadir; Cross, Karissa L.
    • Applied and Environmental Microbiology, Vol. 86, Issue 3
    • DOI: 10.1128/aem.02117-19

    Interspecies Chemical Signaling in a Methane-Oxidizing Bacterial Community
    journal, February 2019

    • Puri, Aaron W.; Liu, Darren; Schaefer, Amy L.
    • Applied and Environmental Microbiology, Vol. 85, Issue 7
    • DOI: 10.1128/AEM.02702-18

    The Connection and Disconnection Between Microbiome and Metabolome: A Critical Appraisal in Clinical Research
    journal, February 2020

    Marine Natural Products from Microalgae: An -Omics Overview
    journal, May 2019

    • Lauritano, Chiara; Ferrante, Maria Immacolata; Rogato, Alessandra
    • Marine Drugs, Vol. 17, Issue 5
    • DOI: 10.3390/md17050269

    Structural basis and designing of peptide vaccine using PE-PGRS family protein of Mycobacterium ulcerans—An integrated vaccinomics approach
    journal, April 2020

    Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika
    journal, February 2021

    Dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria
    journal, January 2019

    • Mutalik, Vivek K.; Novichkov, Pavel S.; Price, Morgan N.
    • Nature Communications, Vol. 10, Issue 1
    • DOI: 10.1038/s41467-018-08177-8

    MbnH is a diheme MauG-like protein associated with microbial copper homeostasis
    journal, September 2019

    • Kenney, Grace E.; Dassama, Laura M. K.; Manesis, Anastasia C.
    • Journal of Biological Chemistry, Vol. 294, Issue 44
    • DOI: 10.1074/jbc.ra119.010202

    gutMDisorder: a comprehensive database for dysbiosis of the gut microbiota in disorders and interventions
    journal, October 2019

    • Cheng, Liang; Qi, Changlu; Zhuang, He
    • Nucleic Acids Research, Vol. 48, Issue D1
    • DOI: 10.1093/nar/gkz843

    Reconstructing the evolutionary history of nitrogenases: Evidence for ancestral molybdenum‐cofactor utilization
    journal, February 2020

    • Garcia, Amanda K.; McShea, Hanon; Kolaczkowski, Bryan
    • Geobiology, Vol. 18, Issue 3
    • DOI: 10.1111/gbi.12381

    Carbon Use Efficiency and Its Temperature Sensitivity Covary in Soil Bacteria
    journal, January 2020

    • Pold, Grace; Domeignoz-Horta, Luiz A.; Morrison, Eric W.
    • mBio, Vol. 11, Issue 1
    • DOI: 10.1128/mbio.02293-19

    Preservation, Characterization and Exploitation of Microbial Biodiversity: The Perspective of the Italian Network of Culture Collections
    journal, December 2019

    Tepidiforma bonchosmolovskayae gen. nov., sp. nov., a moderately thermophilic Chloroflexi bacterium from a Chukotka hot spring (Arctic, Russia), representing a novel class, Tepidiformia, which includes the previously uncultivated lineage OLB14
    journal, February 2020

    • Kochetkova, Tatiana V.; Zayulina, Kseniya S.; Zhigarkov, Vyacheslav S.
    • International Journal of Systematic and Evolutionary Microbiology, Vol. 70, Issue 2
    • DOI: 10.1099/ijsem.0.003902

    Enterococcus faecium secreted antigen A generates muropeptides to enhance host immunity and limit bacterial pathogenesis.
    text, January 2019

    • Kim, Byungchul; Wang, Yen-Chih; Hespen, Charles W.
    • Apollo - University of Cambridge Repository
    • DOI: 10.17863/cam.39488

    Niche differentiation is spatially and temporally regulated in the rhizosphere
    journal, January 2020

    Peptide-based quorum sensing systems in Paenibacillus polymyxa
    journal, August 2020

    • Voichek, Maya; Maaß, Sandra; Kroniger, Tobias
    • Life Science Alliance, Vol. 3, Issue 10
    • DOI: 10.26508/lsa.202000847

    Active subseafloor microbial communities from Mariana back-arc venting fluids share metabolic strategies across different thermal niches and taxa
    journal, May 2019

    • Trembath-Reichert, Elizabeth; Butterfield, David A.; Huber, Julie A.
    • The ISME Journal, Vol. 13, Issue 9
    • DOI: 10.1038/s41396-019-0431-y

    Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere
    journal, November 2019

    Microbial metagenomes and metatranscriptomes during a coastal phytoplankton bloom
    journal, July 2019

    Manipulating nitrogen regulation in diazotrophic bacteria for agronomic benefit
    journal, April 2019

    • Bueno Batista, Marcelo; Dixon, Ray
    • Biochemical Society Transactions, Vol. 47, Issue 2
    • DOI: 10.1042/bst20180342

    Large-scale identification of pathogen essential genes during coinfection with sympatric and allopatric microbes
    journal, August 2019

    • Lewin, Gina R.; Stacy, Apollo; Michie, Kelly L.
    • Proceedings of the National Academy of Sciences, Vol. 116, Issue 39
    • DOI: 10.1073/pnas.1907619116

    gutMDisorder: a comprehensive database for dysbiosis of the gut microbiota in disorders and interventions
    journal, June 2020

    Joint Optimization of Service Caching Placement and Computation Offloading in Mobile Edge Computing Systems
    journal, July 2020

    • Bi, Suzhi; Huang, Liang; Zhang, Ying-Jun Angela
    • IEEE Transactions on Wireless Communications, Vol. 19, Issue 7
    • DOI: 10.1109/twc.2020.2988386

    Comparative Genomics Guides Elucidation of Vitamin B 12 Biosynthesis in Novel Human-Associated Akkermansia Strains
    journal, January 2020

    • Kirmiz, Nina; Galindo, Kadir; Cross, Karissa L.
    • Applied and Environmental Microbiology, Vol. 86, Issue 3
    • DOI: 10.1128/aem.02117-19

    Carbon Use Efficiency and Its Temperature Sensitivity Covary in Soil Bacteria
    journal, January 2020

    • Pold, Grace; Domeignoz-Horta, Luiz A.; Morrison, Eric W.
    • mBio, Vol. 11, Issue 1
    • DOI: 10.1128/mbio.02293-19

    Draft Genome Sequence of Aryl Hydrocarbon Receptor Activator Strains Lactobacillus reuteri R2lc and 2010
    journal, April 2019

    • Özçam, Mustafa; van Pijkeren, Jan-Peter
    • Microbiology Resource Announcements, Vol. 8, Issue 14
    • DOI: 10.1128/mra.00067-19

    Genome Sequences of Four Vibrio parahaemolyticus Strains Isolated from the English Channel and the River Thames
    journal, June 2019

    • Witherall, Lucy; Wagley, Sariqa; Butler, Clive
    • Microbiology Resource Announcements, Vol. 8, Issue 24
    • DOI: 10.1128/mra.00392-19

    Genome Sequence of Colistin-Resistant Bacteremic Shewanella algae Carrying the Beta-Lactamase Gene bla OXA-55
    journal, June 2019

    • Chen, Ying-Ju; Tung, Kwong-Chung; Hong, Yu-Kai
    • Canadian Journal of Infectious Diseases and Medical Microbiology, Vol. 2019
    • DOI: 10.1155/2019/3840563

    Fueling ab initio folding with marine metagenomics enables structure and function predictions of new protein families
    journal, November 2019

    Challenges in the construction of knowledge bases for human microbiome-disease associations
    journal, September 2019

    A pipeline for targeted metagenomics of environmental bacteria
    journal, February 2020

    Evolutionary Relationships Between Low Potential Ferredoxin and Flavodoxin Electron Carriers
    journal, August 2019

    • Campbell, Ian J.; Bennett, George N.; Silberg, Jonathan J.
    • Frontiers in Energy Research, Vol. 7
    • DOI: 10.3389/fenrg.2019.00079

    Chemotaxis Towards Aromatic Compounds: Insights from Comamonas testosteroni
    journal, June 2019

    • Wang, Yun-Hao; Huang, Zhou; Liu, Shuang-Jiang
    • International Journal of Molecular Sciences, Vol. 20, Issue 11
    • DOI: 10.3390/ijms20112701

    Marine Natural Products from Microalgae: An -Omics Overview
    journal, May 2019

    • Lauritano, Chiara; Ferrante, Maria Immacolata; Rogato, Alessandra
    • Marine Drugs, Vol. 17, Issue 5
    • DOI: 10.3390/md17050269

    Broad Environmental Tolerance for a Salicola Host-Phage Pair Isolated from the Cargill Solar Saltworks, Newark, CA, USA
    journal, April 2019

    Preservation, Characterization and Exploitation of Microbial Biodiversity: The Perspective of the Italian Network of Culture Collections
    journal, December 2019

    Enterococcus faecium secreted antigen A generates muropeptides to enhance host immunity and limit bacterial pathogenesis
    journal, April 2019

    Whole genome sequencing of a novel, dichloromethane-fermenting Peptococcaceae from an enrichment culture
    journal, January 2019

    • Holland, Sophie I.; Edwards, Richard J.; Ertan, Haluk
    • PeerJ, Vol. 7
    • DOI: 10.7717/peerj.7775
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