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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 Lab. (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 = {2018},
month = {10}
}
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    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
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