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

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.

doi:10.1093/nar/gky901

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

Journal Article · Fri Oct 05 00:00:00 EDT 2018 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gky901· OSTI ID:1542357

Chen, I-Min A. ^[1]; Chu, Ken ^[1]; Palaniappan, Krishna ^[1]; Pillay, Manoj ^[1]; Ratner, Anna ^[1]; Huang, Jinghua ^[1]; Huntemann, Marcel ^[1]; Varghese, Neha ^[1]; White, James R. ^[2]; Seshadri, Rekha ^[1]; Smirnova, Tatyana ^[1]; Kirton, Edward ^[1]; Jungbluth, Sean P. ^[1]; Woyke, Tanja ^[1]; Eloe-Fadrosh, Emiley A. ^[1]; Ivanova, Natalia N. ^[1]; Kyrpides, Nikos C. ^[1]

USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Resphera Biosciences, Baltimore, MD (United States)

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.

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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); National Energy Research Scientific Computing Center (NERSC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1542357

Journal Information:: Nucleic Acids Research, Vol. 47, Issue D1; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 447 works

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Cytochrome P450 Monooxygenase CYP139 Family Involved in the Synthesis of Secondary Metabolites in 824 Mycobacterial Species Syed, Puleng Rosinah; Chen, Wanping; Nelson, David R. International Journal of Molecular Sciences, Vol. 20, Issue 11 https://doi.org/10.3390/ijms20112690	journal	May 2019
Chemotaxis Towards Aromatic Compounds: Insights from Comamonas testosteroni Wang, Yun-Hao; Huang, Zhou; Liu, Shuang-Jiang International Journal of Molecular Sciences, Vol. 20, Issue 11 https://doi.org/10.3390/ijms20112701	journal	June 2019
Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives Ambrosino, Luca; Tangherlini, Michael; Colantuono, Chiara Marine Drugs, Vol. 17, Issue 10 https://doi.org/10.3390/md17100576	journal	October 2019
Broad Environmental Tolerance for a Salicola Host-Phage Pair Isolated from the Cargill Solar Saltworks, Newark, CA, USA Rodela, Meghan L.; Sabet, Shereen; Peterson, Allison Microorganisms, Vol. 7, Issue 4 https://doi.org/10.3390/microorganisms7040106	journal	April 2019
Structural elucidation and environmental distributions of butanetriol and pentanetriol dialkyl glycerol tetraethers (BDGTs and PDGTs) Coffinet, Sarah; Meador, Travis B.; Mühlena, Lukas Biogeosciences, Vol. 17, Issue 2 https://doi.org/10.5194/bg-17-317-2020	journal	January 2020
Enterococcus faecium secreted antigen A generates muropeptides to enhance host immunity and limit bacterial pathogenesis Kim, Byungchul; Wang, Yen-Chih; Hespen, Charles W. eLife, Vol. 8 https://doi.org/10.7554/elife.45343	journal	April 2019
MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies Kang, Dongwan D.; Li, Feng; Kirton, Edward PeerJ, Vol. 7 https://doi.org/10.7717/peerj.7359	journal	January 2019
Physiological and genomic features of Paraoceanicella profunda gen. nov., sp. nov., a novel piezophile isolated from deep seawater of the Mariana Trench Liu, Ping; Ding, Wanzhen; Lai, Qiliang MicrobiologyOpen, Vol. 9, Issue 2 https://doi.org/10.1002/mbo3.966	journal	November 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
A Division of Labor in the Recruitment and Topological Organization of a Bacterial Morphogenic Complex Caccamo, Paul D.; Jacq, Maxime; VanNieuwenhze, Michael S. Current Biology, Vol. 30, Issue 20 https://doi.org/10.1016/j.cub.2020.07.063	journal	October 2020
Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments Hiraoka, Satoshi; Hirai, Miho; Matsui, Yohei The ISME Journal, Vol. 14, Issue 3 https://doi.org/10.1038/s41396-019-0564-z	journal	December 2019
New insights from uncultivated genomes of the global human gut microbiome Nayfach, Stephen; Shi, Zhou Jason; Seshadri, Rekha Nature, Vol. 568, Issue 7753 https://doi.org/10.1038/s41586-019-1058-x	journal	March 2019
gutMDisorder: a comprehensive database for dysbiosis of the gut microbiota in disorders and interventions Cheng, Liang; Qi, Changlu; Zhuang, He Nucleic Acids Research https://doi.org/10.1093/nar/gkaa511	journal	June 2020
Rariglobus hedericola gen. nov., sp. nov., belonging to the Verrucomicrobia, isolated from a temperate freshwater habitat Pitt, Alexandra; Schmidt, Johanna; Koll, Ulrike International Journal of Systematic and Evolutionary Microbiology, Vol. 70, Issue 3 https://doi.org/10.1099/ijsem.0.003980	journal	March 2020
Comparative Genomics Guides Elucidation of Vitamin B ₁₂ Biosynthesis in Novel Human-Associated Akkermansia Strains Kirmiz, Nina; Galindo, Kadir; Cross, Karissa L. Applied and Environmental Microbiology, Vol. 86, Issue 3 https://doi.org/10.1128/aem.02117-19	journal	January 2020
Interspecies Chemical Signaling in a Methane-Oxidizing Bacterial Community Puri, Aaron W.; Liu, Darren; Schaefer, Amy L. Applied and Environmental Microbiology, Vol. 85, Issue 7 https://doi.org/10.1128/AEM.02702-18	journal	February 2019
The Connection and Disconnection Between Microbiome and Metabolome: A Critical Appraisal in Clinical Research Misra, Biswapriya B. Biological Research For Nursing, Vol. 22, Issue 4 https://doi.org/10.1177/1099800420903083	journal	February 2020
Complete genome sequence analysis of the thermoacidophilic verrucomicrobial methanotroph “Candidatus Methylacidiphilum kamchatkense” strain Kam1 and comparison with its closest relatives Kruse, Thomas; Ratnadevi, Chandini Murarilal; Erikstad, Helge-André BMC Genomics, Vol. 20, Issue 1 https://doi.org/10.1186/s12864-019-5995-4	journal	August 2019
Marine Natural Products from Microalgae: An -Omics Overview Lauritano, Chiara; Ferrante, Maria Immacolata; Rogato, Alessandra Marine Drugs, Vol. 17, Issue 5 https://doi.org/10.3390/md17050269	journal	May 2019
Structural basis and designing of peptide vaccine using PE-PGRS family protein of Mycobacterium ulcerans—An integrated vaccinomics approach Nain, Zulkar; Karim, Mohammad Minnatul; Sen, Monokesh Kumer Molecular Immunology, Vol. 120 https://doi.org/10.1016/j.molimm.2020.02.009	journal	April 2020
Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika Tran, Patricia Q.; Bachand, Samantha C.; McIntyre, Peter B. The ISME Journal, Vol. 15, Issue 7 https://doi.org/10.1038/s41396-021-00898-x	journal	February 2021
Dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria Mutalik, Vivek K.; Novichkov, Pavel S.; Price, Morgan N. Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-018-08177-8	journal	January 2019
MbnH is a diheme MauG-like protein associated with microbial copper homeostasis Kenney, Grace E.; Dassama, Laura M. K.; Manesis, Anastasia C. Journal of Biological Chemistry, Vol. 294, Issue 44 https://doi.org/10.1074/jbc.ra119.010202	journal	September 2019
gutMDisorder: a comprehensive database for dysbiosis of the gut microbiota in disorders and interventions Cheng, Liang; Qi, Changlu; Zhuang, He Nucleic Acids Research, Vol. 48, Issue D1 https://doi.org/10.1093/nar/gkz843	journal	October 2019
Reconstructing the evolutionary history of nitrogenases: Evidence for ancestral molybdenum‐cofactor utilization Garcia, Amanda K.; McShea, Hanon; Kolaczkowski, Bryan Geobiology, Vol. 18, Issue 3 https://doi.org/10.1111/gbi.12381	journal	February 2020
Carbon Use Efficiency and Its Temperature Sensitivity Covary in Soil Bacteria Pold, Grace; Domeignoz-Horta, Luiz A.; Morrison, Eric W. mBio, Vol. 11, Issue 1 https://doi.org/10.1128/mbio.02293-19	journal	January 2020
Preservation, Characterization and Exploitation of Microbial Biodiversity: The Perspective of the Italian Network of Culture Collections De Vero, Luciana; Boniotti, Maria Beatrice; Budroni, Marilena Microorganisms, Vol. 7, Issue 12 https://doi.org/10.3390/microorganisms7120685	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 Kochetkova, Tatiana V.; Zayulina, Kseniya S.; Zhigarkov, Vyacheslav S. International Journal of Systematic and Evolutionary Microbiology, Vol. 70, Issue 2 https://doi.org/10.1099/ijsem.0.003902	journal	February 2020
Enterococcus faecium secreted antigen A generates muropeptides to enhance host immunity and limit bacterial pathogenesis. Kim, Byungchul; Wang, Yen-Chih; Hespen, Charles W. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.39488	text	January 2019
Niche differentiation is spatially and temporally regulated in the rhizosphere Nuccio, Erin E.; Starr, Evan; Karaoz, Ulas The ISME Journal, Vol. 14, Issue 4 https://doi.org/10.1038/s41396-019-0582-x	journal	January 2020
proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes Mende, Daniel R.; Letunic, Ivica; Maistrenko, Oleksandr M. ETH Zurich https://doi.org/10.3929/ethz-b-000387605	text	January 2020
Peptide-based quorum sensing systems in Paenibacillus polymyxa Voichek, Maya; Maaß, Sandra; Kroniger, Tobias Life Science Alliance, Vol. 3, Issue 10 https://doi.org/10.26508/lsa.202000847	journal	August 2020
Joint Optimization of Service Caching Placement and Computation Offloading in Mobile Edge Computing Systems Bi, Suzhi; Huang, Liang; Zhang, Ying-Jun Angela IEEE Transactions on Wireless Communications, Vol. 19, Issue 7 https://doi.org/10.1109/twc.2020.2988386	journal	July 2020
Draft Genome Sequence of Aryl Hydrocarbon Receptor Activator Strains Lactobacillus reuteri R2lc and 2010 Özçam, Mustafa; van Pijkeren, Jan-Peter Microbiology Resource Announcements, Vol. 8, Issue 14 https://doi.org/10.1128/mra.00067-19	journal	April 2019
Evolutionary Relationships Between Low Potential Ferredoxin and Flavodoxin Electron Carriers Campbell, Ian J.; Bennett, George N.; Silberg, Jonathan J. Frontiers in Energy Research, Vol. 7 https://doi.org/10.3389/fenrg.2019.00079	journal	August 2019
Transposon mutagenesis reveals Pseudomonas cannabina pv. alisalensis optimizes its virulence factors for pathogenicity on different hosts Sakata, Nanami; Ishiga, Takako; Nguyen, Viet Tru figshare https://doi.org/10.6084/m9.figshare.9598319	text	January 2019
Whole genome sequencing of a novel, dichloromethane-fermenting Peptococcaceae from an enrichment culture Holland, Sophie I.; Edwards, Richard J.; Ertan, Haluk PeerJ, Vol. 7 https://doi.org/10.7717/peerj.7775	journal	January 2019

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