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 · 04 October 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.

View Accepted Manuscript (DOE)

Cite

Export

Save

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

Sponsoring Organization:: National Energy Research Scientific Computing Center (NERSC); USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1542357

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

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

References (60)

Shotgun metagenomics, from sampling to analysis Quince, Christopher; Walker, Alan W.; Simpson, Jared T. Nature Biotechnology, Vol. 35, Issue 9 https://doi.org/10.1038/nbt.3935	journal	September 2017
Erratum: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea Bowers, Robert M.; Kyrpides, Nikos C.; Stepanauskas, Ramunas Nature Biotechnology, Vol. 36, Issue 7 https://doi.org/10.1038/nbt0718-660a	journal	July 2018
Evaluation of methods for the prediction of membrane spanning regions Moller, S.; Croning, M. D. R.; Apweiler, R. Bioinformatics, Vol. 17, Issue 7 https://doi.org/10.1093/bioinformatics/17.7.646	journal	July 2001
Infernal 1.1: 100-fold faster RNA homology searches Nawrocki, E. P.; Eddy, S. R. Bioinformatics, Vol. 29, Issue 22 https://doi.org/10.1093/bioinformatics/btt509	journal	September 2013
InterProScan 5: genome-scale protein function classification Jones, P.; Binns, D.; Chang, H. -Y. Bioinformatics, Vol. 30, Issue 9 https://doi.org/10.1093/bioinformatics/btu031	journal	January 2014
Microbial species delineation using whole genome sequences Varghese, Neha J.; Mukherjee, Supratim; Ivanova, Natalia Nucleic Acids Research, Vol. 43, Issue 14 https://doi.org/10.1093/nar/gkv657	journal	July 2015
IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses Paez-Espino, David; Chen, I. -Min A.; Palaniappan, Krishna Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw1030	journal	October 2016
antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification Blin, Kai; Wolf, Thomas; Chevrette, Marc G. Nucleic Acids Research, Vol. 45, Issue W1 https://doi.org/10.1093/nar/gkx319	journal	April 2017
Guidelines to Statistical Analysis of Microbial Composition Data Inferred from Metagenomic Sequencing Odintsova, Vera; Tyakht, Alexander; Alexeev, Dmitry Current Issues in Molecular Biology https://doi.org/10.21775/cimb.024.017	journal	January 2017
Genomic Standards Consortium Projects Field, Dawn; Sterk, Peter; Kottmann, Renzo Standards in Genomic Sciences, Vol. 9, Issue 3 https://doi.org/10.4056/sigs.5559608	journal	February 2014
Protein interaction maps for complete genomes based on gene fusion events Enright, Anton J.; Iliopoulos, Ioannis; Kyrpides, Nikos C. Nature, Vol. 402, Issue 6757 https://doi.org/10.1038/47056	journal	November 1999
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea Bowers, Robert M.; Kyrpides, Nikos C.; Stepanauskas, Ramunas Nature Biotechnology, Vol. 35, Issue 8 https://doi.org/10.1038/nbt.3893	journal	August 2017
Shotgun metagenomics, from sampling to analysis Quince, Christopher; Walker, Alan W.; Simpson, Jared T. Nature Biotechnology, Vol. 35, Issue 9 https://doi.org/10.1038/nbt.3935	journal	September 2017
Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software Sczyrba, Alexander; Hofmann, Peter; Belmann, Peter Nature Methods, Vol. 14, Issue 11 https://doi.org/10.1038/nmeth.4458	journal	October 2017
Locating proteins in the cell using TargetP, SignalP and related tools Emanuelsson, Olof; Brunak, Søren; von Heijne, Gunnar Nature Protocols, Vol. 2, Issue 4 https://doi.org/10.1038/nprot.2007.131	journal	April 2007
Spatiotemporal persistence of multiple, diverse clades and toxins of Corynebacterium diphtheriae Will, Robert C.; Ramamurthy, Thandavarayan; Sharma, Naresh Chand Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-21870-5	journal	March 2021
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life Parks, Donovan H.; Rinke, Christian; Chuvochina, Maria Nature Microbiology, Vol. 2, Issue 11 https://doi.org/10.1038/s41564-017-0012-7	journal	September 2017
Extra virgin olive oil improved body weight and insulin sensitivity in high fat diet-induced obese LDLr−/−.Leiden mice without attenuation of steatohepatitis Álvarez-Amor, Leticia; Sierra, Amparo Luque; Cárdenas, Antonio Scientific Reports, Vol. 11, Issue 1 https://doi.org/10.1038/s41598-021-87761-3	journal	April 2021
The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans Tully, Benjamin J.; Graham, Elaina D.; Heidelberg, John F. Scientific Data, Vol. 5, Issue 1 https://doi.org/10.1038/sdata.2017.203	journal	January 2018
Evaluation of methods for the prediction of membrane spanning regions Moller, S.; Croning, M. D. R.; Apweiler, R. Bioinformatics, Vol. 17, Issue 7 https://doi.org/10.1093/bioinformatics/17.7.646	journal	July 2001
Evaluation of methods for the prediction of membrane spanning regions Moller, S.; Croning, M. D. R.; Apweiler, R. Bioinformatics, Vol. 18, Issue 1 https://doi.org/10.1093/bioinformatics/18.1.218	journal	January 2002
Infernal 1.0: inference of RNA alignments Nawrocki, E. P.; Kolbe, D. L.; Eddy, S. R. Bioinformatics, Vol. 25, Issue 10 https://doi.org/10.1093/bioinformatics/btp157	journal	March 2009
Infernal 1.0: inference of RNA alignments Nawrocki, E. P.; Kolbe, D. L.; Eddy, S. R. Bioinformatics, Vol. 25, Issue 13 https://doi.org/10.1093/bioinformatics/btp326	journal	June 2009
Infernal 1.1: 100-fold faster RNA homology searches Nawrocki, E. P.; Eddy, S. R. Bioinformatics, Vol. 29, Issue 22 https://doi.org/10.1093/bioinformatics/btt509	journal	September 2013
InterProScan 5: genome-scale protein function classification Jones, P.; Binns, D.; Chang, H. -Y. Bioinformatics, Vol. 30, Issue 9 https://doi.org/10.1093/bioinformatics/btu031	journal	January 2014
GenBank Benson, Dennis A.; Cavanaugh, Mark; Clark, Karen Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1195	journal	November 2012
TIGRFAMs and Genome Properties in 2013 Haft, Daniel H.; Selengut, Jeremy D.; Richter, Roland A. Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1234	journal	November 2012
Expanded microbial genome coverage and improved protein family annotation in the COG database Galperin, Michael Y.; Makarova, Kira S.; Wolf, Yuri I. Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1223	journal	November 2014
KEGG as a reference resource for gene and protein annotation Kanehisa, Minoru; Sato, Yoko; Kawashima, Masayuki Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1070	journal	October 2015
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases Caspi, Ron; Billington, Richard; Ferrer, Luciana Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1164	journal	November 2015
The Pfam protein families database: towards a more sustainable future Finn, Robert D.; Coggill, Penelope; Eberhardt, Ruth Y. Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1344	journal	December 2015
HMMER web server: 2015 update Finn, Robert D.; Clements, Jody; Arndt, William Nucleic Acids Research, Vol. 43, Issue W1 https://doi.org/10.1093/nar/gkv397	journal	May 2015
Microbial species delineation using whole genome sequences Varghese, Neha J.; Mukherjee, Supratim; Ivanova, Natalia Nucleic Acids Research, Vol. 43, Issue 14 https://doi.org/10.1093/nar/gkv657	journal	July 2015
IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses Paez-Espino, David; Chen, I. -Min A.; Palaniappan, Krishna Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw1030	journal	October 2016
IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes Hadjithomas, Michalis; Chen, I-Min A.; Chu, Ken Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw1103	journal	November 2016
IMG/M: integrated genome and metagenome comparative data analysis system Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw929	journal	October 2016
Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements Mukherjee, Supratim; Stamatis, Dimitri; Bertsch, Jon Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw992	journal	October 2016
Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families Kalvari, Ioanna; Argasinska, Joanna; Quinones-Olvera, Natalia Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx1038	journal	November 2017
antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification Blin, Kai; Wolf, Thomas; Chevrette, Marc G. Nucleic Acids Research, Vol. 45, Issue W1 https://doi.org/10.1093/nar/gkx319	journal	April 2017
The Reconstruction of 2,631 Draft Metagenome-Assembled Genomes from the Global Oceans Tully, Benjamin J.; Graham, Elaina D.; Heidelberg, John F. Scientific Data https://doi.org/10.1101/162503	posted_content	July 2017
Adaptive seeds tame genomic sequence comparison Kielbasa, S. M.; Wan, R.; Sato, K. Genome Research, Vol. 21, Issue 3 https://doi.org/10.1101/gr.113985.110	journal	January 2011
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T. Genome Research, Vol. 25, Issue 7 https://doi.org/10.1101/gr.186072.114	journal	May 2015
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing Benjamini, Yoav; Hochberg, Yosef Journal of the Royal Statistical Society: Series B (Methodological), Vol. 57, Issue 1 https://doi.org/10.1111/j.2517-6161.1995.tb02031.x	journal	January 1995
Maintaining a microbial genome & metagenome data analysis system in an academic setting Chen, I-Min A.; Markowitz, Victor M.; Szeto, Ernest Proceedings of the 26th International Conference on Scientific and Statistical Database Management - SSDBM '14 https://doi.org/10.1145/2618243.2618244	conference	January 2014
Prodigal: prokaryotic gene recognition and translation initiation site identification Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-119	journal	March 2010
CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats Bland, Charles; Ramsey, Teresa L.; Sabree, Fareedah BMC Bioinformatics, Vol. 8, Issue 1 https://doi.org/10.1186/1471-2105-8-209	journal	June 2007
Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system Chen, I-Min A.; Markowitz, Victor M.; Palaniappan, Krishna BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-2629-y	journal	April 2016
Aging features of the migratory locust at physiological and transcriptional levels Guo, Siyuan; Yang, Pengcheng; Liang, Bo BMC Genomics, Vol. 22, Issue 1 https://doi.org/10.1186/s12864-021-07585-3	journal	April 2021
Recovering complete and draft population genomes from metagenome datasets Sangwan, Naseer; Xia, Fangfang; Gilbert, Jack A. Microbiome, Vol. 4, Issue 1 https://doi.org/10.1186/s40168-016-0154-5	journal	March 2016
The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4) Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos Standards in Genomic Sciences, Vol. 10, Issue 1 https://doi.org/10.1186/s40793-015-0077-y	journal	October 2015
The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4) Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos Standards in Genomic Sciences, Vol. 11, Issue 1 https://doi.org/10.1186/s40793-016-0138-x	journal	February 2016
On a Test of Whether one of Two Random Variables is Stochastically Larger than the Other Mann, H. B.; Whitney, D. R. The Annals of Mathematical Statistics, Vol. 18, Issue 1 https://doi.org/10.1214/aoms/1177730491	journal	March 1947
Gene Context Analysis in the Integrated Microbial Genomes (IMG) Data Management System Mavromatis, Konstantinos; Chu, Ken; Ivanova, Natalia PLoS ONE, Vol. 4, Issue 11 https://doi.org/10.1371/journal.pone.0007979	journal	November 2009
Improving Microbial Genome Annotations in an Integrated Database Context Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken PLoS ONE, Vol. 8, Issue 2 https://doi.org/10.1371/journal.pone.0054859	journal	February 2013
Guidelines to Statistical Analysis of Microbial Composition Data Inferred from Metagenomic Sequencing Odintsova, Vera; Tyakht, Alexander; Alexeev, Dmitry Current Issues in Molecular Biology https://doi.org/10.21775/cimb.024.017	journal	January 2017
Genomic Standards Consortium Projects Field, Dawn; Sterk, Peter; Kottmann, Renzo Standards in Genomic Sciences, Vol. 9, Issue 3 https://doi.org/10.4056/sigs.5559608	journal	February 2014
Genomic Standards Consortium Projects Field, Dawn; Sterk, Peter; Kottmann, Renzo Standards in Genomic Sciences, Vol. 9, Issue 3 https://doi.org/10.4056/sigs.5559680	journal	February 2014
The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans Tully, Benjamin; Graham, Elaina; Heidelberg, John figshare https://doi.org/10.6084/m9.figshare.5188273.v13	dataset	January 2018
The Reconstruction of 2,631 Draft Metagenome-Assembled Genomes from the Global Oceans Tully, Benjamin; Graham, Elaina; Heidelberg, John figshare https://doi.org/10.6084/m9.figshare.5188273.v8	dataset	January 2017
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities Kang, Dongwan D.; Froula, Jeff; Egan, Rob PeerJ, Vol. 3 https://doi.org/10.7717/peerj.1165	journal	January 2015

Cited By (109)

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
Active subseafloor microbial communities from Mariana back-arc venting fluids share metabolic strategies across different thermal niches and taxa Trembath-Reichert, Elizabeth; Butterfield, David A.; Huber, Julie A. The ISME Journal, Vol. 13, Issue 9 https://doi.org/10.1038/s41396-019-0431-y	journal	May 2019
Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere Doud, Devin F. R.; Bowers, Robert M.; Schulz, Frederik The ISME Journal, Vol. 14, Issue 3 https://doi.org/10.1038/s41396-019-0557-y	journal	November 2019
Microbial metagenomes and metatranscriptomes during a coastal phytoplankton bloom Nowinski, Brent; Smith, Christa B.; Thomas, Courtney M. Scientific Data, Vol. 6, Issue 1 https://doi.org/10.1038/s41597-019-0132-4	journal	July 2019
Manipulating nitrogen regulation in diazotrophic bacteria for agronomic benefit Bueno Batista, Marcelo; Dixon, Ray Biochemical Society Transactions, Vol. 47, Issue 2 https://doi.org/10.1042/bst20180342	journal	April 2019
Large-scale identification of pathogen essential genes during coinfection with sympatric and allopatric microbes Lewin, Gina R.; Stacy, Apollo; Michie, Kelly L. Proceedings of the National Academy of Sciences, Vol. 116, Issue 39 https://doi.org/10.1073/pnas.1907619116	journal	August 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
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
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
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
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
Genome Sequences of Four Vibrio parahaemolyticus Strains Isolated from the English Channel and the River Thames Witherall, Lucy; Wagley, Sariqa; Butler, Clive Microbiology Resource Announcements, Vol. 8, Issue 24 https://doi.org/10.1128/mra.00392-19	journal	June 2019
Genome Sequence of Colistin-Resistant Bacteremic Shewanella algae Carrying the Beta-Lactamase Gene bla _OXA-55 Chen, Ying-Ju; Tung, Kwong-Chung; Hong, Yu-Kai Canadian Journal of Infectious Diseases and Medical Microbiology, Vol. 2019 https://doi.org/10.1155/2019/3840563	journal	June 2019
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
Fueling ab initio folding with marine metagenomics enables structure and function predictions of new protein families Wang, Yan; Shi, Qiang; Yang, Pengshuo Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1823-z	journal	November 2019
Challenges in the construction of knowledge bases for human microbiome-disease associations Badal, Varsha Dave; Wright, Dustin; Katsis, Yannis Microbiome, Vol. 7, Issue 1 https://doi.org/10.1186/s40168-019-0742-2	journal	September 2019
A pipeline for targeted metagenomics of environmental bacteria Grieb, Anissa; Bowers, Robert M.; Oggerin, Monike Microbiome, Vol. 8, Issue 1 https://doi.org/10.1186/s40168-020-0790-7	journal	February 2020
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
Position-Specific Metabolic Probing and Metagenomics of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities at High Temperatures Thomas, Scott C.; Tamadonfar, Kevin O.; Seymour, Cale O. Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01427	journal	July 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
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
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
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
Additional file 2 of Meta-Apo improves accuracy of 16S-amplicon-based prediction of microbiome function Jing, Gongchao; Zhang, Yufeng; Cui, Wenzhi figshare https://doi.org/10.6084/m9.figshare.13533109	dataset	January 2021
Additional file 3 of Biogeographic traits of dimethyl sulfide and dimethylsulfoniopropionate cycling in polar oceans Teng, Zhao-Jie; Qin, Qi-Long; Zhang, Weipeng figshare https://doi.org/10.6084/m9.figshare.16821533	dataset	January 2021
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
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
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
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
Different roles of two groEL homologues in methylotrophic utiliser of dichloromethane Methylorubrum extorquens DM4 Firsova, Yulia E.; Torgonskaya, Maria L. Antonie van Leeuwenhoek, Vol. 113, Issue 1 https://doi.org/10.1007/s10482-019-01320-5	journal	August 2019
Microbial community analysis using high-throughput sequencing technology: a beginner’s guide for microbiologists Jo, Jihoon; Oh, Jooseong; Park, Chungoo Journal of Microbiology, Vol. 58, Issue 3 https://doi.org/10.1007/s12275-020-9525-5	journal	February 2020
Data mining of metagenomes to find novel enzymes: a non-computationally intensive method Góngora-Castillo, Elsa; López-Ochoa, Luisa A.; Apolinar-Hernández, Max M. 3 Biotech, Vol. 10, Issue 2 https://doi.org/10.1007/s13205-019-2044-6	journal	January 2020
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
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
Active subseafloor microbial communities from Mariana back-arc venting fluids share metabolic strategies across different thermal niches and taxa Trembath-Reichert, Elizabeth; Butterfield, David A.; Huber, Julie A. The ISME Journal, Vol. 13, Issue 9 https://doi.org/10.1038/s41396-019-0431-y	journal	May 2019
High proportions of bacteria and archaea across most biomes remain uncultured Steen, Andrew D.; Crits-Christoph, Alexander; Carini, Paul The ISME Journal, Vol. 13, Issue 12 https://doi.org/10.1038/s41396-019-0484-y	journal	August 2019
Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere Doud, Devin F. R.; Bowers, Robert M.; Schulz, Frederik The ISME Journal, Vol. 14, Issue 3 https://doi.org/10.1038/s41396-019-0557-y	journal	November 2019
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
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
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
MpsAB is important for Staphylococcus aureus virulence and growth at atmospheric CO2 levels Fan, Sook-Ha; Ebner, Patrick; Reichert, Sebastian Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-11547-5	journal	August 2019
A predator-prey interaction between a marine Pseudoalteromonas sp. and Gram-positive bacteria Tang, Bai-Lu; Yang, Jie; Chen, Xiu-Lan Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-019-14133-x	journal	January 2020
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
Cyclic GMP–AMP signalling protects bacteria against viral infection Cohen, Daniel; Melamed, Sarah; Millman, Adi Nature, Vol. 574, Issue 7780 https://doi.org/10.1038/s41586-019-1605-5	journal	September 2019
Giant virus diversity and host interactions through global metagenomics Schulz, Frederik; Roux, Simon; Paez-Espino, David Nature, Vol. 578, Issue 7795 https://doi.org/10.1038/s41586-020-1957-x	journal	January 2020
Microbial metagenomes and metatranscriptomes during a coastal phytoplankton bloom Nowinski, Brent; Smith, Christa B.; Thomas, Courtney M. Scientific Data, Vol. 6, Issue 1 https://doi.org/10.1038/s41597-019-0132-4	journal	July 2019
Microbiomes of Velloziaceae from phosphorus-impoverished soils of the campos rupestres, a biodiversity hotspot Camargo, Antonio Pedro; de Souza, Rafael Soares Correa; de Britto Costa, Patrícia Scientific Data, Vol. 6, Issue 1 https://doi.org/10.1038/s41597-019-0141-3	journal	July 2019
Manipulating nitrogen regulation in diazotrophic bacteria for agronomic benefit Bueno Batista, Marcelo; Dixon, Ray Biochemical Society Transactions, Vol. 47, Issue 2 https://doi.org/10.1042/bst20180342	journal	April 2019
Large-scale identification of pathogen essential genes during coinfection with sympatric and allopatric microbes Lewin, Gina R.; Stacy, Apollo; Michie, Kelly L. Proceedings of the National Academy of Sciences, Vol. 116, Issue 39 https://doi.org/10.1073/pnas.1907619116	journal	August 2019
Genome-wide identification of Pseudomonas syringae genes required for fitness during colonization of the leaf surface and apoplast Helmann, Tyler C.; Deutschbauer, Adam M.; Lindow, Steven E. Proceedings of the National Academy of Sciences, Vol. 116, Issue 38 https://doi.org/10.1073/pnas.1908858116	journal	September 2019
GDGT cyclization proteins identify the dominant archaeal sources of tetraether lipids in the ocean Zeng, Zhirui; Liu, Xiao-Lei; Farley, Kristen R. Proceedings of the National Academy of Sciences, Vol. 116, Issue 45 https://doi.org/10.1073/pnas.1909306116	journal	October 2019
Insights into the mechanism and regulation of the CbbQO-type Rubisco activase, a MoxR AAA+ ATPase Tsai, Yi-Chin Candace; Ye, Fuzhou; Liew, Lynette Proceedings of the National Academy of Sciences, Vol. 117, Issue 1 https://doi.org/10.1073/pnas.1911123117	journal	December 2019
Energy conservation involving 2 respiratory circuits Schoelmerich, Marie Charlotte; Katsyv, Alexander; Dönig, Judith Proceedings of the National Academy of Sciences, Vol. 117, Issue 2 https://doi.org/10.1073/pnas.1914939117	journal	December 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
DeePaC: predicting pathogenic potential of novel DNA with reverse-complement neural networks Bartoszewicz, Jakub M.; Seidel, Anja; Rentzsch, Robert Bioinformatics https://doi.org/10.1093/bioinformatics/btz541	journal	July 2019
AcetoBase: a functional gene repository and database for formyltetrahydrofolate synthetase sequences Singh, Abhijeet; Müller, Bettina; Fuxelius, Hans-Henrik Database, Vol. 2019 https://doi.org/10.1093/database/baz142	journal	January 2019
Thermophilic methanotrophs: in hot pursuit Houghton, Karen M.; Carere, Carlo R.; Stott, Matthew B. FEMS Microbiology Ecology, Vol. 95, Issue 9 https://doi.org/10.1093/femsec/fiz125	journal	August 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
proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes Mende, Daniel R.; Letunic, Ivica; Maistrenko, Oleksandr M. Nucleic Acids Research https://doi.org/10.1093/nar/gkz1002	journal	October 2019
MGnify: the microbiome analysis resource in 2020 Mitchell, Alex L.; Almeida, Alexandre; Beracochea, Martin Nucleic Acids Research https://doi.org/10.1093/nar/gkz1035	journal	November 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
MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis Vallenet, David; Calteau, Alexandra; Dubois, Mathieu Nucleic Acids Research https://doi.org/10.1093/nar/gkz926	journal	October 2019
IMG-ABC v.5.0: an update to the IMG/Atlas of Biosynthetic Gene Clusters Knowledgebase Palaniappan, Krishnaveni; Chen, I-Min A.; Chu, Ken Nucleic Acids Research https://doi.org/10.1093/nar/gkz932	journal	October 2019
High-quality draft genome sequences of Pseudomonas monteilii DSM 14164T, Pseudomonas mosselii DSM 17497T, Pseudomonas plecoglossicida DSM 15088T, Pseudomonas taiwanensis DSM 21245T and Pseudomonas vranovensis DSM 16006T: taxonomic considerations Peña, Arantxa; Busquets, Antonio; Gomila, Margarita Access Microbiology, Vol. 1, Issue 10 https://doi.org/10.1099/acmi.0.000067	journal	December 2019
Aquirufa antheringensis gen. nov., sp. nov. and Aquirufa nivalisilvae sp. nov., representing a new genus of widespread freshwater bacteria Pitt, Alexandra; Schmidt, Johanna; Koll, Ulrike International Journal of Systematic and Evolutionary Microbiology, Vol. 69, Issue 9 https://doi.org/10.1099/ijsem.0.003554	journal	September 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
Fluviispira multicolorata gen. nov., sp. nov. and Silvanigrella paludirubra sp. nov., isolated from freshwater habitats Pitt, Alexandra; Koll, Ulrike; Schmidt, Johanna International Journal of Systematic and Evolutionary Microbiology, Vol. 70, Issue 3 https://doi.org/10.1099/ijsem.0.003947	journal	March 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
AzeR, a transcriptional regulator that responds to azelaic acid in Pseudomonas nitroreducens Bez, Cristina; Javvadi, Sree Gowrinadh; Bertani, Iris Microbiology, Vol. 166, Issue 1 https://doi.org/10.1099/mic.0.000865	journal	January 2020
Geologic legacy spanning >90 years explains unique Yellowstone hot spring geochemistry and biodiversity Payne, Devon; Dunham, Eric C.; Mohr, Elizabeth Environmental Microbiology, Vol. 21, Issue 11 https://doi.org/10.1111/1462-2920.14775	journal	August 2019
Symbiosis of a P2‐family phage and deep‐sea Shewanella putrefaciens Liu, Xiaoxiao; Tang, Kaihao; Zhang, Dali Environmental Microbiology, Vol. 21, Issue 11 https://doi.org/10.1111/1462-2920.14781	journal	August 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
l ‐Rhamnose catabolism in archaea Reinhardt, Andreas; Johnsen, Ulrike; Schönheit, Peter Molecular Microbiology, Vol. 111, Issue 4 https://doi.org/10.1111/mmi.14213	journal	February 2019
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
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
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
Genome Sequences of Four Vibrio parahaemolyticus Strains Isolated from the English Channel and the River Thames Witherall, Lucy; Wagley, Sariqa; Butler, Clive Microbiology Resource Announcements, Vol. 8, Issue 24 https://doi.org/10.1128/mra.00392-19	journal	June 2019
Draft Genome Sequence of Mn(II)-Oxidizing Bacterium Oxalobacteraceae sp. Strain AB_14 Bushman, Timothy J.; Akob, Denise M.; Bohu, Tsing Microbiology Resource Announcements, Vol. 8, Issue 43 https://doi.org/10.1128/mra.01024-19	journal	October 2019
Metatranscriptomic Sequencing of a Cyanobacterial Soil-Surface Consortium with and without a Diverse Underlying Soil Microbiome Bell, Terrence H.; Trexler, Ryan V.; Peng, Xin Microbiology Resource Announcements, Vol. 9, Issue 1 https://doi.org/10.1128/mra.01361-19	journal	January 2020
Complete Genome Sequence for Asinibacterium sp. Strain OR53 and Draft Genome Sequence for Asinibacterium sp. Strain OR43, Two Bacteria Tolerant to Uranium Brzoska, Ryann M.; Huntemann, Marcel; Clum, Alicia Microbiology Resource Announcements, Vol. 8, Issue 14 https://doi.org/10.1128/mra.01701-18	journal	April 2019
Curated BLAST for Genomes Price, Morgan N.; Arkin, Adam P. mSystems, Vol. 4, Issue 2 https://doi.org/10.1128/msystems.00072-19	journal	March 2019
Genome Sequence of Colistin-Resistant Bacteremic Shewanella algae Carrying the Beta-Lactamase Gene bla _OXA-55 Chen, Ying-Ju; Tung, Kwong-Chung; Hong, Yu-Kai Canadian Journal of Infectious Diseases and Medical Microbiology, Vol. 2019 https://doi.org/10.1155/2019/3840563	journal	June 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
Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2 Gonnella, Giorgio; Adam, Nicole; Perner, Mirjam BMC Genomics, Vol. 20, Issue 1 https://doi.org/10.1186/s12864-019-5710-5	journal	May 2019
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
Discovery of 20 novel ribosomal leader candidates in bacteria and archaea Eckert, Iris; Weinberg, Zasha BMC Microbiology, Vol. 20, Issue 1 https://doi.org/10.1186/s12866-020-01823-6	journal	May 2020
Direct pathway cloning of the sodorifen biosynthetic gene cluster and recombinant generation of its product in E. coli Duell, Elke R.; D’Agostino, Paul M.; Shapiro, Nicole Microbial Cell Factories, Vol. 18, Issue 1 https://doi.org/10.1186/s12934-019-1080-6	journal	February 2019
Fueling ab initio folding with marine metagenomics enables structure and function predictions of new protein families Wang, Yan; Shi, Qiang; Yang, Pengshuo Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1823-z	journal	November 2019
Challenges in the construction of knowledge bases for human microbiome-disease associations Badal, Varsha Dave; Wright, Dustin; Katsis, Yannis Microbiome, Vol. 7, Issue 1 https://doi.org/10.1186/s40168-019-0742-2	journal	September 2019
A pipeline for targeted metagenomics of environmental bacteria Grieb, Anissa; Bowers, Robert M.; Oggerin, Monike Microbiome, Vol. 8, Issue 1 https://doi.org/10.1186/s40168-020-0790-7	journal	February 2020
Shotgun metagenomic analysis of microbial communities from the Loxahatchee nature preserve in the Florida Everglades Abraham, Briana S.; Caglayan, Deniz; Carrillo, Natalie V. Environmental Microbiome, Vol. 15, Issue 1 https://doi.org/10.1186/s40793-019-0352-4	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. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.39488	text	January 2019
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
Position-Specific Metabolic Probing and Metagenomics of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities at High Temperatures Thomas, Scott C.; Tamadonfar, Kevin O.; Seymour, Cale O. Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01427	journal	July 2019
Genome Sequences of a Plant Beneficial Synthetic Bacterial Community Reveal Genetic Features for Successful Plant Colonization de Souza, Rafael Soares Correa; Armanhi, Jaderson Silveira Leite; Damasceno, Natália de Brito Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01779	journal	August 2019
Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes García-López, Marina; Meier-Kolthoff, Jan P.; Tindall, Brian J. Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.02083	journal	September 2019
Genomic Insights into the Carbon and Energy Metabolism of a Thermophilic Deep-Sea Bacterium Deferribacter autotrophicus Revealed New Metabolic Traits in the Phylum Deferribacteres Slobodkin, Alexander; Slobodkina, Galina; Allioux, Maxime Genes, Vol. 10, Issue 11 https://doi.org/10.3390/genes10110849	journal	October 2019
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
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
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
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
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
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

Similar Records

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

Journal Article · 2016 · Nucleic Acids Research · OSTI ID:1379657

Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken; +13 more

IMG Annotation Pipeline (IMGAP) v5.1.13

Software · 2023 · OSTI ID:code-134858

Huntemann, Marcel; Ivanova, Natalia

IMG/M 4 version of the integrated metagenome comparative analysis system

Journal Article · 2013 · Nucleic Acids Research · OSTI ID:1625530

Markowitz, Victor M.; Chen, I-Min A.; Chu, Ken; +15 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES

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

Citation Formats

References (60)

Cited By (109)

Similar Records

Related Subjects