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

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.

View Accepted Manuscript (DOE)

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

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1379657

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

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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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
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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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
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 Sequence of Methylocapsa palsarum NE2 ^T , an Obligate Methanotroph from Subarctic Soil Miroshnikov, Kirill K.; Didriksen, Alena; Naumoff, Daniil G. Genome Announcements, Vol. 5, Issue 24 https://doi.org/10.1128/genomea.00504-17	journal	June 2017
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
RNA-Dependent Cysteine Biosynthesis in Bacteria and Archaea Mukai, Takahito; Crnković, Ana; Umehara, Takuya mBio, Vol. 8, Issue 3, Article No. e00561-17 https://doi.org/10.1128/mbio.00561-17	journal	May 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
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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
Validating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of Zetaproteobacteria Iron Mats at Marine Hydrothermal Vents McAllister, Sean M.; Polson, Shawn W.; Butterfield, David A. mSystems, Vol. 5, Issue 1 https://doi.org/10.1128/msystems.00553-19	journal	February 2020
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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
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
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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
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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
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
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
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
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
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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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
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
Linking stream microbial community functional genes to dissolved organic matter and inorganic nutrients Fasching, Christina; Akotoye, Christian; Bižić, Mina Limnology and Oceanography, Vol. 65, Issue S1 https://doi.org/10.1002/lno.11356	journal	January 2020
Comparative Metagenomics Maltez Thomas, Andrew; Prata Lima, Felipe; Maria Silva Moura, Livia Comparative Genomics https://doi.org/10.1007/978-1-4939-7463-4_8	book	December 2017
Genome sequences of two Antarctic strains of Pseudomonas prosekii: insights into adaptation to extreme conditions Snopková, Kateřina; Čejková, Darina; Dufková, Kristýna Archives of Microbiology, Vol. 202, Issue 3 https://doi.org/10.1007/s00203-019-01755-4	journal	November 2019
A Physiological and Genomic Comparison of Nitrosomonas Cluster 6a and 7 Ammonia-Oxidizing Bacteria Sedlacek, Christopher J.; McGowan, Brian; Suwa, Yuichi Microbial Ecology, Vol. 78, Issue 4 https://doi.org/10.1007/s00248-019-01378-8	journal	April 2019
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
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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Advances in protein structure prediction and design Kuhlman, Brian; Bradley, Philip Nature Reviews Molecular Cell Biology, Vol. 20, Issue 11 https://doi.org/10.1038/s41580-019-0163-x	journal	August 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
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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
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
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
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Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments Berube, Paul M.; Biller, Steven J.; Hackl, Thomas Scientific Data, Vol. 5, Issue 1 https://doi.org/10.1038/sdata.2018.154	journal	September 2018
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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
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
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
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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
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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
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
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
Type 4 pili are dispensable for biofilm development in the cyanobacterium Synechococcus elongatus: Pili are dispensable for biofilm development Nagar, Elad; Zilberman, Shaul; Sendersky, Eleonora Environmental Microbiology, Vol. 19, Issue 7 https://doi.org/10.1111/1462-2920.13814	journal	July 2017
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
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
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
Depth distributions of nitrite reductase ( nirK ) gene variants reveal spatial dynamics of thaumarchaeal ecotype populations in coastal Monterey Bay Reji, Linta; Tolar, Bradley B.; Smith, Jason M. Environmental Microbiology, Vol. 21, Issue 11 https://doi.org/10.1111/1462-2920.14753	journal	August 2019
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
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
A microcin processing peptidase‐like protein of the cyanobacterium Synechococcus elongatus is essential for secretion of biofilm‐promoting proteins Parnasa, Rami; Sendersky, Eleonora; Simkovsky, Ryan Environmental Microbiology Reports, Vol. 11, Issue 3 https://doi.org/10.1111/1758-2229.12751	journal	March 2019
Occurrence and diversity of the oxidative hydroxyhydroquinone pathway for the anaerobic degradation of aromatic compounds in nitrate‐reducing bacteria Pacheco‐Sánchez, Daniel; Rama‐Garda, Ramón; Marín, Patricia Environmental Microbiology Reports, Vol. 11, Issue 4 https://doi.org/10.1111/1758-2229.12752	journal	March 2019
Snf2 controls pulcherriminic acid biosynthesis and antifungal activity of the biocontrol yeast Metschnikowia pulcherrima Gore‐Lloyd, Deborah; Sumann, Inés; Brachmann, Alexander O. Molecular Microbiology, Vol. 112, Issue 1 https://doi.org/10.1111/mmi.14272	journal	April 2019
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
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
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
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
Genus-Wide Assessment of Lignocellulose Utilization in the Extremely Thermophilic Genus Caldicellulosiruptor by Genomic, Pangenomic, and Metagenomic Analyses Lee, Laura L.; Blumer-Schuette, Sara E.; Izquierdo, Javier A. Applied and Environmental Microbiology, Vol. 84, Issue 9 https://doi.org/10.1128/aem.02694-17	journal	February 2018
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
Mutations in Escherichia coli Polyphosphate Kinase That Lead to Dramatically Increased In Vivo Polyphosphate Levels Rudat, Amanda K.; Pokhrel, Arya; Green, Todd J. Journal of Bacteriology, Vol. 200, Issue 6 https://doi.org/10.1128/jb.00697-17	journal	January 2018
Modernized Tools for Streamlined Genetic Manipulation and Comparative Study of Wild and Diverse Proteobacterial Lineages Wiles, Travis J.; Wall, Elena S.; Schlomann, Brandon H. mBio, Vol. 9, Issue 5 https://doi.org/10.1128/mbio.01877-18	journal	October 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
Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes Lloyd, Karen G.; Steen, Andrew D.; Ladau, Joshua mSystems, Vol. 3, Issue 5 https://doi.org/10.1128/msystems.00055-18	journal	September 2018
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
Genome-resolved metagenomics analysis provides insights into the ecological role of Thaumarchaeota in the Amazon River and its plume Pinto, Otávio H. B.; Silva, Thais F.; Vizzotto, Carla S. BMC Microbiology, Vol. 20, Issue 1 https://doi.org/10.1186/s12866-020-1698-x	journal	January 2020
Sugar Lego: gene composition of bacterial carbohydrate metabolism genomic loci Kaznadzey, Anna; Shelyakin, Pavel; Gelfand, Mikhail S. Biology Direct, Vol. 12, Issue 1 https://doi.org/10.1186/s13062-017-0200-7	journal	November 2017
Towards a balanced view of the bacterial tree of life Schulz, Frederik; Eloe-Fadrosh, Emiley A.; Bowers, Robert M. Microbiome, Vol. 5, Issue 1 https://doi.org/10.1186/s40168-017-0360-9	journal	October 2017
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
MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis Uritskiy, Gherman V.; DiRuggiero, Jocelyne; Taylor, James Microbiome, Vol. 6, Issue 1 https://doi.org/10.1186/s40168-018-0541-1	journal	September 2018
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
High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460 Matrosova, Vera Y.; Gaidamakova, Elena K.; Makarova, Kira S. Standards in Genomic Sciences, Vol. 12, Issue 1 https://doi.org/10.1186/s40793-017-0258-y	journal	July 2017
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
LurR is a regulator of the central lactate oxidation pathway in sulfate-reducing Desulfovibrio species Rajeev, Lara; Luning, Eric G.; Zane, Grant M. PLOS ONE, Vol. 14, Issue 4 https://doi.org/10.1371/journal.pone.0214960	journal	April 2019
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
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
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
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
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
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
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
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
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
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
Emergence of trait variability through the lens of nitrogen assimilation in Prochlorococcus Berube, Paul M.; Rasmussen, Anna; Braakman, Rogier eLife, Vol. 8 https://doi.org/10.7554/elife.41043	journal	February 2019

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