DRAM for distilling microbial metabolism to automate the curation of microbiome function

Microbial and viral communities transform the chemistry of Earth's ecosystems, yet the specific reactions catalyzed by these biological engines are hard to decode due to the absence of a scalable, metabolically resolved, annotation software. Here, we present DRAM (Distilled and Refined Annotati...

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Published in:	Nucleic acids research Vol. 48; no. 16; pp. 8883 - 8900
Main Authors:	Shaffer, Michael, Borton, Mikayla A, McGivern, Bridget B, Zayed, Ahmed A, La Rosa, Sabina Leanti, Solden, Lindsey M, Liu, Pengfei, Narrowe, Adrienne B, Rodríguez-Ramos, Josué, Bolduc, Benjamin, Gazitúa, M Consuelo, Daly, Rebecca A, Smith, Garrett J, Vik, Dean R, Pope, Phil B, Sullivan, Matthew B, Roux, Simon, Wrighton, Kelly C
Format:	Journal Article
Language:	English
Published:	England Oxford University Press 18.09.2020
Subjects:	Bacteria - classification BASIC BIOLOGICAL SCIENCES Computational Biology Computational Methods Gastrointestinal Microbiome Genomics - methods Humans Metabolomics - methods Metagenome Molecular Sequence Annotation - methods Software Soil Microbiology Viruses - classification
ISSN:	0305-1048, 1362-4962, 1362-4962
Online Access:	Get full text
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Abstract	Microbial and viral communities transform the chemistry of Earth's ecosystems, yet the specific reactions catalyzed by these biological engines are hard to decode due to the absence of a scalable, metabolically resolved, annotation software. Here, we present DRAM (Distilled and Refined Annotation of Metabolism), a framework to translate the deluge of microbiome-based genomic information into a catalog of microbial traits. To demonstrate the applicability of DRAM across metabolically diverse genomes, we evaluated DRAM performance on a defined, in silico soil community and previously published human gut metagenomes. We show that DRAM accurately assigned microbial contributions to geochemical cycles and automated the partitioning of gut microbial carbohydrate metabolism at substrate levels. DRAM-v, the viral mode of DRAM, established rules to identify virally-encoded auxiliary metabolic genes (AMGs), resulting in the metabolic categorization of thousands of putative AMGs from soils and guts. Together DRAM and DRAM-v provide critical metabolic profiling capabilities that decipher mechanisms underpinning microbiome function.
AbstractList	Microbial and viral communities transform the chemistry of Earth's ecosystems, yet the specific reactions catalyzed by these biological engines are hard to decode due to the absence of a scalable, metabolically resolved, annotation software. Here, we present DRAM (Distilled and Refined Annotation of Metabolism), a framework to translate the deluge of microbiome-based genomic information into a catalog of microbial traits. To demonstrate the applicability of DRAM across metabolically diverse genomes, we evaluated DRAM performance on a defined, in silico soil community and previously published human gut metagenomes. We show that DRAM accurately assigned microbial contributions to geochemical cycles and automated the partitioning of gut microbial carbohydrate metabolism at substrate levels. DRAM-v, the viral mode of DRAM, established rules to identify virally-encoded auxiliary metabolic genes (AMGs), resulting in the metabolic categorization of thousands of putative AMGs from soils and guts. Together DRAM and DRAM-v provide critical metabolic profiling capabilities that decipher mechanisms underpinning microbiome function. Microbial and viral communities transform the chemistry of Earth's ecosystems, yet the specific reactions catalyzed by these biological engines are hard to decode due to the absence of a scalable, metabolically resolved, annotation software. Here, we present DRAM (Distilled and Refined Annotation of Metabolism), a framework to translate the deluge of microbiome-based genomic information into a catalog of microbial traits. To demonstrate the applicability of DRAM across metabolically diverse genomes, we evaluated DRAM performance on a defined, in silico soil community and previously published human gut metagenomes. We show that DRAM accurately assigned microbial contributions to geochemical cycles and automated the partitioning of gut microbial carbohydrate metabolism at substrate levels. DRAM-v, the viral mode of DRAM, established rules to identify virally-encoded auxiliary metabolic genes (AMGs), resulting in the metabolic categorization of thousands of putative AMGs from soils and guts. Together DRAM and DRAM-v provide critical metabolic profiling capabilities that decipher mechanisms underpinning microbiome function.Microbial and viral communities transform the chemistry of Earth's ecosystems, yet the specific reactions catalyzed by these biological engines are hard to decode due to the absence of a scalable, metabolically resolved, annotation software. Here, we present DRAM (Distilled and Refined Annotation of Metabolism), a framework to translate the deluge of microbiome-based genomic information into a catalog of microbial traits. To demonstrate the applicability of DRAM across metabolically diverse genomes, we evaluated DRAM performance on a defined, in silico soil community and previously published human gut metagenomes. We show that DRAM accurately assigned microbial contributions to geochemical cycles and automated the partitioning of gut microbial carbohydrate metabolism at substrate levels. DRAM-v, the viral mode of DRAM, established rules to identify virally-encoded auxiliary metabolic genes (AMGs), resulting in the metabolic categorization of thousands of putative AMGs from soils and guts. Together DRAM and DRAM-v provide critical metabolic profiling capabilities that decipher mechanisms underpinning microbiome function.
Author	La Rosa, Sabina Leanti Daly, Rebecca A Rodríguez-Ramos, Josué Gazitúa, M Consuelo Vik, Dean R Zayed, Ahmed A Shaffer, Michael Smith, Garrett J Borton, Mikayla A McGivern, Bridget B Solden, Lindsey M Sullivan, Matthew B Narrowe, Adrienne B Wrighton, Kelly C Pope, Phil B Liu, Pengfei Bolduc, Benjamin Roux, Simon
Author_xml	– sequence: 1 givenname: Michael surname: Shaffer fullname: Shaffer, Michael organization: Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA – sequence: 2 givenname: Mikayla A surname: Borton fullname: Borton, Mikayla A organization: Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA – sequence: 3 givenname: Bridget B orcidid: 0000-0001-9023-0018 surname: McGivern fullname: McGivern, Bridget B organization: Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA – sequence: 4 givenname: Ahmed A surname: Zayed fullname: Zayed, Ahmed A organization: Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA – sequence: 5 givenname: Sabina Leanti orcidid: 0000-0003-3527-8101 surname: La Rosa fullname: La Rosa, Sabina Leanti organization: Faculty of Biosciences, Norwegian University of Life Sciences, Aas 1432, Norway – sequence: 6 givenname: Lindsey M surname: Solden fullname: Solden, Lindsey M organization: Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA – sequence: 7 givenname: Pengfei surname: Liu fullname: Liu, Pengfei organization: Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA – sequence: 8 givenname: Adrienne B surname: Narrowe fullname: Narrowe, Adrienne B organization: Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA – sequence: 9 givenname: Josué surname: Rodríguez-Ramos fullname: Rodríguez-Ramos, Josué organization: Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA – sequence: 10 givenname: Benjamin surname: Bolduc fullname: Bolduc, Benjamin organization: Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA – sequence: 11 givenname: M Consuelo surname: Gazitúa fullname: Gazitúa, M Consuelo organization: Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA – sequence: 12 givenname: Rebecca A surname: Daly fullname: Daly, Rebecca A organization: Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA – sequence: 13 givenname: Garrett J surname: Smith fullname: Smith, Garrett J organization: Department of Microbiology, Radboud University, Nijmegen 6525, Netherlands – sequence: 14 givenname: Dean R surname: Vik fullname: Vik, Dean R organization: Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA – sequence: 15 givenname: Phil B surname: Pope fullname: Pope, Phil B organization: Faculty of Biosciences, Norwegian University of Life Sciences, Aas 1432, Norway – sequence: 16 givenname: Matthew B surname: Sullivan fullname: Sullivan, Matthew B organization: Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA – sequence: 17 givenname: Simon surname: Roux fullname: Roux, Simon organization: Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA – sequence: 18 givenname: Kelly C orcidid: 0000-0003-0434-4217 surname: Wrighton fullname: Wrighton, Kelly C organization: Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/32766782$$D View this record in MEDLINE/PubMed https://www.osti.gov/biblio/1646715$$D View this record in Osti.gov
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Cites_doi	10.1093/nar/gky995 10.1038/s41569-018-0108-7 10.1038/s41586-019-0965-1 10.1186/1471-2105-11-119 10.1038/nmicrobiol.2016.146 10.3389/fmicb.2019.00051 10.1038/ismej.2016.90 10.1038/sdata.2017.203 10.1038/nature11550 10.1093/nar/gkw256 10.1038/nmicrobiol.2016.48 10.7717/peerj.985 10.3389/fgene.2019.00999 10.1021/cr050196r 10.1093/dnares/dsn027 10.1016/j.cell.2015.11.001 10.1038/nature24621 10.1038/nature14447 10.1093/bioinformatics/btu739 10.1093/nar/gkw1099 10.1038/nrmicro1235 10.1038/nbt.4229 10.21105/joss.01057 10.1038/s41579-018-0004-5 10.1016/j.cell.2019.01.001 10.1038/s41591-018-0128-1 10.1126/science.1235872 10.7717/peerj.7359 10.1038/nbt.4306 10.1038/s41564-017-0096-0 10.1371/journal.pbio.0040234 10.1128/mBio.00815-18 10.1038/s41467-017-01753-4 10.1038/s41586-020-2007-4 10.3389/fmicb.2019.02614 10.1101/gr.1239303 10.1038/s41564-018-0190-y 10.1093/bioinformatics/bts174 10.1038/nbt.1754 10.1073/pnas.1409642111 10.1126/science.aaf4507 10.1093/bioinformatics/btz859 10.1093/bioinformatics/btu153 10.1093/nar/gky901 10.1093/bioinformatics/btq249 10.1186/1471-2164-9-75 10.1038/nbt.3893 10.1038/nature05414 10.1038/s41587-019-0209-9 10.1186/s12986-018-0271-1 10.1038/s41564-018-0312-6 10.1007/s13668-018-0248-8 10.1093/nar/gkp971 10.1038/ismej.2016.53 10.1128/IAI.00945-17 10.1073/pnas.1215689109 10.1038/nprot.2015.053 10.1186/1471-2105-14-202 10.1093/nar/gky418 10.1093/nar/gkw1092 10.1038/s41467-019-08672-6 10.1093/bioinformatics/btx713 10.5670/oceanog.2007.58 10.1038/s41564-018-0225-4 10.1093/nar/gkr367 10.1093/nar/gkh885 10.1038/nmicrobiol.2016.180 10.1038/s41598-017-07910-5 10.1038/ncomms13219 10.1038/ismej.2017.126 10.1126/science.1247023 10.1038/nature02340 10.1093/nar/gkm321 10.1186/s13015-016-0082-8 10.1038/s41564-018-0267-7 10.1016/j.mib.2016.04.002 10.1111/j.1758-2229.2010.00192.x 10.1038/s41586-018-0338-1 10.1038/nature13798 10.1038/s41587-019-0100-8 10.1101/gr.186072.114 10.1016/j.neuropharm.2016.08.024 10.1126/science.1224041 10.1016/j.bbapap.2015.04.015 10.1038/s41586-019-1916-6 10.1186/1471-2105-8-209 10.1016/j.cmet.2017.05.002 10.1038/nature19366 10.1038/nature04111 10.1016/B978-0-12-370950-9.50011-9 10.1016/j.tifs.2011.11.002 10.1093/nar/19.suppl.2247 10.1186/s13690-015-0078-8 10.1016/j.chom.2019.05.005 10.1038/s41587-019-0202-3 10.1038/s41586-019-1058-x 10.1093/bioinformatics/btz848 10.1038/nbt.3988 10.1371/journal.pbio.1001377 10.1038/nature11234 10.1038/nrmicro3404
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Copyright	The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. 2020
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References	Tully (2020091720050844700_B19) 2018; 5 Tran (2020091720050844700_B88) 2011; 26 Noguchi (2020091720050844700_B54) 2008; 15 Seemann (2020091720050844700_B30) 2014; 30 Tyson (2020091720050844700_B5) 2004; 428 Steinegger (2020091720050844700_B44) 2017; 35 Frost (2020091720050844700_B64) 2005; 3 Wrighton (2020091720050844700_B74) 2016; 10 Zengler (2020091720050844700_B98) 2018; 16 El-Gebali (2020091720050844700_B46) 2019; 47 Lozupone (2020091720050844700_B85) 2012; 489 Al-Shayeb (2020091720050844700_B23) 2020; 578 Stefler (2020091720050844700_B82) 2015; 73 McCalley (2020091720050844700_B8) 2014; 514 Solden (2020091720050844700_B93) 2018; 3 Chen (2020091720050844700_B34) 2019; 47 Spang (2020091720050844700_B13) 2015; 521 Parks (2020091720050844700_B11) 2018; 36 Stewart (2020091720050844700_B20) 2019; 37 Zeevi (2020091720050844700_B83) 2015; 163 Trifinopoulos (2020091720050844700_B100) 2016; 44 Louca (2020091720050844700_B29) 2016; 353 Wu (2020091720050844700_B92) 2018; 86 Robinson (2020091720050844700_B102) 2011; 29 Imachi (2020091720050844700_B76) 2020; 577 Almeida (2020091720050844700_B18) 2019; 568 Sullivan (2020091720050844700_B62) 2006; 4 Emerson (2020091720050844700_B14) 2018; 3 Nayfach (2020091720050844700_B16) 2019; 568 Hyatt (2020091720050844700_B40) 2010; 11 Enault (2020091720050844700_B39) 2017; 11 Huttenhower (2020091720050844700_B56) 2012; 486 Haiser (2020091720050844700_B10) 2013; 341 Anantharaman (2020091720050844700_B21) 2016; 7 Hug (2020091720050844700_B12) 2016; 1 Rawlings (2020091720050844700_B43) 2010; 38 Roux (2020091720050844700_B15) 2016; 537 Galperin (2020091720050844700_B70) 2004; 32 Chan (2020091720050844700_B50) 2019 UniProt: the universal protein knowledgebase (2020091720050844700_B69) 2017; 45 Smith (2020091720050844700_B71) 2018; 9 Chambers (2020091720050844700_B87) 2018; 7 Vanderplas (2020091720050844700_B52) 2018; 3 Olm (2020091720050844700_B60) 2017; 11 Gerlt (2020091720050844700_B66) 2015; 1854 Woodcroft (2020091720050844700_B7) 2018; 560 Daly (2020091720050844700_B45) 2016; 1 Maxwell (2020091720050844700_B81) 2012; 24 Kang (2020091720050844700_B59) 2019; 2019 Shannon (2020091720050844700_B67) 2003; 13 Daly (2020091720050844700_B22) 2019; 4 Mizuno (2020091720050844700_B95) 2019; 10 Jang (2020091720050844700_B26) 2019; 37 Chaumeil (2020091720050844700_B24) 2018; 36 Johnson (2020091720050844700_B79) 2019; 25 Bolyen (2020091720050844700_B2) 2019; 37 Tanizawa (2020091720050844700_B31) 2018; 34 Sharon (2020091720050844700_B4) 2013; 342 Pasolli (2020091720050844700_B17) 2019; 176 Mehta (2020091720050844700_B78) 2018; 3 Aramaki (2020091720050844700_B49) 2019; 36 Vignais (2020091720050844700_B77) 2007; 107 Zhang (2020091720050844700_B48) 2018; 46 Moriya (2020091720050844700_B35) 2007; 35 Gevers (2020091720050844700_B55) 2012; 10 Finn (2020091720050844700_B47) 2011; 39 Roux (2020091720050844700_B27) 2019; 37 Konwar (2020091720050844700_B33) 2013; 14 Bushnell (2020091720050844700_B57) 2018 Parks (2020091720050844700_B51) 2015; 25 Heintz-Buschart (2020091720050844700_B28) 2016; 2 Bairoch (2020091720050844700_B53) 1991; 19 Reese (2020091720050844700_B97) 2018; 3 Kanehisa (2020091720050844700_B41) 2017; 45 Garneau (2020091720050844700_B96) 2017; 7 Baker (2020091720050844700_B80) 1979 Amaretti (2020091720050844700_B86) 2019; 10 Filpa (2020091720050844700_B89) 2016; 111 Holeček (2020091720050844700_B99) 2018; 15 Brum (2020091720050844700_B37) 2015; 13 Peng (2020091720050844700_B58) 2012; 28 Turnbaugh (2020091720050844700_B91) 2006; 444 Roux (2020091720050844700_B61) 2015; 3 Lindell (2020091720050844700_B63) 2005; 438 Wrighton (2020091720050844700_B3) 2012; 337 Kelley (2020091720050844700_B73) 2015; 10 Suzek (2020091720050844700_B42) 2015; 31 Aziz (2020091720050844700_B36) 2008; 9 Yu (2020091720050844700_B101) 2010; 26 Angle (2020091720050844700_B6) 2017; 8 Hurwitz (2020091720050844700_B38) 2016; 31 Roberts (2020091720050844700_B9) 2018; 24 Tavormina (2020091720050844700_B72) 2011; 3 Thompson (2020091720050844700_B1) 2017; 551 Tang (2020091720050844700_B90) 2019; 16 Broecker (2020091720050844700_B65) 2019; 10 Bland (2020091720050844700_B68) 2007; 8 Korem (2020091720050844700_B84) 2017; 25 Dong (2020091720050844700_B32) 2019; 10 Breitbart (2020091720050844700_B94) 2007; 20 Craciun (2020091720050844700_B104) 2012; 109 Bowers (2020091720050844700_B25) 2017; 35 Ticak (2020091720050844700_B103) 2014; 111 Hobbs (2020091720050844700_B75) 2016; 11
References_xml	– volume: 47 start-page: D427 year: 2019 ident: 2020091720050844700_B46 article-title: The Pfam protein families database in 2019 publication-title: Nucleic Acids Res doi: 10.1093/nar/gky995 – volume: 16 start-page: 137 year: 2019 ident: 2020091720050844700_B90 article-title: Dietary metabolism, the gut microbiome, and heart failure publication-title: Nat. Rev. Cardiol. doi: 10.1038/s41569-018-0108-7 – volume: 568 start-page: 499 year: 2019 ident: 2020091720050844700_B18 article-title: A new genomic blueprint of the human gut microbiota publication-title: Nature doi: 10.1038/s41586-019-0965-1 – volume: 11 start-page: 119 year: 2010 ident: 2020091720050844700_B40 article-title: Prodigal: prokaryotic gene recognition and translation initiation site identification publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-11-119 – volume: 1 start-page: 16146 year: 2016 ident: 2020091720050844700_B45 article-title: Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales publication-title: Nat. Microbiol. doi: 10.1038/nmicrobiol.2016.146 – volume: 10 start-page: 51 year: 2019 ident: 2020091720050844700_B65 article-title: Evolution of immune systems from viruses and transposable elements publication-title: Front. Microbiol. doi: 10.3389/fmicb.2019.00051 – volume: 11 start-page: 237 year: 2017 ident: 2020091720050844700_B39 article-title: Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses publication-title: ISME J doi: 10.1038/ismej.2016.90 – volume: 26 start-page: 1453 year: 2011 ident: 2020091720050844700_B88 article-title: Potential role of chitinases and chitin-binding proteins in host-microbial interactions during the development of intestinal inflammation publication-title: Histol. Histopathol. – volume: 5 start-page: 170203 year: 2018 ident: 2020091720050844700_B19 article-title: The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans publication-title: Sci. Data doi: 10.1038/sdata.2017.203 – volume: 489 start-page: 220 year: 2012 ident: 2020091720050844700_B85 article-title: Diversity, stability and resilience of the human gut microbiota publication-title: Nature doi: 10.1038/nature11550 – volume: 44 start-page: W232 year: 2016 ident: 2020091720050844700_B100 article-title: W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis publication-title: Nucleic Acids Res doi: 10.1093/nar/gkw256 – volume: 1 start-page: 16048 year: 2016 ident: 2020091720050844700_B12 article-title: A new view of the tree of life publication-title: Nat. Microbiol. doi: 10.1038/nmicrobiol.2016.48 – volume: 3 start-page: e985 year: 2015 ident: 2020091720050844700_B61 article-title: VirSorter: mining viral signal from microbial genomic data publication-title: PeerJ doi: 10.7717/peerj.985 – volume: 10 start-page: 999 year: 2019 ident: 2020091720050844700_B32 article-title: An integrated pipeline for annotation and visualization of metagenomic contigs publication-title: Front. Genet. doi: 10.3389/fgene.2019.00999 – volume: 107 start-page: 4206 year: 2007 ident: 2020091720050844700_B77 article-title: Occurrence, classification, and biological function of hydrogenases: an overview publication-title: Chem. Rev. doi: 10.1021/cr050196r – volume: 15 start-page: 387 year: 2008 ident: 2020091720050844700_B54 article-title: MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes publication-title: DNA Res doi: 10.1093/dnares/dsn027 – volume: 163 start-page: 1079 year: 2015 ident: 2020091720050844700_B83 article-title: Personalized nutrition by prediction of glycemic responses publication-title: Cell doi: 10.1016/j.cell.2015.11.001 – volume: 551 start-page: 457 year: 2017 ident: 2020091720050844700_B1 article-title: A communal catalogue reveals Earth's multiscale microbial diversity publication-title: Nature doi: 10.1038/nature24621 – volume: 521 start-page: 173 year: 2015 ident: 2020091720050844700_B13 article-title: Complex archaea that bridge the gap between prokaryotes and eukaryotes publication-title: Nature doi: 10.1038/nature14447 – volume: 31 start-page: 926 year: 2015 ident: 2020091720050844700_B42 article-title: UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches publication-title: Bioinformatics doi: 10.1093/bioinformatics/btu739 – volume: 45 start-page: D158 year: 2017 ident: 2020091720050844700_B69 publication-title: Nucleic Acids Res doi: 10.1093/nar/gkw1099 – volume: 3 start-page: 722 year: 2005 ident: 2020091720050844700_B64 article-title: Mobile genetic elements: the agents of open source evolution publication-title: Nat. Rev. Microbiol. doi: 10.1038/nrmicro1235 – volume: 36 start-page: 996 year: 2018 ident: 2020091720050844700_B11 article-title: A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life publication-title: Nat. Biotechnol. doi: 10.1038/nbt.4229 – volume: 3 start-page: 1057 year: 2018 ident: 2020091720050844700_B52 article-title: Altair: interactive statistical visualizations for Python publication-title: J. Open Source Softw. doi: 10.21105/joss.01057 – volume: 16 start-page: 383 year: 2018 ident: 2020091720050844700_B98 article-title: The social network of microorganisms - how auxotrophies shape complex communities publication-title: Nat. Rev. Microbiol. doi: 10.1038/s41579-018-0004-5 – volume: 176 start-page: 649 year: 2019 ident: 2020091720050844700_B17 article-title: Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle publication-title: Cell doi: 10.1016/j.cell.2019.01.001 – volume: 24 start-page: 1407 year: 2018 ident: 2020091720050844700_B9 article-title: Development of a gut microbe–targeted nonlethal therapeutic to inhibit thrombosis potential publication-title: Nat. Med. doi: 10.1038/s41591-018-0128-1 – volume: 341 start-page: 295 year: 2013 ident: 2020091720050844700_B10 article-title: Predicting and manipulating cardiac drug inactivation by the human gut bacterium Eggerthella lenta publication-title: Science doi: 10.1126/science.1235872 – volume: 2019 start-page: e7359 year: 2019 ident: 2020091720050844700_B59 article-title: MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies publication-title: PeerJ doi: 10.7717/peerj.7359 – volume: 37 start-page: 29 year: 2019 ident: 2020091720050844700_B27 article-title: Minimum information about an uncultivated virus genome (MIUVIG) publication-title: Nat. Biotechnol. doi: 10.1038/nbt.4306 – volume: 3 start-page: 347 year: 2018 ident: 2020091720050844700_B78 article-title: Stability of the human faecal microbiome in a cohort of adult men publication-title: Nat. Microbiol. doi: 10.1038/s41564-017-0096-0 – volume: 4 start-page: e234 year: 2006 ident: 2020091720050844700_B62 article-title: Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts publication-title: PLoS Biol doi: 10.1371/journal.pbio.0040234 – volume: 9 start-page: e00815-18 year: 2018 ident: 2020091720050844700_B71 article-title: Members of the genus methylobacter are inferred to account for the majority of aerobic methane oxidation in oxic soils from a freshwater wetland publication-title: MBio doi: 10.1128/mBio.00815-18 – start-page: 1 volume-title: Methods in Molecular Biology year: 2019 ident: 2020091720050844700_B50 article-title: tRNAscan-SE: searching for tRNA genes in genomic sequences – volume: 8 start-page: 1567 year: 2017 ident: 2020091720050844700_B6 article-title: Methanogenesis in oxygenated soils is a substantial fraction of wetland methane emissions publication-title: Nat. Commun. doi: 10.1038/s41467-017-01753-4 – volume: 578 start-page: 425 year: 2020 ident: 2020091720050844700_B23 article-title: Clades of huge phages from across Earth's ecosystems publication-title: Nature doi: 10.1038/s41586-020-2007-4 – volume: 10 start-page: 2614 year: 2019 ident: 2020091720050844700_B86 article-title: Profiling of protein degraders in cultures of human gut microbiota publication-title: Front. Microbiol. doi: 10.3389/fmicb.2019.02614 – volume: 13 start-page: 2498 year: 2003 ident: 2020091720050844700_B67 article-title: Cytoscape: a software environment for integrated models of biomolecular interaction networks publication-title: Genome Res doi: 10.1101/gr.1239303 – volume: 3 start-page: 870 year: 2018 ident: 2020091720050844700_B14 article-title: Host-linked soil viral ecology along a permafrost thaw gradient publication-title: Nat. Microbiol. doi: 10.1038/s41564-018-0190-y – volume: 28 start-page: 1420 year: 2012 ident: 2020091720050844700_B58 article-title: IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth publication-title: Bioinformatics doi: 10.1093/bioinformatics/bts174 – volume: 29 start-page: 24 year: 2011 ident: 2020091720050844700_B102 article-title: Integrative genomics viewer publication-title: Nat. Biotechnol. doi: 10.1038/nbt.1754 – volume: 111 start-page: E4668 year: 2014 ident: 2020091720050844700_B103 article-title: A nonpyrrolysine member of the widely distributed trimethylamine methyltransferase family is a glycine betaine methyltransferase publication-title: Proc. Natl. Acad. Sci. U.S.A. doi: 10.1073/pnas.1409642111 – volume: 353 start-page: 1272 year: 2016 ident: 2020091720050844700_B29 article-title: Decoupling function and taxonomy in the global ocean microbiome publication-title: Science doi: 10.1126/science.aaf4507 – volume: 36 start-page: 2251 year: 2019 ident: 2020091720050844700_B49 article-title: KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold publication-title: Bioinformatics doi: 10.1093/bioinformatics/btz859 – volume: 30 start-page: 2068 year: 2014 ident: 2020091720050844700_B30 article-title: Prokka: rapid prokaryotic genome annotation publication-title: Bioinformatics doi: 10.1093/bioinformatics/btu153 – volume: 47 start-page: D666 year: 2019 ident: 2020091720050844700_B34 article-title: IMG/M v. 5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes publication-title: Nucleic Acids Res doi: 10.1093/nar/gky901 – volume: 26 start-page: 1608 year: 2010 ident: 2020091720050844700_B101 article-title: PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes publication-title: Bioinformatics doi: 10.1093/bioinformatics/btq249 – volume: 9 start-page: 75 year: 2008 ident: 2020091720050844700_B36 article-title: The RAST server: rapid annotations using subsystems technology publication-title: BMC Genomics doi: 10.1186/1471-2164-9-75 – volume: 35 start-page: 725 year: 2017 ident: 2020091720050844700_B25 article-title: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea publication-title: Nat. Biotechnol. doi: 10.1038/nbt.3893 – volume: 444 start-page: 1027 year: 2006 ident: 2020091720050844700_B91 article-title: An obesity-associated gut microbiome with increased capacity for energy harvest publication-title: Nature doi: 10.1038/nature05414 – volume: 37 start-page: 852 year: 2019 ident: 2020091720050844700_B2 article-title: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 publication-title: Nat. Biotechnol. doi: 10.1038/s41587-019-0209-9 – volume: 15 start-page: 33 year: 2018 ident: 2020091720050844700_B99 article-title: Branched-chain amino acids in health and disease: metabolism, alterations in blood plasma, and as supplements publication-title: Nutr. Metab. (Lond). doi: 10.1186/s12986-018-0271-1 – volume: 4 start-page: 352 year: 2019 ident: 2020091720050844700_B22 article-title: Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing publication-title: Nat. Microbiol. doi: 10.1038/s41564-018-0312-6 – volume: 7 start-page: 198 year: 2018 ident: 2020091720050844700_B87 article-title: Role of gut microbiota-generated short-chain fatty acids in metabolic and cardiovascular health publication-title: Curr. Nutr. Rep. doi: 10.1007/s13668-018-0248-8 – volume: 38 start-page: D227 year: 2010 ident: 2020091720050844700_B43 article-title: MEROPS: the peptidase database publication-title: Nucleic Acids Res doi: 10.1093/nar/gkp971 – volume: 10 start-page: 2702 year: 2016 ident: 2020091720050844700_B74 article-title: RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria publication-title: ISME J doi: 10.1038/ismej.2016.53 – volume: 86 start-page: e00945-17 year: 2018 ident: 2020091720050844700_B92 article-title: Salmonella-mediated inflammation eliminates competitors for fructose-asparagine in the gut publication-title: Infect. Immun. doi: 10.1128/IAI.00945-17 – volume: 109 start-page: 21307 year: 2012 ident: 2020091720050844700_B104 article-title: Microbial conversion of choline to trimethylamine requires a glycyl radical enzyme publication-title: Proc. Natl. Acad. Sci. U.S.A. doi: 10.1073/pnas.1215689109 – volume: 10 start-page: 845 year: 2015 ident: 2020091720050844700_B73 article-title: The Phyre2 web portal for protein modeling, prediction and analysis publication-title: Nat. Protoc. doi: 10.1038/nprot.2015.053 – volume: 14 start-page: 202 year: 2013 ident: 2020091720050844700_B33 article-title: MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-14-202 – volume: 46 start-page: W95 year: 2018 ident: 2020091720050844700_B48 article-title: DbCAN2: A meta server for automated carbohydrate-active enzyme annotation publication-title: Nucleic Acids Res doi: 10.1093/nar/gky418 – volume: 45 start-page: D353 year: 2017 ident: 2020091720050844700_B41 article-title: KEGG: new perspectives on genomes, pathways, diseases and drugs publication-title: Nucleic Acids Res doi: 10.1093/nar/gkw1092 – volume: 10 start-page: 752 year: 2019 ident: 2020091720050844700_B95 article-title: Numerous cultivated and uncultivated viruses encode ribosomal proteins publication-title: Nat. Commun. doi: 10.1038/s41467-019-08672-6 – volume: 34 start-page: 1037 year: 2018 ident: 2020091720050844700_B31 article-title: DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication publication-title: Bioinformatics doi: 10.1093/bioinformatics/btx713 – volume: 20 start-page: 135 year: 2007 ident: 2020091720050844700_B94 article-title: Exploring the vast diversity of marine viruses publication-title: Oceanography doi: 10.5670/oceanog.2007.58 – volume: 3 start-page: 1274 year: 2018 ident: 2020091720050844700_B93 article-title: Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem publication-title: Nat. Microbiol. doi: 10.1038/s41564-018-0225-4 – volume: 39 start-page: W29 year: 2011 ident: 2020091720050844700_B47 article-title: HMMER web server: interactive sequence similarity searching publication-title: Nucleic Acids Res doi: 10.1093/nar/gkr367 – volume: 32 start-page: 5452 year: 2004 ident: 2020091720050844700_B70 article-title: ‘Conserved hypothetical’proteins: prioritization of targets for experimental study publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkh885 – volume: 2 start-page: 16180 year: 2016 ident: 2020091720050844700_B28 article-title: Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes publication-title: Nat. Microbiol. doi: 10.1038/nmicrobiol.2016.180 – volume: 7 start-page: 8292 year: 2017 ident: 2020091720050844700_B96 article-title: PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data publication-title: Sci. Rep. doi: 10.1038/s41598-017-07910-5 – volume: 7 start-page: 13219 year: 2016 ident: 2020091720050844700_B21 article-title: Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system publication-title: Nat. Commun. doi: 10.1038/ncomms13219 – volume: 11 start-page: 2864 year: 2017 ident: 2020091720050844700_B60 article-title: dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication publication-title: ISME J doi: 10.1038/ismej.2017.126 – year: 2018 ident: 2020091720050844700_B57 article-title: BBTools publication-title: BBMap – volume: 342 start-page: 1057 year: 2013 ident: 2020091720050844700_B4 article-title: Genomes from metagenomics publication-title: Science doi: 10.1126/science.1247023 – volume: 428 start-page: 37 year: 2004 ident: 2020091720050844700_B5 article-title: Community structure and metabolism through reconstruction of microbial genomes from the environment publication-title: Nature doi: 10.1038/nature02340 – volume: 35 start-page: W182 year: 2007 ident: 2020091720050844700_B35 article-title: KAAS: an automatic genome annotation and pathway reconstruction server publication-title: Nucleic Acids Res doi: 10.1093/nar/gkm321 – volume: 11 start-page: 19 year: 2016 ident: 2020091720050844700_B75 article-title: A Bayesian inference method for the analysis of transcriptional regulatory networks in metagenomic data publication-title: Algorithms Mol. Biol. doi: 10.1186/s13015-016-0082-8 – volume: 3 start-page: 1441 year: 2018 ident: 2020091720050844700_B97 article-title: Microbial nitrogen limitation in the mammalian large intestine publication-title: Nat. Microbiol. doi: 10.1038/s41564-018-0267-7 – volume: 31 start-page: 161 year: 2016 ident: 2020091720050844700_B38 article-title: Viral metabolic reprogramming in marine ecosystems publication-title: Curr. Opin. Microbiol. doi: 10.1016/j.mib.2016.04.002 – volume: 3 start-page: 91 year: 2011 ident: 2020091720050844700_B72 article-title: A novel family of functional operons encoding methane/ammonia monooxygenase-related proteins in gammaproteobacterial methanotrophs publication-title: Environ. Microbiol. Rep. doi: 10.1111/j.1758-2229.2010.00192.x – volume: 560 start-page: 49 year: 2018 ident: 2020091720050844700_B7 article-title: Genome-centric view of carbon processing in thawing permafrost publication-title: Nature doi: 10.1038/s41586-018-0338-1 – volume: 514 start-page: 478 year: 2014 ident: 2020091720050844700_B8 article-title: Methane dynamics regulated by microbial community response to permafrost thaw publication-title: Nature doi: 10.1038/nature13798 – volume: 37 start-page: 632 year: 2019 ident: 2020091720050844700_B26 article-title: Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks publication-title: Nat. Biotechnol. doi: 10.1038/s41587-019-0100-8 – volume: 25 start-page: 1043 year: 2015 ident: 2020091720050844700_B51 article-title: CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes publication-title: Genome Res doi: 10.1101/gr.186072.114 – volume: 111 start-page: 14 year: 2016 ident: 2020091720050844700_B89 article-title: Role of glutamatergic neurotransmission in the enteric nervous system and brain-gut axis in health and disease publication-title: Neuropharmacology doi: 10.1016/j.neuropharm.2016.08.024 – volume: 337 start-page: 1661 year: 2012 ident: 2020091720050844700_B3 article-title: Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla publication-title: Science doi: 10.1126/science.1224041 – volume: 1854 start-page: 1019 year: 2015 ident: 2020091720050844700_B66 article-title: Enzyme function initiative-enzyme similarity tool (EFI-EST): a web tool for generating protein sequence similarity networks publication-title: Biochim. Biophys. Acta - Proteins Proteomics doi: 10.1016/j.bbapap.2015.04.015 – volume: 577 start-page: 519 year: 2020 ident: 2020091720050844700_B76 article-title: Isolation of an archaeon at the prokaryote–eukaryote interface publication-title: Nature doi: 10.1038/s41586-019-1916-6 – volume: 8 start-page: 209 year: 2007 ident: 2020091720050844700_B68 article-title: CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-8-209 – volume: 25 start-page: 1243 year: 2017 ident: 2020091720050844700_B84 article-title: Bread affects clinical parameters and induces gut microbiome-associated personal glycemic responses publication-title: Cell Metab doi: 10.1016/j.cmet.2017.05.002 – volume: 537 start-page: 689 year: 2016 ident: 2020091720050844700_B15 article-title: Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses publication-title: Nature doi: 10.1038/nature19366 – volume: 438 start-page: 86 year: 2005 ident: 2020091720050844700_B63 article-title: Photosynthesis genes in marine viruses yield proteins during host infection publication-title: Nature doi: 10.1038/nature04111 – start-page: 67 volume-title: Dietary fibers: chemistry and nutrition year: 1979 ident: 2020091720050844700_B80 article-title: Food fiber analysis: advances in methodology doi: 10.1016/B978-0-12-370950-9.50011-9 – volume: 24 start-page: 64 year: 2012 ident: 2020091720050844700_B81 article-title: Pectin–an emerging new bioactive food polysaccharide publication-title: Trends Food Sci. Technol. doi: 10.1016/j.tifs.2011.11.002 – volume: 19 start-page: 2247 year: 1991 ident: 2020091720050844700_B53 article-title: The SWISS-PROT protein sequence data bank publication-title: Nucleic Acids Res doi: 10.1093/nar/19.suppl.2247 – volume: 73 start-page: 29 year: 2015 ident: 2020091720050844700_B82 article-title: Does the consumption of fruits and vegetables differ between Eastern and Western European populations? Systematic review of cross-national studies publication-title: Arch. Public Heal. doi: 10.1186/s13690-015-0078-8 – volume: 25 start-page: 789 year: 2019 ident: 2020091720050844700_B79 article-title: Daily sampling reveals personalized diet-microbiome associations in humans publication-title: Cell Host Microbe doi: 10.1016/j.chom.2019.05.005 – volume: 37 start-page: 953 year: 2019 ident: 2020091720050844700_B20 article-title: Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery publication-title: Nat. Biotechnol. doi: 10.1038/s41587-019-0202-3 – volume: 568 start-page: 505 year: 2019 ident: 2020091720050844700_B16 article-title: New insights from uncultivated genomes of the global human gut microbiome publication-title: Nature doi: 10.1038/s41586-019-1058-x – volume: 36 start-page: 1925 year: 2018 ident: 2020091720050844700_B24 article-title: GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database publication-title: Bioinformatics doi: 10.1093/bioinformatics/btz848 – volume: 35 start-page: 1026 year: 2017 ident: 2020091720050844700_B44 article-title: MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets publication-title: Nat. Biotechnol. doi: 10.1038/nbt.3988 – volume: 10 start-page: e1001377 year: 2012 ident: 2020091720050844700_B55 article-title: The human microbiome project: a community resource for the healthy human microbiome publication-title: PLoS Biol doi: 10.1371/journal.pbio.1001377 – volume: 486 start-page: 207 year: 2012 ident: 2020091720050844700_B56 article-title: Structure, function and diversity of the healthy human microbiome publication-title: Nature doi: 10.1038/nature11234 – volume: 13 start-page: 147 year: 2015 ident: 2020091720050844700_B37 article-title: Rising to the challenge: accelerated pace of discovery transforms marine virology publication-title: Nat. Rev. Microbiol. doi: 10.1038/nrmicro3404
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SubjectTerms	Bacteria - classification BASIC BIOLOGICAL SCIENCES Computational Biology Computational Methods Gastrointestinal Microbiome Genomics - methods Humans Metabolomics - methods Metagenome Molecular Sequence Annotation - methods Software Soil Microbiology Viruses - classification
Title	DRAM for distilling microbial metabolism to automate the curation of microbiome function
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