A Genomic Catalogue of Earth’s Microbiomes - Introductory KBase Narrative

Nayfach, Stephen; Roux, Simon; Seshadri, Rekha; Udwary, Daniel; Varghese, Neha; Schulz, Frederik; Wu, Dongying; Paez-Espino, David; Chen, I-Min; Huntemann, Marcel; Palaniappan, Krishna; Ladau, Joshua; Mukherjee, Supratim; Reddy, T.B.K.; Nielsen, Torben; Kirton, Edward; P. Faria, José; N. Edirisinghe, Janaka; S. Henry, Christopher; P. Jungbluth, Sean; Chivian, Dylan; Dehal, Paramvir; M. Wood-Charlson, Elisha; P. Arkin, Adam; Tringe, Susannah; Visel, Axel; Woyke, Tanja; J. Mouncey, Nigel; N. Ivanova, Natalia; C. Kyrpides, Nikos; Eloe-Fadrosh, Emiley A.

doi:10.25982/53247.64/1670777

Title: A Genomic Catalogue of Earth’s Microbiomes - Introductory KBase Narrative

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Abstract

The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled unprecedented insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this powerful approach to over 10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, human- and animal-host associated microbiomes, engineered environments, and natural and agricultural soils to capture extant microbial metabolic and functional potential. We present a comprehensive catalogue of 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units (OTUs), spanning 135 phyla, which expand the known phylogenetic diversity of Bacteria and Archaea by 44%. We also demonstrate the utility of this collection for secondary metabolite biosynthetic potential and predicting host-virus linkage, which can provide a view into the global distribution of lysogenic viruses. This resource underscores the value of leveraging genome-centric approaches to reveal genomic properties of uncultivated microbes that impact on ecosystem processes.

Authors:

Nayfach, Stephen; Roux, Simon; Seshadri, Rekha;

; Varghese, Neha;

; Wu, Dongying;

;

; Palaniappan, Krishna; Ladau, Joshua;

;

; Nielsen, Torben; Kirton, Edward;

;

USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
Argonne National Lab. (ANL), Argonne, IL (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

Publication Date:: 2020-01-01

Research Org.:: U.S. Department of Energy Joint Genome Institute (JGI) U.S. Department of Energy Systems Biology Knowledgebase

Sponsoring Org.:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Subject:: 59 BASIC BIOLOGICAL SCIENCES

Keywords:: MAGs, metagenome-assembled genomes, metagenomics, metabolic reconstruction, metabolic modeling

OSTI Identifier:: 1670777

DOI:: https://doi.org/10.25982/53247.64/1670777

Citation Formats


                    Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I-Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, T.B.K., Nielsen, Torben, Kirton, Edward, P. Faria, José, N. Edirisinghe, Janaka, S. Henry, Christopher, P. Jungbluth, Sean, Chivian, Dylan, Dehal, Paramvir, M. Wood-Charlson, Elisha, P. Arkin, Adam, Tringe, Susannah, Visel, Axel, Woyke, Tanja, J. Mouncey, Nigel, N. Ivanova, Natalia, C. Kyrpides, Nikos, and Eloe-Fadrosh, Emiley A. A Genomic Catalogue of Earth’s Microbiomes - Introductory KBase Narrative.  United States: N. p., 2020. 
        Web.  doi:10.25982/53247.64/1670777.

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                    Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I-Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, T.B.K., Nielsen, Torben, Kirton, Edward, P. Faria, José, N. Edirisinghe, Janaka, S. Henry, Christopher, P. Jungbluth, Sean, Chivian, Dylan, Dehal, Paramvir, M. Wood-Charlson, Elisha, P. Arkin, Adam, Tringe, Susannah, Visel, Axel, Woyke, Tanja, J. Mouncey, Nigel, N. Ivanova, Natalia, C. Kyrpides, Nikos, & Eloe-Fadrosh, Emiley A. A Genomic Catalogue of Earth’s Microbiomes - Introductory KBase Narrative.  United States.  doi:https://doi.org/10.25982/53247.64/1670777

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                    Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I-Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, T.B.K., Nielsen, Torben, Kirton, Edward, P. Faria, José, N. Edirisinghe, Janaka, S. Henry, Christopher, P. Jungbluth, Sean, Chivian, Dylan, Dehal, Paramvir, M. Wood-Charlson, Elisha, P. Arkin, Adam, Tringe, Susannah, Visel, Axel, Woyke, Tanja, J. Mouncey, Nigel, N. Ivanova, Natalia, C. Kyrpides, Nikos, and Eloe-Fadrosh, Emiley A. 2020.  
"A Genomic Catalogue of Earth’s Microbiomes - Introductory KBase Narrative".  United States.  doi:https://doi.org/10.25982/53247.64/1670777.  https://www.osti.gov/servlets/purl/1670777. Pub date:Wed Jan 01 00:00:00 EST 2020

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@article{osti_1670777,

  title        = {A Genomic Catalogue of Earth’s Microbiomes - Introductory KBase Narrative},

  author       = {Nayfach, Stephen and Roux, Simon and Seshadri, Rekha and Udwary, Daniel and Varghese, Neha and Schulz, Frederik and Wu, Dongying and Paez-Espino, David and Chen, I-Min and Huntemann, Marcel and Palaniappan, Krishna and Ladau, Joshua and Mukherjee, Supratim and Reddy, T.B.K. and Nielsen, Torben and Kirton, Edward and P. Faria, José and N. Edirisinghe, Janaka and S. Henry, Christopher and P. Jungbluth, Sean and Chivian, Dylan and Dehal, Paramvir and M. Wood-Charlson, Elisha and P. Arkin, Adam and Tringe, Susannah and Visel, Axel and Woyke, Tanja and J. Mouncey, Nigel and N. Ivanova, Natalia and C. Kyrpides, Nikos and Eloe-Fadrosh, Emiley A.},

  abstractNote = {The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled unprecedented insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this powerful approach to over 10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, human- and animal-host associated microbiomes, engineered environments, and natural and agricultural soils to capture extant microbial metabolic and functional potential. We present a comprehensive catalogue of 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units (OTUs), spanning 135 phyla, which expand the known phylogenetic diversity of Bacteria and Archaea by 44%. We also demonstrate the utility of this collection for secondary metabolite biosynthetic potential and predicting host-virus linkage, which can provide a view into the global distribution of lysogenic viruses. This resource underscores the value of leveraging genome-centric approaches to reveal genomic properties of uncultivated microbes that impact on ecosystem processes.},

  doi          = {10.25982/53247.64/1670777},

  journal      = {},

  number       = ,

  volume       = ,

  place        = {United States},

  year         = {2020},

  month        = {1}

}

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DOI: https://doi.org/10.25982/53247.64/1670777

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