Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

Rekha Seshadri, Sinead C. Leahy, Graeme T. Attwood, Koon Hoong Teh, Suzanne C. Lambie, Adrian L. Cookson, Emiley A. Eloe-Fadrosh, Georgios A. Pavlopoulos, Michalis Hadjithomas, Neha J. Varghese, David Paez-Espino, Rechelle Perry, Gemma Henderson, Christopher J. Creevey, Nicolas Terrapon, Pascal Lapebie, Elodie Drula, Vincent Lombard, Edward Rubin, Nikos C. Kyrpides & 31 others Bernard Henrissat, Tanja Woyke, Natalia N. Ivanova, William J. Kelly*, Nikola Palevic, Peter H. Janssen, Ron S. Ronimus, Samantha Noel, Priya Soni, Kerri Reilly, Todd Atherly, Cherie Ziemer, Andre Denis Wright, Suzanne Ishaq, Michael Cotta, Stephanie Thompson, Katie Crosley, Nest McKain, R John Wallace, Harry J. Flint, Jennifer C. Martin, Robert J. Forster, Robert J. Gruninger, Tim McAllister, Rosalind Gilbert, Diane J. Ouwerkerk, Rosalind Gilbert, Diane J. Ouwerkerk, Athol J. Klieve, Rafat Al Jassim, Hungate1000 project collaborators

*Corresponding author for this work

Research output: Contribution to journalReview article

39 Citations (Scopus)
6 Downloads (Pure)

Abstract

Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B 12, ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. We estimate that our Hungate genome resource represents â 1/475% of the genus-level bacterial and archaeal taxa present in the rumen.

Original languageEnglish
Pages (from-to)359-367
Number of pages9
JournalNature Biotechnology
Volume36
Issue number4
DOIs
Publication statusPublished - 19 Mar 2018

Fingerprint

Microbiota
Rumen
Genes
Polysaccharides
Gene encoding
Biofuels
Volatile Fatty Acids
Vitamins
Vitamin B 12
Fatty acids
Greenhouse gases
Ruminants
Farms
Nutrients
Bacteria
Productivity
Degradation
Genome
Metagenomics
Archaea

ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering
  • Applied Microbiology and Biotechnology
  • Molecular Medicine
  • Biomedical Engineering

Cite this

Seshadri, R., Leahy, S. C., Attwood, G. T., Teh, K. H., Lambie, S. C., Cookson, A. L., ... Hungate1000 project collaborators (2018). Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnology, 36(4), 359-367. https://doi.org/10.1038/nbt.4110

Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. / Seshadri, Rekha; Leahy, Sinead C.; Attwood, Graeme T.; Teh, Koon Hoong; Lambie, Suzanne C.; Cookson, Adrian L.; Eloe-Fadrosh, Emiley A.; Pavlopoulos, Georgios A.; Hadjithomas, Michalis; Varghese, Neha J.; Paez-Espino, David; Perry, Rechelle; Henderson, Gemma; Creevey, Christopher J.; Terrapon, Nicolas; Lapebie, Pascal; Drula, Elodie; Lombard, Vincent; Rubin, Edward; Kyrpides, Nikos C.; Henrissat, Bernard; Woyke, Tanja; Ivanova, Natalia N.; Kelly, William J.; Palevic, Nikola; Janssen, Peter H.; Ronimus, Ron S.; Noel, Samantha; Soni, Priya; Reilly, Kerri; Atherly, Todd; Ziemer, Cherie; Wright, Andre Denis; Ishaq, Suzanne; Cotta, Michael; Thompson, Stephanie; Crosley, Katie; McKain, Nest; Wallace, R John; Flint, Harry J.; Martin, Jennifer C.; Forster, Robert J.; Gruninger, Robert J.; McAllister, Tim; Gilbert, Rosalind; Ouwerkerk, Diane J.; Gilbert, Rosalind; Ouwerkerk, Diane J.; Klieve, Athol J.; Jassim, Rafat Al; Hungate1000 project collaborators.

In: Nature Biotechnology, Vol. 36, No. 4, 19.03.2018, p. 359-367.

Research output: Contribution to journalReview article

Seshadri, R, Leahy, SC, Attwood, GT, Teh, KH, Lambie, SC, Cookson, AL, Eloe-Fadrosh, EA, Pavlopoulos, GA, Hadjithomas, M, Varghese, NJ, Paez-Espino, D, Perry, R, Henderson, G, Creevey, CJ, Terrapon, N, Lapebie, P, Drula, E, Lombard, V, Rubin, E, Kyrpides, NC, Henrissat, B, Woyke, T, Ivanova, NN, Kelly, WJ, Palevic, N, Janssen, PH, Ronimus, RS, Noel, S, Soni, P, Reilly, K, Atherly, T, Ziemer, C, Wright, AD, Ishaq, S, Cotta, M, Thompson, S, Crosley, K, McKain, N, Wallace, RJ, Flint, HJ, Martin, JC, Forster, RJ, Gruninger, RJ, McAllister, T, Gilbert, R, Ouwerkerk, DJ, Gilbert, R, Ouwerkerk, DJ, Klieve, AJ, Jassim, RA & Hungate1000 project collaborators 2018, 'Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection', Nature Biotechnology, vol. 36, no. 4, pp. 359-367. https://doi.org/10.1038/nbt.4110
Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL et al. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnology. 2018 Mar 19;36(4):359-367. https://doi.org/10.1038/nbt.4110
Seshadri, Rekha ; Leahy, Sinead C. ; Attwood, Graeme T. ; Teh, Koon Hoong ; Lambie, Suzanne C. ; Cookson, Adrian L. ; Eloe-Fadrosh, Emiley A. ; Pavlopoulos, Georgios A. ; Hadjithomas, Michalis ; Varghese, Neha J. ; Paez-Espino, David ; Perry, Rechelle ; Henderson, Gemma ; Creevey, Christopher J. ; Terrapon, Nicolas ; Lapebie, Pascal ; Drula, Elodie ; Lombard, Vincent ; Rubin, Edward ; Kyrpides, Nikos C. ; Henrissat, Bernard ; Woyke, Tanja ; Ivanova, Natalia N. ; Kelly, William J. ; Palevic, Nikola ; Janssen, Peter H. ; Ronimus, Ron S. ; Noel, Samantha ; Soni, Priya ; Reilly, Kerri ; Atherly, Todd ; Ziemer, Cherie ; Wright, Andre Denis ; Ishaq, Suzanne ; Cotta, Michael ; Thompson, Stephanie ; Crosley, Katie ; McKain, Nest ; Wallace, R John ; Flint, Harry J. ; Martin, Jennifer C. ; Forster, Robert J. ; Gruninger, Robert J. ; McAllister, Tim ; Gilbert, Rosalind ; Ouwerkerk, Diane J. ; Gilbert, Rosalind ; Ouwerkerk, Diane J. ; Klieve, Athol J. ; Jassim, Rafat Al ; Hungate1000 project collaborators. / Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. In: Nature Biotechnology. 2018 ; Vol. 36, No. 4. pp. 359-367.
@article{f861c75c21e2489fa4a8245316ddeefd,
title = "Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection",
abstract = "Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B 12, ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. We estimate that our Hungate genome resource represents {\^a} 1/475{\%} of the genus-level bacterial and archaeal taxa present in the rumen.",
author = "Rekha Seshadri and Leahy, {Sinead C.} and Attwood, {Graeme T.} and Teh, {Koon Hoong} and Lambie, {Suzanne C.} and Cookson, {Adrian L.} and Eloe-Fadrosh, {Emiley A.} and Pavlopoulos, {Georgios A.} and Michalis Hadjithomas and Varghese, {Neha J.} and David Paez-Espino and Rechelle Perry and Gemma Henderson and Creevey, {Christopher J.} and Nicolas Terrapon and Pascal Lapebie and Elodie Drula and Vincent Lombard and Edward Rubin and Kyrpides, {Nikos C.} and Bernard Henrissat and Tanja Woyke and Ivanova, {Natalia N.} and Kelly, {William J.} and Nikola Palevic and Janssen, {Peter H.} and Ronimus, {Ron S.} and Samantha Noel and Priya Soni and Kerri Reilly and Todd Atherly and Cherie Ziemer and Wright, {Andre Denis} and Suzanne Ishaq and Michael Cotta and Stephanie Thompson and Katie Crosley and Nest McKain and Wallace, {R John} and Flint, {Harry J.} and Martin, {Jennifer C.} and Forster, {Robert J.} and Gruninger, {Robert J.} and Tim McAllister and Rosalind Gilbert and Ouwerkerk, {Diane J.} and Rosalind Gilbert and Ouwerkerk, {Diane J.} and Klieve, {Athol J.} and Jassim, {Rafat Al} and {Hungate1000 project collaborators}",
year = "2018",
month = "3",
day = "19",
doi = "10.1038/nbt.4110",
language = "English",
volume = "36",
pages = "359--367",
journal = "Nature Biotechnology",
issn = "1087-0156",
publisher = "Nature Publishing Group",
number = "4",

}

TY - JOUR

T1 - Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

AU - Seshadri, Rekha

AU - Leahy, Sinead C.

AU - Attwood, Graeme T.

AU - Teh, Koon Hoong

AU - Lambie, Suzanne C.

AU - Cookson, Adrian L.

AU - Eloe-Fadrosh, Emiley A.

AU - Pavlopoulos, Georgios A.

AU - Hadjithomas, Michalis

AU - Varghese, Neha J.

AU - Paez-Espino, David

AU - Perry, Rechelle

AU - Henderson, Gemma

AU - Creevey, Christopher J.

AU - Terrapon, Nicolas

AU - Lapebie, Pascal

AU - Drula, Elodie

AU - Lombard, Vincent

AU - Rubin, Edward

AU - Kyrpides, Nikos C.

AU - Henrissat, Bernard

AU - Woyke, Tanja

AU - Ivanova, Natalia N.

AU - Kelly, William J.

AU - Palevic, Nikola

AU - Janssen, Peter H.

AU - Ronimus, Ron S.

AU - Noel, Samantha

AU - Soni, Priya

AU - Reilly, Kerri

AU - Atherly, Todd

AU - Ziemer, Cherie

AU - Wright, Andre Denis

AU - Ishaq, Suzanne

AU - Cotta, Michael

AU - Thompson, Stephanie

AU - Crosley, Katie

AU - McKain, Nest

AU - Wallace, R John

AU - Flint, Harry J.

AU - Martin, Jennifer C.

AU - Forster, Robert J.

AU - Gruninger, Robert J.

AU - McAllister, Tim

AU - Gilbert, Rosalind

AU - Ouwerkerk, Diane J.

AU - Gilbert, Rosalind

AU - Ouwerkerk, Diane J.

AU - Klieve, Athol J.

AU - Jassim, Rafat Al

AU - Hungate1000 project collaborators

PY - 2018/3/19

Y1 - 2018/3/19

N2 - Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B 12, ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. We estimate that our Hungate genome resource represents â 1/475% of the genus-level bacterial and archaeal taxa present in the rumen.

AB - Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B 12, ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. We estimate that our Hungate genome resource represents â 1/475% of the genus-level bacterial and archaeal taxa present in the rumen.

UR - http://www.scopus.com/inward/record.url?scp=85045079802&partnerID=8YFLogxK

U2 - 10.1038/nbt.4110

DO - 10.1038/nbt.4110

M3 - Review article

VL - 36

SP - 359

EP - 367

JO - Nature Biotechnology

JF - Nature Biotechnology

SN - 1087-0156

IS - 4

ER -