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Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

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posted on 2023-05-03, 21:12 authored by Rekha Seshadri, Sinead LeahySinead Leahy, Graeme AttwoodGraeme Attwood, Koon Hoong Teh, Suzanne Lambie, Adrian CooksonAdrian Cookson, Rechelle Perry, Gemma Henderson, Bill KellyBill Kelly
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 B12, 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 ∼75% of the genus-level bacterial and archaeal taxa present in the rumen. ** Hungate1000 project collaborators include AgResearch authors. A comprehensive list of authors and affiliations is at the end of the paper.

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This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

Language

  • English

Does this contain Māori information or data?

  • No

Publisher

Springer Nature

Journal title

Nature Biotechnology

ISSN

1087-0156

Citation

Seshadri, R., Leahy, S. C., Attwood, G. T., Teh, K. H., Lambie, S. C., Cookson, A. L., … Kelly, W. J. (2018). Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnology, 36, 359–367. doi:10.1038/nbt.4110

Funder

Ministry of Business Innovation & Employment

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