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Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

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Seshadri, R., Leahy, S. C., Attwood, G. T., Teh, K. H., Lambie, S. C., Cookson, A. L., Eloe-Fadrosh, E. A., Pavlopoulos, G. A., Hadjithomas, M., Varghese, N. J., Paez-Espino, D., Perry, R., Henderson, G., Creevey, C. J., Terrapon, N., Lapebie, P., Drula, E., Lombard, V., Rubin, E., Kyrpides, N. C., Henrissat, B., Woyke, T., Ivanova, N. N., Kelly, W. J., Palevic, N., Janssen, P. H., Ronimus, R. S., Noel, S., Soni, P., Reilly, K., Atherly, T., Ziemer, C., Wright, A., Ishaq, S., Cotta, S., Thompson, S., Crosley, K., McKain, S., Wallace, R. J., Flint, H. J., Martin, J. C., Forster, R. J., Gruninger, R. J., McAllister, T., Gilbert, R. A., Ouwerkerk, D., Klieve, A., Jassim, R. A., Denman, S., McSweeney, C., Rosewarne, S., Koike, S., Kobayashi, Y., Mitsumori, M., Shinkai, T., Cravero, S. and Cerón Cucchi, T. (2018) Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnology, 36 (4). pp. 359-367.


Article Link: https://doi.org/10.1038/nbt.4110


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. © 2018 Nature Publishing Group. All rights reserved.

Item Type:Article
Business groups:Animal Science
Keywords:Agriculture Biosynthesis Gene encoding Greenhouse gases Mammals Cultured bacteria De novo synthesis Environmental stress Greenhouse gas production Human microbiome Plant polysaccharides Polysaccharide degradation Short-chain fatty acids Fatty acids cyanocobalamin genomic DNA polysaccharide RNA 16S short chain fatty acid biofuel lignin lignocellulose Alistipes bacterium culture Bacteroides Bacteroides thetaiotaomicron Bacteroidetes Butyrivibrio Clostridiales clustered regularly interspaced short palindromic repeat comparative study controlled study CRISPR Cas system fermentation gene cluster gene loss gene sequence genome size in vitro study intestine flora Lachnospiraceae metabolism metagenomics methanogenesis microbiome nonhuman phylogeny Prevotella priority journal Review Rikenellaceae rumen microorganism Ruminococcaceae Ruminococcus animal archaeon bacterium chemistry classification genetics human microbiology microflora rumen Animals Archaea Bacteria Biofuels Gastrointestinal Microbiome Humans Microbiota
Subjects:Science > Biology > Genetics
Science > Biology > Ecology
Science > Microbiology
Science > Microbiology > Microbial ecology
Science > Microbiology > Microorganisms in the animal body
Live Archive:12 Jul 2021 00:33
Last Modified:03 Sep 2021 16:46

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