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Taxonomic and functional assessment using metatranscriptomics reveals the effect of Angus cattle on rumen microbial signatures

Published online by Cambridge University Press:  30 October 2019

A. L. A. Neves ,
Y. Chen ,
K.-A. Lê Cao ,
S. Mandal ,
T. J. Sharpton ,
T. McAllister  and
L. L. Guan Open the ORCID record for L. L. Guan [Opens in a new window]
A. L. A. Neves
Affiliation:
Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, T6G2P5 Alberta, Canada
Y. Chen
Affiliation:
Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, T6G2P5 Alberta, Canada
K.-A. Lê Cao
Affiliation:
Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne, Melbourne, Victoria, 3010, Australia
S. Mandal
Affiliation:
Public Health Foundation of IndiaPlot 47, Sector 44, Gurgaon, 122002, India
T. J. Sharpton
Affiliation:
Departments of Microbiology and Statistics, Oregon State University, Corvallis, OR97331, Oregon, USA
T. McAllister
Affiliation:
Lethbridge Research Center, Agriculture and Agri-Food Canada, Lethbridge, T1J4P4, Alberta, Canada
L. L. Guan*
Affiliation:
Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, T6G2P5 Alberta, Canada
*
†E-mail: [email protected]
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Abstract

A greater understanding of the rumen microbiota and its function may help find new strategies to improve feed efficiency in cattle. This study aimed to investigate whether the cattle breed affects specific ruminal taxonomic microbial groups and functions associated with feed conversion ratio (FCR), using two genetically related Angus breeds as a model. Total RNA was extracted from 24 rumen content samples collected from purebred Black and Red Angus bulls fed the same forage diet and then subjected to metatranscriptomic analysis. Multivariate discriminant analysis (sparse partial least square discriminant analysis (sPLS-DA)) and analysis of composition of microbiomes were conducted to identify microbial signatures characterizing Black and Red Angus cattle. Our analyses revealed relationships among bacterial signatures, host breeds and FCR. Although Black and Red Angus are genetically similar, sPLS-DA detected 25 bacterial species and 10 functions that differentiated the rumen microbial signatures between those two breeds. In Black Angus, we identified bacterial taxa Chitinophaga pinensis, Clostridium stercorarium and microbial functions with large and small subunits ribosomal proteins L16 and S7 exhibiting a higher abundance in the rumen microbiome. In Red Angus, nonetheless, we identified the poorly characterized bacterial taxon Oscillibacter valericigenes with a higher abundance and pathways related to carbohydrate metabolism. Analysis of composition of microbiomes revealed that C. pinensis and C. stercorarium exhibited a higher abundance in Black Angus compared to Red Angus associated with FCR, suggesting that these bacterial species may play a key role in the feed conversion efficiency of forage-fed bulls. This study highlights how the discovery of signatures of bacterial taxa and their functions can be used to harness the full potential of the rumen microbiome in Angus cattle.

Keywords

beef cattlefeed efficiencymicrobiomerumen bacteriarumen microbial functions
Type
Research Article
Information
animal , Volume 14 , Issue 4 , April 2020 , pp. 731 - 744
Copyright
© The Animal Consortium 2019 

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