Oral Samples as Non-Invasive Proxies for Assessing the Composition of the Rumen Microbial Community

Ilma Tapio, Kevin J. Shingfield, Nest McKain, Aurélie Bonin, Daniel Fischer, Ali R. Bayat, Johanna Vilkki, Pierre Taberlet, Timothy J. Snelling, R. John Wallace

Research output: Contribution to journalArticle

16 Citations (Scopus)
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Abstract

Microbial community analysis was carried out on ruminal digesta obtained directly via rumen fistula and buccal fluid, regurgitated digesta (bolus) and faeces of dairy cattle to assess if non-invasive samples could be used as proxies for ruminal digesta. Samples were collected from five cows receiving grass silage based diets containing no additional lipid or four different lipid supplements in a 5 x 5 Latin square design. Extracted DNA was analysed by qPCR and by sequencing 16S and 18S rRNA genes or the fungal ITS1 amplicons. Faeces contained few protozoa, and bacterial, fungal and archaeal communities were substantially different to ruminal digesta. Buccal and bolus samples gave much more similar profiles to ruminal digesta, although fewer archaea were detected in buccal and bolus samples. Bolus samples overall were most similar to ruminal samples. The differences between both buccal and bolus samples and ruminal digesta were consistent across all treatments. It can be concluded that either proxy sample type could be used as a predictor of the rumen microbial community, thereby enabling more convenient large-scale animal sampling for phenotyping and possible use in future animal breeding programs aimed at selecting cattle with a lower environmental footprint.

Original languageEnglish
Article numbere0151220
Pages (from-to)1-15
Number of pages15
JournalPloS ONE
Volume11
Issue number3
DOIs
Publication statusPublished - 17 Mar 2016

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Cheek
Rumen
Proxy
microbial communities
mouth
rumen
Animals
Protozoa
digesta
Lipids
Dairies
Nutrition
Chemical analysis
Feces
Genes
Sampling
sampling
Silage
Fluids
DNA

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Tapio, I., Shingfield, K. J., McKain, N., Bonin, A., Fischer, D., Bayat, A. R., ... Wallace, R. J. (2016). Oral Samples as Non-Invasive Proxies for Assessing the Composition of the Rumen Microbial Community. PloS ONE, 11(3), 1-15. [e0151220]. https://doi.org/10.1371/journal.pone.0151220

Oral Samples as Non-Invasive Proxies for Assessing the Composition of the Rumen Microbial Community. / Tapio, Ilma; Shingfield, Kevin J.; McKain, Nest; Bonin, Aurélie; Fischer, Daniel; Bayat, Ali R.; Vilkki, Johanna; Taberlet, Pierre; Snelling, Timothy J.; Wallace, R. John.

In: PloS ONE, Vol. 11, No. 3, e0151220, 17.03.2016, p. 1-15.

Research output: Contribution to journalArticle

Tapio, I, Shingfield, KJ, McKain, N, Bonin, A, Fischer, D, Bayat, AR, Vilkki, J, Taberlet, P, Snelling, TJ & Wallace, RJ 2016, 'Oral Samples as Non-Invasive Proxies for Assessing the Composition of the Rumen Microbial Community', PloS ONE, vol. 11, no. 3, e0151220, pp. 1-15. https://doi.org/10.1371/journal.pone.0151220
Tapio I, Shingfield KJ, McKain N, Bonin A, Fischer D, Bayat AR et al. Oral Samples as Non-Invasive Proxies for Assessing the Composition of the Rumen Microbial Community. PloS ONE. 2016 Mar 17;11(3):1-15. e0151220. https://doi.org/10.1371/journal.pone.0151220
Tapio, Ilma ; Shingfield, Kevin J. ; McKain, Nest ; Bonin, Aurélie ; Fischer, Daniel ; Bayat, Ali R. ; Vilkki, Johanna ; Taberlet, Pierre ; Snelling, Timothy J. ; Wallace, R. John. / Oral Samples as Non-Invasive Proxies for Assessing the Composition of the Rumen Microbial Community. In: PloS ONE. 2016 ; Vol. 11, No. 3. pp. 1-15.
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