title: Oral Samples as Non-Invasive Proxies for Assessing the Composition of the Rumen Microbial Community.
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.
authors.affiliation: Green Technology, Natural Resources Institute Finland, Jokioinen, Finland.
authors.forename: Ilma
authors.initials: I
authors.lastname: Tapio
authors.affiliation: Green Technology, Natural Resources Institute Finland, Jokioinen, Finland.
authors.forename: Kevin J
authors.initials: KJ
authors.lastname: Shingfield
authors.affiliation: Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom.
authors.forename: Nest
authors.initials: N
authors.lastname: McKain
authors.affiliation: Laboratoire d'Ecologie Alpine, CNRS, Grenoble, France.
authors.forename: Aurélie
authors.initials: A
authors.lastname: Bonin
authors.affiliation: Green Technology, Natural Resources Institute Finland, Jokioinen, Finland.
authors.forename: Daniel
authors.initials: D
authors.lastname: Fischer
authors.affiliation: Green Technology, Natural Resources Institute Finland, Jokioinen, Finland.
authors.forename: Ali R
authors.initials: AR
authors.lastname: Bayat
authors.affiliation: Green Technology, Natural Resources Institute Finland, Jokioinen, Finland.
authors.forename: Johanna
authors.initials: J
authors.lastname: Vilkki
authors.affiliation: Laboratoire d'Ecologie Alpine, CNRS, Grenoble, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Taberlet
authors.affiliation: Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom.
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Snelling
authors.affiliation: Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom.
authors.forename: R John
authors.initials: RJ
authors.lastname: Wallace
mesh_terms: D056893:Alveolata / Q000235:genetics / Q000302:isolation & purification*; D000824:Animal Nutritional Physiological Phenomena; D000818:Animals; D001105:Archaea / Q000235:genetics / Q000302:isolation & purification*; D001419:Bacteria / Q000235:genetics / Q000302:isolation & purification*; D002417:Cattle / Q000382:microbiology* / Q000502:physiology; D004032:Diet / Q000662:veterinary; D019587:Dietary Supplements / Q000032:analysis; D005243:Feces / Q000382:microbiology; D005260:Female; D005658:Fungi / Q000235:genetics / Q000302:isolation & purification*; D009055:Mouth / Q000382:microbiology*; D006109:Poaceae / Q000737:chemistry; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012337:RNA, Ribosomal, 18S / Q000235:genetics; D012417:Rumen / Q000382:microbiology*; D012820:Silage / Q000032:analysis
chemical_list: D012336:RNA, Ribosomal, 16S; D012337:RNA, Ribosomal, 18S