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.
Highlights
Ruminant livestock production has a large environmental footprint because of emissions of the greenhouse gas, methane, and to high nitrogenous emissions in urine and faeces [1]
Treatments comprised total mixed rations based on grass silage (forage: concentrate ratio 60:40 on a dry matter (DM) basis) containing no additional fat (CO) or 50 g/kg diet DM of methyl esters of myristic acid (MA), rapeseed oil (RO), safflower oil (SO) or linseed oil (LO)
Treatments comprised total mixed rations based on grass silage containing no additional fat (CO) or supplemented with methyl myristate (MA), rapeseed oil (RO), safflower oil (SO) or linseed oil (LO)
Summary
Ruminant livestock production has a large environmental footprint because of emissions of the greenhouse gas, methane, and to high nitrogenous emissions in urine and faeces [1]. The primary source of these emissions is rumen microbial metabolism [2]. Understanding the ruminal microbiota is a vital prerequisite for improving the environmental credentials of meat and milk production. The introduction of high-throughput sequencing techniques has opened new ways to explore complex microbial ecosystems, including the rumen [3,4,5,6]. Sampling ruminal digesta is essential to enable the technology benefits to be realized.
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
