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.

The composition of the perinatal intestinal microbiota in horse

“…The microbiota of the oral vestibular mucosa in horses has also not been previously investigated. In our mares, the phylum-level composition was more similar to human buccal microbiota than to bovine oral microbiota, which is affected by rumination 46,47 . However, Bacteroidetes were less abundant in the horses than in the human.…”

Validating the use of bovine buccal sampling as a proxy for the rumen microbiota using a time course and random forest classification approach

“…In this study we evaluated the ability of the buccal swabbing method to describe bacterial communities found in two types of rumen samples taken at six distinct sampling times over the course of ten hours. Buccal swab samples are an attractive alternative to more labor-intensive methods of sampling the rumen microbial community, but may suffer from bias due to contamination by the surrounding oral community (9, 10). We first sought to identify the effect of sampling time on buccal swab community composition as we hypothesized that animal rumination patterns and salivary flow may change the relative abundance of key members of the rumen community.…”

“…In order to identify non-rumen taxa in buccal swab samples, we employed a machine learning classifier to assist in the filtering of oral and silage microbial communities in buccal swab samples. As has been noted previously (9), the presence of the commensal oral microbial community in buccal swab samples prevents direct comparisons between rumen content samples and buccal swabs and must be filtered from buccal swab samples prior to analysis using manual and mathematical methods (9, 10). By using a random forest classifier, we were able to assign importance estimates to individual microbial taxa based on their use as a feature in our classification models, as has been done previously (46, 47).…”

“…Given the requirements for surgery or labor-intensive sample collection, respectively, neither method is suitable for the development of a scalable industrial product. In light of the deficiencies of these methods, buccal swabbing has been proposed as a proxy for the rumen microbiota (9, 10). The ease of this method, combined with high-throughput sequencing of the 16S rRNA gene and its lower cost of implementation, make it a tantalizing option for obtaining population-scale rumen microbial samples.…”

“…The identification and exclusion of these contaminants constitute a pre-requisite for the use of buccal swabs as proxy for the rumen microbiota (9). In previous studies, the depletion of these contaminants was performed with mathematical filtering based on the comparison of the relative abundances of a given taxa between rumen and buccal swab samples (9, 10). However, these approaches noted the need for further statistical and qualitative validation for wide-spread adoption of the technique due to confounding factors that could impact microbial taxa counts (9).…”