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ARS Home » Midwest Area » Madison, Wisconsin » U.S. Dairy Forage Research Center » Cell Wall Biology and Utilization Research » Research » Publications at this Location » Publication #352842

Research Project: Investigating Microbial, Digestive, and Animal Factors to Increase Dairy Cow Performance and Nutrient Use Efficiency

Location: Cell Wall Biology and Utilization Research

Title: Buccal swabs as a noninvasive proxy for rumen microbial content

item Emerson, Elianna
item COX, MADISON - University Of Wisconsin
item SUEN, GARRET - University Of Wisconsin
item Bickhart, Derek

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 5/1/2018
Publication Date: N/A
Citation: N/A

Interpretive Summary: The beneficial microbes of the cow rumen contribute directly to dairy milk production; however, it is currently impossible to efficiently identify these microbes in individual cows at large scale. Since cows chew their cud, it is possible to identify rumen microbes by taking DNA samples from the cow's mouth. This represents an inexpensive way to sample rumen microbes from a large herd of cows, and this study is the first to pioneer such a large scale sampling. If successful, the methods pioneered in this study will serve as the basis for the largest sampling of cow rumen microbes ever published.

Technical Abstract: The specific aim of this study was to test the efficacy of buccal (cheek) swabbing as a noninvasive proxy for rumen microbial content of dairy cattle, with the expectation that buccal swabs could become a diagnostic tool for use in the dairy industry. Within this aim, there were two main goals: 1) to optimize buccal sampling methods, processing and analysis and 2) to examine the variance between buccal swabs and rumen samples collected from the same Holstein cows in order to determine how well they correlate in terms of microbial community composition. Following DNA extraction, amplification and pooling, sample DNA was sequenced on an Illumina Miseq and analyzed using Mothur and the Silva 16S rRNA gene reference alignment database. Generation of NMDS and PCoA plots allowed examination of the similarity between microbial communities present on each sample type and from each animal. Preliminary results confirmed that the microbial communities obtained via buccal swabs maintained their individuality, though the samples obtained did not cluster as closely to rumen liquid and solid samples as expected. Following standardization of buccal swab sample collection and processing to minimize the variance between the swabs themselves, we will further assess the correlation between rumen contents and buccal swabs on a population-scale.