Correlating the oral swab microbial community with milk production metrics in holstein dairy cows

Authors: SKARLUPKA, JOSEPH - University Of Wisconsin; COX, MADISON - University Of Wisconsin; STEINBERGER, ANDREW - University Of Wisconsin; SBARDELLATI, DINO - University Of Wisconsin; McClure, Jennifer; BICKHART, DEREK - Hendrix Genetics; SCHEFTGEN, ANDREW - Obihiro University; ZUNIGA-CHAVES, IBRAHIM - University Of Wisconsin; PAGET, ERIC - University Of Wisconsin; SKADRON, CHARLES - University Of Wisconsin; ATTIPETTY, NITHYA - University Of Wisconsin; SUEN, GARRET - University Of Wisconsin

Submitted to: mSphere
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/15/2025
Publication Date: 4/15/2025
Citation: Skarlupka, J.H., Cox, M.S., Steinberger, A.J., Sbardellati, D.L., Mcclure, J.C., Bickhart, D., Scheftgen, A.J., Zuniga-Chaves, I., Paget, E., Skadron, C., Attipetty, N., Suen, G. 2025. Correlating the oral swab microbial community with milk production metrics in holstein dairy cows. mSphere. https://doi.org/10.1128/msphere.00167-25.
DOI: https://doi.org/10.1128/msphere.00167-25

Interpretive Summary: The rumen microbiome is responsible for the digestion of indigestible fibrous feeds and has been associated with dairy cow milk production efficiency (MPE). Collecting rumen samples from a sufficiently large population of cows has been prohibitive so the strength of the relationship between the rumen microbiome and MPE has been difficult to assess. In this study, we evaluated whether the use of oral swabs as a proxy for direct rumen sampling would allow researchers to collect many samples from different dairy cows in a non-invasive manner and to relate these results to performance and MPE. Oral samples were collected from 226 Holstein dairy cows and used to characterize the ruminal bacterial community. Our study demonstrates the utility of using oral swabs at a large scale as a proxy for characterizing the ruminal microbiome and further recapitulates many of the known associations with MPE previously determined using more traditional sampling methods. These results will be valuable to dairy farmers and their advisors and researchers to guide management decisions and research areas based on the ruminal microbial community.

Technical Abstract: A long-standing goal of the dairy industry is to improve milk production efficiency (MPE). Approaches to achieve increased efficiency include genetic selection and diet. More recently, it has been shown that the ruminal microbiome, which is largely responsible for digesting feed, is strongly linked to MPE, and alterations to this microbial community can potentially improve MPE. Integration of the ruminal microbiome into strategies for improving MPE are hindered by the difficulty in directly sampling the rumen at a large scale, given that proxies such as fecal sampling are not representative of the ruminal microbiota. It has been noted that obtaining the large number of samples required for relating the ruminal microbiome to MPE and/or host genetics is difficult, as the more traditional approaches such as direct sampling via a cannula or stomach tubing are infeasible and laborious. Our group, and others, have pioneered the use of oral swabs as a proxy for direct ruminal sampling, and this approach can identify the presence of up to 70% of the rumen microbial community. Here we further extend the utility of this approach by sampling over 226 dairy cows on a research farm in Wisconsin, USA. These samples were subjected to next-generation sequencing of the V4 region of the 16S rRNA gene to characterize the bacterial community. We then correlated these data with average milk yield and days in milk, two phenotypes known to be associated with differences in the ruminal microbiome. We then obtained MPE data for a subset of these animals which comprised Gross Feed Efficiency (GFE) and Residual Feed Intake (RFI) for each individual, and further correlated these metrics against their associated microbial data. We found that when using the oral swabs, we could identify correlations between bacterial genera and days in milk (p < 0.05). We further show that the ruminal microbiota was associated with average milk yield and days in milk for animals in their first lactation. Differential abundance testing identified amplicon sequence variants (ASVs) associated with these two metrics. Our comparison of bacterial communities between high and low efficiency groups, as determined by GFE and RFI, identified a significant difference in Shannon’s diversity in second lactation cows (p < 0.05). We also found RFI was significantly correlated with the structure of the bacterial community in second lactation animals (p < 0.05). Differential abundance analysis again identified multiple oral- and rumen-associated ASVs correlated with GFE and RFI. Our study demonstrates the utility of using oral swabs at a large scale as a proxy for characterizing the ruminal microbiome and further recapitulates many of the known associations with MPE previously determined using more traditional sampling methods.