The bovine epimural microbiota displays compositional and structural heterogeneity across different ruminal locations

Authors: SBARDELLATI, DINO - University Of Wisconsin; FISCHER, AMELIE - Oak Ridge Institute For Science And Education (ORISE); COX, MADISON - University Of Wisconsin; Li, Wenli; Kalscheur, Kenneth; SUEN, GARRET - University Of Wisconsin

Submitted to: Journal of Dairy Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/16/2019
Publication Date: 4/1/2020
Citation: Sbardellati, D., Fischer, A., Cox, M.S., Li, W., Kalscheur, K., Suen, G. 2020. The bovine epimural microbiota displays compositional and structural heterogeneity across different ruminal locations. Journal of Dairy Science. 103(4):3636–3647. https://doi.org/10.3168/jds.2019-17649.
DOI: https://doi.org/10.3168/jds.2019-17649

Interpretive Summary: The goal of this study was to determine if differences exist in the microbial communities associated with different epithelial locations in the dairy cow rumen. Samples were obtained from the rumens of eight Holstein dairy cows at four different locations and their bacterial microbiotas assessed using 16S rRNA gene sequencing. Given the close association of these microbial communities with the host, understanding the spatial heterogeneity across ruminal location will provide insights into how these microbiotas modulate host health and nutrient provisioning. This research will be of interest to researchers and nutritionists interested in understanding how rumen microbiota may affect health and nutrient utilization by the dairy cow.

Technical Abstract: Dairy cattle are globally important agricultural animals. Central to their biology is the rumen, which houses an essential microbial community, or microbiome, important for providing nutrition to the host from indigestible portions of the diet such as fiber. The rumen environment is noted for its substantial spatial heterogeneity, and the majority of research on the rumen microbiome is focused on the microbiota associated with ruminal solids and liquids. However, a third ruminal microbiota also exists and is associated with the ruminal epithelium, although it is less well understood. This community is thought to serve an important role in modulating epithelial tissue and acts as the interface between the host and the entire rumen microbiome, given its direct contact with the epithelium. Due to challenges in sampling the epithelial community, studies to date have almost exclusively focused on characterizing the epimural microbiota found at a single location: the ventral sac. However, given the substantial morphological, physiological, and functional differences across the geographic spread of the rumen epithelium, we hypothesized that the resident microbiota at different epimural locations are also different. To address this, we characterized the bacterial epimural communities at different sites within eight lactating Holstein dairy cows using 16S rRNA gene sequencing. Four different sites were sampled via rumen tissue biopsy, including the Cranial Sac (CS), the Ventral Sac (VS), the Caudodorsal Blind Sac (CDBS), and the Caudoventral Blind Sac (CVBS). We found that the CDBS community had the highest alpha diversity. Significant differences were observed in the epimural bacterial community structure and composition between locations, with both intra- and inter-animal contributions. All four locations were characterized by high abundances of the phyla Bacteroidetes, Firmicutes, and Proteobacteria. Bacteria within Prevotellaceae, Butyrivibrio, Campylobacter, Mogibacterium, and Desulfobulbus all showed high sequence abundance and differential distributions according to sample location. We also identified a core bacterial microbiota that was found at all locations across all cows. To the best of our knowledge, this work represents the first characterization of the ruminal epimural microbiota across different epithelial locations for any bovine ruminant.