A Grain-Based SARA Challenge Affects the Composition of Epimural and Mucosa-Associated Bacterial Communities throughout the Digestive Tract of Dairy Cows

SIMPLE SUMMARY: High-yielding dairy cows must receive high-grain diets in order to meet their high energy requirements. However, these diets depress the pH in the rumen, leading to a condition referred to as subacute ruminal acidosis (SARA), and in the large intestine, and may negatively affect the taxonomic composition and the functionality of the populations of microorganisms in the digestive tract. As cows depend on these microorganisms for nutrient utilization and health, disruptions of their composition and functionality can greatly affect the production, health, and welfare of dairy cows. In our study, SARA was induced experimentally by excessive grain feeding. The taxonomic composition of bacterial populations attached to the epithelia of the digestive tract were determined throughout this tract. Our results show that SARA affected the populations of several taxa of bacteria, which suggests that the beneficial effects of these bacteria may be reduced, and that the digestive tract may be at increased risk of invasion by pathogenic microorganisms. The greatest effects of SARA on the taxonomic composition of bacteria on epithelia were in the rumen and large intestine. Their composition on epithelia in the small intestine was also affected, but the affected groups of bacteria differed from those in the rumen and large intestine. ABSTRACT: The effects of a subacute ruminal acidosis (SARA) challenge on the composition of epimural and mucosa-associated bacterial communities throughout the digestive tract were determined in eight non-lactating Holstein cows. Treatments included feeding a control diet containing 19.6% dry matter (DM) starch and a SARA-challenge diet containing 33.3% DM starch for two days after a 4-day grain step-up. Subsequently, epithelial samples from the rumen and mucosa samples from the duodenum, proximal, middle and distal jejunum, ileum, cecum and colon were collected. Extracted DNA from these samples were analyzed using MiSeq Illumina sequencing of the V4 region of the 16S rRNA gene. Distinct clustering patterns for each diet existed for all sites. The SARA challenge decreased microbial diversity at all sites, with the exception of the middle jejunum. The SARA challenge also affected the relative abundances of several major phyla and genera at all sites but the magnitude of these effects differed among sites. In the rumen and colon, the largest effects were an increase in the relative abundance of Firmicutes and a reduction of Bacteroidetes. In the small intestine, the largest effect was an increase in the relative abundance of Actinobacteria. The grain-based SARA challenge conducted in this study did not only affect the composition and cause dysbiosis of epimural microbiota in the rumen, it also affected the mucosa-associated microbiota in the intestines. To assess the extent of this dysbiosis, its effects on the functionality of these microbiota must be determined in future.