Elucidating the separate and synergistic impacts of ruminal and hindgut acidosis on fermentation and microbiome of dairy cows.

The aim of this study was to evaluate the short-term effects of both SARA and hindgut acidosis (HGA) on the ruminal and fecal fermentation and microbiome of dairy cows. The study was conducted as a changeover design using 9 rumen-cannulated Holstein cows (724 ± 79 kg BW and 198 ± 74 DIM). The SARA was induced by feeding a diet containing 65% concentrate (DM basis), and HGA was induced through daily abomasal infusion of 3 kg of starch (1:1 corn-to-wheat weight ratio). The evaluated treatments were (1) a control diet containing 40% concentrate (CON), (2) CON+HGA, (3) a diet containing 65% concentrate (SARA), and (4) SARA+HGA. Ruminal pH was measured every 15 min, and the fecal pH was measured 3 times per day (0, 6, and 12 h relative to feeding). Ruminal and fecal samples were collected in the morning before first feeding and were analyzed for microbiome through 16S rRNA gene amplicon sequencing. Additionally, rumen and fecal samples were taken at 0, 6, and 12 h relative to feeding and were analyzed for VFA and lactate to evaluate postprandial effects of treatments. Results showed that changing from CON to SARA treatment lowered ruminal pH and increased ruminal propionate, without affecting fecal VFA profile or pH. Compared with CON, SARA treatment shifted the ruminal microbiome, decreased α diversity in the rumen and feces, and increased abundance of several taxa such as Succinivibrionaceae UCG-001 (operational taxonomic unit [OTU] 2994), Lachnospiraceae (OTU 3043), and Acetitomaculum (OTU 80). The HGA decreased fecal pH, increased total fecal VFA at 12 h after feeding, and increased fecal lactate and butyrate at the expense of acetate and propionate. In addition, HGA shifted the fecal microbiome and increased butyrate producing bacteria such as Lachnospiraceae (OTU 18), Blautia (OTU 508), Acetitomaculum (OTU 622), resulting in positive correlations between fecal butyrate and abundance of these taxa; however, family Ruminococcaceae (OTU 1580), and Christensenellaceae (OTU 550) decreased in feces and correlated negatively with fecal butyrate. Moreover, results showed that SARA in combination with HGA aggravates shifts of the fecal microbiome as revealed by further reductions of microbial α diversity indices and families Ruminococcaceae (OTU 1580) and Christensenellaceae (OTU 550) in cows receiving the SARA diet and abomasal starch infusion. Overall, new findings from this study reveal not only separate effects of SARA and HGA on ruminal and fecal fermentation but also show additive negative effects particularly on fecal microbial diversity and increase in fecal butyrate and lactate. Such alterations in microbial profile increase the risk of creating niches for pathogen proliferation and fecal shedding.