Dynamic effects of dietary shifts and temporal variation on the rumen microbiota of dairy goats differing in SARA tolerance.

Subacute ruminal acidosis (SARA) is a common metabolic disorder observed in intensive dairy production systems and is frequently associated with disruptions in rumen microbial homeostasis. In this study, a SARA model was successfully constructed by increasing the proportion of dietary concentrate and rumen-degradable starch (RDS) to examine the dynamic succession of the rumen microbiota across individuals. Forty-seven dairy goats were selected and classified into a control group (CON), low-RDS susceptible/tolerant groups (LRDSS/LRDST), and high-RDS susceptible/tolerant groups (HRDSS/HRDST) according to diet composition and individual sensitivity to SARA. Analysis of the microbial community revealed that the rumen microbiota of healthy and SARA-tolerant goats exhibited a high degree of structural similarity, whereas that of SARA-susceptible individuals underwent a pronounced compositional shift. These microbial shifts were accompanied by distinct alterations in rumen fermentation patterns, characterized by changes in volatile fatty acid (VFA) profiles, indicating functional divergence between tolerant and susceptible goats during SARA development. Notably, the relative abundance of Candidatus_Saccharimonas exhibited opposing trends between tolerant and susceptible goats and was identified as a key discriminant genus in microbial clustering. Moreover, random forest analysis revealed Candidatus_Saccharimonas as one of the most influential taxa contributing to rumen microbial differentiation, suggesting that it may serve as a potential microbial biomarker for distinguishing dairy goats in terms of SARA susceptibility or tolerance. Collectively, these findings suggest that Candidatus_Saccharimonas plays a crucial role in maintaining rumen microecological stability and enhancing the tolerance mechanisms of ruminants against SARA.