Metagenome Analysis of Major Carbohydrate-utilising Rumen Bacteria in Lactating Cows with Sub-acute Rumen Acidosis

Abstract

The study was conducted during the months of December, 2024 to September, 2025 at the College of Veterinary and Animal Sciences, Mannuthy, Thrissur, Kerala, India, with the objective of evaluating the changes in major carbohydrate-utilising rumen bacterial population and their diversity through metagenomic analysis in animals affected with subacute rumen acidosis (SARA) before and after probiotic supplementation. In the present study, rumen microbial communities in healthy, SARA-affected, and probiotic-supplemented SARA cattle were characterised using 16S rRNA (V3-V4) amplicon sequencing of rumen liquor samples collected from lactating crossbred cows. Metagenomic analysis revealed that Bacteroidetes particularly members of the genus Prevotella, and Firmicutes predominated, followed by Proteobacteria and Fibrobacteres. SARA was associated with lowered rumen pH, reduced microbial alpha diversity, depletion of fibrolytic Firmicutes including members of Clostridia, Lachnospiraceae, Oscillospiraceae, along with the enrichment of acid-tolerant Proteobacteria such as Succinivibrio and Ruminobacter, reflecting a dysbiotic microbial community in the rumen. Despite these changes, Bacteroidetes (Prevotella) continued to remain predominant. Probiotic supplementation partially restored rumen pH, improved microbial richness and diversity, reduced Proteobacteria and increased fibrolytic taxa, including Bacteroidetes (Prevotella) and Firmicutes. Furthermore, beta diversity showed distinct clustering among the healthy, SARA, and probiotic supplemented groups, confirming treatment-specific microbial profiles. Overall, these findings indicated that SARA induced major microbial alterations, whereas probiotic supplementation supported the partial restoration of rumen microbial balance and stability.