Comparative Analysis of Bovine Fecal Microbiota and Short-Chain Fatty Acids Variation During Dry Period, Pregnancy and Lactation

The bovine gut microbiota is crucial for many physiological functions, but how microbial interactions and related metabolic processes shift during pregnancy and lactation remains poorly understood. This study utilized fecal samples from 18 Bunaji (White Fulani) cows as a model to examine the gut microbial composition and structure across lactation, pregnancy, and the dry phase using 16S rRNA gene sequencing. Community composition analysis, alpha and beta diversity, LEfSe and correlation analyses were performed to explore the relationship between these reproductive stages, gut microbiota, and concentrations of short-chain fatty acids (SCFAs). Based on the Shannon and Simpson alpha diversity indices, no significant differences among the groups were found. However, beta diversity analysis revealed clear distinctions in microbial community structures between the groups. The most abundant microbial phyla across all three groups were the Bacillota (55–60%) and Bacteroidota (25–33%). At both the family and genus levels, cellulose-degrading bacteria such as Oscillospiraceae, Bacteroidaceae, Sphingobacteriaceae, Intestinimonas, Bacteroides, and Acetivibrio were prevalent across lactating, pregnant, and dry cows. Fifteen genera, including Intestinimonas, Bacteroides, Aristaeella, and Acinetobacter, were identified as potential biomarkers due to their significantly different abundances (p < 0.05) among the groups based on LEfSe. Notably, Spearman’s correlation analysis (p < 0.05) showed significant associations between the levels of specific microbial taxa and SCFA concentrations. In conclusion, although the core gut microbiota was similar across the groups, significant variations in microbial composition were detected. Additionally, these microbial profiles were associated with variations in fecal SCFA levels, indicating a potential interaction between them.