Uterine microbiome dysbiosis associated with subclinical endometritis in crossbred Holstein Friesian cows revealed by 16s rRNA sequencing

Abstract

Reproductive efficiency in dairy cattle depends on timely uterine recovery after calving, and subclinical endometritis (SCE) silently compromises fertility. This study investigated the reproductive tract microbiome of twenty crossbred Holstein Friesian cows in Bengaluru, including ten estrus cows and ten SCE cows between 35-45 days postpartum, using 16S rRNA sequencing of cytobrush collected samples. Cows in estrus showed a diverse microbiota dominated by Proteobacteria, Firmicutes, and Bacteroidota with commensal genera such as Methylobacterium, Brevundimonas, Streptococcus, Acinetobacter, and Alistipes, whereas SCE cows exhibited reduced richness and were dominated by Bacteroidota and Flavobacteria, particularly Myroides and Flavobacterium, with Myroides odoratimimus and Flavobacterium johnsoniae prevailing at the species level. Alpha diversity indices (Shannon, Simpson, and Chao1) confirmed significantly lower richness and evenness in SCE, while beta diversity showed clear clustering between groups; rarefaction curves indicated adequate sequencing depth for estrus but limited diversity in SCE. The limited overlap in genera and the enrichment of SCE specific taxa indicate a disease associated microbial shift, demonstrating that SCE is characterized by uterine dysbiosis marked by loss of commensals and dominance of opportunistic bacteria, and that microbial signatures may serve as biomarkers of uterine health in dairy cattle.