Metagenomic analysis unravels novel taxonomic differences in the uterine microbiome between healthy mares and mares with endometritis

Abstract Background The application of high throughput technologies has enabled unravelling of unique differences between healthy mares and mares with endometritis at transcriptomic and proteomic levels. However, differences in the uterine microbiome are yet to be investigated. Objectives The present study was aimed at evaluating the differences in uterine microbiome between healthy mares and mares with endometritis. Methods Low‐volume lavage (LVL) samples were collected from the uterus of 30 mares classified into healthy ( n = 15) and endometritis ( n = 15) based on their reproductive history, intrauterine fluid accumulation, gross appearance of LVL samples, endometrial cytology and bacterial culture. The samples were subjected to 16S rRNA sequencing. Results Notable differences in the uterine microbiome were observed between healthy mares and mares with endometritis at various taxonomic levels. In healthy mares, the most abundant phylum, class, order and family were Firmicutes , Bacilli , Bacillales and Paenibacillaceae , respectively. In contrast, the most abundant corresponding taxonomic levels in mares with endometritis were Proteobacteria , Gammaproteobacteria , Enterobacterales and Enterobacteriaceae , respectively. At the genus level, Brevibacillus and Paenibacillus were more abundant in healthy mares, whereas Escherichia , Salmonella and Klebsiella were more abundant in mares with endometritis. In healthy mares, Brevibacillus brevis was the most abundant species, followed by Brevibacillus choshinensis and Paenibacillus sp JDR‐2 . However, in mares with endometritis, Escherichia coli was the most abundant species, followed by Salmonella enterica and Klebsiella pneumoniae . Conclusions These results confirmed the previously reported presence of a uterine microbiome in healthy mares and helped unravel some alterations that occur in mares with endometritis. The findings can potentially help formulate new approaches to prevent or treat equine endometritis.