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. The present study was aimed at evaluating the differences in uterine microbiome between healthy mares and mares with endometritis. 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 metagenomic analysis using 16S rRNA sequencing. 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. These results indicate novel differences in the uterine microbiome between healthy mares and mares with endometritis. The findings can potentially help formulate new approaches to prevent or treat equine endometritis.

B ACKGROUND: Endometritis is a major cause of infertility in mares worldwide.In India, information on endometritis in mares is limited. Objectives: The purpose of this study was to identify uterine bacterial isolates from endometritis-affected mares in India and evaluate their antimicrobial susceptibility pattern. Methods: Endometritis was diagnosed based on history of infertility and findings from transrectal examination, visual inspection of low-volume uterine lavage samples, endometrial cytology and bacterial culture. Uterine lavage samples were collected from 15 mares with endometritis and subjected to bacterial culture and antimicrobial susceptibility test. Results: The most common bacterial isolates were Escherichia coli (E. coli, 40.0%), Staphylococcus (26.7%), Streptococcus (20.0%), and Klebsiella (13.3%) species. Most of the E. coli isolates were susceptible to gentamicin (83.3%), netilmicin sulphate (83.3%), tobramycin (83.3%), nitrofurantoin (83.3%), amikacin (66.7%), and ampicillin/sulbactam (66.7%). All of the Staphylococcus isolates were susceptible to gentamicin, amikacin, and ampicillin/ sulbactam. All Streptococcus and Klebsiella isolates were susceptible to gentamicin, amikacin, and netilmicin sulphate. Furthermore, all Klebsiella isolates were susceptible to sparfloxacin, ampicillin/sulbactam, tobramycin, cefadroxil, and co-trimoxazole. Ampicillin and amoxicillin were the least effective antimicrobials with susceptibility percentages ranging between 0 to 33.3% for the various isolates. Conclusions: The results suggest that E. coli is the most common cause of equine endometritis in India. Based on the antimicrobial susceptibility patterns, it can be concluded that gentamicin, amikacin, netilmicin sulphate and ampicillin/sulbactam may be the best first-line antimicrobials for clinical application in equine endometritis cases in India while awaiting antimicrobial susceptibility test results.