Abstract: Endometritis is generally caused by bacterial reproductive tract infection, it is one of the important causes of reproductive disorders in sows, which seriously affected the production efficiency of breeding industry. Understanding the birth canal microbial community of endometritis sows and healthy sows are a key step in developing more effective ways to prevent the occurrence of endometritis and improve the reproductive capacity of sows. In this study, 19 samples of sow endometritis were collected and divided into 3 groups, of which 6 samples were from healthy sows, 6 samples were from mating sows and 7 samples were from lactating sows. Whole gene sequencing of nanopore 16S rRNA was used to evaluate and compare the birth canal microbiota of sows with endometritis and healthy sows. After splicing, filtering, and screening of the experimental data, a total of 1 359 746 clean reads were obtained, and 2 415 operational taxonomic units (OTUs) were identified after alignment. A total of 2 415 microbial species were detected in the vaginal secretions of healthy sows, sows with diseases during the early stage of reproduction, and sows with diseases during lactation. Among these three groups of sows, 699 bacterial species were shared in their vaginal secretions. At the phylum level, the results showed that the relative abundance of Proteobacteria in the birth canal of sows with endometritis was extremely significantly increased(P＜0.01), while Bacterodietes was significantly decreased (P＜0.05), compared with that of healthy sows. At the classification level, compared with the healthy sow group, the relative abundance of A cinetobacter spp. in the mating period sow group of the endometritis-affected sow group was 14.92%, while in the lactation period sow group, it was 21.83%. In the healthy sow group, it was only 1.22%. The abundance of Proteobacteria in the birth tract of sows with endometritis was extremely significantly higher than that of healthy sows(P＜0.01). Proteobacteria might be the main pathogen of endometritis in sows, and might be closely related to endometrial inflammation in sows. This study provided reference for the subsequent prevention and treatment of sow endometritis.

Key words: sow, vaginal microbiota, endometritis, 16S rRNA sequencing, reproductive failure, Proteobacteria, Bacteroidetes