Comparative Genomic Analysis Reveals Intestinal Habitat Adaptation of Ligilactobacillus equi Rich in Prophage and Degrading Cellulase

Ligilactobacillus equi is common in the horse intestine, alleviates the infection of Salmonella, and regulates intestinal flora. Despite this, there have been no genomic studies on this species. Here, we provide the genomic basis for adaptation to the intestinal habitat of this species. We sequenced the genome of L. equi IMAU81196, compared this with published genome information from three strains in NCBI, and analyzed genome characteristics, phylogenetic relationships, and functional genes. The mean genome size of L. equi strains was 2.08 ± 0.09 Mbp, and the mean GC content was 39.17% ± 0.19%. The genome size of L. equi IMAU81196 was 1.95 Mbp, and the GC content was 39.48%. The phylogenetic tree for L. equi based on 1454 core genes showed that the independent branch of strain IMAU81196 was far from the other three strains. In terms of genomic characteristics, single-nucleotide polymorphism (SNP) sites, rapid annotation using subsystem technology (RAST), carbohydrate activity enzymes (CAZy), and predictions of prophage, we showed that strain L. equi JCM 10991T and strain DSM 15833T are not equivalent strains.It is worth mentioning thatthestrain of L. equi has numerous enzymes related to cellulose degradation, and each L. equi strain investigated contained at least one protophage. We speculate that this is the reason why these strains are adapted to the intestinal environment of horses. These results provide new research directions for the future.