Comparative Genomics of Limosilactobacillus pontis Strains: Niche-Specific Variations and Adaptations

Abstract

Limosilactobacillus pontis (L. pontis) is a species of lactic acid bacteria (LAB) found in various products, including fermented milk, sourdough, and broiler chickens’ gastrointestinal tracts. However, the evolutionary strategies and genomic features of the species remain unknown, which limits its application. In this study, whole-genome sequencing was carried out to investigate the genomic characteristics and evolutionary strategies of L. pontis, combined with a comparative genomic approach, providing the necessary theoretical basis for its application. The genomic sequences in this study included three published genomic sequences and two strains isolated from fermented milk in our lab in Inner Mongolia, China. The mean genome size of the five L. pontis strains was 1.70 Mb, and the mean DNA G + C content was 53.06%. L. pontis was a species with higher G + C content in LAB. The phylogenetic evolutionary tree for the core genes showed that the strains from the same sources were aggregated into a cluster. There were some differences in the genomic information and phylogenetic relationships amongst L. pontis from different sources. An analysis of the annotation results identified differences in the functional genes, carbohydrate-active enzymes, and bacteriocins amongst different isolated strains, which were related to the environment. L. pontis was rich in glycosyltransferases, especially in strains isolated from fermented milk, indicating that they had higher sugar synthesis abilities. It is worth mentioning that only the L. pontis strains isolated in our laboratory identified the bacteriocin operon, which may increase its application potential. The genomic characteristics and evolutionary process of L. pontis were analyzed by comparative genomics, and this study explored the differences in the functional genes amongst the strains, aiming to provide new insights into the genetic characteristics and niche adaptations of L. pontis.