Work

Genomic characterization of a novel Lactobacillus species from pangolin feces: phylogenomic placement and unique functional gene repertoire

Year: 2026

Type: article

Abstract: The genus Lactobacillus represents a phylogenetically and ecologically diverse group of lactic acid bacteria intimately linked to host gastrointestinal homeostasis and widely regarded as prime probiotic candidates. Pangolin conservation is severely challenged by high mortality rates driven by digestive tract diseases, yet their native gut microbial ecology, particularly the functional roles of resident lactobacilli, remains largely unexplored. In this study, a novel Lactobacillus strain, designated M44, was isolated from the feces of a wild Formosan pangolin, and its complete genome was resolved via whole-genome sequencing. Genome-wide taxonomic metrics (ANI, AAI, and dDDH) fell substantially below the established thresholds for known species. Phylogenomic reconstruction based on single-copy orthologs confirmed that strain M44 forms a distinct, novel evolutionary lineage clustering adjacent to L. psittaci , L. jensenii , and L. mulieris . Comparative genomic analysis revealed that while M44 shares a core of 936 orthogroups with these phylogenetically related peers, it maintains a unique repertoire of 207 strain-specific orthogroups. Multi-pipeline functional mining identified a robust gene cluster for exopolysaccharide biosynthesis, alongside an array of surface-anchored adhesins that support its strong mucosal colonization potential. From an antimicrobial defense perspective, genome mining identified no canonical bacteriocin gene clusters, while genes associated with organic acid and hydrogen peroxide biosynthesis were present. Metabolic pathway reconstruction identified genomic capacity for exogenous carbohydrate and peptide utilization, including catabolic pathways for trehalose and N-acetylglucosamine, as well as a comprehensive oligopeptide permease system and an extensive intracellular peptidase repertoire. Genomic safety screening confirmed the complete absence of acquired antimicrobial resistance genes and intact mobile genetic elements, reinforced by an active Type I-E CRISPR-Cas adaptive immune system. These genomic insights establish strain M44 as a novel Lactobacillus species with a functional architecture encompassing broad exogenous carbohydrate and peptide utilization capacity, enhanced intestinal adherence capabilities, and organic acid-mediated antimicrobial defense. The demonstration of a favorable genomic safety profile, combined with prior in vitro phenotypic screening, positions Lactobacillus sp. M44 as a scientifically compelling subject for wildlife microbiome exploration and a candidate worthy of further investigation for potential application in captive pangolin management.

Source: BMC Microbiology

DOI: 10.1186/s12866-026-05451-4