Lactobacillus gaiae sp. nov., a novel species isolated from wild boar fecal samples and evidence for an expanded and differentiated pectin-side-chain utilization module

Three strains, WILCCON 0058, WILCCON 0059 T , and WILCCON 0149, were isolated from wild boar fecal samples collected in Pulau Ubin and Lorong Halus, Singapore. Analysis of the 16S rRNA gene sequences revealed that these strains belong to the genus Lactobacillus and are most closely related to the type strain of Lactobacillus delbrueckii , DSM 20074 T (98.53–98.80% similarity), which was corroborated by genome tree analysis showing that these strains form a distinct but closely related cluster. The average nucleotide identity (ANI), digital DNA–DNA hybridization (dDDH) and average amino acid identity (AAI) values between these three strains and the type strains of all L. delbrueckii subspecies (DSM 20074ᵀ, DSM 20081ᵀ, DSM 15996ᵀ, DSM 24966ᵀ, DSM 26046ᵀ, and DSM 20072ᵀ) were 92.2–92.5%, 46.8–48.1%, and 94.5–95.0%, respectively, well below the established thresholds for species-level delineation. Based on our phylogenomic, phenotypic, and chemotaxonomic analyses, we propose a novel species with the name Lactobacillus gaiae sp. nov., with WILCCON 0059 T (=DSM 120975 T =LMG 34196 T ) designated as the type strain. Interestingly, all strains showed growth on pectic galactan, with the products of two GH53 genes, putative galactanases, present in the genomes, being expressed and secreted into the medium. Together with the strains’ tolerance towards porcine bile and their ability to degrade raffinose-family oligosaccharides, this suggests a potential capacity to survive in the gut, to alleviate gastrointestinal dysbiosis, and to enhance fibre digestion.