Genomic diversity of genus Limosilactobacillus

Abstract

The genus Limosilactobacillus (formerly Lactobacillus ) contains multiple species considered to be adapted to vertebrates, yet their genomic diversity has not been explored. In this study, we performed comparative genomic analysis of Limosilactobacillus (22 species; 332 genomes) isolated from different niches, further focusing on human strains (11 species; 74 genomes) and their adaptation features to specific body sites. Phylogenomic analysis of Limosilactobacillus showed misidentification of some strains deposited in public databases and existence of putative novel Limosilactobacillus species. The pangenome analysis revealed a remarkable genomic diversity (only 1.3 % of gene clusters are shared), and we did not observe a strong association of the accessory genome with different niches. The pangenome of Limosilactobacillus reuteri and Limosilactobacillus fermentum was open, suggesting that acquisition of genes is still occurring. Although most Limosilactobacillus were predicted as antibiotic susceptible (83%), acquired antibiotic-resistance genes were common in L. reuteri from food-producing animals. Genes related to lactic acid isoform production (>95 %) and putative bacteriocins (70.2%) were identified in most Limosilactobacillus strains, while prophages (55.4%) and CRISPR-Cas systems (32.0%) were less prevalent. Among strains from human sources, several metabolic pathways were predicted as conserved and completed. Their accessory genome was highly variable and did not cluster according to different human body sites, with some exceptions (urogenital Limosilactobacillus vaginalis , Limosilactobacillus portuensis , Limosilactobacillus urinaemulieris and Limosilactobacillus coleohominis or gastrointestinal Limosilactobacillus mucosae ). Moreover, we identified 12 Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologues that were significantly enriched in strains from particular body sites. We concluded that evolution of the highly diverse Limosilactobacillus is complex and not always related to niche or human body site origin.

Pangenome Analysis Reveals the Genetic Basis for Taxonomic Classification of the Lactobacillaceae Family

“…The pangenomes of most Lactobacillaceae species were found to be moderately open compared to other bacterial species. The vast genome diversity of the species was also discussed in prior pangenome studies of a few of the Lactobacillaceae (Ksiezarek et al, 2022;Zhang et al, 2020). Thus the larger size of the rare genomes observed in this study represents an important marker for characterizing the genomic diversity of lactic acid bacteria.…”

Limosilactobacillus vaginalis Exerts Bifidogenic Effects: A Novel Postbiotic Strategy for Infant Prebiotic Supplementation

“…For this reason, the genome of L. vaginalis BC17 was fully sequenced, and the absence of antibiotic resistance genes was confirmed. This aligns with the finding that Limosilactobacillus strains are generally antibiotic susceptible, although strains from food-producing animals (i.e., L. reuteri strains) are more prone to acquire antibiotic resistance [38]. Moreover, the genome analysis made it possible to exclude the presence of other virulence factors that have been associated with lactobacilli, mainly causing evasion from host defense mechanisms, platelet aggregation, tissue disruption, and host invasion [12].…”

Comparison of metagenomes from fermentation of various agroindustrial residues suggests a common model of community organization

“…A training set was constructed using organisms known to fit into one of the four groups (Supplementary Table S6). Bifidobacterium species and lactic acid bacteria were used for the Ferment to Intermediates training set (Okada et al, 1979;Pokusaeva et al, 2011;Pruckler et al, 2015;Tanner et al, 2016;Eckel and Vogel, 2020;Ferrero et al, 2021;Kasmaei et al, 2022;Ksiezarek et al, 2022), Clostridium and Megasphaera species were used for the Intermediate Chain Elongators training set (Wallace et al, 2003;Seedorf et al, 2008;Jeon et al, 2017;Kobayashi et al, 2017;Tao et al, 2017;Yang et al, 2018;Yoshikawa et al, 2018;Litty and Muller, 2021), Caproicibacter and Roseburia species were used for the Carbohydrate Chain Elongators training set (Kim et al, 2015;Tamanai-Shacoori et al, 2017;Flaiz et al, 2020;Schoelmerich et al, 2020), and Acetobacter, Prevotella, and Sphaerochaeta species were used for the uninvolved training set.…”