Comparative genomics of Lactobacillus salivarius strains focusing on their host adaptation

Abstract

Lactobacillus salivarius is an important member of the animal gut microflora and is a promising probiotic bacterium. However, there is a lack of research on the genomic diversity of L. salivarius species. In this study, we generated 21 L. salivarius draft genomes, and investigated the pan-genome of L. salivarius strains isolated from humans, pigs and chickens using all available genomes, focusing on host adaptation. Phylogenetic clustering showed a distinct categorization of L. salivarius strains depending on their hosts. In the pan-genome, 15 host-specific genes and 16 dual-host-shared genes that only one host isolate did not possess were identified. Comparison of 56 extracellular protein encoding genes and 124 orthologs related to exopolysaccharide production in the pan-genome revealed that extracellular components of the assayed bacteria have been globally acquired and mutated under the selection pressure for host adaptation. We also found the three host-specific genes that are responsible for energy production in L. salivarius. These results showed that L. salivarius has evolved to adapt to host habitats in two ways, by gaining the abilities for niche adhesion and efficient utilization of nutrients. Our study offers a deeper understanding of the probiotic species L. salivarius, and provides a basis for future studies on L. salivarius and other mutualistic bacteria.

Comparative Genomics Analysis of Lactobacillus ruminis from Different Niches

“…According to the genetic characteristics of those 91 L. ruminis strains, both genome size and genes number among those strains isolated from different sources differed, which was similar to that in L. salivarius. Genome size and genes number of piglet-derived L. salivarius strains were larger than those of the human-derived and chicken-derived strains, while the GC content was not different between isolates in relation to their hosts [48]. And the pan-genome and core-genome analysis showed a closed pan-genome for L. ruminis species, pointing out that an enough number of strains had been included in the current research to sufficiently describe the genetic diversity in L. ruminis species.…”

Comparative Genomics of Lactobacillus crispatus from the Gut and Vagina Reveals Genetic Diversity and Lifestyle Adaptation

“…As the number of strains increased, the pan-genome curve gradually converged. The derived mathematical function had an index value of less than 0.5, indicating that L. crispatus has a closed pan-genome [16]. However, the core genome only consisted of 1250 genes.…”

“…Other species of Lactobacillus that have been subjected to comparative genomic analysis are L. reuteri [15], L. salivarius [16], L. curvatus [17], and L. brevis [18]. The results showed that niches affected the genetic characteristics and evolutionary orientations of the given species.…”

<em>Lactobacillus</em> Strains as Opportunistic Pathogens. A Review

“…bulgaricus and lactis homofementative Dairy products [13] Fermented milk and cheese production [13] L. helveticus homofermentative Dairy products [4] Cheese production [4] L. plantarum facultatively heterofermentative Fermented food and feed, GIT [14] Cheese, sausage, fermentation of vegetables, silage production, probiotic [14] L. reuteri heterofermentative GIT, skin and mucosae [15] Probiotic [15] L. rhamnosus facultatively heterofermentative Dairy products, GIT [11] Probiotic [16] L. sakei facultatively heterofermentative Meat, vegetables [17,18] Sausage fermentation [18] L. sanfranciscensis heterofermentative Sourdough [19] Sourdough fermentation [19] L. salivarius homofermentative Human and animal GIT [20] Probiotic [20] Oenococcus oeni heterofermentative Grape berries [21] Wine malolactic fermentation [21] Pediococcus acidilactici homofermentative Plant materials, cheese, fermented meat products, GIT [22] Sausage fermentation, probiotic [22] P.…”