Genomic and phenotypic comparison of Lactobacillus reuteri isolates from food and intestinal ecosystems provides insights to probiotic applications

Abstract

Some of the food fermenting lactobacilli are derived from the animal intestine. Lactobacillus reuteri provides a model organism to study molecular mechanisms of ecological adaptation from gut to food. The overall objective of this dissertation was to characterize ecological fitness of L. reuteri in food and intestinal ecosystems to guide the direction of probiotic applications. The first goal of this dissertation was to assess carbohydrate transport and metabolism of L. reuteri strains to identify key metabolic traits specific to the cereal ecosystems. The genomewide analysis indicates that food and intestinal isolates of L. reuteri do not differ with respect to the number and type of carbohydrate active enzymes. In silico transporter prediction, gene expression experiments, and phenotypic assays demonstrate that L. reuteri is characterized by the absence of ABC and PTS transporters, efficient utilization of cereals-associated oligosaccharides, and lack of glucose catabolite repression. This study provides experimental evidence to explain the co-existence of heterofermentative and homofermentative lactobacilli in a shared niche. The second goal of this dissertation was to identify genetic signatures marking the adaption of cereal strains of L. reuteri from intestinal ancestors. Core- and pan-genome analysis on 16 L. reuteri strains demonstrates that sourdough-specific genes do not exist. Positively selected genes in sourdough isolates, however, are enriched in three functional groups, energy conversion, carbohydrate metabolism and defense systems while in gut ecosystem positively selected genes are significantly enriched in the function of translation. This suggests that sourdough and intestinal ecosystems differ in selection pressure. Competition in rye sourdough demonstrates that sourdough strains have higher or equal ecological fitness compared to rodent strains. The third goal of this dissertation was to assess the ecological fitness of cereal strains of L. reuteri in the gastrointestinal tract of piglets. Host-adapted L. reuteri exhibits better persistence in the gastrointestinal tract of piglets compared to nomadic and free-living lactobacilli. The impact of probiotic lactobacilli on autochthonous lactobacilli was minor, but the antimicrobial reutericyclin produced by L. reuteri exerted a significant effect on autochthonous Lactobacillus communities. This dissertation provides a basic understanding of the adaptation of intestinal L. reuteri to the food ecosystem, from evolution, ecology and metabolism perspectives. Such knowledge may improve current screening strategy for promising probiotics and starter cultures.