Discovering the molecular foundations of Lactobacillus autochthony in the gastrointestinal tract

Molecular technologies have facilitated detection and identification of intestinal lactobacilli and allowed insight into the occurrence, diversity and dynamics of Lactobacillus populations in the human gastrointestinal tract. These techniques showed that the majority of Lactobacillus strains found in human fecal samples are only transiently detectable and therefore likely to be allochthonous, probably originating from food or the oral cavity. Strains of some species, such as Lactobacillus reuteri and Lactobacillus ruminis, have been shown to be true inhabitants (autochthonous) and persist in significant numbers. Very little is known about the molecular traits that enable autochthonous lactobacilli to occupy a niche within the gut ecosystem. The main focus of our research has been to determine the molecular foundations of the ecological success of Lactobacillus reuteri strains that are autochthonous to the rodent gastrointestinal tract. These studies have begun to provide mechanistic explanations of the ecological success of this species as a result of the application of in vivo expression technology (IVET) and the investigation of the ecological performance of isogenic mutants in the murine gastrointestinal tract. Functional and comparative genomic studies with Lactobacillus reuteri have been initiated in order to identify phenotypic and genotypic traits essential for gut colonization and host/microbe coexistence. Research to decipher these ecological interactions is rewarding, as it not only increases fundamental knowledge about the gut ecosystem, but also provides valuable information to select lactobacilli for probiotics.