Global transcriptome analysis of Lactobacillus reuteri in sourdough fermentation.

In this study, we investigated the transcriptional response of the human isolate L. reuteri ATCC 55730 during sourdough fermentation by using whole-genome microarrays. Significant changes of mRNA levels were found for 101 genes involved in diverse cellular processes, e.g., carbohydrate and energy metabolism, cell envelope biosynthesis, exopolysaccharide production, stress responses, signal transduction and cobalamin biosynthesis. Our results evidence extensive changes of the organism’s gene expression to the growth in sourdough as compared to the growth in chemically defined medium, and thus allowed us to uncover pathways involved in the adaptation of L. reuteri to the ecological niche of sourdough. An impact of several genes of L. reuteri for effective growth in sourdough was shown by implementation of mutant strains in sourdough fermentation. This study contributes to the understanding of the molecular fundamentals of L. reuteri’s ecological competitiveness, and provides a basis for further exploration of genetic traits involved in adaptation to the food and/or intestinal environment. Keywords: environment-specific gene expression, sourdough fermentation, chemically defined medium, dye swap RNA of exponetially growing cells grown in chemically defined medium CDML and sourdough was isolated three times (biological replicates). cDNA was synthesized from RNA of each biological replicate, and labeled with both Cy3 and Cy5 separately. cDNA of CDML and sourdough cultures were hybridized in a dye-swap duplicate for each biological replicate, resulting in 6 hybridizations. The duplicate genome per slide results in 12 replicate hybridizations per spot/gene.