Lactobacillus reuteri LTH5531 is a dominant member of the microbiota of type II sourdough fermentations. To investigate the genetic background of the ecological performance of LTH5531, in vivo expression technology was used to identify promoters that show elevated levels of expression during growth of this organism in a type II sourdough fermentation. Thirty-eight sourdough-induced fusions were detected, and 29 genes could be identified on the basis of the available sequence information. Four genes encoded stress-related functions (e.g., acid and general stress response), reflecting the harsh conditions prevailing during sourdough fermentation. Further, eight genes were involved in acquisition and synthesis of amino acids and nucleotides, indicating their limited availability in sourdough. The remaining genes were either part of functionally unrelated pathways or encoded hypothetical proteins. The identification of a putative proteinase and a component of the arginine deiminase pathway is of technological interest, as they are potentially involved in the formation of aroma precursors. Our study allowed insight into the transcriptional response of Lactobacillus reuteri to the dough environment, which establishes the molecular basis to investigate bacterial properties that are likely to contribute to the ecological performance of the organism and influence the final outcome of the fermentation.Sourdough is an intermediate product in bread production and contains a microbiota comprised of lactic acid bacteria and yeasts (reviewed in reference 16). Microbiological studies have revealed that 43 species of lactic acid bacteria, mostly species of the genus Lactobacillus, and more than 23 species of yeast occur in this ecological niche. The metabolic activity of these microorganisms leads to an acidification of the dough and the development of aroma precursors and is therefore of major importance for the quality of the final product. Sourdough breads are characterized by their unique flavor and texture, enhanced nutritional value, and favorable technological properties, such as prolonged shelf life and delayed staling (reviewed in reference 15). Type II sourdoughs serve mainly as dough acidifiers and are fermented for long periods (up to 5 days) at temperatures of Ͼ30°C and with high dough yields to permit pumping of the dough. Strains of Lactobacillus reuteri have been shown to be highly competitive in type II sourdough fermentations and persist over several years of continuous propagation in industrial fermentation processes (13,22). Numerous ecological factors affect the competitiveness of lactobacilli in sourdough fermentations, i.e., temperature, ionic strength, dough yield, and microbial products, such as lactate, acetate, CO 2 , and ethanol as well as factors resulting from substrates present in the cereal fraction and from enzymatic reactions (6, 22). The properties and genetic background responsible for the ecological performance of L. reuteri in sourdough fermentation are, however, poorly understood.In vivo ex...