The thermophilic lactic acid bacterium Streptococcus thermophilus is widely and traditionally used in the dairy industry. Despite the vast level of consumption of S. thermophilus through yogurt or probiotic functional food, very few data are available about its physiology in the gastrointestinal tract (GIT). The objective of the present work was to explore both the metabolic activity and host response of S. thermophilus in vivo. Our study profiles the protein expression of S. thermophilus after its adaptation to the GIT of gnotobiotic rats and describes the impact of S. thermophilus colonization on the colonic epithelium. S. thermophilus colonized progressively the GIT of germ-free rats to reach a stable population in 30 days (10 8 cfu/g of feces). This progressive colonization suggested that S. thermophilus undergoes an adaptation process within GIT. Indeed, we showed that the main response of S. thermophilus in the rat's GIT was the massive induction of the glycolysis pathway, leading to formation of lactate in the cecum. At the level of the colonic epithelium, the abundance of monocarboxylic acid transporter mRNAs (SLC16A1 and SLC5A8) and a protein involved in the cell cycle arrest (p27 kip1 ) increased in the presence of S. thermophilus compared with germ-free rats. Based on different mono-associated rats harboring two different strains of S. thermophilus (LMD-9 or LMG18311) or weak lactate-producing commensal bacteria (Bacteroides thetaiotaomicron and Ruminococcus gnavus), we propose that lactate could be a signal produced by S. thermophilus and modulating the colon epithelium.Streptoccocus thermophilus belongs to the group of the thermophilic lactic acid bacteria and is traditionally and widely used as a starter in manufacturing dairy products (Emmental, Gruyere, Parmigiano, mozarella, yogurt, etc.). Yogurt, which results from the fermentation of milk by S. thermophilus and Lactobacillus delbrueckii sp. bulgaricus (L. bulgaricus), fulfills the current specifications required to be recognized as a probiotic product (1). The health beneficial effect of yogurt consumption is linked to the metabolic properties of S. thermophilus and L. bulgaricus. As such, it improves lactose digestion in the gastrointestinal tract (GIT) 3 through their lactose-hydrolyzing activity present in yogurt and in the GIT, thus reducing symptoms of lactose intolerance (2, 3).Yogurt cultures have been shown to induce other health benefits, such as reduction of diarrhea or allergic disorders as well as modulation of the immune system (1, 4). S. thermophilus is also present at high concentration in VSL#3, a probiotic mixture of eight different bacterial strains that possesses beneficial effects in several intestinal conditions (5, 6).Recent data indicate that strains related to S. thermophilus LMD-9 are among the 57 bacteria species found in the intestinal microbiota of 90% of 124 European individuals (7). In comparison with the overall human intestinal microbiota, S. thermophilus is a numerically nondominant species with variable levels...