Lactobacilli are common inhabitants of the gastrointestinal tracts of mammals and have received considerable attention due to their putative health-promoting properties. Little is known about the traits that enhance the ability of these bacteria to inhabit the gastrointestinal tract. In this paper we describe the development and application of a strategy based on in vivo expression technology (IVET) that enables detection of Lactobacillus reuteri genes specifically induced in the murine gut. A plasmid-based system was constructed containing ermGT (which confers lincomycin resistance) as the primary reporter gene for selection of promoters active in the gastrointestinal tract of mice treated with lincomycin. A second reporter gene, bglM (-glucanase), allowed differentiation between constitutive and in vivo inducible promoters. The system was successfully tested in vitro and in vivo by using a constitutive promoter. Application of the IVET system with chromosomal DNA of L. reuteri 100-23 and reconstituted lactobacillus-free mice revealed three genes induced specifically during colonization. Two of the sequences showed homology to genes encoding xylose isomerase (xylA) and peptide methionine sulfoxide reductase (msrB), which are involved in nutrient acquisition and stress responses, respectively. The third locus showed homology to the gene encoding a protein whose function is not known. Our IVET system has the potential to identify genes of lactobacilli that have not previously been functionally characterized but which may be essential for growth of these bacteria in the gastrointestinal ecosystem.The gastrointestinal tracts of vertebrate animals are colonized by a complex microflora containing several hundred different species, some of which are present at high levels (29). Bacteria belonging to the genus Lactobacillus are common inhabitants of this ecosystem and have received considerable attention due to their putative health-promoting properties when they are ingested as probiotics (19,36). Lactobacillus species comprise only a minor part of the bacterial community in human feces (19,25), but in animals such as pigs, chickens, mice, and rats lactobacilli are the predominant bacteria in proximal regions of the gut. They can also be detected as minority members of the large bowel ecosystem in these animals (19). In order to persist in the gastrointestinal tract, which is a lotic and highly competitive ecosystem, the bacteria must have appropriate multiplication rates and metabolic activities. Ecological studies have suggested that only a minority of the lactobacilli found in intestinal samples meet these requirements and are truly autochthonous, but the bacterial factors that allow lactobacilli to become established and persist in the gastrointestinal tract are unknown (22,34,37).In the last decade, promoter-trapping technologies have been developed to overcome the limitations of in vitro models for studying the traits that enhance ecological performance in complex ecosystems. In vivo expression technology (IVET...