AIMS: we performed this case-control observational study to evaluate the effects of early administration of Lactobacillus reuteri DSM 17938 on microbial composition in infants' gastrointestinal tract. METHODS: early fecal microbiota composition was analyzed by using selective and differential cultural methods. Genomic DNA from positive Escherichia coli and Cronobacter sakazakii colonies was extracted and DNA was processed by multiplex PCR assay. RESULTS: fecal samples of 30 hospitalized infants who previously received probiotics and 30 not receiving probiotics were analyzed. We find that the two groups showed differences in gut microbial strains composition and richness. Infant treated with probiotics have a lower total anaerobic gramnegative counts (p=0.03) and a higher total anaerobic gram-positive counts (p=0.02). Enterobacteriaceae and enterococci were significantly higher (p=0.04) in the control group. No significant differences were observed for total aerobic counts, lactobacilli and bifidobacteria. C. sakazaki was found only in one infant recruited in the control group. Infants not previously treated with probiotics showed a higher colonization by diarrheagenic E. coli (EPEC) (p=0.04). CONCLUSIONS: our findings enhanced our understanding of the effects of probiotics on gut health in pediatric subjects. Early administration of L.reuteri in infancy could improve gut health by reducing pathogens colonization. Our trial underlines the efficacy of an early probiotic administration in improving gut health in infancy.Informed consent was obtained from each child's parent.The study has been approved by a research ethics committee.There are no prior publications or submissions with any overlapping information, including studies and patients.These data have not been published previously and are not under consideration for publication by any other journal. The manuscript has not been and will not be submitted to any other journal while it is under consideration by Clinica Chimica Acta Journal.All authors have read and approved the version of the article being submitted.No an honorarium, grant, or other form of payment was given to anyone to produce the manuscript.All authors declare no conflict of interest.No affiliations with or financial involvement in any organization or entity with a direct financial interest in the subject matter or materials of the research discussed in the manuscript were present. Probiotics and gut health in infants: a case-control observational study about early treatment with Lactobacillus reuteri DSM 17938.