Lactobacillus reuteri DSM 17938 (L. reuteri DSM 17938) is a well-studied probiotic strain. Studies have shown that it can reduce morbidity in infants with very low birth weight, it is used in modulating gut microbiota, reducing infections, and treating antibiotic-associated diarrhoea. The aim of our study, which was part of randomized, placebo-controlled trial on the effect of L. reuteri DSM 17938 on antibiotic-treated infants (ClinicalTrials.gov: NCT02865564), was to examine differences in intestinal microbiota of infants, treated with antibiotics, and infants who received the probiotic strain L. reuteri DSM 17938 concurrently with antibiotic therapy. A total of 161 fecal samples from 87 infants, who were randomized into intervention group (TS = 43 infants) and placebo group (P = 44 infants), were collected 6 weeks after the start of therapy and at 1 year of age and then analysed. Quantitative PCR analysis was performed for Lactobacillus genus, Enterobacteriaceae family, Bifidobacterium genus, L. reuteri DSM 17938 strain and entire bacterial population. We also examined the influence of gender, feeding method and mode of delivery. Breastfeeding influenced the formation of the intestinal microbiota, as infants who were supplemented at 2 months of age had higher proportions of Enterobacteriaceae, L. reuteri and Lactobacillus in their fecal samples, taken 6 weeks after the start of therapy. The mode of delivery and gender didn't influence the composition of the fecal microbiota in samples taken 6 weeks after the start of therapy and at 1 year of age. The presence of L. reuteri 17938 strain was detected in 28 % of fecal samples of infants in intervention group at 6 weeks after the start of therapy. Despite the fact that we confirmed the presence of L. reuteri DSM 17938 strain and that it is able to colonize the intestines, it did not affect the proportion of the investigated representatives of the microbiota. Consumption of the strain did not affect the size of microbial populations of bifidobacteria, enterobacteria and lactobacilli in the stool samples taken 6 weeks after the start of therapy and at 1 year of age.
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