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Objective  To analyze the global microbial composition, using large-scale DNA sequencing of 16 S rRNA genes, in faecal samples from colicky infants given  L. reuteri  DSM 17938 or placebo.    Methods  Twenty-nine colicky infants (age 10–60 days) were enrolled and randomly assigned to receive either  Lactobacillus reuteri  (10 8  cfu) or a placebo once daily for 21 days. Responders were defined as subjects with a decrease of 50% in daily crying time at day 21 compared with the starting point. The microbiota of faecal samples from day 1 and 21 were analyzed using 454 pyrosequencing. The primers: Bakt_341F and Bakt_805R, complemented with 454 adapters and sample specific barcodes were used for PCR amplification of the 16 S rRNA genes. The structure of the data was explored by using permutational multivariate analysis of variance and effects of different variables were visualized with ordination analysis.    Results  The infants’ faecal microbiota were composed of  Proteobacteria ,  Firmicutes ,  Actinobacteria  and  Bacteroidetes  as the four main phyla. The composition of the microbiota in infants with colic had very high inter-individual variability with  Firmicutes / Bacteroidetes  ratios varying from 4000 to 0.025. On an individual basis, the microbiota was, however, relatively stable over time. Treatment with  L. reuteri  DSM 17938 did not change the global composition of the microbiota, but when comparing responders with non-responders the group responders had an increased relative abundance of the phyla  Bacteroidetes  and genus  Bacteroides  at day 21 compared with day 0. Furthermore, the phyla composition of the infants at day 21 could be divided into three enterotype groups, dominated by  Firmicutes ,  Bacteroidetes , and  Actinobacteria , respectively.    Conclusion    L. reuteri  DSM 17938 did not affect the global composition of the microbiota. However, the increase of  Bacteroidetes  in the responder infants indicated that a decrease in colicky symptoms was linked to changes of the microbiota.    Trial Registration  ClinicalTrials.gov  NCT00893711

454 Pyrosequencing Analysis on Faecal Samples from a Randomized DBPC Trial of Colicky Infants Treated with Lactobacillus reuteri DSM 17938