title: 454 pyrosequencing analysis on faecal samples from a randomized DBPC trial of colicky infants treated with Lactobacillus reuteri DSM 17938.
abstract: 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.
  
  
  CONCLUSIONS
  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.
  
  
  BACKGROUND
  ClinicalTrials.gov NCT00893711.
authors.affiliation: Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
authors.forename: Stefan
authors.initials: S
authors.lastname: Roos
authors.forename: Johan
authors.initials: J
authors.lastname: Dicksved
authors.forename: Valentina
authors.initials: V
authors.lastname: Tarasco
authors.forename: Emanuela
authors.initials: E
authors.lastname: Locatelli
authors.forename: Fulvio
authors.initials: F
authors.lastname: Ricceri
authors.forename: Ulf
authors.initials: U
authors.lastname: Grandin
authors.forename: Francesco
authors.initials: F
authors.lastname: Savino
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics; D003085:Colic / Q000628:therapy*; D005243:Feces / Q000382:microbiology*; D005260:Female; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D052200:Limosilactobacillus reuteri / Q000502:physiology*; D008297:Male; D054892:Metagenome