Rarefaction curves were calculated to compare microbial richness [39]. Principal coordinate analysis (PCoA) was applied to evaluate the phylogenetic beta diversity [40] of the bacterial profiles at different time points. Multivariate partial least-square analysis (PLS) modeling (SIMCA P+, version 12.0; Umetrics AB, Umeå, Sweden) was performed to search if microbiota structures were related to L. reuteri consumption (y-variables) [41,42]. Tested models included those with pyrosequencing data only and those to which lactobacilli and streptococci culture and PCR data had been added. Variables were autoscaled to unit variance and cross-validated Y predictions were calculated. Subject clustering was displayed in score loading plots, and the importance of each x-variable was displayed in loading plots. Variables, where the 95% CI of the PLS correlation coefficient did not inlude zero were considered statistically significant [42]. The Q2 value yielded the capacities of the x-variables to predict the outcome (test or placebo group allocation). Univariate analyses of single taxa were not applied because of the combination of small groups and a high number of repeated tests.