Effect of diet on infant microbiota. BF (breast-fed) infants (green) exhibited more heterogeneity than FF (formula-fed) infants (blue) with respect to phylogenetic composition. (a) Taxon assignment (phylum level) variability for BF and FF samples using 16S rRNA alignments to GreenGenes (see Materials and methods). A diet label permutation test using the statistic ∑s |∑iεBF pis/6 - ∑iεFF pis/6|, where s indexes phylum and iεBF and iεFF denote that sample i is BF or FF infant, respectively, and p denotes the associated taxon proportion, rejected the null hypothesis that variability in phylogenetic composition was unrelated to BF/FF status with a P-value of 0.011. (b) Taxon assignments for all the shotgun reads (not just 16S rRNA homologs) using PhymmBL . (c) Shannon-Weiner index for BF and FF infants, indicating alpha-diversity for each sample.
Schwartz et al. Genome Biology 2012 13:r32 doi:10.1186/gb-2012-13-4-r32