Extended Data Figure 8: Diet-dependent changes in composition of the faecal microbiota of gnotobiotic mice.

Indicator species analysis was used to identify taxa from the RF-derived model of gut microbiota maturation whose abundances varied consistently by diet treatments (n = 9,999 permutations with ‘mouse’ as the grouping variable). The top 60 ranked OTUs in the model (on the basis of their feature importance scores) were included in the analysis; those OTUs with statistically significant diet-dependent partitioning (P < 0.05) after FDR correction and with an indicator value >0.5 are shown, ranked from highest to lowest indicator value for infant formula-discriminatory (upper portion of figure) and ‘infant formula plus fruits and vegetables’-discriminatory (lower portion of figure) (see Supplementary Table 19 for results of the indicator species analysis). Mean values for relative abundances in the faecal microbiota at each time point are plotted ± s.d.