Fig. 3. Bacterial microbiota change with age and supplementation. (a) Relative abundances of 801 bacterial phyla in 12 (top) and 24 (bottom) month old children based on 16S data. Samples are 802 sorted by the proportion of Firmicutes along the horizontal axis. (b) Rarefaction curves comparing 803 mean species richness by age group, micronutrient supplementation, nutritional status and place 804 of residence (study site). Shaded regions represent standard errors and the dotted lines denote the 805 read depth at which significance was tested. (c) Non-metric multidimensional scaling of bacterial 806 compositions in samples based on Bray-Curtis dissimilarities. Samples are coloured by age and 807 ellipses represent 95% confidence intervals. Arrows indicate the direction of cosines of the top 10 808 bacterial OTUs significantly correlated with the ordination axes, and are scaled by their strength 809 of correlation (r2). (d) Mean DESeq2-transformed abundance of Actinobacteria and Firmicutes 810 grouped by nutritional status and treatment. (e) Compositional variance among samples grouped 811 by supplementation arm and age measured as distances to centroid, based on NMDS of weighted 812 Unifrac dissimilarity scores. *p < 0.05, **p < 0.01, ***p < 0.001 (f) Venn diagram showing the 813 numbers of bacterial taxa with significantly increased or decreased abundance, as indicated by 814 arrows, in supplemented groups relative to the control group. The pairs of numbers within brackets 815 refer to taxa at 12 and 24 months of age respectively, and select taxa are listed in boxes. (g) 816
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