Fig 1. Functional development of the gut microbiomes of Malawian twin pairs concordant for healthy status, and twin pairs who became discordant for kwashiorkor.

(A) PCoA of Hellinger distances between KEGG EC profiles. The position of each fecal microbiome along principal coordinate 1 (PC1), which describes the largest amount of variation (17%) in this dataset of 308 sequenced twin fecal microbiomes, is plotted against age. Each sphere represents a microbiome colored by the age of the human donor. PC1 is strongly associated with age (and with family membership) (linear mixed-effects model, table S4). We did not find significant associations between the positions of samples along other principal coordinates and the other host parameters presented in table S2A). On average the degree of intrapersonal variation in a co-twin was not smaller than the variation between co-twins (fig. S2). Similar to twins who remained healthy, the temporal variation within a co-twin member of a discordant twin pair was equal to the variation between co-twins, but still smaller compared to unrelated children (fig. S2). (B) Average ± SEM PC1 coordinate obtained from the data shown in panel A for microbiomes sampled at three consecutive time points from nine twin pairs who remained well-nourished (healthy) during the study (subjects surveyed between three weeks and 24.5 months of age). (C) Average ± SEM PC1 coordinate obtained from panel A for microbiomes sampled before, during and after RUTF treatment from co-twins discordant for kwashiorkor. *p<0.05, Friedman test with Dunn’s post-hoc test applied to data shown in panels B and C. Similar results were obtained using other distance metrics [Bray Curtis, Euclidian, and Kulzyncki (fig. S3)]. (See fig. S4 which shows how changes in the relative proportion of Actinobacteria parallel the patterns observed with the changes along PC1; children with kwashiorkor manifested a statistically significant decrease in Actinobacteria with introduction of RUTF, unlike their healthy co-twins).