3.2. Gut Microbiota
diarrheal, well-nourished
MALNOURISHED, WASTED
Beta Diversity: We first assessed the beta diversity of the gut microbial community composition from all the children at each time point, in both locations (urban and rural) and within each intervention arm using PCoA of weighted UniFrac distances. The UniFrac algorithm measures similarity among microbial communities based on the degree to which their component taxa share branch length on a phylogenetic tree [Differences in weighted Unifrac distances between age groups were statistically significant at 9 (Alpha Diversity: As age appeared to be the factor that most accounted for differences in beta diversity of microbial communities, we focused on the analysis of the effect of age on alpha diversity and relative abundance of major taxa at the highest and lowest taxonomic levels, i.e., phyla and genera. To account for covariates, we used a linear mixed-effects model adjusted for gender, residential location, and reported diarrheal episodes. Although there were no significant differences overall in beta diversity of the gut microbiota of children residing in urban and rural locations, we wanted to determine if there were significant differences in alpha diversity indices between children residing in these locations at each of the 3-monthly time points. While all alpha diversity indices have doubled over the study period, as shown in Relative Abundance: Overall, the most abundant phyla were Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes (Overall, the 10 most abundant genera were Differentially abundant taxa: In order to identify differentially abundant taxa at all taxonomic levels between the microbiota of all of the children in rural and urban locations in all intervention arms combined between the first and second years of life, we used the LEfSe algorithm, which identifies genomic features characterizing the differences between two or more biological conditions [We also used the LEfSe algorithm to identify differentially abundant taxa at all taxonomic levels between the microbiota of children in the urban and rural locations and in the three intervention arms, in each age group. These analyses revealed specific taxa that were enriched in the microbiota of children in urban versus rural locations in all intervention groups combined (There were very few differentially abundant taxa in the microbiota of children who received different interventions (The numbers of malnourished (underweight, wasted, stunted) or well-nourished children at each age, in each intervention arm, and at urban or rural sites were too small to determine if there were significant differences in alpha or beta diversity or differentially abundant taxa among them.