Intestinal microbiota diversity in children from three African countries

In children, the gut microbiota is a dynamic ecosystem derived from breastfeeding, oral microbiota and diet. Diversity can vary from one country to another, and the aim of this study was to compare microbiota of well-nourished children between three African countries using fully standardized protocols from sampling to data analysis. Well-nourished (WHZ weight for height z-score ≥ -1.5) children aged 18-24 months were enrolled. Libraries were constructed using Illumina 16S protocol. Sequences were aligned to the Silva.nr and clustered into OTUs (organism taxonomic unit) using greedy clustering (dgc). Consensus determination was done using classify.otu and the OTU table, taxonomy and metadata were assembled using Phyloseq. Alpha diversity was assessed using Chao1, Shannon and Simpson's index using Mothur. 106 well-nourished children were selected (31 in Madagascar, 40 in Senegal and 35 in Centrafrican Republic CAR). Richness was higher in Senegal than in CAR or Madagascar, but diversity was lowest in Senegal and highest in CAR. As the quality of drinking water increased, richness increased and diversity decreased. Microbiota shared five dominant phyla in different proportions: Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Verrucomicrobia. The composition of the microbiota in Madagascar and Centrafrica republic (CAR) was more similar, with more Prevotella 9 in Madagascar and more Bifidobacterium in CAR. Only two taxa were markers from CAR (Prevotella 9 and Ruminococcus 2). Apart from a pool of common species, a large proportion of rare species may characterize each geographical context. Therefore, the microbiota of children in Africa cannot be considered comparable between countries. Each biotope harbors specific species on a common background.