Gut microbiomes of agropastoral children from the Adadle region of Ethiopia

The composition and function of the intestinal microbiota are major determinants of human health and are influenced by factors such as diet, antibiotic treatment, and lifestyle. Previously, consistent differences between pre-industrial and industrial societies were shown. Here, we aimed at assessing the microbiota composition in an agropastoral community with a pre-industrial, yet nutritionally distinct lifestyle. For this purpose, 59 fecal samples were obtained from children aged two to five years living a traditional agropastoral lifestyle in the Adadle district in the Somali Regional State of Ethiopia where milk and starch-rich food are predominant components of the local diet. Due to their unique way of life and their specific diet, we hypothesized that these children might harbor a distinct microbiome profile. Fecal samples were subjected to both 16S rRNA gene amplicon and shotgun metagenomic sequencing. Microbiota composition, function and the resistome were described in the feces and compared to 1'384 publicly available fecal sequencing datasets from children living in other traditional, transitional, and industrial communities with different subsistence strategies. We find that samples from Adadle are distinctly low in Bacteroidaceae, Prevotellaceae and Succinivibrionaceae but high in Akkermansiaceae, Erysipelatoclostridiaceae Bifidobacteriaceae, Lactobacillaceae and Streptococcaceae. Additionally, genes participating in pathways related to the degradation of lactose, D-galactose and simple carbohydrates are enriched in samples from Adadle compared to samples from other communities. Finally, resistances against tetracycline, fluoroquinolone, penam and macrolide antibiotic are observed in the feces of children from Adadle. Unlike other non-industrialized communities, the samples from agropastoralists from Adadle are low in Prevotellaceae, Spirochaetaceae and Succinivibrionaceae, some of the main bacterial representatives in the feces of children living a traditional lifestyle. The high abundance of specific taxa and the enrichment of carbohydrate degradation pathways suggest that dietary choices strongly influence the microbiota composition and may overshadow the industrialization gradient. Our study revealed that the fecal microbiota of agropastoral children from Adadle significantly differs from the microbiota of children living a similar traditional lifestyle, highlighting the need to further characterize the fecal bacterial composition of diverse communities to better understand microbiota dynamics and better define what is a healthy microbiome on a global scale