Gut microbial signatures expose the westernized lifestyle of urban Ethiopian children

Gut microbiota composition has been extensively studied in European and North American pediatric cohorts, as well as in rural African children. Much less attention has been paid to urban African children, whose families have transitioned to a "Western" lifestyle characterized by smaller family sizes, access to perinatal care including C-section delivery, non-traditional food sources and widespread availability of antibiotics. We analyzed fecal samples from ~200 Ethiopian children aged 2-5 years from Adama, Ethiopia, using 16S rRNA gene sequencing and shotgun metagenomics. We found that well-studied factors such as delivery mode, breastfeeding and family size have only minor effects on α-diversity, whereas household crowding (single vs. multiple rooms) and consumption of the traditional fermented cereal Eragrostis tef predict higher α-diversity. Stunted growth and absence of Helicobacter pylori infection were additional factors associated with increased fecal microbial diversity. Metagenomic profiling revealed that rural African signature genera such as Segatella and Prevotella were largely absent; instead, urban Ethiopian children displayed a high Firmicutes/Bacteroidota ratio and enrichment of metabolic pathways linked to a westernized diet, resembling European rather than rural Ethiopian children. These results indicate that an urban westernized lifestyle alters gut microbiota composition, which may be partially offset by a traditional fermented diet.