Co-occurrence of Species in Children From Eastern Ethiopia, and Their Association With Environmental Enteric Dysfunction, Diarrhea, and Host Microbiome.

High prevalence during early childhood has been associated with stunting and environmental enteric dysfunction (EED), especially in low resource settings. This study assessed the prevalence, diversity, abundance, and co-occurrence of spp. in stools from children in a rural area of eastern Ethiopia and their association with microbiome, diarrhea, and EED in children. Stool samples ( = 100) were collected from randomly selected children (age range: 360-498 days) in five kebeles in Haramaya District, Ethiopia. Diarrhea, compromised gut permeability, and gut inflammation were observed in 48, 45, and 57% of children, respectively. prevalence and species diversity were assessed using PCR and meta-total RNA sequencing (MeTRS). The prevalence of spp. in the children's stools was 50% (41-60%) by PCR and 88% (80-93.6%) by MeTRS ( < 0.01). Further, seven species ( sp. RM6137, uncultured sp., and sp. RM12175) were detected by MeTRS in at least 40% of children stools in high abundance (>1.76-log read per million per positive stool sample). Four clusters of species (5-12 species per cluster) co-occurred in the stool samples, suggesting that colonization of children may have occurred through multiple reservoirs or from a reservoir in which several species may co-inhabit. No associations between spp., EED, and diarrhea were detected in this cross-sectional study; however, characteristic microbiome profiles were identified based on the prevalence of spp., EED severity, and diarrhea. Forty-seven bacterial species were correlated with , and 13 of them also correlated with gut permeability, gut inflammation and/or EED severity. Forty-nine species not correlated with were correlated with gut permeability, gut inflammation, EED severity and/or diarrhea. This study demonstrated that (1) in addition to and , multiple non-thermophilic spp. (i.e., , and ) were frequently detected in the children's stools and (2) the , gut permeability, gut inflammation, EED severity, and diarrhea were associated with characteristic microbiome composition. Additional spatial and longitudinal studies are needed to identify environmental reservoirs and sources of infection of children with disparate species and to better define their associations with EED in low-income countries.