We analyzed a total of 1’104 samples representing 212 gastric, 187 duodenal, and 705 fecal samples using a metabarcoding approach targeting the full ITS2 region for fungi, and the V4 hypervariable region of the 18S rRNA gene for the overall eukaryome.. Our study is of one of the largest cohorts analyzing the human intestinal eukaryome to date and the first to compare the eukaryome across different compartments of the gastrointestinal tract. Our 3 results highlight the importance of studying populations across the world to uncover common features of the eukaryome in health.. The eukaryome of African children is influenced by geographic location, gut biogeography, and nutritional status

Eukaryotes are a normal part of the mammalian gut ecosystem. They have historically been studied as parasites but high prevalence in healthy individuals suggest they may be indicators of a healthy gut ecosystem. Here, we describe the eukaryome along the gastrointestinal tract of children aged 2- 5 years in two different cities of Sub-Saharan Africa and test for associations between the eukaryome and clinical factors such as anaemia, intestinal inflammation, chronic undernutrition and age. Children were included in the context of the Afribiota project in Bangui, Central African Republic and Antananarivo, Madagascar from December 2016—May 2018. We analyzed a total of 1’104 samples representing 212 gastric, 187 duodenal, and 705 fecal samples using a metabarcoding approach targeting the full ITS2 region for fungi, and the V4 hypervariable region of the 18S rRNA gene for the overall eukaryome. Roughly half of all fecal samples showed microeukaryotic reads. We find high inter-subject variability, only a handful of fungal, helminth, and protist taxa that are likely residents of the gastrointestinal tract, and frequent co-occurrence of eukaryotes within an individual. Results from this large cohort thus echo those from around the world and reinforce our understanding of the eukaryome and mycobiome. We also find that the eukaryome differs between the stomach, duodenum and feces and is strongly influenced by country of origin. The eukaryome is poorly corelated with clinical variables including chronic undernutrition, anemia, intestinal inflammation, and age. Our data show trends toward higher levels of GiberellaGibberella intricans, syn. Fusarium equiseti, a mycotoxin producing fungus, and lower levels of the common gut protist Blastocystis in stunted children compared to non-stunted controls, mirroring findings that Blastocystis is less common in individuals with inflammatory or gastrointestinal disease compared to healthy individuals in other parts of the world. Our study is of one of the largest cohorts analyzing the human intestinal eukaryome to date and the first to compare the eukaryome across different compartments of the gastrointestinal tract. Our 3 results highlight the importance of studying populations across the world to uncover common features of the eukaryome in health.