The eukaryome of African children is influenced by geographic location, gut biogeography, and nutritional status
Author:
Vonaesch Pascale1ORCID, Billy Vincent2, Mann Allison E2, Morien Evan2, Habib Azimdine3, Collard Jean-Marc3, Dédé Michel4, Kapel Nathalie5, Sansonetti Philippe J1, Parfrey Laura Wegener2ORCID, Barbot-Trystram Laurence, Barouki Robert, Bastaraud Alexandra, Collard Jean-Marc, Doria Maria, Duffy Darragh, Finlay B Brett, Djorie Serge Ghislain, Giles-Vernick Tamara, Hasan Milena, Godje Bolmbaye Privat, Gody Jean-Chrysostome, Hunald Francis Allen, Kapel Nathalie, Lombart Jean-Pierre, Manirakiza Alexandre, Nigatoloum Synthia Nazita, Parfrey Laura Wegener, Raharimalala Lisette, Rakotondrainipiana Maheninasy, Randremanana Rindra, Randriamizao Harifetra Mamy Richard, Randrianirina Frédérique, Robinson Annick, Rubbo Pierre-Alain, Sansonetti Philippe, Schaeffer Laura, Gouandjika-Vassilache Ionela, Vonaesch Pascale, Vondo Sonia Sandrine, Vigan-Womas Inès,
Affiliation:
1. Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur , 25-28 Rue du Dr Roux, 75015 Paris, France 2. Departments of Botany and Zoology, and Biodiversity Research Centre, University of British Columbia , 3200-6270 University Boulevard, V6T1Z4 Vancouver, Canada 3. Unité de Bactériologie Expérimentale, Institut Pasteur de Madagascar , BP1274 Ambatofotsikely Avaradoha 101 Antananarivo , Madagascar 4. Laboratoire d’Analyse médicale, Institut Pasteur de Bangui , Avenue De Independence Bangui, 923 Central African Republic 5. Laboratoire de Coprologie Fonctionnelle, Assistance Publique- Hôpitaux de Paris, Hôpital Pitié-Salpêtrière , 47-83 Bd de l’Hôpital, 75013 Paris, France
Abstract
Abstract
Eukaryotes have historically been studied as parasites, but recent evidence suggests they may be indicators of a healthy gut ecosystem. Here, we describe the eukaryome along the gastrointestinal tract of children aged 2–5 years and test for associations with clinical factors such as anaemia, intestinal inflammation, chronic undernutrition, and age. Children were enrolled from December 2016 to May 2018 in Bangui, Central African Republic and Antananarivo, Madagascar. We analyzed a total of 1104 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 intersubject variability, only a handful of taxa that are likely residents of the gastrointestinal tract, and frequent co-occurrence of eukaryotes within an individual. We also find that the eukaryome differs between the stomach, duodenum, and feces and is strongly influenced by country of origin. Our data show trends towards higher levels of Fusarium equiseti, a mycotoxin producing fungus, and lower levels of the protist Blastocystis in stunted children compared to nonstunted controls. Overall, the eukaryome is poorly correlated with clinical variables. 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 results highlight the importance of studying populations across the world to uncover common features of the eukaryome in health.
Funder
Early Postdoctoral Fellowship Advanced Postdoctoral Fellowship Swiss National Science Foundation Human Frontier Science Program
Publisher
Oxford University Press (OUP)
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