Contributors: Pathogénie microbienne moléculaire; Institut Pasteur Paris (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM); University of British Columbia Canada (UBC); Institut Pasteur de Madagascar; Pasteur Network (Réseau International des Instituts Pasteur); Institut Pasteur de Bangui (IPB); CHU Pitié-Salpêtrière AP-HP; Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU); This project was funded by the Total Foundation, Institut Pasteur, Pasteur Foundation Switzerland and a donation by the Odyssey Re-Insurance Company. P.V. was supported by an Early Postdoctoral Fellowship (P2EZP3_152159), an Advanced Postdoctoral Fellowship (P300PA_177876) as well as a Return Grant (P3P3PA_177877) from the Swiss National Science Foundation, a Roux-Cantarini Fellowship (2016), and a L’Oréal-UNESCO for Women in Science France Fellowship (2017) and the Forschungsfonds of the University of Basel. P.J.S. is a HHMI Senior Foreign Scholar and CIFAR scholar in the human microbiota consortium. Work in LWP’s group is funded by the Human Frontier Science Program RGY0078/2015 and Canada Research Chair in Protist Ecology and work in P.V.’s group is funded by the NCCR Microbiomes NCCR Microbiomes, a National Centre of Competence in Research, funded by the Swiss National Science Foundation (grant number 180575).; Afribiota Investigators : Laurence Barbot-Trystram, Hôpital Pitié-Salpêtrière, Paris, France. Robert Barouki,Hôpital Necker-Enfantsmaladies,Paris,France. Alexandra Bastaraud,Institut Pasteur de Madagascar,Antana- narivo,Madagascar. Jean-Marc Collard, Institut Pasteur de Madagascar, Antana- narivo,Madagascar. Maria Doria,Institut Pasteur,Paris,France. Darragh Duffy,Institut Pasteur,Paris,France. B. Brett Finlay, University of British Columbia, Vancouver, Canada. Serge Ghislain Djorie, Institut Pasteur de Bangui, Bangui, Cen- tral African Republic. Tamara Giles-Vernick,Institut Pasteur,Paris,France. Milena Hasan,Institut Pasteur,Paris,France. Bolmbaye Privat Godje, Complexe Pédiatrique de Bangui, Ban- gui,Central African Republic. Jean-ChrysostomeGody,ComplexePédiatriquedeBangui,Ban- gui,Central African Republic. Francis Allen Hunald, Service de Chirurgie pédiatrique, Cen- tre Hospitalier Universitaire Joseph Ravoahangy Andrianavalona (CHU-JRA),Antananarivo,Madagascar. Nathalie Kapel,Hôpital Pitié-Salpêtrière,Paris,France. Jean-PierreLombart,InstitutPasteurdeBangui,Bangui,Central African Republic. AlexandreManirakiza,InstitutPasteurdeBangui,Bangui,Cen- tral African Republic. Synthia Nazita Nigatoloum, Complexe Pédiatrique de Bangui, Bangui,Central African Republic. LauraWegenerParfrey,UniversityofBritishColumbia,Vancou- ver,Canada. Lisette Raharimalala,Centre de Santé Materno-Infantile,Tsar- alalana,Antananarivo,Madagascar. Maheninasy Rakotondrainipiana,Institut Pasteur de Madagas- car,Antananarivo,Madagascar. Rindra Randremanana, Institut Pasteur de Madagascar, An- tananarivo,Madagascar. HarifetraMamyRichardRandriamizao,CentreHospitalierUni- versitaire Joseph Ravoahangy Andrianavalona (CHU-JRA), An- tananarivo,Madagascar. Frédérique Randrianirina, Institut Pasteur de Madagascar, An- tananarivo,Madagascar. Annick Robinson,Centre Hospitalier Universitaire Mère Enfant de Tsaralalana,Antananarivo,Madagascar. Pierre-Alain Rubbo, Institut Pasteur de Bangui, Bangui, République Centrafricaine. Philippe Sansonetti,Institut Pasteur,Paris,France. Laura Schaeffer,Institut Pasteur,Paris,France. Ionela Gouandjika-Vassilache,Institut Pasteur de Bangui,Ban- gui,République Centrafricaine. Pascale Vonaesch,Institut Pasteur,Paris,France. Sonia Sandrine Vondo, Complexe Pédiatrique de Bangui, Ban- gui,Central African Republic. Inès Vigan-Womas, Institut Pasteur de Madagascar, Antana- narivo,Madagascar.
نبذة مختصرة : International audience ; 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.
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