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Socioeconomic and nutritional determinants outweigh gut microbiota influence on neurodevelopment in young children from Antananarivo, Madagascar
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  • Published: 17 January 2026

Socioeconomic and nutritional determinants outweigh gut microbiota influence on neurodevelopment in young children from Antananarivo, Madagascar

  • Jeanne Tamarelle  ORCID: orcid.org/0000-0003-0956-03491 na1,
  • Maria V. Doria2 na1,
  • Valérie Rambolamanana3,
  • Tatamo Rajaonarivo3,
  • Ana Sousa Ferreira4,5,
  • Maheninasy Rakotondrainipiana  ORCID: orcid.org/0000-0001-7932-97033,
  • Rindra Vatosoa Randremanana  ORCID: orcid.org/0000-0002-6174-88273,
  • Philippe Sansonetti  ORCID: orcid.org/0000-0001-7542-45276,7 &
  • Pascale Vonaesch  ORCID: orcid.org/0000-0002-1064-65051
  • On behalf of the Afribiota investigators

Scientific Reports , Article number:  (2026) Cite this article

  • 987 Accesses

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We are providing an unedited version of this manuscript to give early access to its findings. Before final publication, the manuscript will undergo further editing. Please note there may be errors present which affect the content, and all legal disclaimers apply.

Subjects

  • Clinical microbiology
  • Malnutrition
  • Microbiome
  • Paediatric neurological disorders
  • Risk factors

Abstract

In 2024, stunted child growth affected 150 million children under the age of five years, underscoring its critical impact on global health. Stunting has also been associated with neurodevelopmental delays. This study explores the relationship between stunting, the fecal microbiota, and neurodevelopment in 2–5-year-old children from the Afribiota cross-sectional study in Madagascar. Children were assessed using the Ages and Stages Questionnaire (ASQ-3), covering five developmental domains (communication, personal-social, problem-solving, fine and gross motor). Fecal samples were analyzed via 16S rRNA gene amplicon sequencing. Classical bi- and multivariate analysis was combined with Structural Equation Modelling to evaluate direct and indirect associations between different clinical factors, the microbiota and neurodevelopment. Our study shows that stunting and low socioeconomic status are consistently linked to poorer neurodevelopmental outcomes, while low branched-chain amino acids and hemoglobin levels are associated with stunting. Furthermore, a higher microbial diversity within individuals (α-diversity—specifically the Shannon index-) was directly linked to improved neurodevelopment scores in one of the tested models, while gut microbiota variation between individuals (β-diversity) was not associated with neurodevelopment. These findings support the hypothesis of neurodevelopment being primarily influenced by nutritional and social factors, with a more limited role for microbiota diversity.

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Data availability

All metataxonomic data are deposited on ENA ([https://www.ebi.ac.uk/ena/browser/view/PRJEB48119](https:/www.ebi.ac.uk/ena/browser/view/PRJEB48119)). Access to the remaining data is regulated through a Scientific Advisory Board, under the supervision of Institut Pasteur. Data requests should be directed to the corresponding author (PV), who will redirect them to the Access Committee.

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Acknowledgements

We would like to thank Kurt Long for helpful discussions regarding the SEM model approach. We further would like to thank all field workers, doctors, community health workers and families implicated in Afribiota.

Funding

The Afribiota project was funded by the Total Foundation, Institut Pasteur, the Bill and Melinda Gates Foundation (OPP1204689, INV-004352 and INV-002525), the Fondation Petram and a donation by the Odyssey Re-Insurance company. PV was supported by an Early Postdoctoral Fellowship (P2EZP3_152159), an Advanced Postdoctoral Fellowship (P300PA_177876) as well as a Return Grant (P3P3PA_177877), an Eccellenza Professorial Fellowship (PCEFP3_194545) and a SNSF Starting Grant (TMSGI3_218455) from the Swiss National Science Foundation. This study has been further supported as a part of the NCCR Microbiome, a National Center of Competence and research, funded by the Swiss National Science Foundation (Grant number 180575). JT is a Marie Curie Slodowska Actions Global Fellow.

Author information

Author notes

  1. These authors contributed equally: Jeanne Tamarelle and Maria V. Doria.

Authors and Affiliations

  1. Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland

    Jeanne Tamarelle & Pascale Vonaesch

  2. Institut Pasteur, 25-28 Rue du Docteur Roux, Paris, France

    Maria V. Doria

  3. Unité d’Epidémiologie et de Recherche Clinique, Institut Pasteur de Madagascar, BP 1274, Ambatofotsikely, 101, Antananarivo, Madagascar

    Valérie Rambolamanana, Tatamo Rajaonarivo, Maheninasy Rakotondrainipiana & Rindra Vatosoa Randremanana

  4. Faculdade de Psicologia, Universidade de Lisboa, Alameda da Universidade, 1649-013, Lisbon, Portugal

    Ana Sousa Ferreira

  5. Business Research Unit (BRU-IUL), Instituto Universitário de Lisboa (ISCTE-IUL), Lisbon, Portugal

    Ana Sousa Ferreira

  6. Unité de Pathogénie Microbienne, Institut Pasteur, 25‑28 Rue du Dr Roux, Paris, France

    Philippe Sansonetti

  7. Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, 25-28 Rue du Dr. Roux, 75015, Paris, France

    Philippe Sansonetti

  8. Hôpital Necker- Enfants Maladies, 149 rue de Sèvres, 75015, Paris, France

    Robert Barouki

  9. Institut Pasteur de Madagascar, BP1274, Ambatofotsikely 101, Antananarivo, Madagascar

    Alexandra Bastaraud, Jean-Marc Collard, Maheninasy Rakotondrainipiana, Rindra Vatosoa Randremanana & Inès Vigan-Womas

  10. Institut Pasteur, 25-28 Rue du Docteur Roux, Paris, France

    Maria Doria, Darragh Duffy, Tamara Giles-Vernick, Milena Hasan, Philippe Sansonetti & Laura Schaeffer

  11. Biodiversity Research Center, University of British Columbia, 2212 Main Mall, Vancouver, Canada

    B. Brett Finlay & Laura Wegener Parfrey

  12. Institut Pasteur de Bangui, BP923, Bangui, Central African Republic

    Serge Ghislain Djorie & Jean-Pierre Lombart

  13. Complexe Hospitalier Universitaire Pédiatrique de Bangui, Bangui, Central African Republic

    Bolmbaye Privat Gondje, Jean-Chrysostome Gody, Synthia Nazita Nigatoloum & Sonia Sandrine Vondo

  14. Hôpital Pitié-Salpêtrière, 47-83 Bd de l’Hôpital, 75013, Paris, France

    Nathalie Kapel

  15. Centre Hospitalier Universitaire Mère Enfant de Tsaralalana, Antananarivo, Madagascar

    Annick Robinson

  16. Institut Pasteur de Bangui, BP923, Bangui, Central African Republic

    Pierre-Alain Rubbo & Ionela Gouandjika-Vasilache

Authors
  1. Jeanne Tamarelle
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  2. Maria V. Doria
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  3. Valérie Rambolamanana
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  4. Tatamo Rajaonarivo
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  5. Ana Sousa Ferreira
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  6. Maheninasy Rakotondrainipiana
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  7. Rindra Vatosoa Randremanana
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  8. Philippe Sansonetti
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  9. Pascale Vonaesch
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Consortia

On behalf of the Afribiota investigators

  • Robert Barouki
  • , Alexandra Bastaraud
  • , Jean-Marc Collard
  • , Maria Doria
  • , Darragh Duffy
  • , B. Brett Finlay
  • , Serge Ghislain Djorie
  • , Tamara Giles-Vernick
  • , Bolmbaye Privat Gondje
  • , Jean-Chrysostome Gody
  • , Milena Hasan
  • , Nathalie Kapel
  • , Jean-Pierre Lombart
  • , Synthia Nazita Nigatoloum
  • , Laura Wegener Parfrey
  • , Maheninasy Rakotondrainipiana
  • , Rindra Vatosoa Randremanana
  • , Annick Robinson
  • , Pierre-Alain Rubbo
  • , Philippe Sansonetti
  • , Laura Schaeffer
  • , Ionela Gouandjika-Vasilache
  • , Pascale Vonaesch
  • , Sonia Sandrine Vondo
  •  & Inès Vigan-Womas

Contributions

PS, PV and the Afribiota investigators conceived and implemented the Afribiota cross-sectional study in Madagascar and the Central African Republic. In Madagascar, the study was coordinated by MR and RVR. For this substudy on cognitive development, MVD and PV conceived the study. MVD, VR and TR coordinated the cognitive assessment of children on site. JT and ASF performed statistical analyses. JT wrote the manuscript. JT and PV performed the revisions of the article. The final article was read and approved by all authors.

Corresponding authors

Correspondence to Maria V. Doria or Pascale Vonaesch.

Ethics declarations

Competing interests

The authors declare no competing interests.

Ethical approval

The study protocol of Afribiota was approved by the Institutional Review Board of the Institut Pasteur (2016-06/IRB) and the National Ethical Review Boards of Madagascar (55/MSANP/CE, 19 May 2015). All participants received oral and written information about the study. The legal representatives of the children provided written consent to participate in the study. The present analysis (AfriGutBrain) was approved by the Swiss Cantonal Ethics Commission CER-VD (BASEC-ID 2023-01834).

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Tamarelle, J., Doria, M.V., Rambolamanana, V. et al. Socioeconomic and nutritional determinants outweigh gut microbiota influence on neurodevelopment in young children from Antananarivo, Madagascar. Sci Rep (2026). https://doi.org/10.1038/s41598-026-35174-5

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  • Received: 19 June 2025

  • Accepted: 02 January 2026

  • Published: 17 January 2026

  • DOI: https://doi.org/10.1038/s41598-026-35174-5

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