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Updated: Sep 10, 2025

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Intestinal microbiota diversity in children from three African countries.

Catherine Dauga1, Valentine Gilbart1, Azimdine Habib2

  • 1Institut Pasteur, F-75015 Paris, France.

Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases
|August 20, 2025
PubMed
Summary

The gut microbiota of well-nourished children varies significantly across African countries, with distinct species compositions influenced by geography and water quality. This highlights the need for country-specific considerations in understanding child gut health.

Keywords:
16SCentrale African RepublicGut microbiotaMadagascarSenegal

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Area of Science:

  • Microbiology
  • Pediatrics
  • Nutritional Science

Background:

  • The gut microbiota in children is a complex ecosystem influenced by diet, breastfeeding, and environmental factors.
  • Microbiota diversity can exhibit significant geographical variation, necessitating localized studies.
  • Understanding these variations is crucial for pediatric health and nutritional interventions.

Purpose of the Study:

  • To compare the gut microbiota composition of well-nourished children across three African nations: Madagascar, Senegal, and the Central African Republic (CAR).
  • To identify geographical and environmental factors influencing microbiota diversity and composition in young children.
  • To establish whether African child microbiota can be considered uniform across different countries.

Main Methods:

  • Standardized protocols were employed for sample collection, DNA extraction, and 16S rRNA gene sequencing (Illumina).
  • Bioinformatic analyses included sequence alignment (Silva.nr), Operational Taxonomic Unit (OTU) clustering (dgc), and taxonomic assignment (classify.otu).
  • Phylogenetic analysis (Phyloseq) and diversity metrics (Chao1, Shannon, Simpson) were used to assess microbiota richness and diversity.

Main Results:

  • Microbiota richness was highest in Senegal, while diversity was lowest in Senegal and highest in CAR.
  • Increased drinking water quality correlated with increased richness and decreased diversity.
  • Five dominant phyla (Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Verrucomicrobia) were common, but proportions varied; CAR and Madagascar shared more similarities than Senegal. Specific taxa (Prevotella 9, Bifidobacterium, Ruminococcus 2) were identified as regional markers.

Conclusions:

  • The gut microbiota composition in children differs significantly between Madagascar, Senegal, and CAR.
  • Geographical location and environmental factors, such as water quality, play a substantial role in shaping the pediatric gut microbiome.
  • A common microbial background exists, but rare species contribute to distinct geographical profiles, making a generalized comparison of African child microbiota inappropriate.