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Published on: December 31, 2017
Intestinal microbiota diversity in children from three African countries
Catherine Dauga1, Valentine Gilbart1, Azimdine Habib2
1Institut Pasteur, F-75015 Paris, France.
Insights
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.
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.
Abstract:
In children, the gut microbiota is a dynamic ecosystem derived from breastfeeding, oral microbiota and diet. Diversity can vary from one country to another, and the aim of this study was to compare microbiota of well-nourished children between three African countries using fully standardized protocols from sampling to data analysis. Well-nourished (WHZ weight for height z-score ≥ -1.5) children aged 18-24 months were enrolled. Libraries were constructed using Illumina 16S protocol. Sequences were aligned to the Silva.nr and clustered into OTUs (organism taxonomic unit) using greedy clustering (dgc). Consensus determination was done using classify.otu and the OTU table, taxonomy and metadata were assembled using Phyloseq. Alpha diversity was assessed using Chao1, Shannon and Simpson's index using Mothur. 106 well-nourished children were selected (31 in Madagascar, 40 in Senegal and 35 in Centrafrican Republic CAR). Richness was higher in Senegal than in CAR or Madagascar, but diversity was lowest in Senegal and highest in CAR. As the quality of drinking water increased, richness increased and diversity decreased. Microbiota shared five dominant phyla in different proportions: Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Verrucomicrobia. The composition of the microbiota in Madagascar and Centrafrica republic (CAR) was more similar, with more Prevotella 9 in Madagascar and more Bifidobacterium in CAR. Only two taxa were markers from CAR (Prevotella 9 and Ruminococcus 2). Apart from a pool of common species, a large proportion of rare species may characterize each geographical context. Therefore, the microbiota of children in Africa cannot be considered comparable between countries. Each biotope harbors specific species on a common background.
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