Environmental exposures and child and maternal gut microbiota in rural Malawi

Abstract

Background: Gut microbiota composition is associated with child health, but the effect of the environment on microbiota composition is not well understood. Few studies have been conducted in low-income settings where childhood malnutrition is common and possibly related to microbiota composition.

Objectives: To investigate whether gut microbiota composition in young children and their mothers is associated with different environmental exposures in rural Malawi. We hypothesized that more adverse environmental exposures would be associated with lower levels of microbiota maturity and diversity.

Methods: Faecal samples from up to 631 children and mothers participating in a nutrition intervention trial were collected at 1, 6, 12, 18, and 30 months (children) and at 1 month (mothers) after birth and analysed for microbiota composition with 16S rRNA sequencing. Bacterial OTU and genus abundances, measures of microbiota maturity and diversity, and UniFrac distances were compared between participants with different environmental exposures. The exposure variables included socio-economic status, water source, sanitary facility, domestic animals, maternal characteristics, season, antibiotic use, and delivery mode.

Results: Measures of microbiota maturity and diversity in children were inversely associated with maternal education at 6, 18, and 30 months and did not otherwise differ consistently between participants with different environmental exposures. Phylogenetic distance was related to season of stool sample collection at all time points. At the level of individual OTUs and genera, season of stool sample collection, type of water source, and maternal education showed most associations with child gut microbiota, while HIV status was the most important predictor of relative OTU and genus abundances in mothers.

Conclusion: The results do not support the hypothesis that adverse environmental exposures are broadly associated with lower microbiota maturity and diversity but suggest that environmental exposures influence the abundance of several bacterial OTUs and genera and that low maternal education is associated with higher microbiota maturity and diversity.

Keywords: child health; environment; gut microbiota; seasons; socio-economic factors.

Figure 1

Participant flow

Figure 2

Genera and OTUs with highest relative abundances as percentage of all reads at 18 and 30 mo [Colour figure can be viewed at http://wileyonlinelibrary.com]

Figure 3

Differences in OTU abundances at 30 mo between samples collected in the dry and cold season and samples collected in the dry and hot or rainy seasons. Results from zero‐inflated negative binominal model adjusted for other environmental predictor variables and covariates. The dots represent OTUs arranged according to ln fold change (lnFC) in OTU abundance between samples collected in different seasons and the corresponding fdr‐corrected P‐values. Positive lnFC values represent OTUs that are less abundant in samples collected in the dry and cold season compared with the dry and hot and rainy seasons. Differences in OTUs in orange and blue above the solid line were significant at level q = 0.05 [Colour figure can be viewed at http://wileyonlinelibrary.com]