Gut microbiomes from Gambian infants reveal the development of a non-industrialized Prevotella-based trophic network

Marcus C De Goffau,Niamh Meagher,Julian Parkhill,David J Price,Chilel Sanyang,Dora I A Pereira,Josef Wagner,Peter A Revill,Amadou T Jallow,Andrew M Prentice

doi:10.1038/s41564-021-01023-6

Abstract

Distinct bacterial trophic networks exist in the gut microbiota of individuals in industrialized and non-industrialized countries. In particular, non-industrialized gut microbiomes tend to be enriched with Prevotella species. To study the development of these Prevotella-rich compositions, we investigated the gut microbiota of children aged between 7 and 37 months living in rural Gambia (616 children, 1,389 stool samples, stratified by 3-month age groups). These infants, who typically eat a high-fibre, low-protein diet, were part of a double-blind, randomized iron intervention trial (NCT02941081) and here we report the secondary outcome. We found that child age was the largest discriminating factor between samples and that anthropometric indices (collection time points, season, geographic collection site, and iron supplementation) did not significantly influence the gut microbiome. Prevotella copri, Faecalibacterium prausnitzii and Prevotella stercorea were, on average, the most abundant species in these 1,389 samples (35%, 11% and 7%, respectively). Distinct bacterial trophic network clusters were identified, centred around either P.stercorea or F.prausnitzii and were found to develop steadily with age, whereas P.copri, independently of other species, rapidly became dominant after weaning. This dataset, set within a critical gut microbial developmental time frame, provides insights into the development of Prevotella-rich gut microbiomes, which are typically understudied and are underrepresented in western populations.

Highlights

Distinct bacterial trophic networks exist in the gut microbiota of individuals in industrialized and non-industrialized countries
Children were enroled between the ages of 7 and 37 months, and samples were collected at three different time points during an iron intervention trial in The Gambia[9]
In this study, we utilized a large cohort of children from an iron intervention trial in a rural region of The Gambia

Summary

Introduction

Distinct bacterial trophic networks exist in the gut microbiota of individuals in industrialized and non-industrialized countries. Distinct bacterial trophic network clusters were identified, centred around either P. stercorea or F. prausnitzii and were found to develop steadily with age, whereas P. copri, independently of other species, rapidly became dominant after weaning This dataset, set within a critical gut microbial developmental time frame, provides insights into the development of Prevotella-rich gut microbiomes, which are typically understudied and are underrepresented in western populations. Bacterial trophic networks can be understood as microbial populations that form clusters and, at the trophic level, constitute a food web of metabolically interdependent organisms[10,11] To date, such analyses have been performed mostly on Prevotella-poor cohorts from industrialized countries using combinations of adults and children, or to some degree, on smaller paediatric groups in non-industrialized countries[12].

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Results

Conclusion