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

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.

Robust Variation in Infant Gut Microbiome Assembly Across a Spectrum of Lifestyles

“…The microbiome assembly process of infants living in industrialized nations is well-studied, and tends to follow a series of characterized steps that lead to the low-diversity gut microbiome composition characteristic of industrialized adults ( 4 ). The microbiome assembly process that occurs in infants living non-industrialized lifestyles (which results in the characteristically diverse adult microbiomes of non-industrialized adults ( 2 )) is largely unknown ( 5 ). Of particular interest are the timing at which the microbiomes of infants from different lifestyles diverge, the microbes and functions that are characteristic of infants from different lifestyles, and whether there are differences in the taxa that are vertically transmitted from mothers to infants and seed the microbiome assembly process.…”

Robust variation in infant gut microbiome assembly across a spectrum of lifestyles

“…The microbiome assembly process of infants living in industrialized nations is well studied and tends to follow a series of characterized steps that lead to the low-diversity gut microbiome composition characteristic of industrialized adults ( 2 ). The microbiome assembly process that occurs in infants living nonindustrialized lifestyles (which results in the characteristically diverse adult microbiomes of nonindustrialized adults) ( 3 ) is largely unknown ( 4 ). Of particular interest are the following: the timing at which the microbiomes of infants from different lifestyles diverge, the microbes and functions that are characteristic of infants from different lifestyles, and whether there are differences in the taxa that are vertically transmitted from mothers to infants, which seed the microbiome assembly process.…”

Effect of intra-partum azithromycin on the development of the infant nasopharyngeal microbiota: A post hoc analysis of a double-blind randomized trial

“…In the Gambia, like other LMIC, household congestion and poor ventilation are common, which may further increase bacterial exposure during the neonatal period. 36 Also, a recent publication on gut microbiota development in Gambian children showed differences in patterns of microbiota assembly between high income and low income settings, 37 giving further support to this argument.…”