Gut microbiome strain-sharing within isolated village social networks (extended metadata)

Abstract

When humans assemble into face-to-face social networks, they create an extended environment that permits exposure to the microbiome of other people, thereby shaping the composition and diversity of the microbiome at individual and population levels. Here, we use comprehensive social network mapping and detailed microbiome sequencing data in 1,787 adults within 18 isolated villages in Honduras to investigate the relationship between social network structure and gut microbiome composition. Using both species-level and strain-level data, we show that microbial sharing occurs between many relationship types, notably including non-familial and non-household connections. Using strain-sharing data alone, we can confidently predict a wide variety of relationship types (AUC ~0.72). This strain-level sharing extends to second-degree social connections in a network, suggesting the relevance of the extended network with respect to microbiome composition. We also observe that socially central individuals are more microbially similar to the overall village than socially peripheral individuals. Using a subset of 301 people in 4 villages whose microbiome was also measured 2 years later, we observed greater convergence in strain-sharing in connected versus otherwise similar unconnected co-villagers. Finally, we observe that clusters of both species and strains occur within clusters of people in the village social networks, providing the social niches within which microbiome biology and phenotypic impact are manifested.

Data Description

Additional access-restricted sample-level metadata. Variables included in this release are:

Variable descriptions are included in the hnl_hmb_nature_beghini_item6_metadata_2024-05-08.xlsx file