Family SES Is Associated with the Gut Microbiome in Infants and Children

Abstract

Background: While early life exposures such as mode of birth, breastfeeding, and antibiotic use are established regulators of microbiome composition in early childhood, recent research suggests that the social environment may also exert influence. Two recent studies in adults demonstrated associations between socioeconomic factors and microbiome composition. This study expands on this prior work by examining the association between family socioeconomic status (SES) and host genetics with microbiome composition in infants and children.

Methods: Family SES was used to predict a latent variable representing six genera abundances generated from whole-genome shotgun sequencing. A polygenic score derived from a microbiome genome-wide association study was included to control for potential genetic associations. Associations between family SES and microbiome diversity were assessed.

Results: Anaerostipes, Bacteroides, Eubacterium, Faecalibacterium, and Lachnospiraceae spp. significantly loaded onto a latent factor, which was significantly predicted by SES (p < 0.05) but not the polygenic score (p > 0.05). Our results indicate that SES did not predict alpha diversity but did predict beta diversity (p < 0.001).

Conclusions: Our results demonstrate that modifiable environmental factors influence gut microbiome composition at an early age. These results are important as our understanding of gut microbiome influences on health continue to expand.

Keywords: childhood; infant; microbiome; socioeconomic status; stress.

Figure 1

Full Sample Taxonomic Summaries. Stacked bar plots showing the average relative abundance of the top ten. Different colored bars represent different genus (indicated by the key). Any other genus are classified as ‘’Other’’.

Figure 2

SEM Model Taxonomic Summaries. Stacked bar plots showing the average relative abundance of the genera assessed with socioeconomic status (SES). Different colored bars represent different genus (indicated by the key).

Figure 3

Latent Variable Path Model-Socioeconomic Status (SES) and Microbiome. Gut microbiome genera previously associated with SES in adulthood load onto a single latent variable which is predicted by SES and age in young children. The shapes in the graph represent variables where squares are observed variables and circles are latent variables. The single headed arrows are regression effects, solid lines indicates a significant path and dashed line indicates non-significance. Unstandardized estimates are above the standardized estimates, which are in parentheses. * p < 0.05, ** p < 0.001. RMSEA = 0.062; SRMR = 0.047.

Figure 4

Socioeconomic Status (SES) and Beta Diversity. Beta diversity was calculated based on Bray-Curtis Dissimilarity Distances and visualized using a Non-metric Multidimensional Scaling (NMDS) plot. The NMDS plot projects dissimilarity onto a plane with the two axes representing the largest variance. Data points represent individual beta-diversity values and have been colored by SES score to visualize the relationship between SES and beta-diversity. F(1, 432) = 8.46, p = 0.0001; R2 = 0.0192; Stress value = 0.17.