Socioeconomic position and gut microbiome composition and function: evidence from the Lifelines Cohort

The gut microbiome has emerged as a potential biological mechanism through which socioeconomic position (SEP) may shape health inequalities, yet the extent and consistency of this relationship remains poorly understood, with existing evidence largely drawn from studies with small sample sizes and outdated sequencing methods. Using shotgun metagenomic data from two Lifelines cohort studies (n ≈ 1,170 and n ≈ 8,200; 400 participants with longitudinal data), we examined associations between four SEP indicators — educational attainment, household income, occupational prestige, and neighbourhood-level SEP — and gut microbiome diversity, taxonomic and functional composition, and short-chain fatty acid (SCFA)-related functional potential. We ran hierarchical linear regression models, first fitting minimally adjusted models before sequentially adjusting for BMI and health behaviours to assess whether any observed associations were attenuated. Disadvantaged SEP was consistently associated with reduced gut microbiome alpha diversity, and PERMANOVA analyses revealed that all four SEP indicators were significantly associated with microbiome composition, with educational attainment explaining the greatest variance in both analyses. Several bacterial species and functional pathways were associated with SEP in terms of both abundance and prevalence, including depletion of butyrate-producing species such as Roseburia hominis and Faecalibacterium SGB15346, and enrichment of mucus-degrading and flavonoid-degrading species including Ruminococcus torques and Flavonifractor plautii in individuals with disadvantaged SEP, with socioeconomic patterning also extending across a substantial proportion of taxonomically unresolved species.