Living in deprived neighborhoods reshapes the gut microbiome

By Dr. Liji Thomas, MDReviewed by Lauren HardakerMar 2 2026

A large UK twin study reveals that neighborhood deprivation is linked to measurable shifts in gut bacteria and metabolic pathways, offering new clues about how social inequality may become biologically embedded.

Study: Gut microbiome composition and function reflect socioeconomic deprivation. Image credit: sulit.photos/Shutterstock.com

Socioeconomic status (SES) is an important marker of health. A recent paper in the journal NPJ Biofilms and Microbiomes explored the effects of socioeconomic deprivation on gut microbiome composition and whether this helps explain the mental and metabolic ill effects of deprivation.

How neighborhood deprivation shapes long-term health

Lower SES is strongly associated with a number of chronic medical disorders, including mental health conditions and type 2 diabetes. Socioeconomic status encompasses factors such as income, education, and the environments at home, school, work, and within neighborhoods. These determinants influence levels of personal and environmental cleanliness, diet quality, pollution exposure, housing conditions, and antibiotic exposure.

Chronic stress linked to socioeconomic disadvantage has been associated with dysregulation of inflammatory and neuroendocrine signaling pathways, which may further worsen stress and perpetuate cycles of disease. Such stress can arise from financial and housing insecurity, neglected neighborhoods, and limited access to supportive resources.

The gut microbiome appears central to these relationships, as it is highly responsive to environmental and social influences, sometimes referred to as the “sociobiome,” alongside host genetics. It also plays a major role in the gut–brain axis, which influences neurodevelopment, stress responses, and mental health. Prior research has linked mental stress to disruptions in the gut–brain axis and to biochemical changes that may shift the gut microbiome toward dysbiosis, potentially worsening mental health.

Early-life socioeconomic conditions may shape the microbiome in ways that persist across the lifespan. Although preclinical studies suggest that gut microbes can influence depressive behaviors, the precise biological mechanisms remain unclear.

The current study examined correlations between socioeconomic deprivation and gut microbiome composition and function. The researchers aimed to determine whether specific microbial features might represent biological pathways linking deprivation to poorer mental and metabolic health.

Mapping neighborhood disadvantage to gut biology

The study included 1,390 women from the TwinsUK cohort who had their stool samples subjected to shotgun metagenomic sequencing. Socioeconomic deprivation was assessed using the Townsend Deprivation Index, an area-level measure of neighborhood material deprivation. The researchers evaluated associations between this index and both structural and functional characteristics of the gut microbiome. They also conducted mediation analyses to examine whether specific microbial features might partially explain links between deprivation and health outcomes.

Deprivation linked to reduced microbial richness

Higher Townsend deprivation scores were associated with reduced gut microbiome richness, measured as observed features. Other alpha diversity indices, including Shannon and Simpson diversity, were not significantly associated after statistical adjustment. Deprivation was also linked to distinct shifts in microbial composition. Twelve bacterial species were significantly associated with deprivation, nine of which belonged to the Firmicutes class.

Several species, including Intestinimonas massiliensis, Eubacterium siraeum, and Lawsonibacter sp_NSJ_51, were depleted among participants with greater deprivation. These taxa are known producers of short-chain fatty acids (SCFAs), metabolites linked to gut and brain health. In contrast, three species were positively associated with higher deprivation.

Functional analyses identified 22 MetaCyc pathways associated with deprivation. Many of these were related to energy metabolism, including fatty-acid beta-oxidation and central carbon metabolism pathways, and were negatively associated with higher deprivation. These findings suggest that social deprivation may be linked to alterations in how gut microbes process and extract energy from nutrients.

Machine learning classification models using microbial species or functional pathways distinguished participants in the most deprived versus the least deprived groups, with area under the curve values of approximately 0.73-0.74. These models distinguished between high- and low-deprivation groups but did not predict individual-level deprivation status. Importantly, most associations remained significant after adjusting for diet quality, indicating that factors beyond dietary differences, such as stress or broader environmental exposures, may contribute to the observed patterns.

Socioeconomic deprivation was also associated with higher odds of anxiety, with an odds ratio of 1.09, and higher odds of diabetes, with an odds ratio of 1.16. These effect sizes were modest and do not establish causality or directionality. SCFAs are thought to support serotonin production in the gut, although serotonin levels were not directly measured in this study. Deprivation was negatively associated with microbial L-tryptophan biosynthesis pathways, suggesting reduced microbial production of a serotonin precursor. This finding is biologically plausible in the context of anxiety, but remains indirect evidence.

The association between deprivation and anxiety was partially mediated by two microbial species, Intestinimonas massiliensis and Lawsonibacter sp_NSJ_51. Lawsonibacter sp_NSJ_51 also partially mediated the association between deprivation and diabetes. In both cases, mediation was partial, indicating that multiple biological and social pathways are likely involved.

The findings align with some previous research linking socioeconomic disadvantage to alterations in the microbiome, although inconsistencies across studies may reflect differences in how SES is measured and variations in study populations.

Study limitations

The study has several limitations. The Townsend Deprivation Index captures neighborhood-level material deprivation but does not provide a comprehensive measure of individual socioeconomic status. Mental health outcomes were self-reported, which may introduce reporting bias. The number of participants with anxiety or diabetes was relatively small, although the inclusion of borderline categories in the statistical models improved stability. As an observational study, the analysis cannot establish causal relationships. Additionally, the cohort consisted entirely of women from the United Kingdom, limiting generalizability to other populations.

New clues to how disadvantage affects health

This study integrates socioeconomic deprivation measures with gut microbiome profiling to explore potential biological pathways linking social disadvantage to health. The findings demonstrate associations between higher deprivation and reduced microbial richness, depletion of SCFA-producing bacteria, and alterations in energy metabolism pathways. Some microbial features partially mediated associations between deprivation and anxiety or diabetes. However, because the study is observational, the results identify associations rather than proving that socioeconomic deprivation directly causes microbiome changes or disease outcomes.

The authors conclude that the "adverse impact of social deprivation extends beyond mental ill-health, influencing key metabolic pathways through microbiome-driven mechanisms," while emphasizing that further research is needed to clarify causal pathways.

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