Background The incidence of Crohn’s disease (CD) has increased obviously in newly industrialized countries including China, of which gut dysbiosis caused by environmental exposures is prone to contribute to this upward trend. Few studies examined the influence of the rural environment on gut microbiota and metabolome, as well as their interaction in CD development within a country undergoing rapid urbanization. We aimed to identify rural living-related microbial and metabolic signatures potentially associated with CD development and provide insights into CD prevention.

Methods A case-control study including 140 CD and 140 healthy controls (HCs) was conducted to investigate risk factors for CD development. Fecal 16S rRNA and metagenomics sequencing were performed in 54 CD and 266 HCs to compare the difference between microbial composition and function. The integrations of environmental information, metagenome and targeted metabolome profiles, which included 46 CD, 50 from Urban and 29 from Rural, were performed by correlation and mediation analysis.

Results (1) We identified various protective and hazardous environmental factors related to CD. Rural living at infant (OR = 0.62) or at child age (OR = 0.63) showed marginally significant associations with lower CD risk. (2) Rural HCs were further away from CD than urban HCs in terms of microbial diversity. Rural HCs, urban HCs and CD had distinct gut microbial and metabolic profiles. Bacteria and metabolic pathways involved in fiber and complex carbohydrate metabolism were enriched in rural HC. (3) Important microbial or metabolic associations with environmental factors were captured by the Hierarchical All-against-All association, which could be used to differentiate the human living environment. (4) Species-metabolite links that were enriched in rural settings, such as the connection between Prevotella copri and suberic acid in feces and hippuric acid in serum, may potentially play a role in the metabolism of fiber and polyphenol. Notably, these links were diminished in CD patients.

Conclusions Living in rural areas appears to protect against CD and help preserve beneficial species with complex metabolic functions. These advantages of bacteria-metabolites interaction, indicated by mediation analysis, might provide new indications in CD pathogenesis and potential microbiota-based disease prevention and treatment.