Neighborhood deadwood and yard rewilding modulate commensal microbiomes and inflammatory signals among urbanites

Urbanization and biodiversity loss reduce human exposure to diverse microbiomes. Current evidence suggests that the vanishing microbiomes in industrialized populations are a central factor in the rising prevalence of non-communicable immune-mediated diseases. Rewilding has been proposed as an approach to diversify urban microbial communities and promote immunological resilience.

We rewilded 21 urban private yards with deadwood, vegetation, and microbially rich soil. Control yards (15) were analyzed for comparison. We analyzed skin bacteria and oral microbiomes and used vegetation and deadwood inventories, satellite data, and questionnaires to determine the effects of rewilding, living environment, and lifestyle factors on skin and oral microbiota, functional gene pathways, and cytokine levels (IL-6, IL-10). Neighborhood deadwood within 200-m radii around home yards was used as an indicator of environmental biodiversity. Samples were collected before the rewilding in summer and three months later in autumn. Skin microbial diversity stayed constant and was associated with plant richness in the rewilding group, despite the normal seasonal decline and reduced outdoor time in autumn. Rewilding was associated with a decrease in tetrahydrofolate biosynthesis and salvage, and L-histidine degradation gene pathways and other changes in oral microbiota. In the rewilding group in autumn, picking of berries and fruits was directly associated with immunoregulatory IL-10 and pleiotropic IL-6 in saliva, and neighborhood deadwood abundance with the fatty acid biosynthesis superpathway in oral microbiomes. When groups were analyzed jointly, the diversity of oral microbial functional gene pathways was negatively correlated with IL-6 levels, and neighborhood deadwood abundance was directly linked to skin Gammaproteobacterial taxa, and typically soil-derived Cytobacillus sp. CY-G and Streptomyces sp. HSG2 in saliva.

Our findings are consistent with the biodiversity hypothesis, suggesting that biodiversity exposure may influence commensal microbiomes and biological pathways involved in host-microbe interactions. Our results suggest that the amount of decaying deadwood in the neighborhood, in addition to conventional measures of greenness and vegetation diversity, may provide advantageous information in studies examining human-environment microbiome interactions. This may inform biodiversity-related ecosystem services related to impacts on human health. Our findings provide an incentive for future studies and strategic investments for rewilding urban microbiomes to support planetary health. Video Abstract.