The Garden(er) Microbiome Project

Garden soil contains tens of thousands of different microbial species, including bacteria, fungi, viruses, and archaea, and millions to billions of individual microorganisms. Humans evolved for millenia in the presence of these environmental microbes associated with vegetation, soil, water, and wildlife. Our immune systems are not only adapted to coexist with the majority of these microbes, but may even require that interaction to function properly. Emerging scientific evidence suggests that exposure to soil microbes trains the immune system, reduces inflammation, and improves mental health (Rook, 2013). For example, the common soil bacterium Mycobacterium vaccae has been found to have positive impacts on stress tolerance and mental health (Matthews and Jenks, 2013), while other research has shown that children exposed to greater microbial diversity, such as that encountered in farming environments, tend to have lower prevalence of autoimmune disorders, including allergies and asthma, than their urban counterparts (Hanski et al., 2012).

Therefore, the primary goals of this study were to understand how much microbial transfer from soil to skin occurs during gardening activities, what types of microorganisms are transferred, and how long they can persist on the skin. We were also interested in exploring how soil microbial communities vary with different management practices (e.g., organic vs. conventional) and geographic locations, as we know that microbes play critical roles in soil nutrient cycling, carbon sequestration, pollutant degradation, and water purification.

To accomplish this study, we recruited 40 gardeners to collect microbial samples from their garden soil and from the surface of their skin (hands). All samples were collected in July–September, 2020, and were equally distributed between Oregon’s Willamette Valley and High Desert regions, as well as between self-reported organic and non-organic management practices. Each volunteer was asked to collect soil samples from three different garden beds and skin microbiome swabs at four timepoints (before, after, ~12 hours after, and 24 hours after gardening). To identify bacterial taxa (different types of bacteria) present in the samples, we used Earth Microbiome Project protocols to sequence the V4 region of the bacterial 16S rRNA gene.

The map below provides an interactive tool to explore results of this study.