Impact of Compost Amendments on the Human Gut Microbiota During Gardening

OBJECTIVES: To measure associations between gardening with three different types of compost amendments and the human gut microbiota composition. METHODS: Gardeners (n = 25) were provided with one of three types of compost: chicken manure (CM), compost with dairy manure and plant material (DMP), or plant-based compost (P). Stool samples were collected before gardening (T1), after amending soil with compost (T2), and at the peak of garden harvest (T3). Compost and soil samples were also collected. DNA was extracted from the samples, 16S rRNA libraries were made, and libraries were sequenced by Illumina MiSeq. Sequences were processed using mothur, and data were analyzed in R. Kruskal-Wallis with post hoc Dunn test was performed to compare Shannon Alpha diversity. Individual taxa were compared between time points using a negative binomial test. Fast expectation-maximization microbial source tracking (FEAST) analysis was used to determine stool bacteria sources. Proportions were compared by Chi-Square. RESULTS: At T2 and T3, gut bacterial communities of participants who used P compost had lower Shannon alpha diversity compared to the gut bacterial communities of participants using the other two compost types, and this was also the trend at T1. In T2 stool, Ruminococcus 1 and Ruminococcus 2 were less abundant in the microbiotas of those using P compost as compared to those using CM or DMP. However, at T1, Ruminococcus 2 was less abundant in the microbiotas of individuals that later used P as well as those that later used CM compared to those who later used DMP. During T2, Prevotella 9 had the highest abundance in the microbiotas of those using P compost. In participants who used CM compost to amend their gardening plots, a larger proportion of the human stool bacteria were sourced from CM compared to soil. CONCLUSIONS: Soil exposure through gardening was associated with a small but detectable change in the gardeners’ gut microbiota composition. These results suggest that human interactions with soil through gardening could potentially impact health through alterations to the gut microbiota. FUNDING SOURCES: USDA NIFA AFRI.