Upcycling human excrement: the gut microbiome to soil microbiome axis

Human excrement composting (HEC) is a sustainable strategy for human excrement (HE) management that recycles nutrients and mitigates health risks while reducing reliance on freshwater, fossil fuels, and fertilizers. A mixture of HE and bulking material was collected from 15 composting toilets and composted as 15 biological replicates in modified 19-liter buckets under mesophilic conditions with weekly sampling for one year. We hypothesized that (i) the microbiome of 1 year old compost would resemble that of a soil and/or food and landscape waste compost microbiome more closely than the original HE; and (ii) the human fecal indicators, <i>Escherichia coli</i> and <i>Clostridium perfringens</i>, would be undetectable after 52 weeks using qPCR and culturing. This investigation identified unique successional trajectories within buckets (i.e. biological replicates) and significant shifts in microbial communities around 25 weeks across buckets, with reductions in fecal-associated taxa and increases in environmental taxa indicating effective composting. We present a comprehensive microbial time series analysis of HEC and show that the initial gut-like microbiome of HEC systems transitions to a microbiome similar to soil and traditional compost but that pathogen risk assessment is important if thermophilic temperatures are not achieved. This study also produced the highest resolution composting microbiome data to date, establishing a baseline for HEC optimization and thermophilic composting studies while serving as a resource for bioprospecting for enzymes and organisms relevant to upcycling waste.