Application of microbiome-based medicine software tools to track microbial community transitions during composting of human excrement

During our lab’s initial human excrement compost (HEC) investigation (Meilander et al. 2025), Andrew Manley utilized ANCOMBC (Analysis of Compositions of Microbiomes with Bias Correction) and q2-FMT (Herman et al. 2025), a QIIME 2 plugin originally designed to track microbiome engraftment in fecal microbiota transplants, to monitor microbial succession during a 52-week mesophilic composting process. His findings showed that HEC microbiomes become increasingly dissimilar to their gut-associated origins and increasingly similar to soil and compost communities, with enriched taxa linked to soil functions such as nutrient cycling and plant growth promotion. This work demonstrates the ecological importance of using HEC in closed-loop nutrient cycles and expands the analytical utility of q2-FMT beyond its original clinical context.

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