From the ancient “Yellow Soup” to modern microbiome medicine: the scientific renaissance of fecal microbiota transplantation and the phyllosphere logic of herbal bioactivation

Abstract

Fecal microbiota transplantation (FMT) has become one of the most robustly substantiated – yet culturally contentious – interventions in microbiome medicine over the past decade, particularly for recurrent Clostridioides difficile infection (rCDI). This paper surveys the historical roots of FMT from the ancient Chinese “Yellow Soup” (huanglongtang) tradition to contemporary randomized clinical trials, and outlines the mechanistic basis of efficacy: restoration of colonization resistance, reconstruction of microbial community functions (metabolite profiles), and the role of the primary–secondary bile acid axis in the ecological suppression of C. difficile (Gurung et al., 2024; McMillan et al., 2024; van Nood et al., 2013). The systems-level, “ecosystem-therapeutic” framework is then extended to questions of herbal bioavailability by introducing the concept of a “metabolic gap”: under dysbiosis, reduced gut-microbial biotransformation capacity may prevent a substantial fraction of phytochemicals from being converted into bioactive metabolites (Alqudah et al., 2024; Chen, 2025). As a plausible natural-biotechnological solution, the paper discusses the use of phyllosphere microbial communities in microbiome-assisted fermentation–extraction workflows, drawing on the natural fermentation analogy of bee bread (perga) (Bakour et al., 2022; El-Didamony et al., 2024). In conclusion, the paper argues that supporting health and regeneration – both in clinical microbiome therapeutics and botanical approaches – progressively converges on the logic of restoring, or partially substituting for, ecological balance and microbial functions (Du et al., 2019; U.S. FDA, 2022; U.S. FDA, 2023).