The human microbiome encompasses all microorganisms living in and on the human body. The gut microbiota — the largest and most extensively studied component — numbers approximately 100 trillion bacteria. The NIH launched the Human Microbiome Project (HMP) in 2007 to systematically map the human microbiota; the EU launched MetaHIT in 2010 to reveal gut microbiota genetic diversity through metagenomic sequencing.
## Core Functions of the Gut Microbiome
**Immune regulation**: the gut is the body’s largest immune organ, housing approximately 70-80% of immune cells. The gut microbiome trains and regulates the immune system by producing short-chain fatty acids (SCFAs — e.g., butyrate), influencing inflammation, allergy rates, and autoimmune disease risk. Germ-free mouse studies prove: without gut microbiota, the immune system cannot develop normally.
**Gut-brain axis**: the enteric nervous system (ENS) contains over 100 million neurons and communicates bidirectionally with the brain. Neurotransmitter precursors produced by gut bacteria (serotonin precursors — the gut produces approximately 95% of the body’s 5-HT), neuroactive metabolites, and vagus nerve signals influence mood, cognition, and sleep. Research associates gut microbiome composition with depression, autism, and Parkinson’s disease.
**Metabolic regulation**: the gut microbiome influences energy metabolism, insulin sensitivity, and lipid metabolism. Transplanting obese mice’s gut microbiota into germ-free mice causes weight gain even without dietary changes — demonstrating the causal role of microbiota in obesity. Specific strains (e.g., Akkermansia muciniphila) correlate positively with metabolic health and are becoming the next-generation probiotic research focus.
## TCM and Gut Microbiome Intersection
TCM theory’s “spleen-stomach as postnatal foundation” has a striking resonance with modern microbiome science:
Multiple studies show that many TCM formulas (e.g., Four Gentlemen Decoction, Middle Qi Supplementing Decoction) significantly alter gut microbiome structure, increasing beneficial bacteria and reducing harmful species. Part of Berberine’s glucose-lowering mechanism operates through gut microbiome regulation (increasing Akkermansia muciniphila) rather than direct insulin signaling — a finding that deeply connects TCM research with modern microbiome science.
## Clinical Applications
**Fecal Microbiota Transplantation (FMT)**: transplanting healthy donor fecal microbiota to patients achieves over 90% efficacy for Clostridioides difficile (C. diff) infection — FDA approved (Rebyota, 2022). Clinical trials continue in ulcerative colitis, inflammatory bowel disease, and obesity.
**Probiotic clinical evidence**: commercial probiotics (Lactobacillus, Bifidobacterium) have strong evidence for preventing antibiotic-associated diarrhea and improving lactose intolerance; evidence in other indications remains contested.
See [TCM Modernization Overview](https://sunqi.org/tcm-modernization-overview-en/) and [Human Microbiome Project](https://hmpdacc.org/).
