The Gut Microbiome & Systemic Health
Humans host roughly as many bacterial cells as human cells (Sender 2016), and the gut microbiome participates in digestion, immune regulation, metabolism and gut-brain signaling (Cryan 2019). Diet measurably reshapes microbial composition within weeks (Valdes 2018, BMJ). Testing is genuinely informative for guiding nutrition strategy — but it is an assessment tool, not a diagnostic, and single-sample results require careful interpretation.
Written/Reviewed by: Dr. Michael Ellis, DO — Medical Director
Scientific/Technical contribution: John Campetella
Last medical review: June 2026
What is established
The revised cell-count estimates put bacteria at ~38 trillion cells — a 1:1 order of magnitude with human cells. Microbial genes vastly outnumber human genes, and microbial metabolites (short-chain fatty acids, neurotransmitter precursors) have measurable systemic effects on immunity, metabolism and the nervous system.
The gut-brain axis
Cryan's comprehensive Physiological Reviews synthesis documents bidirectional gut-brain communication via the vagus nerve, immune signaling and microbial metabolites, with animal and growing human evidence connecting microbiome composition to stress physiology, mood and cognition.
Modifiability
Dietary fiber diversity, fermented foods and overall dietary pattern shift microbiome composition within weeks — making the microbiome one of the most modifiable systems in the body, and dietary intervention the best-supported lever.
Limitations
A single stool sample is a snapshot of a dynamic ecosystem; healthy microbiome composition varies widely between individuals; and direct causal evidence in humans for many microbiome-condition links is still developing. Generic probiotic supplementation unmatched to sequencing results has inconsistent evidence.
The Integrated Wellness approach
We sequence composition and functional capacity, read the results against inflammatory labs, food-response and recovery data in the Matrix Engine, and target intervention at the specific functions your ecosystem is missing — then retest to confirm the shift.
A = consistent RCT/meta-analytic · B = strong observational/mixed · C = limited · Emerging = active research
- Sender R, Fuchs S, Milo R (2016). Revised estimates for the number of human and bacteria cells in the body. PLoS Biology.
- Cryan JF, et al. (2019). The microbiota-gut-brain axis. Physiological Reviews.
- Valdes AM, et al. (2018). Role of the gut microbiota in nutrition and health. BMJ.