HPC › Nutrition › Glossary
Microbiome refers to the complete community of microorganisms, including bacteria, viruses, fungi, and archaea, together with their collective genetic material, that inhabit the human body. The gut alone harbours an estimated 39 trillion microbial cells representing thousands of species, whose collective genome encodes more than 8 million distinct genes, dwarfing the approximately 20,000 protein-coding human genes.1
The term is often used interchangeably with microbiota, which refers strictly to the microbial organisms themselves; microbiome technically includes the organisms together with their collective genetic catalogue.
How it works
The gut microbiome's primary mechanism is fermentation. Resident bacteria break down dietary fibre via saccharolytic fermentation, producing short-chain fatty acids, principally acetate, propionate, and butyrate.24 These metabolites fuel colonocytes, activate immune-regulatory G-protein-coupled receptors, and inhibit histone deacetylases, reducing systemic inflammation at the genomic level. This functional range is underwritten by a collective microbial genome encoding over 8 million genes, compared with approximately 20,000 protein-coding human genes.1
A second major pathway runs along the gut-brain axis. Approximately 90-95% of the body's serotonin is synthesised not in the brain but in the gut, where enterochromaffin cells produce it under microbiome influence.3 The microbiota regulates this synthesis, directly shaping enteric nervous system maturation and modulating signalling along the hypothalamic-pituitary-adrenal axis. The microbiome functions like an internal chemical plant: running on dietary inputs and delivering neurotransmitter precursors throughout the body, not solely through the bloodstream.
Microbial composition is not fixed. A shift towards a diverse, high-fibre, plant-based diet consistently increases species richness and SCFA output within days, while low-fibre, high-fat diets reduce diversity at comparable speed.24 Consuming 30 or more distinct plant species per week is associated with significantly greater diversity and higher SCFA production than diets restricted to fewer than 10 plant varieties.4 Antibiotic use can collapse microbial diversity within days; some keystone species fail to reconstitute for months or permanently.2
Example
An endurance athlete with persistent low-grade fatigue and variable recovery adopts a structured dietary change: replacing refined carbohydrates with a rotation of legumes, varied vegetables, and other distinct plant foods, targeting 30 or more plant species per week. Within weeks, self-reported energy consistency improves alongside a stool diversity assessment showing increased species richness and higher short-chain fatty acid output.
The shift to botanical variety delivers measurable gains in microbial diversity and metabolic output within days to weeks, driven by diet alone.
Why it matters
Dysbiosis, a persistent imbalance in microbial composition, is implicated in an unusually broad disease spectrum. Obesity, type 2 diabetes, inflammatory bowel disease, cardiovascular disease, depression, and neurodegenerative conditions including Parkinson's disease have each been associated with characteristic microbiome disruptions, and in several cases microbiome changes precede clinical onset rather than follow it.43 A compromised gut allows microbial products to enter circulation through a leaky intestinal barrier, triggering chronic low-grade inflammation central to metabolic syndrome and insulin resistance.2
Via the microbiota-gut-brain axis, dysbiosis disrupts hypothalamic-pituitary-adrenal regulation and neurotransmitter production, contributing to heightened stress reactivity, anxiety, and mood disorders.3 Because the gut synthesises approximately 90-95% of the body's serotonin, a disrupted microbiome is not merely a digestive problem; it is a neurochemical one with consequences for stress tolerance, emotional regulation, and psychiatric health.
What is the difference between microbiome and microbiota?+
Microbiota refers to the living microorganisms themselves, such as bacteria, fungi, and archaea, that inhabit the body. Microbiome technically encompasses the microorganisms together with their collective genetic material. In practice, the terms are used interchangeably in scientific literature, though precision-focused texts maintain the distinction.{{cite:10.1038/nature06244}}
How does diet affect the gut microbiome?+
Dietary composition is one of the most powerful modifiers of microbial community structure. High-fibre, plant-diverse diets increase species richness and short-chain fatty acid output within days, while low-fibre patterns reduce diversity comparably quickly. Consuming 30 or more distinct plant species per week is associated with notably higher microbiome diversity than diets limited to fewer plant varieties.{{cite:10.1038/nature18846}}{{cite:10.1038/s41579-024-01068-4}}
Can the microbiome affect mood and mental health?+
Yes. The gut synthesises approximately 90-95% of the body's serotonin, and the microbiota directly regulates that synthesis. Via the gut-brain axis, microbial imbalances disrupt hypothalamic-pituitary-adrenal regulation and neurotransmitter production, elevating stress reactivity and contributing to anxiety and mood disorders.{{cite:10.1152/physrev.00018.2018}}
What causes an unhealthy microbiome (dysbiosis)?+
Low dietary diversity and low fibre intake are the primary dietary drivers, shrinking microbial richness and short-chain fatty acid output. Antibiotic use can collapse diversity within days, with some keystone species failing to reconstitute for months or permanently. High-fat, low-fibre diets produce similar shifts even without antibiotics.{{cite:10.1038/s41579-024-01068-4}}{{cite:10.1038/nature18846}}
