The second genome — what the gut microbiome is and why it matters more than we thought
Your gut contains roughly 100 trillion microorganisms encoding 150 times more genes than your own genome. They are not passengers — they are active participants in nearly every system in your body.
science
The human gut microbiome is a community of bacteria, fungi, archaea and viruses inhabiting the gastrointestinal tract, with the highest density in the large intestine. The total number of microbial cells is roughly equal to the number of human cells in the body, and the genes they encode outnumber human genes by a factor of 150. This has led researchers to describe the microbiome as a second genome — one that is far more variable between individuals than the human genome itself, and far more responsive to environmental inputs like diet, stress and medication.
The functions of the gut microbiome extend far beyond digestion. Gut bacteria ferment dietary that human digestive enzymes cannot break down, producing short-chain fatty acids — particularly butyrate, propionate and acetate — that serve as the primary fuel for colonocytes, maintain the integrity of the gut lining, regulate immune cell activity and communicate with the brain via the vagus nerve and the bloodstream. Without microbial fermentation, the gut barrier becomes more permeable, immune tone shifts toward chronic activation, and systemic inflammation increases.
Approximately 70% of the immune system resides in or immediately adjacent to the gut. The microbiome continuously trains immune cells to distinguish between harmless food and genuine pathogens — a process called immune tolerance. Disruption of the microbiome in early life, when this training is most critical, is associated with significantly higher rates of allergies, asthma and autoimmune conditions in adulthood
Roughly 90% of the body's serotonin is produced in the gut — not the brain. Gut bacteria modulate tryptophan availability, the precursor from which serotonin is synthesised, and influence the activity of the enzymes that convert it. Dysbiosis — an imbalance in the microbial community — is associated with altered serotonin signalling and has been linked to anxiety, depression and irritable bowel syndrome through multiple converging mechanistic pathways
The gut microbiome degrades nitrate from vegetables into nitrite, which is then converted to nitric oxide in the body — the molecule that regulates blood pressure, vascular tone and insulin sensitivity. Antibacterial mouthwash and certain medications that reduce stomach acid can disrupt this pathway, reducing the cardiovascular benefit of vegetable intake independently of how many vegetables are consumed
Microbial diversity — the number of distinct species present — is one of the most consistent predictors of metabolic and immune health. Higher diversity is associated with lower inflammation, better insulin sensitivity, lower BMI and greater resilience to pathogenic infection. Ultra-processed food, low-fibre diets, antibiotic use and chronic stress all reduce diversity; a variety of coloured plant foods, fermented foods and sources all support it
The gut microbiome has its own circadian rhythm, cycling through different metabolic activities across the 24-hour day in synchrony with the host's feeding and fasting cycle. Eating late at night, chronic sleep deprivation and shift work disrupt the microbiome's timing as well as the host's — providing a mechanistic link between irregular eating patterns and metabolic disease that operates through the gut
The microbiome is established in early life and shaped continuously thereafter. Vaginal birth, breastfeeding, diverse food exposure, outdoor play and limited early antibiotic use all contribute to a more diverse initial colonisation. These early exposures set a baseline that influences immune and metabolic health for decades. This is not a reason for anxiety in parents — most healthy childhood microbiomes develop robustly — but it explains why early dietary diversity matters beyond simple nutrition.
The most evidence-based dietary strategy for supporting the microbiome is also the simplest: eat a wide variety of plant foods. A landmark study found that people consuming 30 or more different plant foods per week had significantly more diverse microbiomes than those eating fewer than 10, regardless of whether they were vegetarian, vegan or omnivorous. The variety matters more than the category. Coloured vegetables, legumes, whole grains, nuts, seeds, herbs and fermented foods each contribute different types that feed different microbial populations.