When you feel butterflies in your stomach before an important presentation, or lose your appetite in a moment of intense stress, your gut is responding to signals from the brain. But it works in the other direction too. The gut sends three times more signals to the brain than the brain sends to the gut. This isn’t a metaphor; it’s why the idea that the gut is the second brain has solid scientific foundations. Find out how trillions of bacteria in your gut shape mood, immunity, and longevity!
What’s worth knowing about the gut and microbiome:
- The enteric nervous system contains more than 500 million neurons – as many as the spinal cord
- 90% of serotonin – the neurotransmitter responsible for mood – is produced in the gut
- The gut microbiome weighs 1-2 kg and contains ten times more cells than the human body
- The gut-brain axis communicates via the vagus nerve, the immune system, and hormones
- Diet and lifestyle change the microbiome’s composition within 24-48 hours of a shift in habits
Why is the gut called the second brain?
The enteric nervous system (ENS) contains more than 500 million neurons distributed throughout the entire digestive tract. That’s fewer than the brain (86 billion), but far more than the spinal cord. The ENS operates independently of the brain: it regulates peristalsis (the muscular contractions that move food through the gut), the secretion of digestive juices, and blood flow in the gut. Claim that the gut is the second brain is therefore more than a figure of speech. The ENS can function autonomously even without a connection to the brain.
Metaphor of a “second brain” has anatomical justification. The gut synthesises neurotransmitters identical to those produced by the brain: 90% of serotonin, 50% of dopamine, and 100% of melatonin in the body originates in the gut or depends closely on gut processes. When the gut’s microbial balance is disrupted, it can affect the production of these substances. And through them, mood, sleep, and the ability to concentrate.
How does the gut communicate with the brain?
The gut communicates with the brain mainly through the vagus nerve. Transmitting signals in both directions, with around 80% of the vagus nerve’s fibres running from the gut to the brain, and only 20% going the other way. This explains why the state of the gut has such a significant effect on wellbeing. Chronic stress disrupts this communication, leading to gut dysbiosis (a disrupted microbial balance).
Gut bacteria – who are they and what do they do?
How many bacteria live in the gut?
The human gut is home to around 38 trillion bacteria belonging to more than 1,000 different species. Total mass of the gut microbiome is 1-2 kilograms – about the same as the liver. Dominant strains are Firmicutes and Bacteroidetes, which together account for 90% of the microbiome. The ratio between these groups is one indicator of gut health. An excess of Firmicutes is associated with obesity and inflammation.
Key functions of gut bacteria:
- Production of short-chain fatty acids – butyrate nourishes the gut lining and reduces inflammation
- Vitamin synthesis – bacteria produce vitamin K2, B12, folic acid, and biotin
- Immune system regulation – 70-80% of immune cells are found in gut-associated tissue
- Drug and toxin metabolism – bacteria activate or deactivate chemical substances absorbed from food
- Communication with the brain – via the vagus nerve and neurotransmitter production
How does the microbiome affect mood and emotions?
The microbiome influences mood through the production of serotonin and GABA. Neurotransmitters that regulate mood and anxiety – and via direct vagus nerve signals to the brain. Dr Emeran Mayer, a gastroenterologist at UCLA and author of research on the gut-brain axis, states: “The gut microbiome is involved in regulating mood, emotions, and cognitive function in ways we couldn’t have imagined 20 years ago.” Anxiety and depression frequently co-occur with gut disorders – and that’s no coincidence.
Gut bacteria produce or stimulate the production of GABA (gamma-aminobutyric acid, a neurotransmitter that calms the nervous system), serotonin, and other neurotransmitters. Shifts in the microbiome’s composition – for instance after a course of antibiotics – can trigger temporary mood fluctuations. Germ-free mice (raised without any microbiome) have higher stress hormone levels and are more anxious than mice with a normal microbiome.
What destroys gut microflora?
Antibiotics, a highly processed diet, and chronic stress are the three main factors that destroy the gut microbiome. A single course of antibiotics can destroy up to 30% of bacterial species, and full restoration takes months. A highly processed diet with little fibre starves bacteria that need fermentable plant substrates. Chronic stress, through cortisol, disrupts peristalsis and alters gut permeability.
Main threats to the microbiome:
- Antibiotics – essential for treatment, but when taken too often or without clear indication, they destroy beneficial bacteria
- A diet high in sugar and processed food – feeds harmful strains while starving beneficial ones
- Chronic stress – cortisol alters the gut’s pH and microbiome composition
- Poor sleep – the microbiome has its own circadian rhythm, and disrupted night-time sleep disturbs its composition
- Pesticides and preservatives – some herbicide compounds and additives such as E-221 have demonstrated antibacterial effects
Foods that support a healthy gut
Fermented foods are one of the best ways to deliver live bacteria directly to the gut. Kefir, kimchi, miso, tempeh, and sauerkraut contain anywhere from millions to billions of colony-forming units (CFU) per serving. Fermented foods are a more effective way to support the microbiome than most probiotic supplements, as they contain live cultures within a natural food matrix.
Foods that support the microbiome:
- Kefir and natural yoghurt – contain Lactobacillus and Bifidobacterium, supporting gut barrier integrity
- Sauerkraut and kimchi – rich in Lactobacillus plantarum and fibre; unpasteurised versions retain live cultures
- Legumes and wholegrains – prebiotic fibre that feeds beneficial bacteria
- Garlic, onion, and leek – contain inulin, which selectively feeds Bifidobacterium
- Extra virgin olive oil – polyphenols act as selective prebiotics
Do probiotics really help?
Probiotic supplements have proven uses in several specific situations. Antibiotic-associated diarrhoea, irritable bowel syndrome, and some forms of inflammatory bowel disease. Beyond these indications, the evidence is less clear. Probiotics in capsule form rarely colonise the gut permanently – bacteria pass through the digestive tract and are excreted within a few weeks. Even so, they can temporarily improve the gut environment and stimulate the body’s own microbiome.
How to look after gut health every day
The most effective way to care for your gut is to eat 30 different types of plants a week – that level of variety produces a microbiome twice as species-rich as in people eating fewer than 10 plant types, as the American Gut Project, the world’s largest microbiome study, consistently confirms. You don’t need supplements – eating a varied diet, choosing minimally processed foods, and adding fermented products is enough. Bacterial composition shifts within just 24-48 hours of changing eating habits.
FAQ: Frequently asked questions about the gut and microbiome
Does the gut affect mental health?
The gut-brain axis is a well-documented mechanism through which the gut microbiome influences mood, anxiety levels, and cognitive function – mainly via the production of serotonin, GABA, and short-chain fatty acids.
How quickly can gut microflora be improved?
The first changes in microbiome composition can appear within 24-48 hours of modifying the diet, though lasting shifts in bacterial populations require consistent changes maintained over several weeks.
Do antibiotics destroy gut bacteria?
Antibiotics destroy both harmful and beneficial gut bacteria – a single course can eliminate up to 30% of species, and full microbiome recovery takes anywhere from several months to a year.
References:
- Cryan, J. F., et al. (2019). The microbiota-gut-brain axis. Physiological Reviews. https://doi.org/10.1152/physrev.00018.2018
- Sonnenburg, J. L., & Bäckhed, F. (2016). Diet-induced alterations in gut microflora contribute to lethal pulmonary damage in TLR2/TLR4-deficient mice. Nature. https://doi.org/10.1038/nature18846
