Your gut contains more microorganisms than there are stars in the Milky Way — and most of them are working hard to keep you well
The gut microbiome is the community of trillions of bacteria, fungi, viruses, and other microorganisms that live in your digestive tract. Most of them are found in the large intestine, and together they weigh roughly 1–2 kg.
That might sound alarming. But the vast majority of these organisms aren’t harmful. They’re essential. Without them, your immune system, digestion, mood, and metabolism wouldn’t function properly.
Here’s what the research actually shows about your gut microbiome — and why looking after it may be one of the most important things you can do for your long-term health.
What the Gut Microbiome Does
The gut microbiome isn’t just a passive resident in your digestive system. It’s an active participant in hundreds of processes across your body.
Digestion and nutrient absorption
Many of the nutrients in plant foods — particularly fibre — can’t be broken down by your own digestive enzymes. Gut bacteria do that work instead, fermenting fibres and producing short-chain fatty acids (SCFAs) like butyrate, acetate, and propionate.
Butyrate in particular is the primary energy source for the cells lining your colon. A well-fed microbiome keeps the gut lining intact and reduces intestinal permeability (sometimes called “leaky gut”).
Immune regulation
Around 70–80% of your immune system is in your gut. The microbiome trains immune cells to distinguish between harmless substances and genuine threats. Research published in Cell (2021) found that gut bacteria directly regulate the activity of T-cells and other immune components.
A disrupted microbiome — a state called dysbiosis — is associated with increased inflammation and a higher risk of autoimmune conditions.
Mood and mental health
The gut and brain communicate constantly through the vagus nerve, the immune system, and a class of signalling molecules called neurotransmitters. Your gut bacteria produce or influence around 90% of the body’s serotonin.
Research from Psychosomatic Medicine (2017) found associations between gut microbiome composition and symptoms of depression and anxiety. This connection is known as the gut-brain axis — and it’s one of the most active areas of current research. You can read more about it in our post on the gut-brain axis and mood.
Metabolism and weight regulation
The microbiome plays a role in how efficiently your body extracts energy from food and how fat is stored. Studies in Nature (Turnbaugh et al., 2006) showed that germ-free mice gained significantly more body fat when colonised with microbiomes from obese donors — even without eating more calories.
Microbiome Diversity: Why It Matters So Much
Not all gut microbiomes are equal. The key measure of a healthy microbiome isn’t any single strain of bacteria — it’s diversity.
A diverse microbiome contains a wider range of bacterial species, each contributing different functions. Lower diversity is consistently associated with obesity, type 2 diabetes, inflammatory bowel disease, and depression.
Research from the American Gut Project (McDonald et al., mSystems, 2018) — one of the largest microbiome studies ever conducted — found that people who ate 30 or more different plant foods per week had significantly more diverse gut microbiomes than those eating fewer than 10.
The variety of fibre sources matters as much as the quantity. Different bacterial species feed on different types of fibre. Eating a wide range of vegetables, fruits, legumes, and whole grains feeds a wider range of bacteria.
What Disrupts the Gut Microbiome
Several common lifestyle factors can reduce microbiome diversity and shift it towards dysbiosis.
- Antibiotics — necessary when prescribed, but they kill beneficial bacteria alongside harmful ones. Studies show it can take 6–12 months for the microbiome to recover after a course of antibiotics.
- Ultra-processed foods — emulsifiers, artificial sweeteners, and preservatives found in many packaged foods can alter microbiome composition. Research in Nature (Suez et al., 2022) found that commonly used artificial sweeteners changed gut bacteria in ways associated with glucose intolerance.
- Chronic stress — sustained stress alters gut motility and the composition of the microbiome, partly through the cortisol-gut axis.
- Low fibre intake — the average UK adult eats around 18g of fibre per day, well below the NHS recommended 30g. Without adequate fibre, the bacteria that produce butyrate starve.
- Lack of sleep — disrupted sleep patterns alter the composition and activity of the gut microbiome, according to research in Sleep Medicine Reviews (2019).
How to Support a Healthy Gut Microbiome
The good news: the microbiome is responsive. Unlike your DNA, it can change relatively quickly — sometimes within days — in response to what you eat.
Increase plant variety
The 30 plants per week target from the American Gut Project is a useful benchmark. This includes vegetables, fruits, whole grains, legumes, nuts, seeds, and herbs. Diversity matters more than eating large amounts of any single food.
Eat more fibre — different types
Prebiotic fibres (found in garlic, onions, leeks, oats, and bananas) specifically feed beneficial bacteria. Resistant starch (in cooked-then-cooled potatoes and rice) feeds butyrate-producing bacteria that competitors low in fibre can’t provide.
Include fermented foods
Fermented foods — yoghurt, kefir, sauerkraut, kimchi, kombucha, miso — contain live bacteria that may contribute to microbiome diversity. A randomised trial in Cell (Wastyk et al., 2021) found that a high-fermented food diet increased microbiome diversity more effectively than a high-fibre diet alone.
For more on this, see our post on fermented foods and gut health.
Consider a quality probiotic supplement
Probiotic supplements provide specific strains of beneficial bacteria. The evidence is strain-specific — not all probiotics do the same thing. The most researched strains include Lactobacillus rhamnosus, Lactobacillus plantarum, Lactobacillus casei, and Saccharomyces boulardii.
Our Biome Bliss supplement contains five clinically researched strains, fermented in organic honey and apple juice with 25 organic herbs — a format that mirrors the gut-supporting properties of fermented food rather than a standard encapsulated powder. If you’re specifically looking for a dairy-free option, see our guide to dairy-free probiotic drinks.
Manage stress and sleep
Regular physical activity, adequate sleep (7–9 hours), and stress management all support microbiome health. These factors are often overlooked but are as important as diet.
How the Microbiome Changes With Age
The gut microbiome isn’t static — it shifts throughout life. Infants have relatively simple microbiomes that diversify rapidly. By adulthood, the microbiome stabilises — though it continues to respond to diet, illness, and lifestyle.
After 40, microbiome diversity tends to decline gradually. Research published in Gut (2012) found that older adults have lower levels of Bifidobacterium and other beneficial species compared to younger adults eating similar diets.
This makes active microbiome support — through diet and targeted supplementation — particularly relevant for people in midlife and beyond.
The Microbiome Is Still Being Mapped
It’s worth being clear about the limits of current knowledge. Microbiome science is moving fast, but much of it is still observational. Studies can show associations between microbiome composition and health outcomes — but proving causation is harder.
What is clear: diversity is consistently associated with better health outcomes. Feeding your gut bacteria a varied, plant-rich diet — and limiting the things that disrupt them — is supported by the best available evidence.
For a deeper look at how specific probiotic strains work, see our guide to probiotic bacteria strains.
FAQ
What is the gut microbiome made of?
The gut microbiome is a community of trillions of microorganisms — primarily bacteria, but also viruses, fungi, and archaea — that live mainly in the large intestine. It’s estimated to contain over 1,000 different bacterial species, though most people host around 150–400 distinct species at any one time.
Can you improve your gut microbiome?
Yes. The microbiome responds relatively quickly to dietary changes. Increasing plant food variety, eating more fibre, adding fermented foods, and reducing ultra-processed food intake can all shift microbiome composition within days to weeks. Probiotic supplements may also help restore beneficial strains.
What are signs of an unhealthy gut microbiome?
Common signs associated with disrupted gut microbiome (dysbiosis) include bloating, irregular bowel movements, frequent infections, fatigue, mood changes, and food sensitivities. These symptoms have many possible causes, so it’s worth speaking to your GP if they’re persistent.
Does everyone have the same gut microbiome?
No. Your microbiome is as individual as a fingerprint. It’s shaped by how you were born (vaginal vs. caesarean), whether you were breastfed, your early diet, antibiotic history, and your ongoing lifestyle. Even identical twins have meaningfully different gut microbiomes.
How long does it take to change your gut microbiome?
Some changes in microbiome composition can be detected within 24–48 hours of dietary change. More significant, sustained shifts take weeks to months. Consistency matters more than short-term interventions — a temporary change in diet produces a temporary change in the microbiome.
References
- Turnbaugh PJ et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006;444:1027–1031. PubMed
- McDonald D et al. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 2018;3(3). PubMed
- Wastyk HC et al. Gut-microbiota-targeted diets modulate human immune status. Cell. 2021;184(16):4137–4153. PubMed
- Suez J et al. Personalized microbiome-driven effects of non-nutritive sweeteners on human glucose tolerance. Cell. 2022;185(18):3307–3328. PubMed
- Claesson MJ et al. Gut microbiota composition correlates with diet and health in the elderly. Nature. 2012;488:178–184. PubMed
This article is for informational purposes only and does not constitute medical advice. If you have a digestive health condition or are considering supplementation, speak to your GP or a registered dietitian before making changes.
