“Your Gut Is Talking to Your Brain. Here’s How.”

There are an estimated 38 trillion bacteria living in the human body, roughly the same order of magnitude as the number of human cells.

Most of them live in your gut.

But the interesting part isn’t how many are there. It’s what they are doing.

Gut microbes break down parts of food we cannot digest ourselves, produce metabolites that interact with our immune system, influence the intestinal barrier and communicate with nerves running between the gut and the brain.

In 2025, scientists went one step further. In mice, they identified a neural circuit capable of detecting a molecule produced by gut bacteria and relaying that information towards the brain.

Your gut, it turns out, is much more than a digestive tube.

First: what exactly is your microbiome? (1)

Your microbiota is the collection of microorganisms living in and on you, including bacteria, viruses, fungi and other microbes. The microbiome includes those microorganisms along with their genes, products and surrounding environment.

The largest microbial community lives in the gastrointestinal tract, particularly the colon.

One widely cited calculation estimates that a typical 70 kg adult male contains around 38 trillion bacterial cells and 30 trillion human cells. The exact number varies enormously between people, but it corrected an older myth that bacteria outnumber our own cells by 10 to 1.

The ratio is actually much closer to one to one.

So are we half bacteria?

By cell count, roughly.

By mass, definitely not. Those bacteria together are estimated to weigh only around 200 grams.

What are all those bacteria doing? (2,3)

Some of the most important work happens when your microbes get access to food that your own digestive enzymes cannot completely break down.

Dietary fibre is a good example.

Certain gut bacteria ferment fibre and produce molecules called short-chain fatty acids, predominantly acetate, propionate and butyrate.

These are not simply waste products.

Butyrate is used extensively by cells lining the colon, while short-chain fatty acids can interact with immune cells, receptors, metabolism and intestinal barrier function. A major 2025 review in Nature Reviews Microbiology describes them as microbial metabolites with effects extending well beyond the bacteria that produced them.

This means something quite strange is happening every time you eat fibre.

You do not possess all the enzymes necessary to extract everything from it yourself. Instead, some of what you eat becomes food for your microbes, and what they make from it can then interact with you.

It is less like feeding one organism and more like feeding an ecosystem.

So how can something in your gut communicate with your brain? (4)

The phrase gut-brain axis can make this sound slightly mystical.

It isn't.

There are several physical communication routes between the gut and brain, including the nervous system, immune signalling, hormones and molecules produced or modified by gut microbes.

One of the major neural routes is the vagus nerve, which carries sensory information from internal organs towards the brain.

The gut lining also contains specialised sensory cells capable of detecting what is happening inside the intestine. Some sit remarkably close to sensory nerve endings, creating a route by which information in the gut can be translated into a nervous-system signal.

A major 2025 review described this interface between microorganisms, intestinal sensory cells and nerves as an emerging biological system through which microbial information can reach the nervous system.

And then researchers actually watched one of these circuits work.

In 2025, scientists found what they called a “neurobiotic sense” (5)

This is one of the most interesting recent findings in gut-brain research.

Researchers publishing in Nature studied flagellin, a structural protein found in the flagella used by many bacteria.

They found specialised sensory cells in the mouse colon capable of detecting this microbial signal.

Those cells then released PYY, which activated neurons connected to the vagus nerve. The signal travelled towards the brain and changed feeding behaviour.

When researchers disrupted the system, the mice ate more and gained more weight.

The scientists called it a “neurobiotic sense”: a sensory mechanism through which the animal could detect a molecular pattern associated with the microorganisms living inside it.

This was a mouse study, so we cannot assume exactly the same mechanism controls human behaviour.

But mechanistically, it is important.

Gut-to-brain communication is no longer just an abstract idea based on associations between microbes and mood. Researchers can now trace specific sensory cells, receptors and neurons involved in transmitting microbial information.

Does your gut really make serotonin? (6)

Yes.

But this is also one of the most misunderstood facts in microbiome science.

Around 95% of the body's serotonin is produced outside the brain, predominantly in the gastrointestinal system, much of it by specialised enterochromaffin cells in the intestinal lining. Gut microbes and microbial products can influence this production.

This has led to the often repeated claim that your gut “makes your happiness hormone”.

That is not quite how it works.

Serotonin produced in the gut does not cross the blood-brain barrier and simply become serotonin inside your brain. Peripheral and brain serotonin largely operate as separate pools.

Gut serotonin still matters enormously. It is involved in intestinal movement, secretion, sensation and other signalling processes. The microbiome can also affect tryptophan metabolism and other pathways that may influence communication between the gut and nervous system.

But “95% of serotonin is made in the gut” does not mean “95% of your happiness comes from your gut”.

The real biology is more interesting than the slogan.

Your microbiome can change surprisingly quickly (7)

Your microbiome is partly shaped over years, but parts of it can respond to what you eat remarkably fast.

In a well-known controlled study published in Nature, researchers gave participants diets made entirely from either animal or plant foods and tracked what happened to their gut microbes.

The microbial community responded within days.

On the animal-based diet, bile-tolerant species increased while several bacteria involved in breaking down plant polysaccharides decreased. Microbial gene activity also changed substantially.

So the microbiome is not a fixed collection of organisms you acquire in childhood and keep forever.

It is an ecosystem constantly responding to its environment.

Food is part of that environment.

So are medication, illness, age and many other aspects of daily life.

Does eating more fibre automatically create a “better” microbiome?

Not necessarily, and this is where microbiome science gets more interesting.

A Stanford randomised dietary study compared diets high in fibre with diets high in fermented foods in healthy adults over 10 weeks.

The fermented-food group showed an increase in microbial diversity and reductions across a panel of inflammatory proteins. The high-fibre group, unexpectedly, did not show an overall increase in microbial diversity over the same period.

That does not mean fibre is unimportant. Fibre remains fundamental to gastrointestinal and wider health, and different fibres feed different microbial communities.

Instead, the study showed that microbiomes do not all respond identically to the same intervention.

Researchers also found that participants' starting microbiomes appeared to influence how they responded to increased fibre.

Which brings us to one of the biggest problems with the phrase “healthy gut”.

We still don't know what the perfect microbiome looks like (8)

There probably isn't one.

Two healthy people can have remarkably different collections of gut microbes.

A major 2025 Nature Reviews Microbiology paper involving an international group of microbiome researchers examined exactly this question and concluded that defining one universally “healthy” microbiome remains extremely difficult.

Microbial communities vary by person, geography, age, diet, medication, environment and over time. Different bacterial communities can also perform overlapping biological functions.

So a microbiome test telling you that one particular bacterium is “low” does not necessarily mean something is wrong.

And simply having more microbial diversity does not automatically equal better health in every context.

What the microbes do may ultimately be as important as exactly which names appear on the list.

Can changing the gut microbiome actually change cognition? (9)

This is where the evidence becomes particularly interesting, but also where we need to separate promising research from established fact.

In 2024, researchers studied 36 pairs of twins aged 60 or older in a double-blind randomised controlled trial.

One twin received a daily prebiotic containing inulin and fructo-oligosaccharides, while the other received a placebo. Both groups also received protein supplementation and an exercise programme.

After 12 weeks, the prebiotic changed the gut microbiome, including an increase in Bifidobacterium.

The researchers also found a statistically significant improvement in a combined cognitive score in the prebiotic group compared with placebo. There was no significant improvement in the trial's primary physical outcome.

It was a relatively small study in older adults, so it would be a big leap to claim that prebiotics generally make people smarter.

But it matters because this is human randomised evidence, not simply an observational link between certain bacteria and certain behaviours.

The next question is whether findings like this can be reproduced in larger groups, across different ages, with different fibres and with clearly defined mechanisms.

What about the microbiome and ADHD? (10)

This area has grown quickly, but the results are nowhere near as settled as social media sometimes suggests.

A systematic review published in June 2026 examined 23 human studies comparing the gut microbiota of children with and without ADHD.

Most studies found no significant difference in alpha diversity, meaning the overall diversity within an individual's microbiome was not consistently lower or higher in ADHD.

Differences in beta diversity, which looks at how microbial communities differ between groups, appeared more frequently. Some bacterial patterns also appeared repeatedly, including lower abundance of certain butyrate-producing bacteria such as Faecalibacterium.

But results were inconsistent between studies and affected by differences in diet, age, geography, medication, sequencing methods and other potential confounders.

So there is a signal worth studying.

There is not yet an “ADHD microbiome”.

And there is currently no convincing evidence that changing one particular bacterial species treats ADHD.

That distinction is important.

The gut-brain axis works both ways

We normally hear about the gut influencing the brain.

The brain also influences the gut.

Stress, autonomic nervous system activity, intestinal movement, secretions and eating behaviour can all alter the environment microbes live in. Recent mechanistic research has even shown brain circuits capable of rapidly changing gut microbial composition in mice.

So the gut-brain axis is not:

gut → brain

It is:

gut ↔ brain

with the immune system, nervous system, diet, microbial metabolites and hormones sitting between them.

This is why reducing everything to “good bacteria” and “bad bacteria” misses most of the interesting biology.

So what do we actually know?

We know the human gut contains an enormous microbial ecosystem. We know microbes metabolise parts of our diet that our own enzymes cannot, producing compounds that interact with intestinal, metabolic and immune systems. We know the gut has direct neural connections with the brain, and animal experiments can now trace some microbial signals through specific gut sensory cells and neurons.

We also know diet can change microbial activity quickly, that different people respond differently to the same foods, and that human trials are beginning to show measurable effects of microbiome-targeted interventions outside the gut.

What we do not yet have is a universal definition of the perfect microbiome, a single bacterial profile that explains cognition or ADHD, or evidence that manipulating one microbe gives predictable effects in everyone.

The science is moving quickly.

The most interesting shift may be a fairly simple one: the gut is no longer being studied as an organ that just processes food.

It is being studied as an ecosystem, an immune interface, a metabolic organ and a sensory system communicating continuously with the rest of the body.

And we are only beginning to understand the conversation.

References
Sender R, Fuchs S, Milo R. Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLoS Biology. 2016.
Mukhopadhya I, Louis P. Gut microbiota-derived short-chain fatty acids and their role in human health and disease. Nature Reviews Microbiology. 2025.
Sanz Y, Cryan JF, Deschasaux-Tanguy M, et al. The gut microbiome connects nutrition and human health. Nature Reviews Gastroenterology & Hepatology. 2025.
Ohara TE, Hsiao EY. Microbiota-neuroepithelial signalling across the gut-brain axis. Nature Reviews Microbiology. 2025.
Liu WW, Reicher N, Alway E, et al. A gut sense for a microbial pattern regulates feeding. Nature. 2025.
Banskota S, Ghia JE, Khan WI. Serotonin in the gut: Blessing or a curse. Biochimie. 2019; together with subsequent reviews of gut-derived serotonin signalling.
David LA, Maurice CF, Carmody RN, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014.
Joos R, Boucher K, Lavelle A, et al. Examining the healthy human microbiome concept. Nature Reviews Microbiology. 2025.
Ni Lochlainn M, et al. Effect of gut microbiome modulation on muscle function and cognition: the PROMOTe randomised controlled trial. Nature Communications. 2024.
Rodrigues B, Miranda IM, Costa de Oliveira S. Gut Microbiota Composition and Diversity in Attention-Deficit/Hyperactivity Disorder: A Systematic Review. Microorganisms. 2026.

This journal is for general education and is not medical advice.