You have probably been told that your gut microbiome is the key to everything: weight, mood, immunity, even your skin. Shops sell probiotics and home test kits, and social media counts plants by the week. If you already eat reasonably well, it is hard to know what deserves your attention and what is simply marketing.
The confusing part is that some of it is true. Diet does change your gut community within days, and antibiotics do disturb it.410 But much of what you read rests on mouse experiments and on associations in people, not on proof.6 The real science and the sales pitch often use exactly the same words.
This guide walks you through it in order: what the microbes in your gut actually do, which claims hold up in people, what shapes your microbiome from one week to the next, and the free habits with the best evidence. It ends with the signs that need a doctor first, and where we fit.
Before deciding what to eat, it helps to know who lives in your gut and what they do all day.
Trillions of microbes, and no single healthy pattern#
Your gut microbiome is the community of bacteria, with smaller numbers of fungi and viruses, living in your intestines, together with their genes. Every person's community is different, and no single pattern counts as the healthy one.
A careful recount in 2016 estimated about 38 trillion bacteria in a reference adult, roughly the same number as human cells, weighing about 0.2 kg in total. The old claim of ten bacteria for every human cell was wrong.1
The Human Microbiome Project, which sampled a large cohort of healthy adults, found that even healthy people differ remarkably in which microbes they carry. What the microbes could do, their metabolic pathways, was more stable between people than which species were present.2
Microbiome, in one sentence
The microbes living in a place, such as the gut, together with their genes. "Microbiota" means the microbes themselves; the two words are often used interchangeably.
Your microbes turn fibre into fuel for your colon#
Of everything these microbes do, one job is understood best: turning the fibre you cannot digest into short-chain fatty acids that feed your colon lining and act as signals elsewhere in the body. They also change bile acids and interact with your immune system.
Fibre that reaches the colon undigested is fermented by specialist microbes into short-chain fatty acids, mainly acetate, propionate and butyrate, and into gases. Butyrate is the main energy source for the cells lining the colon, and propionate travels to the liver, where it takes part in regulating glucose production.5
Gut microbes also transform bile acids into molecules that act as signals in metabolism.5 When fibre intake is low, fermentation shifts towards other nutrients, and a BMJ review describes evidence that a low-fibre Western diet degrades the protective mucus layer of the colon.5
Short-chain fatty acids, in one sentence
Small fatty acids, mainly acetate, propionate and butyrate, that gut bacteria make when they ferment fibre. Butyrate fuels the cells lining the colon.
Understand your gut better
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Knowing what the microbes do makes it tempting to credit them with everything. This chapter sorts what has been shown in people from what still rests on animal studies.
Much of the science still comes from mice#
The headlines run ahead of the evidence. In people, diet and antibiotics clearly change the microbiome, and donor stool clears a recurrent gut infection; most claims that microbes cause weight gain, mood changes or chronic disease rest on mice or on associations.
| Claim | Where the evidence stands |
|---|---|
| Diet changes the microbiome quickly | Shown in people: switching to an all-plant or all-animal diet changed the community within days.4 |
| Antibiotics disturb the microbiome | Shown in people, with a loss of diversity within days of starting a course.1011 |
| Donor stool can treat a gut infection | Shown in a randomised trial in people with recurrent C. difficile infection.7 |
| Low diversity goes with many diseases | Seen repeatedly in people, but an association: it does not show which comes first.5 |
| Gut microbes drive weight gain | Strongest evidence comes from mice; in people, mainly associations.5 |
| Specific microbes cause chronic disease | Mostly unproven in people; causal claims rest largely on transferring human microbes into mice.6 |
The gap between mice and people matters. A systematic review found that 95% of published studies (36 of 38) that transferred human gut microbes into germ-free rodents reported that the disease came across with them. The authors argue that such a high success rate is implausible and overstates the role of the microbiome in human disease.6
The clearest human example runs the other way. In a Dutch randomised trial in recurrent C. difficile infection, 13 of 16 people (81%) were free of the infection after one infusion of donor stool, compared with 4 of 13 (31%) on the antibiotic vancomycin alone.7 That is one specific infection, not evidence for gut health products in general.
One idea comes up in almost every microbiome headline, and it deserves a closer look: diversity.
Diversity is a useful marker, not a target to chase#
In general, a more varied gut community goes with better health, and lower diversity has turned up in several chronic conditions. Cause and effect are still being untangled, so diversity is best read as a sign of the ecosystem rather than a number to push up.
Lower bacterial diversity has been reported repeatedly in people with inflammatory bowel disease, coeliac disease, obesity, type 2 diabetes and atopic eczema, compared with healthy controls. A species-rich community may be more robust, because other microbes can take over a missing function.5
Diversity is not the whole story. Large increases in fibre can temporarily reduce diversity, because the microbes that digest that fibre multiply, and fibre trials can show clinical benefits without any change in diversity.5
Diversity, in one sentence
A measure of how many different microbial species live in a community and how evenly they are spread. It describes the ecosystem, not whether any single microbe is good or bad.
With the evidence in perspective, the practical questions come into view: how many plants, which foods, what antibiotics change, and whether a test can guide you.
Thirty plants is a prompt, not a proven threshold#
The popular figure of 30 comes from a single observational comparison, in which people who reported more than 30 types of plants a week had more diverse gut bacteria than those who reported 10 or fewer.3 The comparison was small, so the number works as a prompt, not a rule.
The American Gut Project collected stool samples from more than 10,000 volunteers. People who answered "more than 30" to the question "In an average week, how many different plants do you eat?" had higher bacterial diversity than people who answered 10 or fewer, and the variety of plants explained more than labels such as vegan.3
The limits matter: participants chose to take part, plant counts were self-reported, and the detailed comparison involved about 85 people at the two extremes.3 No trial has tested 30 plants against 20; the finding supports the direction, variety, not the number.
Fibre itself has much stronger evidence. In a series of meta-analyses covering 185 prospective studies and 58 trials, people with the highest fibre intakes had 15 to 30% lower all-cause and cardiovascular mortality, and lower rates of heart disease, stroke, type 2 diabetes and colorectal cancer, than those with the lowest. The benefits were greatest at 25 to 29 g of fibre a day.8
Fermented foods look promising in one small trial#
Fermented foods may help as well. In one small Stanford randomised trial, healthy adults who built up to about six servings a day for ten weeks gained microbiome diversity and lowered several inflammatory markers, a promising result that still needs confirming.
In the trial, 36 healthy adults were randomised to a high-fermented-food or a high-fibre diet, with 18 in each arm, ramping up over four weeks and then keeping it up for six. The fermented-food group went from about 0.4 to 6.3 servings a day of foods such as yoghurt, kefir, kombucha, kimchi and fermented vegetables. Their microbiome diversity rose steadily, and 19 of 93 inflammatory proteins measured in the blood fell, including interleukin 6.9
The high-fibre group doubled their intake, from about 21 to 45 g a day. Their microbiome diversity stayed stable, while the microbial enzymes that break down fibre increased.9 The trial's main planned measure, a cytokine response score, did not change, so the findings need confirming in larger studies.9
Food is what you add to your gut. Antibiotics are the clearest example of what can take something away.
Antibiotics reduce diversity, and recovery can be partial#
A single course quickly thins out the community. In healthy adults it mostly recovers within weeks, yet some species can still be missing months later, and the long-term consequences are not yet known.
In a study that followed three adults for ten months through two courses of the antibiotic ciprofloxacin, diversity fell within three to four days of starting. The communities began to return a week after each course ended, but the recovery was often incomplete and differed from person to person.10
In twelve healthy men given four days of three broad-spectrum antibiotics, the microbiome returned to near its starting composition within about six weeks. Nine common species, present in everyone at the start, were still undetectable in most of them six months later.11 Antibiotics save lives; the lesson is to use them when needed, not to refuse them.
After a course of antibiotics, many people wonder whether a test could show what is missing, and what to eat about it.
No microbiome test can yet tell you what to eat#
The tests on sale cannot carry that weight yet. An international expert consensus found too little evidence to recommend routine microbiome testing, and an independent evaluation found that commercial tests disagree with each other as much as different people's microbiomes do.
In 2025, an international panel of experts published a consensus statement on microbiome testing. They noted that direct-to-consumer tests are sold without proven value in clinical practice, that there is not enough information to set strict healthy reference ranges for the abundance of species, and that dysbiosis scores lack sufficient evidence. They also discouraged testing providers from giving treatment advice based on results.12
In 2026, a study sent the same standardised stool material to seven direct-to-consumer services. The results differed substantially within and between providers, and the variation between providers was on the same scale as the real biological difference between different donors.13
Biology adds to the problem: healthy people carry very different communities,2 so there is no single normal profile to compare yours with.
Most of what shapes your microbiome sits in ordinary days. Here is how to start, which signs need a doctor first, and how we can help.
The same gut worries come up again and again#
Worries about the gut tend to arrive in a handful of familiar phrases, often after antibiotics, a stomach bug or years of trying to eat well. These are the ones we hear most.
- My gut is out of balance
- Should I take a probiotic?
- I want a microbiome test
- Ever since those antibiotics
- I eat healthily but my gut is not right
- I am bloated after fibre
- Is my gut flora damaged?
- How do I rebuild my gut?
Four free habits to start this week#
Four habits can begin this week, and none of them costs anything: count the different plants you eat, add fibre gradually, try a fermented food you enjoy, and ask whether an antibiotic is really needed before you take one.
Some gut changes need a doctor, not a new diet#
A few signs call for a medical assessment rather than a change of diet: blood in your stool, unexplained weight loss, anaemia, a lasting change in your bowel habit, or symptoms that wake you at night.
We work on daily habits, alongside your doctor#
Our work sits alongside medical care, never in place of it, and it centres on the everyday habits that shape your microbiome: what you eat, and how you sleep, move and handle stress.
What reliably shapes the gut microbiome sits in daily life: the fibre and variety on your plate, sleep, movement and stress. These are also the hardest things to change alone.
At FunctionAlps we work on nutrition, sleep, movement, stress and digestion, and we coordinate with your doctor whenever something needs medical attention. We do not sell a microbiome reading of your diet. If you would like to look at your own habits, talk it through with our care team on a free call.
Quick answers12 questions this guide covers, in short
What is the gut microbiome, exactly?
The gut microbiome is the community of bacteria, and smaller numbers of fungi and viruses, that live in your intestines, together with their genes. Each person's community is different, and there is no single healthy pattern. Read the section
What does the gut microbiome actually do for you?
Its best understood job is fermenting the fibre you cannot digest into short-chain fatty acids, which feed the cells lining your colon and act as signals elsewhere in the body. It also changes bile acids and interacts with the immune system. Read the section
How much of microbiome science is proven in humans?
Less than the headlines suggest. Diet and antibiotics clearly change the microbiome in people, and donor stool clears a recurrent gut infection, but most claims that microbes cause weight gain, mood changes or chronic disease come from mice or from associations. Read the section
Why does microbiome diversity matter?
A more diverse gut community is generally linked with better health, and lower diversity has been found in several chronic conditions. But it is a marker, not a target to chase, and its causes and effects are still being untangled. Read the section
Do you really need 30 different plants a week?
Thirty is a useful prompt, not a proven threshold. In the American Gut Project, people who reported eating more than 30 types of plants a week had more diverse gut bacteria than those who reported 10 or fewer, but that comparison was observational and small. Read the section
Do fermented foods help your gut microbiome?
Possibly. In one small Stanford randomised trial, healthy adults who built up to about six servings of fermented foods a day for ten weeks gained microbiome diversity and lowered several inflammatory markers. The result is promising but not yet confirmed. Read the section
What do antibiotics do to the gut microbiome?
A course of antibiotics quickly reduces gut diversity. In healthy adults the community recovers mostly within weeks, but some species can still be missing months later, and the long-term consequences are not yet known. Read the section
Can a microbiome test tell you what to eat?
Not yet. An international expert consensus concluded that there is insufficient evidence to recommend routine microbiome testing, and an independent evaluation found that commercial tests disagree with each other as much as different people's microbiomes do. Read the section
What do people say when they worry about their gut?
The same handful of phrases comes up again and again, often after antibiotics, a stomach bug or years of trying to eat well. These are the ones we hear most. Read the section
What can you do this week for your gut microbiome?
Count the different plants you eat, add fibre gradually, try a fermented food you enjoy, and ask whether an antibiotic is really needed before you take one. All four are free. Read the section
When should gut changes be checked by a doctor?
When there is blood in your stool, unexplained weight loss, anaemia, a lasting change in your bowel habit, or symptoms that wake you at night. Those need a medical assessment, not a change of diet. Read the section
Where does a functional approach fit in looking after your gut?
Alongside medical care, never instead of it. The habits that shape your microbiome, what you eat, how you sleep, move and handle stress, are the ones we work on with you. Read the section
- Sender R, Fuchs S, Milo R. Revised estimates for the number of human and bacteria cells in the body. PLoS Biol. 2016;14(8):e1002533. PMID : 27541692. Link
- Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486(7402):207-214. PMID : 22699609. Link
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- Walter J, Armet AM, Finlay BB, Shanahan F. Establishing or exaggerating causality for the gut microbiome: lessons from human microbiota-associated rodents. Cell. 2020;180(2):221-232. PMID : 31978342. Link
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- Reynolds A, Mann J, Cummings J, et al. Carbohydrate quality and human health: a series of systematic reviews and meta-analyses. Lancet. 2019;393(10170):434-445. PMID : 30638909. Link
- Wastyk HC, Fragiadakis GK, Perelman D, et al. Gut-microbiota-targeted diets modulate human immune status. Cell. 2021;184(16):4137-4153.e14. PMID : 34256014. Link
- Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci U S A. 2011;108 Suppl 1:4554-4561. PMID : 20847294. Link
- Palleja A, Mikkelsen KH, Forslund SK, et al. Recovery of gut microbiota of healthy adults following antibiotic exposure. Nat Microbiol. 2018;3(11):1255-1265. PMID : 30349083. Link
- Porcari S, Mullish BH, Asnicar F, et al. International consensus statement on microbiome testing in clinical practice. Lancet Gastroenterol Hepatol. 2025;10(2):154-167. PMID : 39647502. Link
- Servetas SL, Gierz KS, Hoffmann D, et al. Evaluating the analytical performance of direct-to-consumer gut microbiome testing services. Commun Biol. 2026;9(1):269. PMID : 41748906. Link
- Manichanh C, Eck A, Varela E, et al. Anal gas evacuation and colonic microbiota in patients with flatulence: effect of diet. Gut. 2014;63(3):401-408. PMID : 23766444. Link
Articles published by FunctionAlps are educational and written within ASCA and EMR scope. They do not replace personalised clinical advice. When findings warrant medical evaluation, we coordinate with a referring physician.