Your gut in ten minutes

Who lives there, what do they do, and why is balance more important than individual germs?

How solid is the research? Well supported

That the microbiome breaks down food, produces fatty acids and shapes the immune system is well established. What exactly makes a “healthy” microbiome, however, has not yet been fully defined.

Healthy state

The gut is a tube about five metres long in the living body in which digestion, immune system, nervous system and microbes work together. Digestion starts in the mouth: chewing breaks food down, and saliva contains an enzyme that splits starch. In the stomach, acid dissolves food further and kills many germs swallowed with the meal. Then the pancreas and the liver release their digestive juices into the small intestine, where protein, fat and most carbohydrates are broken down and absorbed.

Between meals the small intestine runs a kind of cleaning wave (the Migrating motor complex A wave of muscle contractions that sweeps the stomach and small intestine empty about every one and a half to two hours when fasting. Eating interrupts it. More in the chapter “Intermittent fasting and meal timing: 16:8, 5:2 and Ramadan”) that sweeps leftovers and germs towards the large intestine. At the junction lies a sphincter, the ileocaecal valve, which is meant to stop colon contents from flowing back. That is why only few germs live in the stomach and small intestine. The great mass sits in the large intestine.

There live trillions of microorganisms: bacteria, fungi, archaea and viruses, mainly Bacteriophages Viruses that only infect bacteria. In the gut there are probably about as many phages as bacteria, perhaps more, and they help determine which bacteria prevail. More in the chapter “Bacteriophages: the hunters in the gut” that infect bacteria. By a more recent estimate there are roughly as many bacterial cells in the body as human cells, a ratio closer to one to one than the often-quoted ten to one. Together they form an ecosystem that breaks down fibre the body cannot digest on its own.

This fibre is turned into Short-chain fatty acids Acids such as acetate, propionate and butyrate that gut bacteria make from fibre. They nourish the gut wall and act throughout the body. More in the chapter “Butyrate and other short-chain fatty acids” such as Butyrate A short-chain fatty acid and the main energy source for the cells of the colon wall. It strengthens the barrier and dampens inflammation. More in the chapter “Butyrate and other short-chain fatty acids”. They supply the cells of the gut lining with energy, strengthen the Mucus layer A gel layer of mucins on the gut wall that keeps bacteria at a distance. In the colon, the inner layer is almost free of microbes. More in the chapter “The mucus layer and additives” and send calming signals to the immune system. The gut wall is border and door at once: a tight layer of cells with mucus on top lets nutrients through and keeps germs out, and a large part of the immune system sits right beneath it. It learns to tolerate harmless bacteria and food and to fight dangers.

The ecosystem is stable when many different species live side by side. No single species dominates, and for almost every task there are several species that can step in. There are also links to the rest of the body: the Vagus nerve The tenth cranial nerve and the most important nerve of the rest-and-digest system. It connects the brainstem and the abdominal organs; most of its fibres tell the brain what is happening in the gut. More in the chapter “The vagus nerve: the data line between belly and head” and the gut's own nervous system exchange signals with the brain, and hormones control hunger and the pace of digestion. That is why stress often hits the belly.

Many different species live in the colon. They ferment fibre into short-chain fatty acids.

Disrupted state: causes and effects

Antibiotics, a one-sided low-fibre diet, infections and some medications can reduce diversity. Then individual species that are normally kept small take over. Acid blockers or missing cleaning waves also let more germs advance into the small intestine, where they ferment food before the body could absorb it. That can lead to gas, a bloated belly and nutrient deficiencies.

The result is often non-specific symptoms: bloating, changing stools, a feeling of fullness. Usually there is not a single pathogen behind it, but a shifted overall picture. Other points along the digestive route that have nothing to do with microbes can contribute: too little stomach acid or enzymes, sluggish bile, oversensitive nerves, activated Mast cells Immune cells beneath the skin and mucous membranes, filled with histamine and other messengers. They raise the alarm in allergies, infections and stress. More in the chapter “Mast cells: alarm cells in the gut, histamine and the disputed MCAS” or a more permeable lining. That is why symptoms from different causes resemble each other so much.

Important: everyone's Microbiome, gut microbiota The community of all microbes in the gut, mainly bacteria, plus viruses, fungi and archaea. Most live in the colon. More in the chapter “Building microbial diversity” is different. There is no “perfect” microbiome to measure yourself against. Commercial stool tests therefore cannot reliably tell you whether your gut is “healthy”. Reference values from tests are mostly based on averages and say little about the individual case.

Two warnings for perspective. First: with symptoms, transit often matters more than the microbiota. Someone who goes to the toilet very rarely or very often has different starting points from someone with bloating after meals. Second: certain signs should always be checked by a doctor, such as blood in the stool, unintended weight loss, night-time diarrhoea, persistent fever or trouble swallowing. They are not candidates for self-experiments.

A little reassurance to finish: the gut is robust, the microbiota changes within days of a dietary change, and many symptoms improve with simple steps. The further chapters look at each station of this journey in more detail.

Less fibre and fewer species: a few species take over.

What often helps

Lifestyle

Diet, exercise, sleep, social contact and dealing with stress.

Plant diversity Spread as many different vegetables, legumes, nuts, seeds, herbs and whole grains as possible over the week. The goal of “30 plants per week” is a rule of thumb from a large observational study, not a proven threshold. Plausible How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [1]
Fermented foods Include yoghurt, kefir, sauerkraut or kimchi regularly. In a randomised trial this increased diversity, and several inflammatory markers went down. Promising How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [2]
Regular exercise In one study, endurance training shifted the gut microbiota towards more butyrate producers, independently of diet. The effect disappeared again when participants stopped. Plausible How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [3]
Eat calmly, chew well, leave gaps between meals Good chewing and calm eating ease the load on stomach and small intestine. If you leave a few hours between meals, the small intestine's cleaning wave can work, which runs mainly when fasting. Constant snacking interrupts it. Plausible How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [4]
Think of stress and sleep too Ongoing stress changes gut movement, sensitivity and, according to studies, the composition of the microbiota. Sleep, breaks and relaxation are part of the gut programme. Plausible How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [5]

Natural supplements

Supplements do not replace a medical check-up. Discuss dosage and interactions with your doctor or pharmacist.

Soluble fibre, such as psyllium husk They can help if your diet provides too little fibre. For IBS, the guideline recommends soluble fibre, but not bran. Increase slowly and drink plenty. Established How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [6]

Medical treatments

Information, not a treatment recommendation. Decide together with a doctor. Approval and availability differ from country to country.

Use antibiotics wisely Antibiotics are often lifesaving. If it is unclear whether you need them, for example with a viral infection, ask whether they are really necessary. Promising How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [7]
Have persistent symptoms checked If symptoms last several weeks, a doctor should rule out other causes such as coeliac disease, lactose intolerance or inflammatory bowel disease. Established How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [6]
Do not wait on warning signs Blood in the stool, unintended weight loss, night-time diarrhoea, persistent fever or swallowing problems should be examined by a doctor promptly rather than treated with diet or supplements. Well supported How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open.

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How we rate the evidence

Trust score 5 of 5:Established: Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies.
Trust score 4 of 5:Well supported: Several randomised studies in humans with largely consistent results.
Trust score 3 of 5:Promising: Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies.
Trust score 2 of 5:Plausible: Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms.
Trust score 1 of 5:Experimental: Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open.

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