What are the real signs of a healthy gut? A user’s guide

What is the gut?

The gut, or gastrointestinal system, is the long and winding route that food and drink takes through the body. It ensures that all the beneficial nutrients are absorbed and used for energy, growth and repair. You can think of it as a number of hollow organs connected by a tube which starts at the mouth and ends at the anus. Once food has been swallowed, the oesophagus delivers it to the stomach. It then goes through the small and large intestines before waste – the material the body cannot use – is expelled as a stool. Solid organs help along the way: the liver, pancreas and gall bladder. The entire digestive tract is about 5m long in a typical adult, with the small intestine making up two-thirds, but there is plenty of variation between people. Spread the whole lot out, and the surface area of the gut that comes into contact with food is about 32m2. That’s about half the size of a badminton court.

How does it work?

The gut is built for digestion: the breaking down of food and drink into nutrients that can be absorbed into the bloodstream. Chewing food turns it into smaller lumps for the gut to digest, a process helped by saliva. Saliva contains enzymes that break down starches and fats in food before it reaches the stomach.

Food is moved through the digestive tract by peristalsis, where the gut walls squeeze behind the contents, much as toothpaste is squeezed from a tube. Once swallowed, food is pushed down into the stomach, which releases strong acids and enzymes to break the food down further. This produces a thick fluid called chyme which is slowly released into the small intestine.

Nearly all of the nutrients the body absorbs – from carbohydrates and vitamins to fats, proteins and minerals – are absorbed in the small intestine. Here, the solid organs lend a hand. Small ducts from the pancreas deliver digestive juice that helps break down carbohydrates, fats and proteins. Another digestive juice called bile is made by the liver and either fed into the small intestine or stored in the gall bladder to use later. Bacteria in the small intestine also get involved, releasing enzymes that help with digestion. Once in the bloodstream, nutrients are circulated around the body, where they are used and stored by the tissues and organs.

The ideal stool is a medium-to-dark-brown sausage shape that has a soft-to-firm consistency

Once the small intestine has absorbed all the nutrients it can, the large intestine takes on the waste. Peristalsis moves it through the colon, where water is removed to produce a stool made up of undigested food material and bacteria. It takes six to eight hours for food to pass through the stomach and small intestine, and a further 36 hours to move through the colon. At the end of the large intestine is the rectum, which stores stools until they are passed in a bowel movement.

From mouth to anus, the human gut is lined with more than 100m nerve cells that make up the enteric nervous system. This dense collection of nerves can send messages back and forth to the brain. Signals are exchanged along the left and right vagus nerves, which run from the brain down the corresponding side of the body to the large intestine. The nerves play a crucial role in healthy digestion, mucus and saliva production, immune responses, taste and bladder control, not to mention heart rate, blood pressure, breathing, mood and speech.

What keeps the gut healthy?

Given the gut’s role, it’s not surprising that doctors recommend a healthy diet for a healthy gut. That means fruit and vegetables every day, cutting back on sugary and fatty foods, and choosing poultry or fish over red meat. Dr Megan Rossi, a registered dietitian and research fellow at King’s College London, recommends eating 30 different plant foods each week. If that sounds a bit much, bear in mind that it includes fruit and veg, wholegrains, legumes, nuts and seeds. Hitting the target could be as easy as sprinkling mixed seeds on your breakfast in the morning.

Some foods are obviously healthier than others and, although there’s no formal designation, dozens are often described as “superfoods”. The label means they are particularly rich in healthy nutrients, such as vitamins, minerals and antioxidants, though some are also high in fibre, healthy unsaturated fats and flavonoids. The latter include plant compounds such as apigenin, found in parsley, chamomile and celery, which has anti-inflammatory and anti-cancer properties. Dark, leafy greens such as spinach and kale, berries, avocados, cinnamon, root vegetables, garlic, ginger, green tea, lentils and salmon are regarded as superfoods, but it’s not always easy to establish the health benefits of particular foods: most studies test specific constituents on cells in petri dishes or in mice.

Adults in the UK are advised to eat 30g of fibre a day but typically consume only 20g. A high-fibre diet can help digestion and prevent constipation, and is linked to lower risk of heart disease, type 2 diabetes and colorectal cancer. Fibre should come from a variety of sources, including fruit and veg, beans, nuts, seeds, oats, wholemeal bread and pasta and brown rice. It is important to drink enough water, too, which helps food pass through the digestive system. Too little can lead to dehydration, a common cause of constipation.

Physical activity, such as a walk after dinner, also helps with digestion. Moving around and letting gravity do its thing helps food to move through the gastrointestinal tract. A healthy gut has benefits far beyond the intestines themselves. “A wealth of research is coming together to highlight that gut health is central to the health of every other element of the body,” says Rossi.

The UK has some of the highest rates of IBD in the world, but estimates vary, partly because of ambiguous diagnoses

What are the signs of a healthy gut?

Your gut has many ways of telling you when it isn’t healthy. Infections such as gastroenteritis can cause stomach pain, vomiting and diarrhoea. Lactose intolerance – an inability to digest a form of sugar found in milk and other dairy products – can leave you feeling bloated. Coeliac disease, when gluten causes the immune system to attack the gut, can trigger abdominal pain and indigestion. So an absence of pain and bloating are starters for good gut health. Bowel movements are a decent indicator, too: these should be regular and pain-free and shouldn’t involve too much pushing. The ideal stool is a medium-to-dark-brown sausage shape that has a soft-to-firm consistency. Healthy ones tend to sink and don’t stick to the toilet bowl. Floating stools are less dense, usually because they contain more gas or fat. High-fibre diets can lead to more gas in stools, as it’s released when bacteria in the colon go to work on the material. If you are eating more fat than usual, any excess that can’t be digested could make your stools float. But fatty stools can also signify problems with absorption in the gut or an inflamed pancreas (pancreatitis).

What causes common gut problems?

A whole host of conditions affect the gut from indigestion, heartburn and diarrhoea to constipation, irritable bowel syndrome and cancer. Indigestion happens when stomach acid irritates the stomach lining, or a raw patch of the stomach wall, such as an ulcer. Heartburn is similar: the burning feeling in the chest is caused by stomach acid flowing back up the oesophagus. It’s often a sign that the band of muscle at the bottom of the oesophagus isn’t working properly. When heartburn happens regularly it’s called gastro-oesophageal reflux disease, or Gord. Some foods such as chillies, onions, garlic, tomatoes and citrus fruits can trigger heartburn, as can certain drinks, such as tea, coffee and fizzy drinks. Reducing stress and anxiety can help.

Constipation and diarrhoea are extremely common gut health problems. Constipation generally means having fewer than three bowel movements a week, and finding it difficult to pass stools. Often, constipation is the result of eating too little fibre, not drinking enough fluids, and not being physically active, but sometimes there is no obvious cause. Diarrhoea – when the stools become loose and watery – is often caused by bacterial, viral or parasitic infections in the gut.

Irritable bowel syndrome is still something of a medical mystery. The causes are unclear, but the condition can develop after severe diarrhoea-causing infections. Studies suggest that changes in gut microbes and early life stress play a role, too.

More serious diseases also affect the digestive system. Doctors estimate there are about 5m new gastrointestinal cancers each year, accounting for about a quarter of new cancers worldwide. Eating red meat, including beef, lamb and pork, and processed meats, such as sausages, bacon and salami, raise the risk of bowel cancer by an estimated 13%. Nearly a third of bowel cancers are linked to eating too little fibre, 11% to obesity and about 7% to smoking, according to Cancer Research UK.

Peanut and tree-nut allergies were uncommon before the 1990s, but have risen to affect between 0.5% to 2.5% of children

In the UK, an estimated two million people have a diagnosed food allergy. Peanut and tree-nut allergies were uncommon before the 1990s, but have risen to affect between 0.5% to 2.5% of children. The range of foods people are allergic to has expanded, too. According to a 2007 study by St George’s, University of London, UK hospital admissions for anaphylaxis due to food allergies rose sevenfold, from 16 to 107 per million children, between 1990 and 2004. What is driving the rise is unknown. One theory is that babies and infants are not as exposed to microbes that help train the immune system as much as they were in the past. Another suggests that at-risk babies – those with severe eczema, for example – have foods such as peanuts introduced into their diet too late, preventing them from building tolerance in their first year.

At least 1% of the UK population has coeliac disease. The real figure is probably much higher because mild cases can go undiagnosed or are misdiagnosed. The autoimmune disorder affects genetically susceptible people and often runs in families. It happens when the immune system mistakes gliadin, a component of gluten found in cereals such as wheat, barley and rye, for a threat. The immune system responds by releasing antibodies that inflame the gut. This flattens down the hair-like fronds called villi, which line the small intestine in their millions, impairing their ability to absorb nutrients. Coeliac disease causes symptoms ranging from weight loss and fatigue to diarrhoea, abdominal pain and bloating. Cases have risen in the UK in recent decades, with researchers noting a four-fold increase between 1990 and 2011, but they suspect this is down to better diagnoses, rather than the condition becoming more common.

Inflammatory bowel disease, IBD, is also common. The two most prevalent forms are Crohn’s disease, which can affect any part of the digestive system, and ulcerative colitis, which affects only the colon. Both involve long-term inflammation, but their root causes are unclear. The UK has some of the highest rates of IBD in the world, but estimates vary a lot, partly because of ambiguous diagnoses. As a long-term but rarely fatal disease, the total number of people with IBD in the UK population is rising, with a 2021 study in BMC Gastroenterology finding a 34% rise in prevalence in the decade to 2016. According to a 2020 report in BMJ Open, which looked at IBD in the UK between 2000 and 2018, new diagnoses were stable in children under 10, stable or falling in adults, but rising in 10- to 16-year-olds. This could be down to earlier diagnosis – people who are diagnosed with IBD at 15 are not diagnosed again at 40 – but if it reflects a surge in disease, “this is of great concern”, the authors warn.

What is the gut microbiome?

Trillions of microbes, comprising thousands of species of bacteria, fungi, viruses and parasites, live inside the human gut. Most are symbiotic, meaning both the human and the microbe do well from them being there, but some can raise the risk of disease, or ramp up levels of toxins if exposed to a poor diet. As with most communities, the good tend to outnumber the bad and keep them in check, but the balance can be thrown out by diet, infections or a long course of antibiotics. This can cause the bad bacteria to proliferate, increasing the risk of diseases such as IBD, IBS, obesity and colon cancer.

In recent years, this mass of microbes, and its role in human health, has become one of the hottest topics in medicine. As a collective, they help to break down food and support digestion. Some gut bugs synthesise vitamins we struggle to obtain from our diets. In the large intestine, bugs ferment indigestible fibres, producing short chain fatty acids that reinforce the gut wall, possibly preventing certain cancers and bowel conditions.

Does the microbiome affect our broader health?

Absolutely. The microbiome is thought to affect virtually every aspect of human health. Compounds that are either produced by the bugs, or released when they degrade food, help regulate hormones, metabolism and immunity. Beyond their impact on diseases, these can affect anxiety, mood, cognition and pain. Hundreds of clinical trials are now either planned or under way to investigate what role the gut microbiome plays in a whole host of issues including the brain development of babies, autism, obesity, diabetes, coronary artery disease, gastric cancer, arthritis, Parkinson’s, Alzheimer’s, depression, mood disorders, anxiety, anorexia nervosa, pain and sleep quality. There’s even evidence to suggest the microbiome can boost motivation in exercise.

How can we keep the microbiome healthy?

A healthy microbiome is a diverse microbiome. Dr Karen Scott, a microbiologist at the University of Aberdeen, says diversity helps to maintain a balanced microbiome. “It allows you to degrade all types of food and release the full variety of products, all of which are useful in different ways,” she says. One way to feed the good bugs is to eat prebiotics. This is indigestible fibre that reaches the large intestine intact. It acts as a food source for the microbes, which metabolise and ferment the material. The process produces byproducts that are healthy for the gut. The usual suspects – fruit, veg, legumes and grains – are good sources of prebiotic fibre. “If you are eating 30-plus plant foods per week, you are going to be getting enough prebiotics,” says Rossi.

Trillions of microbes, comprising thousands of species of bacteria, fungi, viruses and parasites, live inside the gut

Prebiotics should not be confused with probiotics. Probiotics are live bacteria found in certain yoghurts and other fermented foods, such as kimchi, sauerkraut, kefir and kombucha. These “good” bacteria may help to maintain a healthy, diverse population of gut microbes, but the science is unclear on whether they prevent many health problems. There is some evidence that certain probiotics can ease irritable bowel syndrome, for example, but none that they help with eczema. Frequent reviews of the evidence by the Cochrane collaboration find that many studies are too weak to draw conclusions from, or that probiotics have little or no effect, though they may help prevent common colds and other upper respiratory tract infections. “For someone who is healthy, prebiotics are the way to go, because they feed the bacteria that are already there,” says Scott. “Probiotics have had a lot of bad press, with people saying they don’t work, but people forget that bacteria are not all the same. You need to use a specific probiotic for a specific purpose. It has to be the right one that has been tried and tested.”

Consuming a lot of fast food, sugar, processed foods and alcohol is bad for the microbiome. In 2021, researchers linked the western diet, rich in processed food and animal-derived products, along with alcohol and sugar, to microbiomes that drive inflammation. Further work has shown that alcohol can disrupt the balance between good and bad bacteria, leading to an overgrowth of harmful microbes that release toxins.

In one remarkable 2015 study, researchers invited African American and rural African volunteers to swap diets for two weeks. The rural Africans, who were used to a diet rich in beans and vegetables, fared worse on the US diet, which was rich in fat and animal protein, but low on dietary fibre. Their metabolism switched to that seen in diabetes and their risk of colon cancer rose. The African Americans did better out of the deal: they had less inflamed colons and their biomarkers for cancer dropped. The only negative was a ramping up of flatulence. The beneficial effect of the rural African diet was attributed to microbes that break down fermentable fibre in the colon to produce butyrate, known for its anti-inflammatory and anti-cancer effects. Prof Jeremy Nicholson, an author on the study at Imperial College London, said it was “startling” how profoundly the microbes, metabolism and cancer risk changed in just two weeks.