How to maintain a healthy gut

Need to know

Difficulties and discomfort related to the gut are very common. But even so, because of embarrassment and stigma, many of us don’t talk about them, even with our closest friends and family. As a practising gastroenterologist, I’ve seen first-hand how these problems can affect people’s lives.

The first step in maintaining gut health and overcoming gut symptoms is having a willingness to learn more about the subject. In this Guide, I invite you to take a journey into the gut and the ‘gut microbiome’, and to learn more about what you can do to help improve and maintain your gut health.

If you have concerns about your gut health, or someone you know does, a vital message is to realise you are far from alone. Here are a few examples of people I’ve helped in my medical practice. I wonder if you can identify with any of them?

One patient came to my clinic complaining of severe bloating. She felt on certain days that her abdomen was so distended that she looked like she was nine months pregnant. She is in her early 20s, works as a receptionist for a large company, is medically well and very mystified why her gut was unhealthy. We started a good conversation about the gut microbiome, diet and what a healthy gut means.

Another patient of mine in his late 50s arrived at my clinic complaining of passing a small amount of fresh red blood in his stools. He is a farmer and very physically active with no known medical issues. This was the first time that he had ever seen blood in his stools. He generally avoided seeing doctors, but his wife prompted him to come in for a checkup. We started a chat about the importance of ‘alarm symptoms’ such as blood in the stools.

I saw a man in his early 30s with a perplexing story of burping that started shortly after a relationship breakdown. He was severely affected by this burping – it would occur non-stop with several hundred burps a day! The burping really started to affect his social engagements and he would avoid leaving the house because he felt anxious and ashamed. Fortunately, his job allowed him to work from home, so he was able to continue working. We began a good dialogue around the role of mental health and how it can affect the gut.

As you can see, I began helping patients like these by providing them with essential information about good gut health, the links between mental health and gut health, and beneficial lifestyle changes. In this Guide, I will share some of this information and advice with you.

What is a healthy gut?

Defining good gut health is challenging: it means something different for researchers, doctors and the community. However, most medical experts would agree that a healthy gut is one not affected by gut diseases or troubling gut symptoms – and one that has a healthy microbiome.

It can help to know something about the properties that make up a healthy gut. A healthy gut has a mucus-lined barrier that is ordinarily very effective at preventing gut contents, such as its microbes, undigested food particles and toxins, from escaping into the bloodstream.

However, various factors, from poor diet to medical conditions to infections, can cause a disruption of your gut barrier, which allows bacteria or small food particles to escape into your bloodstream, where they are recognised as foreign invaders, triggering the immune system to respond.

The medical term for this disruption of the gut barrier is ‘intestinal permeability’ but it is better known as ‘leaky gut’. There is evidence that increased intestinal permeability can lead to continuous immune activation and inflammation of the lining of your gut. In turn, increased intestinal permeability is believed to be a key mechanism underpinning gut diseases such as coeliac disease and inflammatory bowel disease.

A healthy gut has important functions, such as digestion, synthesis and absorption of nutrients that are essential for the body. Sometimes, specific nutrients such as lactose may not be absorbed well because of a deficiency in the enzyme (lactase) found in the small bowel that breaks it down. Lactose intolerance is not considered a true gut disease, but if people with this condition ingest lactose-containing foods, they can be troubled by persistent symptoms, such as bloating, cramping and diarrhoea.

The gut and your brain

There is increasing recognition that an important factor in maintaining gut health is the gut-brain axis. This refers to the physical and chemical connections between your gut and brain. There are many hundreds of millions of neurons in the gut, and the gut is often thought of as a ‘mini-brain’. The gut also produces a large amount of neurotransmitters, which are chemicals that transmit messages within the nervous system, including to the brain. One good example of a neurotransmitter is serotonin, which is responsible for regulating your mood, appetite and sleep. The gut provides approximately 95 per cent of the body’s total serotonin. Your gut microbes (more on them in a moment) and immune cells also play an important role in the gut-brain axis.

The gut-brain axis helps explain why your gut health can affect your mental health and vice versa. Irritable bowel syndrome (IBS; a condition that can cause digestive discomfort and irregular bowel movements) is regarded as a disorder of gut-brain interaction. More women than men suffer from IBS, and symptoms often first occur in early adulthood. There is no single cause of IBS, but environmental factors – such as changes of routine, stress, anxiety or depression, infection and diet – can trigger symptoms. These symptoms can then be perpetuated by ongoing chronic stress, anxiety, depression, maladaptive coping strategies and negative beliefs.

Your gut microbiome

Another key factor in gut health is your gut microbiome. Your body is home to a vast collection of microorganisms and this ecosystem is known as a biome. The word ‘micro’ is used to indicate that this ecosystem is a hidden world invisible to the naked eye. Your body’s microbiome is mostly teeming with bacteria, but also contains other organisms such as viruses, fungi and a group of single-celled organisms called archaea that resemble bacteria. The number of microbes in your body is around 40 trillion, similar to your total number of cells.

The terms ‘microbiome’ and ‘microbiota’ are often used interchangeably but they have slightly different meanings. ‘Microbiota’ refers specifically to the microbes, while ‘microbiome’ refers to the microbes and their genes. Therefore, your gut microbiome refers to the trillions of microbes and their genetic material that reside in your intestinal tract.

The bacteria in your gut, and some other microbes, play an important role in the digestion of food and also the absorption and synthesis of nutrients. They are also involved in other bodily processes such as metabolism, immune regulation and even brain function and mood.

Indeed, your gut microbiome and the immune system are critically intertwined, with 70 to 80 per cent of your body’s immune cells located in the gut. These immune cells interact with the gut microbiome and are directly influenced by your diet and lifestyle. The foods you eat affect the diversity and composition of your gut bacteria, which in turn affects your immune cells.

A healthy gut microbiome is essential to a healthy gut. Your individual microbiome is thought to be akin to a bacterial fingerprint. This high degree of variability makes interpretation of the gut microbiome difficult and therefore it is hard to know exactly what constitutes a healthy gut microbiome. That being said, a rich diversity of bacterial species is generally associated with a healthier gut. Resilience, which is the property of an ecosystem to resist changes under stress or to recover quickly and fully from stress, is another surrogate measure of good gut microbial health.

The role of dysbiosis in physical and mental health

In some instances, your gut microbiome can become imbalanced or disrupted, shifting away from its normal state. This is called dysbiosis. Dysbiosis can be caused by multiple factors including stress, chronic illness, overuse of antibiotics or unhealthy eating.

Short-term disruption to the gut microbiome, such as from an infection, often has no lasting health consequences. However, chronic dysbiosis – a sustained disruption to the gut microbiome – is being investigated as a potential risk factor for various diseases, including inflammatory bowel disease, obesity, Type 1 diabetes mellitus and autism.

Thanks to the gut-brain axis, dysbiosis can also play a role in mood disorders such as depression and anxiety. On the flip side, there is the potential for good bacteria to positively influence mental health. It’s thought that good bacteria can generate compounds that send signals to your brain that elicit positive mood, cognition and stress reduction. Some scientists have called such good bacteria ‘psychobiotics’ and this is a fascinating emerging research area.

This Guide will give you an insight into the inner workings of the gut, canvass what makes for good gut health, including the gut microbiome; and provide practical steps that you can follow to improve your gut health. I am hoping that the Guide will be of help to those dealing with everyday gut difficulties or worried that they might have a more serious problem, as well as to anyone interested in looking after this most important part of their body.

What to do

Make lifestyle changes to protect your gut health

The most significant steps you can take to protect your gut health concern your diet. However, before I share some specific dietary advice with you, here are some basic lifestyle interventions that can also help you maintain a healthy gut:

• Practise good sleep hygiene. A disturbance in your circadian rhythm (the internal 24-hour body clock that influences when you feel alert and when you sleep) can disturb your gut, for instance leading to irregular bowel motions. A good sleep routine – aim to go to bed and rise at a similar time each day – is good for your mental and physical health in general, and this includes helping to improve the regularity of your bowel motions.
• Avoid alcohol and smoking. Alcohol and smoking both contribute to gut dysbiosis and bring with them a whole host of other health hazards. Even if you don’t want to give up alcohol completely, cutting back your consumption is one of the simplest steps you can take to improve your gut health.
• Reduce stress. Of course this is easier said than done, but another key way to look after your gut health is to look after your mental health. As I mentioned earlier, stress and depression can increase intestinal permeability and produce an inflammatory response that can harm your gut microbiome. Psyche magazine has many articles to help you better manage stress and overcome emotional difficulties.
• Undertake regular moderate-intensity exercise. Regular moderate-intensity exercise has been shown to enhance colon health, improve the diversity of gut microbes and increase key antioxidant enzymes. If you have concerns about your gut health, bear in mind that intense, strenuous exercise could be counterproductive. It’s been shown to produce a classical stress response that, combined with a reduced blood supply to the gut lining, can lead to increased gut intestinal permeability, which can cause inflammation.
• Limit your unnecessary use of antibiotics. Sometimes antibiotics are essential. But it is important to use them only when necessary because they can adversely affect your gut microbiome. Widespread indiscriminate use of antibiotics, for example in the treatment of a common cold, can increase the risk of dysbiosis. This is especially important to consider when it comes to children. Disruption of the gut microbiota early in life is linked to the development of immune-related and metabolic disorders later in life.

Aim for a diverse diet

The above lifestyle factors are all important, but the most significant influence on your gut microbiome – and therefore on your gut health – is the food you consume every day. If you want to make just one beneficial change to your diet, aim for diversity.

Diet diversity or food variety is an important part of healthy eating because it helps to ensure adequate amounts of nutrients for normal human bodily function. A systematic review published in 2021 found that greater dietary diversity across major food groups, and in particular a diversity of different fruits and/or vegetables, was associated with a reduced risk of Type 2 diabetes and a reduced incidence of depression and cognitive decline. Therefore, it’s recommended for a healthy gut that you regularly consume a diverse diet of predominantly healthy foods (unsurprisingly perhaps, the review found that consuming a greater diversity of unhealthy foods such as sweets, snacks and soft drinks was associated with obesity).

You should be eating a variety of foods across each of the five core food groups:

• grain (cereal) foods, mostly wholegrain;
• vegetables and legumes/beans;
• fruit;
• milk, yoghurt, cheese or alternatives, such as soy, if you are lactose intolerant; and
• lean meats and poultry, fish, eggs, tofu, nuts and seeds.

Vegans and vegetarians can be reassured that appropriately planned vegetarian (including vegan) diets are healthy, nutritionally adequate and appropriate for all stages of the lifecycle including pregnancy, breastfeeding, infancy and older adulthood. Vegans will need to ensure they include reliable sources of vitamin B12 in their diet, such as from fortified foods or supplements.

In addition to eating across each of the five core groups, you should eat a range of foods within each group. This is supported by research from the American Gut Project, which found that people eating 30 or more different plant foods a week had a more favourable gut microbiome diversity, compared with those who ate 10 or less.

Keep a food diary

In practice, it can be quite difficult to make the transition to a very diverse diet. Eating 30 different plant foods a week is a lot for most people! A simple first step is to begin recording your current diet each day, at least for a few weeks.

Assign the healthy foods that you’re eating into each of the five core groups. Then you can see where you may wish to increase the different types of foods within each group. For example, if you’re consuming only two different types of fruits a week you may wish to increase that to four.

You’ll also quickly see if there are unhealthy highly processed foods or sweetened beverages in your diet that you can reduce (eg, if you currently consume three Coca-Cola drinks a day, aim to reduce to this to one a day).

You don’t need to make the full set of changes overnight. Behavioural adjustment takes time, so don’t be worried if you can’t make all the changes immediately. The most important thing is to try to stick with the positive changes you make.

Ensure you’re consuming enough fibre

Dietary fibre, which is the part of plant foods that the body can’t digest, is also important for our digestive health and regular bowel movements. Fibre-rich foods include fruits, grains, legumes, vegetables, nuts and seeds.

Fibre can also help one feel fuller for longer, improve blood sugar and cholesterol levels, and assist in preventing some diseases such as diabetes, heart disease and colon cancer. Adults should aim for at least 30 grammes of fibre a day for the general health benefits.

How can you know how much fibre is in different foods? The first thing is to find a standard reference table for how much fibre is contained in different foods. It can be surprising just how little fibre is found in some of the foods that we regularly consume. For example, a medium-sized apple holds 2.2 grammes of fibre; a slice of wholegrain bread contains 2.4 grammes.

Next, use your food diary from the previous step to map how much fibre you’re consuming daily. Remember, your diet will vary from day to day, so it’s worth keeping your diary for at least a few weeks to get an accurate assessment. Finally, you can start to phase different fibre-containing foods into your diet. Plant foods are a great source of dietary fibre and offer the ability to score two wins: by increasing your fibre intake, you will also be increasing the diversity of foods in your diet.

It’s important to not feel pressured to increase your dietary fibre to the daily recommended intake straight away. Bloating and abdominal discomfort can be side-effects of consuming too much fibre too quickly. Take your time.

Try a Mediterranean diet

The Mediterranean diet, which is known for its lower intake of saturated fats, refined carbohydrates, red meat and dairy products, has been shown to have a positive effect on the microbial balance within the gut and a protective effect on the gut mucus barrier. The Mediterranean diet has also been linked to a lower risk of Type 2 diabetes in older adults. It’s also associated with many other health benefits including increased longevity. If you would like to give it a try, the foundational principles for the Mediterranean diet are:

• Eating an abundance of fresh, minimally processed plant foods including fruits, vegetables, whole grains, nuts and legumes.
• Eating fish and poultry in low to moderate amounts a few times a week.
• Using olive oil as the principal source of fat.
• Eating cheese and yoghurt daily in low to moderate amounts.
• Eating red meat infrequently and in small amounts.
• Using fresh fruit for dessert and minimising sweets that contain added sugars.

You can see that if you are already following the previous steps – eating a diverse diet with foods from each of the five groups and minimising your intake of highly processed foods – you will already be following a routine that is fairly similar to a Mediterranean diet. You can go further by incorporating the foundational principles outlined above into a meal plan, and adopting a Mediterranean diet can be made easier by switching over whatever fats you use to extra virgin olive oil and beginning each meal with a salad.

Consider a low FODMAPs diet

If you are prone to symptoms such as bloating and abdominal discomfort, especially after eating (perhaps you’ve been diagnosed with IBS), then you might like to try a so-called low FODMAPs diet.

Researchers from Monash University in Australia came up with the concept of FODMAPs (fermentable oligosaccharides, disaccharides, monosaccharides and polyols) in 2004, referring to certain food products, such as simple sugars, that were shown to distend the small bowel through water and gas production, thereby leading to bloating and related symptoms. The idea of the low FODMAPs diet was then born, with the premise that a diet restrictive in FODMAPs could help improve symptoms.

The key to starting the diet is to know which foods are high and low in FODMAPs – to avoid high FODMAP foods while maintaining diversity in your diet. Below, I’ve provided examples of some foods that you can eat and others to avoid in a low FODMAPs diet, categorised into each of the five core food groups:

Grains

• EAT – potatoes, tortilla chips, quinoa, rice noodles
• AVOID – wheat pasta, legumes, multigrain bread, muffins, sweetcorn

Vegetables and legumes/beans

• EAT – cucumber, lettuce, carrot, eggplant
• AVOID – onions, garlic, beans, lentils

Fruit

• EAT – strawberries, grapes, oranges, kiwi fruit
• AVOID – peaches, apples, watermelon, mango, pear, avocado

Milk, yoghurt, cheese or alternatives

• EAT – butter, hard cheeses, soy milk, almond milk
• AVOID – soft cheeses, regular milk, custard, ice cream and yoghurt

Lean meats and poultry, fish, eggs, tofu, nuts and seeds

• EAT – chicken, eggs, tofu, fish
• AVOID – breaded meats, sausage, battered fish, almonds, pistachio

In preparing a low FODMAPs diet plan, it’s important to know that you don’t have to change your diet entirely. It’s easier to focus on substituting some high FODMAP foods with low FODMAP foods. Over the course of around six weeks, aim to substitute those high FODMAP foods with low FODMAP alternatives across all five core food groups. Then, over the next eight to 12 weeks, aim to reintroduce some high FODMAP foods, one at a time over a three-day period. You’ll quickly realise which foods are likely to trigger off your IBS symptoms and learn to avoid them.

It can be tempting after your symptoms significantly improve to remain on a very restricted diet, but that’s unhealthy and you should be aiming to diversify your diet. Eventually, you’ll come up with a diet that is as reasonably diverse as possible but limited in those FODMAP foods that are triggering. This can be a challenging diet to undertake, so if you have any concerns or feel like you need help, I’d recommend seeking the assistance of a dietitian to support you along the journey.

In the case of my patient with bloating who was otherwise healthy, it turns out that after a lot of investigations she was diagnosed with IBS. She had an excellent response to the low FODMAPs diet and has remained symptom-free for the past two years.

Know the alarm symptoms and when to seek treatment

It’s very common to have mild gut symptoms such as changes in bowel habits or mild abdominal discomfort. The vast majority of the time, these symptoms disappear by themselves. However, if they persist for more than a few days or if the symptoms change to become more severe, then it’s certainly worthwhile seeking medical advice.

If it transpires that your gut symptoms are the result of a disease, then treatment of that disease will be appropriate. For instance, if you are diagnosed with a condition such as inflammatory bowel disease, there are multiple medications that can be effective to achieve disease remission. Some gut conditions will have a diet-based treatment: ie, a gluten-free diet in coeliac disease or a low FODMAPs diet in my patient with IBS. Other conditions or symptoms might require psychological intervention.

Take my patient with severe burping – a condition called supragastric belching, which is considered to be a behavioural disorder with psychological causes. The understanding that the gut-brain axis is disturbed in these kinds of disorders has led to tailored treatments, which have been shown to improve gut symptoms and mood as well as decreasing anxiety. Such treatments include meditation, yoga, breathing exercises, gut-directed hypnotherapy and cognitive behavioural therapy.

For my patient with supragastric belching, his symptoms all started after a particularly stressful and traumatic relationship breakdown. I referred him to see a psychologist for cognitive behavioural therapy and he had an excellent response with complete disappearance of symptoms.

For most people who don’t have gut diseases, it is still important to care for your gut health, be alert to any concerning gut symptoms (see below) and follow the advice of national cancer screening guidelines. For instance, the increasing prevalence of bowel cancer around the world, especially among people aged over 50, has led to the introduction of non-invasive population-based screening programmes in many countries. This usually involves the health authorities issuing diagnostic faecal occult blood test kits to persons over the age of 50 annually or biannually.

Please note that if you are healthy with no gut symptoms, you do not need to order a test to check the health of your gut microbiome – and, anyway, these tests have limited validity. If you are concerned that you might have dysbiosis, the relevant investigations should be carried out in a clinical setting by medical experts.

The alarm symptoms

Sometimes, there are worrying symptoms that are reflective of a structural abnormality in the gut. These ‘alarm’ symptoms always need further evaluation:

Blood. The presence of gastrointestinal bleeding whether vomiting blood or passing blood in stool is always concerning. It implies that there is a break in the lining of the gut or bleeding from a blood vessel. Causes could include conditions such as haemorrhoids, peptic ulcer, inflammatory bowel disease or even something more sinister such as a tumour arising in the gastrointestinal tract.

Unexplained vomiting. Unexplained vomiting needs further evaluation, especially if it is severe and persistent.

Fever. Fever may be due to acute conditions such as infectious gastroenteritis but other conditions such as inflammatory bowel disease can result in a fever.

Unexplained weight loss. Unexplained weight loss is always concerning and there is a need to rule out serious pathologies such as cancers of the gastrointestinal tract.

Difficulty in swallowing. A difficulty in swallowing (medically known as dysphagia) needs to be investigated to determine if a benign condition such as an oesophageal stricture is the cause or if there is something else more worrying such as an oesophageal cancer.

Persistent change in bowel habits. An unexplained and persistent change in bowel habits can be emblematic of chronic gut conditions such as coeliac disease or inflammatory bowel disease. In some cases, particularly in older individuals, it could herald the onset of bowel cancer.

Loss of appetite. A loss of appetite also needs further consideration because it may signify a chronic gastrointestinal illness.

If you experience any of these alarm symptoms, it’s highly advisable to see your local doctor. You may be referred to a gastroenterologist to carry out further tests which may include an endoscopy or colonoscopy. These are flexible long thin cameras that can assess your upper gastrointestinal tract (oesophagus, stomach and first part of the small bowel) and lower gastrointestinal tract (colon) respectively.

If these investigations reveal conditions such as bowel or oesophageal cancer, your medical professionals will discuss with you whether this warrants surgery and potentially specific cancer treatments such as chemotherapy or radiotherapy.

In the case of my farmer patient with blood in his stools, I found a large tumour in his colon while carrying out a colonoscopy. Fortunately, the tumour was caught in time and hadn’t spread beyond the colon. After surgery and a course of chemotherapy, he has remained well and tumour-free.

Links & books

If you’d like to learn more about gut health and gut science, I have a collection of gut 3D animations on my website, Gut Dr.

By the end of the first 1,000 days of life, most of the development of the gut microbiome has occurred, but it continues to evolve after that time. To learn more about the developing gut microbiome, you can read my book The Healthy Baby Gut Guide (2020). I explain how the gut microbiome is intimately connected to the immune system, and how strategies employed in early life can help prevent children’s allergies.

The excellent Gut Health Podcast is a collaboration between the gastrointestinal dietitian Kate Scarlata and the psychologist Megan Riehl that explores the interplay between gut health, wellbeing, mood and microbes.

To find out more about the gut-brain axis, fermented foods and the microbiome, I’d recommend the Gut Health Gurus Podcast.

The Butts and Guts podcast run by the surgeon Scott Steele from the Cleveland Clinic covers a lot of topics in digestive health and is a great one to listen to if you particularly want to learn more about gut surgery.

There is a terrific Netflix documentary about the gut called Hack Your Health: The Secrets of Your Gut (2024) that explores the impact of gut health on brain function and mental health, featuring Giulia Enders who wrote the compelling blockbuster book Gut (rev ed, 2018).

Emeran Mayer’s book The Mind-Gut Connection (2016) is a fascinating read into how microbiome research has revolutionised our understanding of the human body and brain. It’s a great book to explore the gut-brain axis in detail.

Another book I’d suggest reading if you want to do a deep dive into the microbiome and IBS/small intestinal bacterial overgrowth is The Microbiome Connection: Your Guide to IBS, SIBO, and Low-Fermentation Eating (2022) by two doctors, Mark Pimentel and Ali Rezaie.

If you have IBS and would like to read a book by the definitive authority behind the low FODMAPs diet, I’d highly recommend the Monash University Low FODMAP: The Cookbook (2023). This practical book has more than 120 newly developed recipes and is very easy to use. Best of all, proceeds from the cookbook go back into research. If you want to do a deeper comprehensive dive into FODMAPs, you can buy a set of three books produced by the Monash University team.