The 10 common causes of poor gut health

Gut health is about far more than digestion alone. The gut plays a crucial role in other areas too, like immune function, mental wellbeing, metabolism and even weight regulation (Valdes et al 2018). At the centre of this system is the gut microbiome - the diverse community of trillions of bacteria, fungi and other microorganisms that live primarily in the large intestine.

Each person’s gut microbiome is unique, shaped by many factors such as genetics, early life exposures, diet, lifestyle, medications and environment. Maintaining a healthy balance of gut microbes (often referred to as microbial diversity and symbiosis) is important  for good gut health. However, many aspects of modern life can work against this balance.

What we eat, our stress levels, physical activity, sleep patterns and medication use are some of the factors that can impact our gut health. For example, chronic stress can increase gut inflammation and sensitivity, making the digestive system more reactive to certain foods (Konturek et al 2011). Poor sleep can disrupt appetite hormones and alter gut bacteria (Benedict et al 2016), while a lack of dietary fibre may reduce the production of beneficial compounds that protect the gut lining  (Valdes et al 2018).

While certain foods and lifestyle habits are commonly associated with poorer gut health, it is important to recognise that individual responses vary. What causes symptoms for one person may not affect another in the same way.

This article provides general, evidence-based information; anyone experiencing ongoing digestive symptoms should seek advice from a registered dietitian, GP or other qualified healthcare professional.

Meet our expert: Nichola Ludlam-Raine

Foods That Can Throw Gut Balance Off

Fried Foods

Fried foods are typically high in saturated fats and, depending on preparation methods, may also contain trans fats. Research suggests that diets high in saturated fat can influence the balance and variety of microbes in the gut. These changes may affect how the digestive system functions, particularly for people who are more sensitive  (Jamar and Pisani 2023).

Frying foods at high temperatures can also produce compounds that irritate the gut lining. Regular consumption of fried foods has been associated with disruption of the gut barrier and increased intestinal permeability (often known as “leaky gut”), contributing to inflammation and poorer gut health outcomes (Statovci et al 2017).

Healthier alternatives such as baking, air-frying, grilling or stir-frying with small amounts of unsaturated fats (such as olive or rapeseed oil) can support gut health while still allowing people to enjoy familiar foods.

High-Sugar Foods

Sugar occurs naturally in many foods, including lactose in dairy products, like yoghurt and fructose in fruit. These naturally occurring sugars are typically consumed alongside fibre, protein, vitamins and minerals and are important in the diet

Added sugars, however, are often overlooked in the diet. They are commonly found in confectionery, baked goods, sugary drinks and foods which offer little nutritional value. While some sugar can fit into a balanced diet, excessive intake of added sugars has been linked to negative effects on gut health (Zinöcker and Lindseth 2018).

Diets high in added sugars and low in fibre may make it harder to maintain a healthy balance of gut microbes. Over time, this can affect the gut’s natural protective lining and may be linked to irritation in the digestive system. High sugar intake has also been linked to poorer oral health, which could indirectly influence gut health through changes in the bacteria in the mouth  (Desai et al 2016).

Reducing added sugar does not mean eliminating all sweet foods. Focusing on whole foods, checking labels for hidden sugars (and monitoring intake) and choosing naturally sweet options such as those with fruit can help support gut health.

Lack of Diverse Plant Foods and Fibre-Containing Foods

Dietary fibre is one of the most important nutrients for gut health, yet many adults (96%) fail to meet the recommended intake of 30g a day (NDNS, 2025). Fibre is not digested by the body but is fermented by gut microbes, producing beneficial compounds called short-chain fatty acids (SCFAs). These compounds help nourish the cells lining the gut, reduce inflammation and support immune function  (Makki et al 2018).

A lack of plant diversity in the diet limits the range of fibres and polyphenols (beneficial compounds found in foods) available to different gut microbes. Each species of microbes prefers different foods for fuel, so eating a narrow range of foods can reduce microbial diversity over time.

A practical way to improve variety is aiming for around 30 different plant foods per week. This includes fruits, vegetables, wholegrains, legumes, nuts, seeds, herbs and spices. Even small additions, such as mixing vegetables into meals or rotating different grains, can have meaningful benefits.

Foods with a Low Nutritional Content

Foods high in saturated fat, salt and added sugars (often referred to as HFSS foods) are generally considered less supportive of gut and overall health when consumed frequently. It is important to focus on the overall quality and nutrient density of foods, as well as their main ingredients, rather than simply the length of an ingredient list or the presence of one or two additives used to keep a product safe or stable (Ludwig et al 2018).

For example, although yogurt is processed, it is a nutrient-dense food that provides protein, calcium and, in many cases, live cultures that can support gut health. Some foods are also fortified to improve nutritional quality, such as cereals fortified with iron or vitamin D-enriched plant-based products. Fortification can play an important role in addressing population nutrient gaps.

Certain ingredients are also necessary to ensure food safety, shelf life and consistency. Rather than categorising foods as “good” or “bad,” a balanced approach that prioritises overall dietary patterns is more helpful for long-term gut health.

Drinks That Can Disrupt Your Gut Health

Alcohol

Alcohol has a direct toxic effect on the digestive system, damaging the gut lining, increasing intestinal permeability and disrupting the gut microbiome, which may promote inflammation and contribute to digestive symptoms (Bishehsari et al 2017).

Frequent or high alcohol intake has been associated with changes to the gut microbiome that may affect immune function and metabolic health. Over time, this disruption may worsen digestive symptoms such as bloating, diarrhoea or abdominal pain.

There is some nuance when it comes to red wine, which contains polyphenols that may have prebiotic-like effects when consumed in small amounts. However, these potential benefits are only observed with moderate intake, and alcohol is not necessary for gut health, as polyphenols are abundant in many other, more nutritious foods and drinks, including tea, coffee, fruits, vegetables, herbs and spices.

Sugary Soft Drinks and Energy Drinks

Sugary soft drinks and energy drinks are often high in added sugars and provide little nutritional value. Regular consumption can increase the growth of less beneficial gut microbes and contribute to gut inflammation (Satokari 2020).

High sugar intake from drinks is also linked to weight gain and poorer metabolic health, both of which can indirectly affect gut function. The acidic nature of many fizzy drinks may further irritate the digestive tract in some individuals.

Choosing water, sparkling water, herbal teas or lower-sugar alternatives can help reduce sugar intake while supporting hydration - an often-overlooked factor in digestive health.

Lifestyle Factors That Can Impact Your Gut Health

Antibiotic Overuse

Antibiotics are essential for treating bacterial infections and can be lifesaving. However, they do not distinguish between harmful and beneficial bacteria. A course of antibiotics can significantly reduce gut microbial diversity, sometimes for weeks or months.

Repeated or unnecessary antibiotic use may increase the risk of long-term gut imbalance because antibiotics can affect both harmful and beneficial bacteria. However, if antibiotics are prescribed, it is important to take them exactly as directed and complete the full course, even if symptoms improve, to ensure the infection is properly treated. If you experience side effects or have concerns while taking antibiotics, you should seek advice from a healthcare professional.

Supporting the gut before, during and after antibiotic treatment may also help recovery. Eating a varied, fibre-rich diet that includes foods such as vegetables, fruit, wholegrains, beans and oats can help nourish beneficial gut bacteria. Foods containing live cultures, such as yoghurt or kefir, may also be helpful for some people, particularly during or after a course of antibiotics, as they can help reintroduce beneficial microbes and support the restoration of the gut microbiome (World Gastroenterology Organisation Global Guidelines, 2023).

Chronic Stress

The gut and brain are closely connected via the gut–brain axis, a two-way communication network linking the digestive system with the central nervous system. Chronic stress can reduce blood flow to the digestive system, alter gut motility and increase intestinal sensitivity.

Stress hormones such as cortisol can also influence the composition of gut bacteria and increase inflammation. Common sources of prolonged stress, such as work pressure, caregiving responsibilities or exam stress, may therefore contribute to digestive symptoms even in the absence of dietary changes (Cryan et al 2019).

Stress-management techniques, including mindfulness, yoga, breathing exercises and regular breaks, can play a meaningful role in supporting gut health.

Poor Sleep Patterns

The gut microbiome follows a circadian rhythm that aligns with sleep-wake cycles. Disrupted sleep, shift work or irregular routines can alter this rhythm and negatively affect gut balance (Thaiss et al 2014).

Poor sleep has been associated with changes in appetite regulation, increased inflammation and a higher risk of weight gain and metabolic issues - all of which may impact gut health (Supasitdikul et al 2025). Prioritising consistent bedtimes, limiting caffeine later in the day, reducing screen time before bed and creating a calming evening routine are all part of good sleep hygiene and can support both sleep and digestion.

Lack of Physical Activity

Regular moderate physical activity has been shown to increase gut microbial diversity and the abundance of beneficial bacteria (Clarke et al 2014). Exercise supports the production of short-chain fatty acids,which help reduce gut inflammation and strengthen the gut barrier.

In contrast, prolonged inactivity is associated with reduced microbial diversity and poorer gut health outcomes. While moderate exercise is beneficial, very intense or prolonged training without adequate recovery may temporarily disrupt the gut microbiome in some individuals and lead to dysbiosis (Monda et al 2017).

Finding a sustainable balance, and an activity you enjoy, such as walking, cycling, swimming or strength training, is key to consistent movement for gut health.

Smoking

Smoking has been shown to negatively affect gut microbial composition and increase inflammation throughout the digestive tract. It is associated with a higher risk of gastrointestinal conditions and may impair the gut’s ability to maintain a healthy microbial balance.

Stopping smoking can lead to improvements in gut health over time, alongside well-established benefits for overall health (Biedermann et al 2013).

How to Support Your Gut Health

Supporting gut health does not require perfection or extreme changes. Small, consistent habits can have a powerful impact over time.

• Eat prebiotic- and probiotic-rich foods: Include fibre-rich foods such as onions, garlic, leeks and wholegrains, alongside fermented foods like yoghurt and kefir.
• Prioritise sleep and stress management: Aim for regular sleep patterns and incorporate stress-reducing practices into daily life such as mindfulness, controlled breathing and meditation.
• Move your body regularly: Move your body regularly: Regular moderate physical activity supports the growth of beneficial gut bacteria and overall health. Aim for around 30 minutes of activity on most days of the week, alongside two strength-based sessions per week to support muscle strength and overall resilience.
• Diversify your diet: Eating a wide variety of plant foods helps nourish a diverse microbiome. Aim for around 30 different plant foods each week, including wholegrains, lentils, beans, fruits, vegetables, nuts, seeds, herbs and spices.