What are gut bacteria?

The human gastrointestinal tract is home to a vast community of over 100 trillion microorganisms, mainly bacteria. One of the many jobs of these bacteria is to help us digest and use the nutrients from our food. They also serve other important functions that regulate our overall health, such as supporting our immune system¹ .

Each person has a unique community of microorganisms living in their gut – this is called the gut microbiota. The gut microbiota is first influenced by genetics and birth, but changes throughout a person’s life due to factors like diet, age, geographical location, and the use of certain medications, like antibiotics ^2,3. The gut microbiota, together with its genetic material and associated metabolites living in the intestinal tract, is called the gut microbiome.

While there isn’t a consensus definition of a “healthy gut microbiome” – partly because everyone’s microbiome is unique (even identical twins!) and because your microbiome changes throughout your lifetime – there are certain indicators that can help us understand features that contribute to positive or negative health outcomes. Importantly, we know that having a lot of diversity in our gut bacteria makes our microbiome more capable and resilient². In adults, a microbiome with many different types of bacteria works more effectively than one with only a few types, because if one bacteria can’t do its job, another can take over.

Fig 1 – Illustration of the difference between microorganisms, microbiota, microbiome

How do gut bacteria impact our health?

Our gut bacteria support many essential body functions, including vitamin production and nutrient absorption, immune system response, hormone regulation, metabolism regulation, and protection against harmful pathogens⁴.

When the balance of microorganisms in the gut is disrupted, it can negatively impact these functions, and a condition known as dysbiosis may occur. Gut dysbiosis has been linked to health issues including allergies, autoimmune diseases, certain cancers, asthma, metabolic diseases like type 2 diabetes and obesity, and mental health disorders like anxiety and depression¹. However, it is still unclear whether the changes in gut bacteria cause these diseases or are a result from them⁴.

Researchers have also found that people with certain diseases often have different kinds of bacteria living in their gut compared to those who do not have the disease. For instance, individuals with inflammatory bowel disease (IBD) or type 2 diabetes tend to have gut microbiota that is noticeably different from those without these conditions.

How do gut bacteria affect our immune system?

A large part of our immune system, about 70-80% of the body’s immune cells, is found in the gut. Here, the immune cells continuously interact with gut bacteria. This close relationship is crucial for shaping the immune system because it helps to create, develop, and regulate various immune cells, while also protecting against harmful pathogens. In return, immune cells help stabilise the balance of gut microorganisms. This partnership is vital for maintaining stability in the immune system and keeping the body healthy. However, if the structure and function of gut microbiota are disrupted, it can lead to an overgrowth of harmful bacteria, increasing the risk of infections and other health problems³.

Can gut bacteria affect mental health?

There is a significant connection between the gut and the brain, commonly referred to as the ‘gut-brain axis’. This two-way communication system means that the gut can influence cognitive performance, mood, and behaviour. For example, gut-related issues like irritable bowel syndrome (IBS) can affect what’s happening in the brain, and vice-versa, stress is a major trigger for IBS symptoms and the disease is closely related to anxiety disorders, early-life trauma or depression^5,6. Hence, our mind and mental health can have a significant impact on our gut – expanding our understanding of mental health beyond just the brain itself ^7,8.

Several studies suggest that the diversity and composition of gut microbiota play a role in conditions like depression, anxiety, and other psychological disorders. Research is also exploring the role of gut microbiota in the progression of neurological disorders such as Alzheimer’s, cerebrovascular stroke, Parkinson’s disease, and schizophrenia^4,9.

New research is investigating how improving gut microbiome functions could support better mental health. For example, existing clinical trials have demonstrated that probiotics, beneficial bacteria that influence the gut-brain link, might help reduce anxiety, improve mood, and even enhance cognitive function in conditions like bipolar disorder . This has led to the term ‘psychobiotic’ to describe how probiotics (and prebiotics) might relieve mental health symptoms^8,9,10.

Dietary patterns, which strongly impact gut microbiota, are also being studied for their impact on mental health . For instance, high-fat diets rich in animal products have been shown to disrupt the balance of gut microorganisms, while on the other hand, the Mediterranean diet (rich in fibre and prebiotics from whole grains, nuts, and vegetables) has been linked to reducing the occurrence of psychiatric conditions and the risk of depression^4,11.

How do gut bacteria influence weight loss?

Many studies have identified significant links between gut bacteria, weight gain, and obesity. Our gut bacteria help regulate body weight by influencing energy levels, appetite, how we absorb nutrients, and the function of adipose tissue which impacts how our bodies store fat^5,12,13. For example, in people with obesity, gut bacteria are better at extracting energy from food compared to those with a normal weight. Notably, people with obesity often have less diverse gut bacteria and different types of gut bacteria compared to those without obesity – and the types of bacteria found in the gut can vary depending on how severe the obesity is^14,15. An imbalance in gut bacteria can both contribute to the development of obesity by affecting metabolism and fat storage, and it can also result from obesity, where gut bacteria becomes disbalanced from the impact of weight gain1. The development of the microbiota in early childhood can also influence a child’s growth and risk of obesity later in life.

Much of the evidence linking gut bacteria and obesity comes from animal studies. Many studies have been carried out with humans, but are limited due to underrepresented populations and outcomes with opposing results¹⁵. Existing studies have shown associations between changes in gut bacteria – like those caused by antibiotics – and the development of weight gain^1,16. As findings from animal studies cannot be directly applied to humans, more research is necessary to understand how, and to what extent, the gut microbiome may impact human metabolism .

Modifying the gut microbiota composition through diet, probiotics or prebiotics has shown promise as a weight management strategy. Personalised approaches and combined interventions may be necessary to see improvements for individuals . Importantly, it’s crucial that any microbiome-related treatments should be conducted under professional medical guidance to ensure they are safe and effective.

• Research highlight: The EU-funded BETTER4U project is working to develop personalised interventions to address obesity and weight gain. The project aims to understand how factors like genetics, epigenetics, lifestyle, environment, and the gut microbiome influence weight gain and to identify potential microbial strains that could aid in weight loss.

What factors influence the composition of gut bacteria?

Birth mode and early life

The gut microbiome begins to form early in life. How a baby is born – whether through vaginal delivery or caesarean section – can influence the types of bacteria that settle in their gut. Babies born through vaginal delivery mainly get their gut bacteria from the mother’s vaginal bacteria. Babies born via caesarean section pick up different bacteria from the surrounding environment, for example from the mother’s skin, the medic’s skin, and the surrounding environment. This tends to impact the composition of the gut microbiota in infants for up to 6 months after birth¹⁶.

Feeding is also an important factor in the development of an infant’s microbiota, whether it is breastfeeding or formula feeding. Human milk is rich in essential nutrients such as fats, proteins, carbohydrates, and immunoglobulins, all which support microbiota diversity. Improvements in infant milk formula, such as the addition of specific oligosaccharides, aim to promote a microbiota rich in beneficial bacteria strains that are linked to positive health outcomes. As an infant grows, their microbiota evolve, and by the time they reach three years of age the gut microbiota becomes quite similar to an adult’s ^19,20.

Effects of antibiotics

Antibiotics help us combat (life-threatening) bacterial infections, however, while doing so, they can also harm beneficial microorganisms in our gut. Antibiotics reduce microbial diversity and alter functional attributes of the gut microbiome, which can lead to dysbiosis²¹. The extent of these changes depends on several factors, such as the specific antibiotic used, dosage, and period of use¹⁷. While the impact of antibiotics is usually short-term, disturbances of the gut microbiota for extended periods of times have also been documented, with some cases associated with increased risk of asthma, food allergies, or weight gain ²¹.

Antibiotic usage can lead to mild or more severe cases of diarrhoea, caused by the pathogen Clostridioides difficile. Taking probiotics during antibiotic treatment can reduce the risk of developing antibiotic-associated diarrhoea .

It is important to be aware of the dangers of use, misuse and abuse of antibiotics²³. Only take antibiotics when prescribed by your doctor (and not self-medicate), follow your GP’s advice and finish the whole prescription.

Diet and lifestyle

Diet and lifestyle have a major impact on shaping the composition and function of our gut bacteria in the long-term^19,23 . Gut bacteria highly depend on the foods we eat, which can either help or harm their functioning. For example, gut bacteria ferment non-digestible substrates such as dietary fibres (for example, prebiotics), a process that produces short-chain fatty acids, which are important for regulating metabolism and inflammation, and reducing the risk of disease^13,24. In general, diets rich in high-fibre, plant-based foods, and whole grains help support a diverse microbiome. In contrast, diets characterised by low-fibre foods can reduce microbial diversity¹².

Consuming probiotics or prebiotics, either in the form of supplements or via certain foods, can improve intestinal health as they promote the presence of beneficial gut bacteria²⁶. Probiotic treatments have the potential to restore gut dysbiosis by limiting the growth of harmful bacteria and strengthening the functions of the gut barrier^1,21. It is for this reason that probiotics have been studied in clinical trials for their therapeutic potential in treating a wide range of health conditions, from type 2 diabetes and obesity to mental health disorders.

In terms of lifestyle factors, regular physical exercise, interacting with pets, spending time in nature and getting adequate sleep can all foster a diverse and healthy microbial community in the gut. On the other hand, exposure to environmental pollutants, smoking and drinking too much alcohol can reduce microbial diversity and disrupt the balance between beneficial and harmful bacteria. This can lead to increased inflammation and a higher risk of disease. Managing stress is also important, as chronic stress can negatively impact digestion, reduce the presence of beneficial bacteria, and cause problems in the gut barrier, leading to inflammation ^25,26.

Fig. 2 – What factors influence the gut microbiota?

What foods help promote healthy gut bacteria?

Overall, a balanced diet rich in a diversity of fruits and vegetables, fermented products with live microorganisms, and healthy fats (i.e., unsaturated fats) is key to fostering a diverse gut microbiome. Some foods that can support a healthy gut include:

Foods that are high in saturated fat, such as fried foods, and foods high in added and free sugars, like soft drinks and sweets, can negatively impact gut bacteria. Try swapping potato chips with raw veggies and hummus or replacing a sugary dessert with a bowl of fresh fruit salad.

• Research highlight: The EU funded DOMINO project is researching the impact of fermented foods on the gut microbiome, and the links to health benefits. This project will contribute to a better understanding of how dietary recommendations based on fermented foods can support recovery for individuals with metabolic syndrome.

Conclusion

The bacteria living in the human gut are crucial for human health. Exactly how, to what extent, and what areas of human health are influenced by our microbial “inhabitants” is an exploding area of research. While gaps in the knowledge remain, there are well-established links showing that gut bacteria influence the way we function: from digestion and immune function to mental health and weight management. The balance and diversity of gut bacteria, which indicates how well a microbe community functions, is shaped by a complex interplay of factors, including diet, lifestyle, genetics, epigenetics, and microbial exposure in early life. Maintaining a diverse gut microbiome through a balanced diet rich in fibre, fermented foods, and prebiotics, alongside positive lifestyle choices like regular exercise and stress management, can support not only digestive health but also contribute to reducing the risk of various chronic diseases.

This article was written in collaboration with EUFIC and researchers from the DOMINO and BETTER4U projects. View the article on EUFIC’s website, here.

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