How the gut microbiome protects us from chronic conditions

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The gut microbiome consists of trillions of different types of bacteria and other microbes, some of which are considered beneficial to our body while others may be harmful under certain conditions. Whilst not a new discovery, scientists are only recently starting to understand that the gut microbiome is one of the most powerful influences on long-term health, playing a crucial role in digestion, metabolism, immune function, disease risk, healthy ageing and inflammation control. 

An imbalance in the microbiome (gut dysbiosis) has been linked to a higher risk of chronic diseases, while a well-balanced microbiome can help prevent and protect against these conditions. 

Understanding how the microbiome protects us from chronic disease can help you take steps to improve, optimise and maintain your gut health. 

Scientific research has linked a healthy gut microbiome to a lower risk of many chronic conditions, including: 

Inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) 

The two main types of IBD are Crohn’s disease and ulcerative colitis. 

Individuals with ulcerative colitis (UC) tend to have lower levels of beneficial bacteria Bifidobacterium longum, while both Crohn’s disease (CD) and UC are associated with a decline in beneficial gut bacteria like Eubacterium rectale, Faecalibacterium prausnitzii, and Roseburia intestinalis. In contrast, harmful bacteria such as Bacteroides fragilis appear to thrive, with their numbers and growth rates increasing. 

In individuals with IBS, improving the gut microbiome can reduce many of the common symptoms associated with the conditions such as diarrhoea, constipation and bloating. A balanced gut microbiome also helps to regulate gut motility. 

Clinical studies have shown that individuals with IBS have a lower gut diversity than healthy individuals. This further supports our argument that the gut microbiome is directly involved in the development and severity of IBS symptoms.

A healthy microbiome produces anti-inflammatory compounds like butyrate, which can help reduce gut inflammation and maintain a strong intestinal barrier. 

Obesity and type 2 diabetes 

People with obesity and type 2 diabetes often have lower microbial diversity, meaning fewer beneficial bacteria and sometimes an overgrowth of harmful microbes. This imbalance in bacteria can impact several important functions the microbiome carries out to help regulate our weight, fat storage, insulin resistance and metabolism. 

• Certain gut bacteria regulate blood glucose levels and reduce insulin resistance. 
• A diverse microbiome supports efficient energy extraction from food, preventing excess fat accumulation. 
• Beneficial bacteria produce short-chain fatty acids (SCFAs), which help reduce inflammation and improve metabolic function.  
• A lack of beneficial bacteria reduces the efficiency of the microbiome in carrying out these functions, increasing our risk of obesity and type 2 diabetes. 

Cardiovascular disease 

A healthy microbiome can lower cholesterol levels and reduce the risk of cardiovascular disease. There are several ways in which the microbiome can support healthy cholesterol levels and reduce our overall risk of cardiovascular disease: 

• Some beneficial bacteria help to convert cholesterol into a less harmful form. 
• The production of short-chain fatty acids can suppress synthesis of cholesterol in the liver, helping to lower cholesterol levels in the body. 
• The production of short-chain fatty acids is vital in reducing systemic inflammation. Chronic inflammation is a key indicator of heart disease. 
• Certain harmful gut bacteria produce trimethylamine N-oxide (TMAO), a compound linked to heart disease. A disrupted microbiome can increase TMAO levels, raising cardiovascular risk. 

Autoimmune diseases (rheumatoid arthritis, multiple sclerosis, lupus) 

With 70% of our immune system located within the gut, the gut microbiome plays a huge role in regulating and training our immune system. Dysbiosis is strongly linked to autoimmune diseases and inflammation. 

• The microbiome is in constant communication with our immune system and even helps to regulate it. It can calm and prevent overactive immune responses that can lead to autoimmune conditions. 
• People with autoimmune diseases often have gut dysbiosis, characterised by lower levels of anti-inflammatory bacteria and higher levels of pro-inflammatory bacteria. This imbalance can impair the immune system’s ability to regulate and calm inflammation, potentially triggering an immune attack on the body’s own tissues. 
• SCFAs, like butyrate, reduce excessive immune responses and help regulate inflammation, potentially suppressing autoimmune diseases. 

Mental health disorders (depression, anxiety, Alzheimer’s disease, Parkinson’s disease) 

• The gut produces neurotransmitters like serotonin and dopamine, which influence mood, cognition, and mental well-being. 
• Dysbiosis disrupts gut-brain communication and has been linked to depression and anxiety. This is due to increased inflammation, which affects brain function. 
• Research suggests that SCFAs, particularly butyrate, protect neurons and reduce neuroinflammation, lowering the risk of cognitive decline in conditions like Alzheimer’s and Parkinson’s disease.  
• In patients with Parkinson’s disease, butyrate levels may be reduced. Butyrate is believed to play a major role in the development and progression of Parkinson's disease. 

Fatty liver disease and metabolic syndromes 

Increased gut permeability (leaky gut) has been identified in individuals with metabolic syndrome and liver disease. This happens because increased gut permeability allows harmful toxins to enter the bloodstream and trigger inflammation in the liver. A study found that 39.1% of people with Non-alcoholic fatty liver disease showed signs of increased intestinal permeability compared to just 6.8% in healthy individuals. 

Cancer 

The microbiome influences cell growth and immune surveillance, helping to prevent colon cancer and other types of cancer. 

• A healthy gut helps neutralise carcinogens and toxins. 
• SCFAs, can inhibit the growth and migration of cancer cells. 

How does the microbiome lower our risk of disease? 

The microbiome protects us from chronic conditions through several key mechanisms: 

Metabolising food for nutrient absorption 

The gut microbiome plays a significant role in vitamin synthesis and absorption. When the microbiome is imbalanced (dysbiosis), the beneficial bacteria responsible for synthesising these vitamins decrease in number. This can impair nutrient absorption, making it harder for the body to utilise vitamins from food. In essence, it doesn't matter how many vitamins or minerals a food contains or how much you consume if your microbiome is unable to extract and absorb them effectively. 

Vitamin deficiencies can arise when the gut microbiome is unable to properly synthesise and absorb essential vitamins and minerals. Over time these deficiencies can contribute to fatigue, cognitive decline, weakened immunity, poor bone health, and increased inflammation, all of which are risk factors for chronic conditions such as cardiovascular disease, autoimmune disorders, metabolic syndromes and more. 

Digesting and processing fibre 

You might be surprised to learn that the human body cannot digest fibre, so why is the recommended daily intake for adults 30g if we can’t break it down? 

The answer lies in our gut bacteria. They ferment the dietary fibre we cannot digest, converting it into beneficial compounds like short-chain fatty acids (SCFAs). These SFCAs have huge benefits to our overall health, and without fibre in our diet, they wouldn’t exist. 

Benefits of effective fibre digestion: 

• Promotes regular digestion and prevents constipation. 
• Feeds beneficial bacteria, allowing them to multiply in numbers and maintain a healthy and diverse microbiome. 
• Lowers inflammation, reducing the risk of chronic conditions. 
• Regulates blood glucose by slowing carbohydrate absorption. 

A low-fibre diet starves beneficial gut bacteria, contributing to dysbiosis and an increased risk of disease. While humans cannot digest fibre in its natural form, our gut microbiome relies on it, using it in ways that are vital for our overall health. 

Producing short-chain fatty acids 

Short-chain fatty acids are produced when gut bacteria ferment dietary fibre. They are essential compounds and vital to our overall health in many ways. There are three primary SCFAs: butyrate, propionate and acetate, each playing a role in protecting against chronic disease, but butyrate and propionate are particularly important. 

Butyrate strengthens the gut lining, preventing harmful substances from entering the bloodstream (increased gut permeability), while also reducing inflammation, supporting brain health, and regulating metabolism.  

Propionate helps control appetite, lower cholesterol, and balance blood sugar levels, reducing the risk of cardiovascular disease and type 2 diabetes.  

Low SCFA levels are linked to poor digestion, chronic conditions, metabolic disorders and even certain cancers. 

How to ensure your gut microbiome is healthy

Understanding what a healthy microbiome looks like can ensure that you are able to identify any symptoms early on and make dietary and lifestyle changes to improve it.

A gut-friendly diet 

Eat a variety of fibre-rich foods - Fibre feeds your good bacteria, helping them thrive. 

Add fermented foods and probiotic rich foods (kefir, kimchi, sauerkraut) - Probiotic foods introduce beneficial bacteria into your gut. 

Add probiotics and prebiotics into your diet. Learn the difference between probiotics and prebiotics to understand how they can improve your overall gut health. 

Limit processed foods and sugar - Processed foods and excess sugar can feed harmful bacteria, leading to gut imbalances. Aim to: 

• Reduce fast food and ultra-processed snacks 
• Cut back on added sugars and artificial sweeteners 
• Choose whole, natural foods whenever possible 

Stay hydrated 

Water helps with digestion and keeps your gut microbiome in balance. Drink 6-8 glasses a day to support your gut health. 

To learn about what foods that are good for gut health, read our guide that details what types of foods are the best for supporting your gut health and why. 

Lifestyle changes 

• Manage stress 
• Regular exercise 
• Getting enough sleep (7–9 hours per night) 

Limit antibiotic use 

Antibiotics can kill both good and bad bacteria, leading to imbalances. If you need them: 

• Take probiotics during and after your course 
• Eat fibre-rich and fermented foods to help restore gut health 

If you want more ways to improve your gut health, take a look at our guide. 

Saskia's thoughts

A healthy gut microbiome is essential for preventing chronic diseases by: 

• Processing fibre and producing SCFAs like butyrate and propionate. 
• Enhancing immune function and reducing inflammation. 
• Maintaining gut barrier integrity, preventing systemic inflammation. 
• Regulating metabolism, reducing the risk of obesity, diabetes, and heart disease. 

Supporting your microbiome through a high-fibre diet, fermented foods, and a balanced lifestyle can lower your risk of disease and promote long-term health.