More and more research is showing how important the health of the gut is to physical and mental wellbeing and the number of papers published on the subject has grown exponentially; now thought to be around 75,000. The bacteria, yeast and viruses that live in our gut are called the gut microbiome and there are around 100 trillion of them. Many of these microbes are beneficial and even essential to human health, while others can be harmful. This symbiotic relationship benefits microbes and their hosts as long as the body is in a healthy state. Sometimes dysbiosis develops when the more harmful bacteria get to overwhelm the system leading to ill health (Magill, 2023). By reducing factors that harm the good microbiome and increasing factors that help it to be restored to the right balance, much can be done for wellbeing. 

This two-part article explores why a good balance of microbiota is important and what factors encourage a healthy microbiota and what factors cause an imbalanced one. It is in two parts because it is now such a vast and popular subject; with this first part exploring why the gut microbiome is so important for health and wellbeing and what an unbalanced microbiota (otherwise known as dysbiosis) can lead to.
 

Why is it important?

Understanding of the gut microbiota’s importance evolved gradually; with the idea that beneficial microbes lived in the gut emerging in the late nineteenth and early twentieth centuries. The terms ‘microbiota’ and ‘microbiome’ appeared in scientific literature around 1927 and 1949 respectively (Nature Portfolio, 2019).
 
A person’s gut microbiota develops from the first microbial exposure, generally agreed to be at birth, with birth through the birth canal claimed to ‘seed’ the correct type of bacteria compared to a caesarean birth (Neu and Rushing, 2011). The gut microbiota typically reaches a more adult-like state by around 2–3 years of age, with the majority of the development and maturation occurring during early childhood. Disturbances to these early exposures can hamper the development of the microbiota (Magill, 2023). 
 
It is now known that the microbiota can reduce the incidence and severity of a wide range of human diseases, including obesity, psoriasis, autism and mood disorders. This is because the gut microbiome is now known to interact with many organs in the body, including the brain (Cleveland Clinic, 2023).
 
Our relationship with the gut microbiota is symbiotic; we provide an environment for the microorganisms in which to live and nutrients for them to feed on. In turn, they participate in several functions that are important for human health, such as fermentation of non-digestible dietary fibres, production of vitamin K and prevention of colonisation by pathogenic microorganisms. The following are some more functions performed by the gut microbiome.
 

Helping to break down food in the gut

 
Beneficial bacteria feed on fibre and resistant starch in a process called fermentation. The fermentation of carbohydrates produces beneficial compounds such as short-chain fatty acids (SCFAs), which can help to keep the gut lining healthy and reduce inflammation (Shin et al, 2023). In general, the breakdown of food by gut bacteria contributes to better nutrient absorption, ensuring the body gets the most from the food consumed (Valdes, 2018). Once broken down, these waste products leave the body easily and smoothly.
 

Protecting against pathogens

Gut bacteria protect against pathogens, which can cause stomach upsets and diarrhoea, by inhibiting pathogenic bugs from colonising the gut, or at least weakening them. These bugs include norovirus, Clostridioides difficile, Campylobacter, Escherichia coli, Salmonella enterica Typhimurium and Shigella species. It does this through several mechanisms, including: 
  • Crowding out harmful bacteria by competitive exclusion where the beneficial bacteria compete with harmful bacteria for nutrients and space in the gut, effectively limiting the harmful bacteria’s ability to multiply and cause illness. Good bacteria can also use direct inhibition by producing substances that can directly kill or inhibit the growth of harmful bacteria (Gut Clinic UK, 2025)
  • Stimulating the host’s immune response (Zheng et al, 2020) 
  • Helping to maintain the integrity of the intestinal barrier (Paone and Cani, 2020)
  • Teaching the immune system to distinguish between harmful and beneficial microbes (Pickard et al, 2017)
  • Breaking down toxic substances taken in with food (Cleveland Clinic, 2023). 


Supporting the immune system

Around three-quarters of our immune system is in the gut. Beneficial bacteria help to develop and support this system by training immune cells, competing with pathogens and producing beneficial metabolites (Zheng et al, 2020). The right kind of gut microbiota also prevents excessive inflammation and maintains a healthy gut barrier. During early life, the developing gut microbiota is crucial for the proper maturation and regulation of the immune system and helps prevent the development of immune-related disorders such as allergies, eczema, asthma and autoimmune diseases (Zheng et al, 2020). At the other end of life, the immune system works less efficiently (this is called immunosenescence), but supporting a healthy gut microbiome can give the ageing gut a boost (Goyani et al, 2024). Because of the declining immune system, vaccinations do not ‘take’ so well with age, but improving the gut microbiome can boost immunity (Bosco and Noti, 2024). 
 

Reducing the risk of metabolic disorders

Metabolic disorders include high cholesterol levels and raised blood sugars, especially post prandial. Gut microbiota can reduce these levels and so also help lessen inflammation. One way this is done is by the production of SCFAs which stimulate hormones such as glucagon-like peptide-1 (GLP-1) which, in turn, can help regulate blood sugar levels (Tolhurst et al, 2012; Bussell, 2021).
 

Influencing bile acid metabolism

This is important for lipid digestion and absorption. The microbiota helps to convert primary bile acids into secondary bile acids, regulating bile acid signalling and impacting gut microbial composition. This interaction is crucial for both host metabolism and gut health (Feng et al, 2023). 
 

Producing beneficial short chain fatty acids

SCFAs, such as butyric acid, improve the gut health through a number of local effects, including maintenance of the intestinal barrier integrity, mucus production, protection against inflammation and reduction of the risk of colorectal cancer (Magill, 2023).
 

‘Talking’ to the brain via a communication pathway between the brain and gut

This works in both directions and is often referred to as the gut–brain axis. Studies now suggest a healthy balance of gut bacteria may affect our mental wellbeing, perhaps even protecting against conditions like anxiety and depression (Magill, 2023). More research is needed to understand how the brain and gut communicate, and the effect this may have on mental health.
 

Reducing risk of getting certain cancers

The gut microbiome can contribute to reducing cancer risk, including colorectal cancer, and improving treatment outcomes through its modulating and enhancing effect on the immune system and by influencing tumour growth. It can also make tumour cells more susceptible to conventional treatments. Conversely, dysbiosis can promote cancer development and progression by increasing inflammation and altering cellular pathways (Akbar et al, 2022).
 

Preventing the gut from allowing harmful substances to enter through the gut lining

Good bacteria can bind to sites on the layer of cells lining the gut and provide a barrier preventing penetration by toxins, adhesion and infiltration by harmful bacteria. This ‘contra-biotic’ effect can inhibit the sensitisation of the gut and may help prevent the symptoms of irritable bowel syndrome (IBS) (Cleveland Clinic, 2023).
 

Helping to convert plant oestrogens (from foods such as soya) into equol

During the menopause, equol can exert a weak oestrogenic effect thus possibly lessening some menopausal symptoms, such as hot flushes, and also protect bone health (Lv et al, 2024).
 

Helping absorption of essential minerals

Many minerals are easily inhibited from being absorbed, such as iron and calcium, but the gut microbiota plays a significant role in enabling mineral absorption. It does this by increasing the bioavailability of minerals in the gut and producing enzymes that aid in mineral release from food (Hadadi et al, 2021).
 

Helping to synthesise certain vitamins

This includes vitamin K (half of our requirement is provided by gut bacteria), B vitamins and vitamin C (Cleveland Clinic, 2023). 
 

What can an unbalanced microbiota cause?

While a varied and balanced microbiota can help promote good health as outlined above, research has shown that a less varied and an imbalanced gut bacteria may be linked with a whole host of diseases. 
 

Irritable bowel syndrome and inflammatory bowel disease 

Although not a direct cause in all cases, dysbiosis is strongly associated with the development and progression of these conditions. In IBS, it is believed that altered gut bacteria can affect gut motility, pain perception, and overall gut health, all of which contribute to IBS symptoms (Cheng et al, 2024). In IBD, an alteration of the gut microbiome can lead to both Crohn’s disease and ulcerative colitis due to disruption of the gut barrier, resulting in increased inflammation and immune system activation, which are hallmarks of IBD (Newman, 2024).
 

Constipation, diarrhoea, bloating and gas

These common digestive symptoms can be a sign of an imbalanced gut microbiome and can be a symptom of IBS (Cleveland Clinic, 2024).
 

Food intolerances and sensitivities

Gut dysbiosis can create an environment that is more prone to both food intolerance and allergy. This is thought to be due to disruption of the gut barrier and immune function, as well as altering the way the body processes food (Berin, 2021). 
 

Autoimmune conditions

Dysbiosis promotes inflammation in the gut and throughout the body, which is a key factor in the development of autoimmune diseases, potentially leading to conditions like rheumatoid arthritis, type 1 diabetes, and thyroid issues (Mousa et al, 2022). These conditions arise due to an overactive or inappropriately targeted immune response and an increase in the permeability of the gut lining, allowing more substances (like bacteria and toxins) to enter the bloodstream evoking the autoimmune response. Also, gut microbes can in some cases trigger the production of antibodies that mistakenly attack the body’s own tissues (De Luca and Shoenfield, 2019).
 

Anxiety and depression

As said, emerging research suggests a strong link between gut health and mental wellbeing, with an imbalanced gut also potentially contributing to mood disorders and accelerated cognitive decline. The effect is believed to occur through the gut–brain axis; impacting mental health through various mechanisms (Boehme et al, 2023). 
 

Sleep disturbances

Similarly, sleep disorders and dysbiosis are linked through the gut–brain axis, with both sleep disruptions and imbalances in the gut microbiota affecting each other (Neroni et al, 2021). 
 

Obesity

An imbalanced gut microbiota can disrupt metabolic processes, potentially leading to weight gain and obesity (Thwaini, 2024).
 
Other diseases linked to dysbiosis include:
  • Type 2 diabetes
  • Cardiovascular disease
  • Hypertension
  • Cancer
  • Chronic fatigue
  • Kidney disease
  • Parkinson’s disease
  • Fatty liver disease
(Cleveland Clinic, 2024).
 
Again, the conditions above can result because of gut microbiome imbalance with too many harmful gut microbes crowding out the good ones. Some of the harmful microbes include Clostridioides difficile, Salmonella enterica, Escherichia coli, Shigella species, Helicobacter pylori, Bacteroides fragilis, Candida, Campylobacter jejuni, and Vibrio cholera (Floré, 2025). Some of the good microbes include Lactobacillus species (such as L. acidophilus, L. plantarum, L. rhamnosus, L. casei), Bifidobacterium species (such as B. longum, B. breve, B. animalis), Saccharomyces boulardii, Streptococcus thermophilus, Enterococcus faecium, Faecalibacterium prausnitzii, and Ruminococcus (Linares et al, 2016).
 

Conclusions

Outlined above is why the microbiome is being increasingly seen as important not just for gut health, but also general health, including metabolic diseases and brain health. What an unbalanced microbiota (dysbiosis) can result in as far as health implications are concerned is also outlined. As more and more evidence gathers at a rapid pace in this area, part 2 will look at how a certain healthy diet and lifestyle can help to restore the diversity and number of microbiomes so that normal gut balance can be improved and hence health and wellbeing restored.
 
Originally published in Journal of General Practice Nursing: Bussell G (2025) Gut microbiome: does it matter, what harms it, what helps it? Journal of General Practice Nursing 11(4): 46-49. https://www.journalofpracticenursing.co.uk/journals/issue/12-2025/article/gut-microbiome-does-matter-harms-helps 
 

Key points

  • The bacteria, yeast and viruses that live in our gut are called the gut microbiome. Many of these microbes are beneficial and even essential to human health, while others can be harmful.
  • Gut bacteria protect against pathogens, which can cause stomach upsets and diarrhoea.
  • The microbiome is being increasingly seen as important not just for gut health, but also general health, including metabolic diseases and brain health.

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