What is the Gut Microbiome and How Does it Affect Your Health?

The gut microbiome has become a hot topic as it is thought to play an important role in good health and disease prevention.

It’s made up of trillions of live microbes living within the human intestine known as the gut microbiota.

Here we will explore what the gut microbiome is, how it is related to our health, and how we can best support it.

What is the Gut Microbiome?

What is the Gut Microbiome?

Microbes include bacteria, viruses and fungi that exist within our bodies.

There are approximately 100 trillion microbes living in the gastrointestinal (GI) tract alone, mostly within the large intestine. These microbes are collectively referred to as the gut microbiome, and can be thought of as a separate, multi-functional organ within the body (1).

The development of the gut microbiome begins at birth, when a newborn baby’s GI tract is first exposed to microbes in the vaginal birth canal. However, emerging evidence suggests babies may come into contact with microbes even earlier while in the womb (2).

As you get older, your gut microbiome continues to grow and develop, and it’s influenced by factors such as diet, lifestyle, medications and stress (3, 4).

Many of these gut microbes are beneficial to health, though some can be harmful and promote infection or disease. To prevent ill-health, it’s important that the gut bacteria maintain a natural balance of “good” bacteria, such as Lactobacillus and Bifidobacterium, and “bad” bacteria, like Staphylococcus or Clostridium. (5, 6).

Summary: The gut microbiome contains a complex community of microbes that live within the gastrointestinal tract. Many of these microbes are beneficial to our health, though some can be harmful and promote infection or disease. Maintaining a natural balance of the “good” and “bad” microbes is important for maintaining good health.

Roles of the Gut Microbiome

Roles of the Gut Microbiome

Due to its sheer volume, the gut microbiome is able to perform a wide range of functions, including metabolism of fiber, immune support and communication with the central nervous system.

Metabolism of Fiber

The gut microbiome plays an important role in the metabolism (breakdown) of fiber.

Fiber (or roughage) describes the indigestible parts of plant foods. High-fiber foods include wholegrain cereals, beans, pulses, nuts, seeds and fruits and vegetables.

Most foods are broken down and digested by human enzymes in the small intestine, but this isn’t the case for fiber (7).

Instead, fiber passes through to the large intestine, where it’s broken down by gut microbes in a process known as fermentation. This fermentation results in the production of short-chain fatty acids (SCFAs), primarily propionate, acetate and butyrate.

These SCFAs are involved in numerous physiological health-promoting processes, including:

Summary: The gut microbiome plays an important role in the digestion and metabolism of fiber. This process produces short-chain fatty acids (SCFAs), which play an important role in promoting health.

Immune Support

Immune Support

The immune system protects against the spread of harmful, pathogenic microbes in the GI tract, and also allows for the colonization of beneficial microorganisms.

The bacteria in the gut microbiome support the early development and ongoing function of the immune system. The exact mechanism by which it does so is unclear, but the SCFA butyrate appears to play a role (12).

Butyrate, which is produced from microbial fermentation of fiber in the large intestine, helps to maintain the gut’s intestinal lining, which separates the digestive system from other parts of the body. This helps prevent pathogens from entering the immune system.

Recently, scientists have discovered that butyrate also boosts immunity by acting as a switch for the production of important immune cells called regulatory T cells and macrophages. These immune cells prevent harmless and even useful microorganisms in the intestine from being attacked by the immune system (13, 14).

Scientists also believe that both the immune system and gut microbiome mutually contribute to establishing and maintaining the balance in the gut (15).

Studies in mice have found an association between the gut microbiome and the innate immune system. They’ve concluded that a microbial imbalance may predispose individuals to immune-related conditions such as type 1 diabetes and inflammatory bowel disease (IBD). (16, 17).

Summary: The gut microbiome is important for supporting a healthy immune system. The exact mechanism by which it does so is unclear, but the SCFA butyrate (produced by microbial fermentation of fiber) plays an important role in turning on production of immune cells.

The Gut-Brain Axis and the Gut Microbiome

The Gut-Brain Axis

The gut microbiome is also linked to the brain through a bi-directional communication system called the gut-brain axis.

Gut microbes communicate with the central nervous system through nervous-, endocrine- and immune-signaling mechanisms. This allows the brain to control gut function, but also provides an opportunity for the gut microbiome to influence the brain (18).

Specific psychiatric disorders, such as depression and schizophrenia, have been shown to be associated with microbial imbalance (also known as dysbiosis) (19).

For example, one study found that people with depression had an overgrowth of potentially harmful bacteria and a lack of beneficial bacteria. However, it’s not possible to infer a causal link here, as these differences may be due to other factors such as diet or lifestyle (20).

Animal studies have provided further evidence for the effect of the gut microbiome on the brain and behavior. A study in rodents demonstrated that treatment with the bacterial strain Lactobacillus rhamnosus reduced anxiety and depression-related behavior, perhaps by increasing neurotransmitters in the brain (21).

Further studies in humans are needed, but we may start seeing new mental health therapies emerging that involve microbes.

Summary: The gut microbiome is able to communicate with the central nervous system via the gut-brain axis. An imbalance of gut bacteria has been associated with mental health disorders, including depression, anxiety and schizophrenia. Future mental health therapies may involve manipulating the bacteria in the gut microbiome.

The Gut Microbiome and Disease

Dysbiosis is thought to play a role in the cause of many diseases, including IBS and IBD, obesity, diabetes, cardiovascular disease, and even c-19.

Irritable Bowel Syndrome (IBS)

Irritable bowel syndrome (IBS) is a chronic gastrointestinal condition that affects up to 1 in 7 people worldwide.

It’s characterised by recurrent abdominal symptoms, including:

It’s been suggested that abnormalities in gut motility, infections of the GI tract and gut-brain axis problems may be involved in IBS (22, 23, 24).

In one study, people with IBS showed a significantly altered microbiome composition compared with a healthy control group (25).

This imbalance in the gut microbiome is believed to contribute to the low-level intestinal inflammation and entrance of pathogenic bacteria associated with IBS (26, 27).

Summary: IBS is a common condition characterized by chronic gastrointestinal symptoms. Its exact cause is unknown, but evidence suggests that microbiome dysbiosis may be a contributory factor.

Inflammatory Bowel Disease (IBD)

Inflammatory bowel disease (IBD) refers to a group of long-term inflammatory conditions that affect the digestive tract.

The most common types of IBD are Crohn’s disease, ulcerative colitis and microscopic colitis. Common symptoms include:

  • Diarrhea
  • Bleeding ulcers
  • Stomach pain, cramping and bloating
  • Weight loss
  • Anemia

As with IBS, the gut microbiome composition in IBD patients often differs from healthy people.

In 128 patients with Crohn’s disease, ulcerative colitis, lymphocytic colitis or collagenous colitis, one analysis demonstrated that their gut microbiome fluctuated more than that of healthy individuals.

This study also found an association between fluctuations in gut microbiome composition and a need for stronger medication during symptom flare-ups (28).

Summary: IBD is associated with an altered microbiome profile. In particular, some evidence has demonstrated that fluctuation in microbiome composition is more common in IBD patients compared with healthy people, and these fluctuations are associated with increased symptom severity.

Weight Gain and Obesity

Weight Gain and Obesity

Gut dysbiosis has also been associated with weight gain and obesity through a range of mechanisms, including (29).

  • Altered energy regulation
  • Altered gut hormone regulation
  • Promotion of inflammation due to pathogens entering the bloodstream via the intestinal wall (30).

Interestingly, overweight and obese people have been found to have lower gut microbial diversity compared with lean people (31).

One study compared 154 identical twins, one of whom was obese and the other whom was lean. The twins had significant differences in their gut microbiome composition, including the classes of microbes present and bacterial diversity. This suggests that differences in the microbiome are not genetic (32).

A similar study analyzed four pairs of twins. The gut microbiome from each twin was then introduced into mice. Despite the mice eating the same low-fat, high-fiber diet, the mouse hosting the obese twin’s microbiome gained more fat mass and presented more obesity-associated metabolic markers than the mouse hosting the non-obese twin’s microbiome (33).

Meanwhile, a long-term human study of 1,632 women found that low gut microbial diversity, especially in those with low dietary fiber intake, was associated with a higher degree of weight gain compared with those women who had a high microbiome diversity and fiber intake (34).

Summary: The causes of obesity are complex, but it appears that the gut microbiome may play a role. Eating a varied and diverse diet, high in fiber, may be beneficial in helping to maintain a healthy body weight and gut microbiome.



The gut microbiome may help control blood sugar, which could decrease a person’s risk of diabetes.

A recent study looked at 33 infants who were at high risk of developing type 1 diabetes due to genetic predisposal. They found that the diversity of the microbiome dropped suddenly before the onset of type 1 diabetes and that the number of “bad” bacteria increased just before diagnosis (35).

As mentioned above, SCFAs produced from the microbial fermentation of fiber play an important role in regulating blood sugar levels.

SCFAs are absorbed in the blood circulation, where they affect glucose (sugar) storage in the muscle, liver and fat cells. One specific type of SCFA, acetate, influences appetite to decrease food consumption, which may reduce risk of type 2 diabetes (36).

In a study of type 2 diabetes, 49 patients were randomly assigned to either a control group receiving usual diabetes care, or an experimental group where they were given a high-fiber diet to follow.

Almost three months later, the group eating a high-fiber diet had greater diversity and abundance of bacterial species that produce SCFAs compared with the control group. The high-fiber group patients also had reduced insulin resistance (37).

Summary: The gut microbiome plays an important role in controlling blood sugar levels and may affect a person’s risk of developing type 1 and type 2 diabetes.

Cardiovascular Disease

Cardiovascular Disease

The gut microbiome may play a role in cardiometabolic conditions as well (38).

It can benefit heart health through promoting good cholesterol (HDL) and moderating bad cholesterol (LDL and triglycerides), which can have an effect on cardiovascular health (39).

A study of 893 volunteers found that gut microbiome composition was accountable for the differences seen in blood lipid levels (LDL cholesterol and triglycerides) between individuals. The researchers concluded that altering the microbiome could be a potential treatment option for people with high blood lipid levels and high cholesterol (40).

Also, certain species within the gut microbiome could have negative effects on cardiovascular health by producing trimethylamine N-oxide (TMAO). Such species may convert choline and L-carnitine—nutrients found in red meat and dairy—to TMAO, potentially increasing a person’s risk of heart disease (41, 42).

Summary: A healthy gut microbiome appears to positively influence cardiovascular health by controlling cholesterol levels. However, some species within the microbiome can have a negative impact on heart health; this may be more of an issue for people who eat lots of red meat and dairy.

How to Improve the Gut Microbiome

 Fortunately, you can improve the composition and diversity of your gut microbiome by making changes in your diet.

Consuming a varied and diverse diet is important for maintaining a healthy gut microbiome (43).

A study comparing the diets and gut microbiomes in people from Europe and rural regions of Africa—where a more diverse and predominantly plant-based diet is consumed—found a significant difference in the gut microbiome. People from Africa had greater diversity of microbes and less harmful bacteria in their guts compared with Europeans (44).

In particular, you want to focus on consuming high-fiber foods.

High-Fiber Foods

High-Fiber Foods

Eating a diet rich in fiber is one of the best ways to diversify your diet and help your gut microbiome flourish.

High-fiber foods include:

  • Wholegrain cereals
  • Potatoes with skin on
  • Fruits and vegetables
  • Nuts and seeds
  • Beans and pulses

The recommended daily fiber intake in the UK is 30 grams per day, and 25-30 grams per day in the U.S. – though most people don’t achieve this.

Prebiotic Foods

Prebiotic Foods

Prebiotics are types of dietary fiber that feed the friendly bacteria in your gut (45).

Prebiotic foods include:

  • Jerusalem artichoke
  • Garlic
  • Onions
  • Leeks
  • Bananas
  • Asparagus
  • Barley
  • Oats
  • Flaxseeds
  • Wheat bran
  • Apples

Resistant Starch

Resistant Starch

Resistant starch, which “resists” normal digestion, is another type of dietary fiber and prebiotic.

Instead of being digested in the small intestine, resistant starch is broken down in the large intestine, where it’s fermented by gut bacteria. Studies have shown that resistant starch can help with weight loss, blood sugar control and digestive health (46, 47, 48).

You can change the starch content of a food depending on how you cook and prepare it. Cooking or heating destroys most resistant starches, but if you cook and cool a starchy food, you can increase the resistant starch in it.

Foods high in resistant starch include:

  • Cooked and cooled potatoes, pasta and rice
  • Oats
  • Legumes
  • Green bananas

Fermented Foods

Fermented Foods

Another way to improve your gut microbiome is by consuming fermented foods.

These are foods that have been broken down by bacteria or yeast, promoting the growth of beneficial bacteria such as lactobacilli.

Fermented foods include:

  • Plain, natural yogurt
  • Kefir
  • Kimchi
  • Sauerkraut
  • Miso
  • Tempeh

A study investigating the effect of yogurt consumption found that adults who consumed at least 200 grams of yogurt per day had significantly higher levels of beneficial bacteria and lower levels of harmful bacteria in their gut microbiome (49).

A seperate study of 24 obese women found that daily consumption of 180 grams of fermented kimchi for 8 weeks had a beneficial effect on gut microbiome composition (50).

Another study also demonstrated that fermented kimchi had positive effects on blood pressure, body fat percentage, fasting glucose levels and total cholesterol (51).



Many types of probiotics have been shown to restore the balance of the gut bacteria.

Probiotics can be consumed in foods or as a supplement. Probiotic foods include:

  • Natural yogurt
  • Kefir
  • Sauerkraut
  • Kimchi
  • Tempeh
  • Miso
  • Some cheeses, such as gouda, mozzarella, cheddar and cottage cheese

A meta-analysis on specific gastrointestinal diseases found that probiotics offered significant positive effects on symptoms of several diseases, including IBS, infectious diarrhea, pouchitis and antibiotic-associated diarrhea (52).

Another review found that probiotic use was associated with a significant reduction in “bad” cholesterol (LDL) and total cholesterol, as well as other inflammatory biomarkers for cardiovascular disease (53).

However, not all probiotics work in the same way. Research has shown that different probiotic bacterial strains have different effects on health and disease, so what works for one person might not work for another.

Probiotics research is still in its infancy and we don’t yet have enough information to make specific recommendations about which strains of probiotics are best for particular diseases.

Summary: You can beneficially influence the composition and diversity of your gut microbiome by eating a healthy, balanced diet that is high in fiber, comprises a wide variety of foods, and contains whole grains, fruits and vegetables. Eating prebiotic, probiotic and fermented foods can also improve your gut microbiome.

What to Avoid to Support the Gut Microbiome

Part of supporting your gut microbiome means avoiding restrictive diets, foods like artificial sweeteners and other lifestyle factors.

Restrictive Diets

Restrictive Diets

Following restrictive diets such as a gluten-free or low-FODMAP diet without a medical reason to do so could have adverse effects on the balance and diversity of the gut microbiome (54).

Prolonged exclusion of a particular nutrient or food group from your diet is likely to result in a microbial imbalance (dysbiosis). This reduced microbial diversity was demonstrated in mice who were fed a low-fiber diet over several generations (55).

A separate four-week study of 21 healthy (non-celiac) people found that following a gluten-free diet significantly altered their gut microbiome composition, with most of the participants showing a decrease in several key beneficial microbes (56).

While we need more research into the effects of long-term restrictive diets on the gut microbiome, it makes sense to avoid any unnecessary long-term restrictions in your diet.

Artificial Sweeteners

Artificial Sweeteners

Artificial sweeteners are widely used as an alternative for sugar, often as a tool for reducing total calorie intake.

However, research suggests that they may have a negative impact on gut microbiome. A 12-week study found that regular consumption of artificial sweeteners in rats resulted in a significant reduction in several beneficial microbes compared with a control group (57).

Another group of researchers conducted a series of studies examining the link between artificial sweeteners, the gut microbiome and negative health outcomes. Mice that were fed artificial sweeteners for 11 weeks developed glucose intolerance compared with mice fed regular sugar. The researchers concluded that these differences were attributable to altered composition of the gut microbiome (58).

The same researchers investigated long-term artificial sweetener consumption in 381 healthy humans. They found a positive association between consumption of artificial sweeteners, adverse changes in the microbiome and several indicators of metabolic syndrome (59).

This is still a relatively new field of research, but the existing evidence suggests that artificial sweetener consumption may have an adverse effect on metabolic health (namely, glucose intolerance), which could be caused by changes in the gut microbiome.

Lifestyle factors

Lifestyle factors

Lifestyle factors other than nutrition can play a role in the health of the gut microbiome.

Alcohol consumption appears to have a negative effect. A study of the gut bacteria of alcoholics demonstrated dysbiosis in 27% compared with 0% prevalence in mild and non-drinkers (60). This research also suggested that these changes persisted even after an extended period of sobriety.

However, the type of alcohol may produce different effects. A small study comparing the influence of red wine and gin consumption in 10 healthy men found that while the gin reduced the amount of beneficial gut bacteria, red wine increased beneficial bacteria and reduced harmful bacteria (61). This effect was attributed to the polyphenol content of red wine.

Medications, in particular antibiotics, have the potential to alter the gut microbiome, creating dysbiosis. A review of the scientific evidence on this topic found that antibiotic use can result in long-term consequences including decreased microbial diversity, altered microbe ratios, overgrowth of harmful bacteria, and reduced resistance to pathogens (62). Therefore antibiotics should always be prescribed with caution and taken in adherence with your doctor’s advice.

Stress is an inevitable part of daily life, however chronic stress has been shown to negatively influence the composition of the gut microbiome in animal studies (63). This may be due to physical changes to the microbiome environment, either as a result of changes to the structure of the intestinal lining or gut secretions.

Therefore, learning to manage your stress levels through exercise, meditation or mindfulness is one way that you can positively influence your gut microbiome.

Summary: Along with eating a varied, high-fiber diet, you should avoid restrictive diets and artificial sweeteners to help your gut microbiome to flourish. Paying attention to your alcohol intake, antibiotic usage, and stress levels will also contribute to keeping your gut microbiome healthy.

Why the Gut Microbiome is So Important

The gut microbiome is home to trillions of bacteria, viruses and fungi, all of which collectively play an important role in maintaining good health.

It can almost be thought of as a separate, multifunctional organ given its important functions within the body.

These include the metabolism of fiber, immune system support, and communication with the central nervous system via the gut-brain axis.

The gut microbiome has been heavily researched over the past few years.

While there’s still much to be learned, most scientists agree that an altered gut microbiome—specifically reduced microbial diversity and dysbiosis (microbial imbalance)—may play a role in a number of diseases, including IBS, IBD, obesity, diabetes, and cardiovascular disease.

The mechanisms by which the gut microbiome can influence these diseases are wide-ranging and still being discovered. More research is required to inform treatment options.

In the meantime, one of the best ways to look after your gut microbiome is by eating a varied and diverse diet that is high in fiber and predominantly plant-based.

Try to include lots of prebiotic- and probiotic-containing foods and, if possible, avoid unnecessary restrictive diets and artificial sweeteners.

You should also be mindful of your alcohol intake and stress levels, and be sure to use antibiotics carefully.

Taking probiotic supplements is another way to potentially optimise your gut health, though there’s still not enough research to recommend specific strains for particular diseases.

While there’s so much more to be learned about the gut microbiome, it definitely influences our health in multiple ways, so it’s worth looking after by following a healthy and balanced diet and lifestyle.


About Harriet Smith, BSc (Hons), RD

Harriet is an award-winning Dietitian who is registered with the British Dietetic Association (BDA) and Health and Care Professions Council (HCPC). She runs her own business, ’Surrey Dietitian’, which provides private dietetic consultations and consultancy services (PR & Media and Health Writing).