Microbiome Diversity: Here’s How To Have A Diverse And Balanced Microbiome

Your gut is home to an ecosystem of microbes, mostly residing in the colon. These bacteria live in balance with your body, contributing to your metabolism and wellbeing in return for nourishment from the gut. 

Microbiome diversity (how many types of bacteria are in your gut) is an important measure of microbiome health. Indeed, research shows that low microbiome diversity is linked to many common problems like weight gain, digestive problems and even chronic diseases, but high diversity is representative of good gut health

What is gut microbiome diversity?

What makes your gut different to other people is in part determined by differences in your gut microbiome diversity. Low diversity is so important that it’s even associated with serious chronic diseases, such as obesity, type II diabetes, inflammatory bowel disease, and chronic fatigue syndrome. Even allergies and cancer can be linked to changes in the microbiome bacteria. 

So what is gut microbiome diversity? Approximately 1,000 bacterial species live in your gut, 90% of which are either Bacteroidetes or Firmicutes. To measure diversity, products like the Atlas Microbiome Test by Atlasbiomed.com use DNA sequencing to analyse the bacteria in your stool and calculate microbial species richness and abundance in your gut. 

Abundance refers to how many different species of bacteria there are, while richness tells you how different those species are relative to one another. An additional measure is how different the microbiome is across different parts of the gut. 

The relationship between your body and its gut bacteria is symbiotic: you help them, and they help you. Basically you give them a home and food and, in return, their activities and beneficial substances contribute to your health. What food you may wonder? Well, gut bacteria largely digest carbohydrates, plant fibre, and other substances found in your food for energy

For example, a diverse microbiota produces butyrate, a short-chain fatty acid (SCFA) that is the main source of energy for colonocytes, the cells that line your gut. The activities of your gut microbes help control inflammation and reinforce your gut lining, thus protecting you against infection and pathogens.

In addition to butyrate, gut bacteria make a few other important short-chain fatty acids (acetate and propionate) that can help control appetite and enhance the functions of your digestive tract. They also produce a range of vitamins that support microbiome health.

But your microbiome diversity can still be significantly altered by factors within your control. One landmark study found that environmental factors (like diet and antibiotics) accounted for up to 16% of microbiome diversity. 

However, there is only one way to check your microbiome diversity, and that is with a microbiome test that uses advanced sequencing technology on a stool sample. Nowadays, you can actually buy these tests online and do them at home, like with AtlasBioMed.

Why is having a diverse and balanced microbiome important?

A diverse and balanced microbiome boosts your immune system, helps protect against illness, and even contributes to maintaining a healthy body weight. That’s because it can respond better to health challenges as it has more ‘workers’ to perform each job (like controlling opportunistic microbes) while a less diverse one has fewer specialised workers for specific jobs. 

Meanwhile, a less diverse gut microbiome may result in dysbiosis, where the body switches from a positive to a combative relationship with its gut bacteria because of imbalanced microbial populations. This can cause digestive symptoms and inflammation because it triggers your body’s own immune system. 

Higher microbiome diversity is also linked to healthy body weight. This is probably because it helps maintain the gut lining, while regulating your appetite and fat deposits. Short-chain fatty acids, like butyrate, propionate and acetate are responsible for many of these effects. Some other factors that influence diversity include:

Biological sex

If you’re a woman, you’re in luck! Female study participants have been found to have higher gut microbiome diversity, on average, than male participants. This may be due to the influence of female sex hormones on microbiome diversity, during events like puberty, the monthly cycle, and pregnancy. 


Ageing makes gut microbiomes less diverse: less beneficial bacteria and more potential pathogens, leading to a greater risk of dysbiosis and infection. This loss of diversity depletes the microbiome’s ability to keep you healthy. However, one study on Irish people over 60 showed that those living with family had greater diversity than those in care facilities and hospitals.


Antibiotics wipe out a variety of bacteria in your gut (not just the “bad” ones) and their effects on the microbiota can be seen months and years after taking them. In fact, antibiotics can permanently alter the gut bacterial make-up. Long-term antibiotics cause resistance and prevent your gut cells from recognising and responding to pathogenic bacteria with their usual efficiency. 

Diversity, weight and appetite

Interestingly, being overweight or obesity is linked to lower gut diversity, less bacteria associated with healthy body weight and more bacteria associated with the storage of body fat. Studies in mice confirm that dysbiosis and body mass are linked.

Obese mice have greatly reduced levels of Bacteroidetes and an increase of Firmicutes bacteria. The ratio of these two bacteria are reversed in lean humans and can be achieved by a diet that restricts calorie intake. Furthermore, athletes and people with low BMI had higher levels of Akkermansia muciniphila compared to overweight and obese people.

Akkermansia works to regulate blood sugar, protecting against diabetes type II. It does this mainly by maintaining the thickness of the mucous lining the gut, preventing ‘leaky gut’ and keeping your immune system functioning smoothly. In addition, Akkermansia make acetate, a short-chain fatty acid that regulates appetite through the production of hunger and satiety hormones.

How to increase microbiome diversity

A diverse diet high in fibre and nutritious foods helps create a melting pot of happy commensal bacteria. So, what can people do to maintain a diverse and balanced microbiome? The answer is, thankfully, lots. 

A healthy diet is associated with high gut bacterial diversity.  In a study of 858 French people, increased diversity was associated with healthy foods (such as fruits and fish), while lower was associated with unhealthy foods, like high-fat, high-sugar products, that are often found in a Western diet. 

How to have a healthy microbiome

FactorAssociation with gut microbiome diversity
Fibre-rich diet
Being female
Good sleep
Stress and depression 
Overweight, obesity
Low-fibre, unhealthy diet

Another study showed that 9 months after migration from Thailand to the US, participants experienced dramatic reduction in microbial diversity in their guts and an increased risk of obesity. This goes to show that changing environment, food traditions and culture can influence your health and microbes for better and for worse.

Overall, scientists want us to know that gut microbiome diversity is decreasing in the West and emerging economies that are adopting Western diets. At the same time, the rates of diseases related to inflammation and the gut, such as obesity, inflammatory bowel disease, diabetes, psoriasis, allergies, and asthma are increasing. 

Eat the rainbow is sound advice for microbiome health: the more diverse your intake of plants, the more diverse your microbiome according to an American Gut Project study. People who ate more than 30 different plant types a week had more diverse guts than those who ate 10 or fewer types of plants per week. 

What is more, low fibre intake is associated with a decline in microbiota diversity in adults, but it also generally slows the transit of food through the gut, which can cause constipation, discomfort, flatulence and bloating.

Ways to increase fibre intake

  1. Add more wholegrains and bran to your diet, like brown rice, wholewheat pasta and oat bran.
  2. Snack on fruit, nuts, or wholemeal crackers.
  3. Add barley, wheat or oats to your breakfast cereal. 
  4. When baking, swop all-purpose flour for oat, nut or wholegrain flours.


Physical activity is another simple way you can benefit your gut diversity and improve your overall health. Studies on elite athletes have shown that they have greater gut microbiome diversity, including higher levels of beneficial Akkermansia microbes. 

What is the best kind of exercise? Aerobic exercise – such as running, swimming, or cycling – is the most effective, accounting for more than 20% of the variation in species richness. It can also promote the presence of butyrate-producing bacteria. 

Exercise indirectly improves your gut diversity by contributing to weight loss and reducing stress. You can read about some recommended workout routines to increase microbiome diversity here. Working out also reduces the risk of colon cancer by up to 50%.


Are you getting a good night’s sleep, or do you find sleep hard to come by? It turns out that the richness of both Bacteroides and Firmicutes bacteria is positively correlated with increased sleep efficiency and total sleep time.

Several bacteria (Lachnospiraceae, Corynebacterium, and Blautia) may negatively influence sleep. Practising good sleep hygiene, such as avoiding caffeine close to bedtime, setting a regular sleep routine to relax before bed, and getting lots of sunlight during the day can help sync your sleep cycles with your gut bacteria.

For microbiome diversity remember this

The gut microbiome is a relatively new discovery and shows that bacteria in your large intestine play many roles in your health. Microbial diversity is when you have a variety of different bacteria in the gut, and it is a sign of health. However, when diversity is low, it is linked to chronic diseases, weight gain and dysbiosis. 

Fortunately, you can help your microbiome diversity by adding diversity to your diet, in the form of colourful plant foods. Exercise and regular sleeping habits can also contribute to gut health and diversity because everyday choices can have a big impact on your gut, bacteria and overall wellbeing.