What is the Link Between Beneficial Gut Bacteria and Good Health?

The link between gut bacteria and type 2 diabetes explained


The gut microbiome is a living ecosystem that exists deep within our gut and is intimately linked to our health.

Like any ecosystem, the gut microbiome is vulnerable to change and these changes can either help or hurt us. 

Decades of research have shown us that changes in our microbiome that increase the presence of specific types of bacteria may help protect us from conditions like type 2 diabetes. 

On the other hand, the gut microbiome can also grow to exclude these beneficial bacteria, resulting in an increased likelihood of developing type 2 diabetes. 

Fortunately, there are steps you can take to encourage the growth of the beneficial bacteria and reduce the influence of the bad bacteria.  

In the following sections, we’ll explore the link between the gut microbiome and human health.


The link between type 2 diabetes and the gut microbiome

There is a close relationship that exists between the gut microbiome and type 2 diabetes.

Your gut microbiome is where trillions of bacteria reside. Your gut microbiome is an ecosystem where many diverse species co-exist in some state of competition and harmony. 

And, like these other ecosystems, the gut microbiome is vulnerable to change. 

What species of bacteria live in your gut depend on several factors including:

  • Your diet
  • Your exercise levels and routines
  • Medicine you may be taking
  • Travel to foreign countries
  • Your stress levels
  • Your sleep habits
  • Your genetics 

Because of this, the exact composition of any one person’s microbiome might change over time and can differ from another person’s1.  

Sometimes, these differences are meaningless. Other times, however, when specific types of bacteria are missing, it could lead to type 2 diabetes1

Scientists have compared the composition of people’s gut microbiomes and found that people with type 2 diabetes tend to be missing certain types of bacteria1,2,3.

For example, multiple studies have found that species belonging to the genera of Bifidobacterium, Bacteroides, Faecalibacterium, Akkermansia muciniphila and Roseburia were often missing (or severely reduced) in people who have type 2 diabetes1

How does the lack of certain gut bacteria strains lead to type 2 diabetes?

The effects of losing a type of gut microbiome bacteria can vary depending on the strain. However, the types of bacteria that are frequently absent in people with type 2 diabetes tend to:

  • Strengthen the gut mucosal lining
  • Prompt the release of butyrate 

Each of these functions is important to our health, and the loss of the bacteria responsible for carrying out these activities can leave a person vulnerable to several conditions, including type 2 diabetes.

Butyrate production

Many of the strains of bacteria that are missing in people with type 2 diabetes are involved in the production of the important short-chain fatty acid known as butyrate, which can be used for energy by the cells that line the colon (colonocytes) and can act like a hormone in certain contexts4

Butyrate is produced in the large intestine as a byproduct of soluble-fiber metabolism, and is an incredibly important molecule with far-reaching effects on the human body.

Dietary fibers are complex molecules that human cells are unable to break down. Were it not for some species of bacteria in the gut, dietary fibers would go right through us.

Fortunately, though, there are bacteria in the gut microbiome that use fiber like food—they consume it by breaking it down and stripping it for useful parts.

In this process, butyrate is made and cast aside5

Once made, most of the butyrate is used by cells in the gut called colonocytes as a source of energy. (Usually, cells use sugar for energy, but colonocytes are some of the only cells we have that need butyrate to produce energy). 

You could try and address some symptoms of type 2 diabetes by taking supplements that are specifically designed to deliver butyrate to the colon8. However, such an approach would be similar to buying a box of nails and a hammer instead of hiring a carpenter—the butyrate delivered through the supplement is only a temporary solution and one that fails to compensate for the many different roles that gut bacteria play.  

Additionally, when bacteria produce butyrate, they do so while occupying many different locations in the gut. This means that butyrate can be moved closer to—or further from—the cells lining the gut depending on where the butyrate-producing bacteria are.

By producing butyrate in various locations, the body can ensure that the right cell types get this precious nutrient. 

What specific strains of bacteria affect type 2 diabetes?

Many types of bacteria have been suggested to have a positive role to play in protecting us from type 2 diabetes.1,2,3 

Glucose Control is a synbiotic that contains some of these strains, including: 

  • Akkermansia muciniphila—a strain of bacteria that plays a critical role in supporting a healthy gut lining
  • Anaerobutyricum hallii—a butyrate-producing bacteria.
  • Clostridium butyricum and Clostridium beijerinckii— two more butyrate-producing bacteria that are often missing in people with type 2 diabetes
  • Bifidobacterium infantiswhich supports digestive health by aiding in the breakdown of complex carbohydrates that are otherwise difficult for the human body to digest
Why are people with type 2 diabetes deficient in these strains?

There are many potential reasons why a person might start to lose the aforementioned strains of bacteria. 

The gut microbiome is a diverse and harsh ecosystem where bacteria must compete with one another for space, food, and other resources. As a result, the species that survive in the gut are those that have found a competitive advantage—such as the ability to live deep inside a layer of mucus despite the lack of certain nutrients. 

However, the specialization of some species leaves them vulnerable to environmental change. if they rely on fiber as their main food source, for example, they’ll have a hard time surviving if your diet changes and no longer includes fiber—especially soluble fiber. 

With this in mind, here are some of the known factors that, if changed, can lead to deficiencies in certain strains of important bacterial species. 

Diet & Nutrition

Changes in your diet and nutrition can lead to a decrease or loss of some bacterial species that are thought to protect you from type 2 diabetes. 

This means that when the amount of fibrous foods in your diet (such as oats, nuts, and whole-grain foods) decreases, and the amount of high-fat foods increases (such as red meats, fried foods, and cheese), you’re likely to start losing some beneficial bacteria1,4,5

One reason for this change is that many types of bacteria that help protect us from type 2 diabetes rely on soluble fiber as an energy source. 

When fiber is present, it can thrive and outcompete other bacteria. In turn, they also produce various molecules, including butyrate, that help us regulate our blood sugar levels1,4,5

When fiber levels are low or absent in the diet, these bacteria will struggle to survive and can be overrun by other, less beneficial species that do not rely on fiber as a food source.

This is one of the reasons it is generally recommended that a healthy eating plan is high in fiber. 


Lack of exercise

Multiple studies have demonstrated a difference in the microbiome following exercise (both mild and exhaustive exercise). 

In most studies, results suggest that people who exercise tend to have more beneficial bacteria in their microbiome relative to people who have a more stationary lifestyle10

It’s not yet known, though, exactly how exercise causes this difference.

One suggestion is that physiological changes brought on by exercise—specifically changes in blood flow to the gut as well as an increase in the speed at which food moves through the gut—could lead to temporary changes in the gut microbiome environment. 

When these momentary changes in the environment happen frequently enough, it can favor the survival of beneficial bacteria that thrive in those conditions10.  

Another possibility is that exercise itself does not directly affect the gut microbiome but has an indirect effect that results from weight loss10

In this scenario, exercise slowly leads to weight loss which in turn alters the gut microbiome. 

A recurring challenge in this field of study is overcoming confusion around cause and effect. Is it weight loss and exercise that causes a change in the microbiome? Or does a change in the microbiome lead to weight loss? 

At the moment, there’s not enough evidence to draw firm conclusions about how exercise alters the gut microbiome, but it’s likely related to a number of large and small physiological changes in the gut environment that ultimately make it easier for beneficial bacteria to survive.



Unlike most other factors, antibiotics have a clear cause-and-effect explanation for how they change the gut microbiome11

Broadly speaking, antibiotics work by disrupting parts of bacteria that are critical to their survival, essentially throwing a wrench into the cellular machinery that helps them stay alive.  

Most species of bacteria have their own unique set of cellular machinery, but they also tend to rely on some of the same core components. 

It may help to think of differences between bacterial species as being similar to differences in models of cars. A pickup truck is fundamentally different from a sports car, but they both rely on wheels and an engine to move. 

When antibiotics are designed to target these core components, they can be very effective but may also have collateral damage, especially in the gut.

Because of this, antibiotics can sometimes have a devastating effect on the gut microbiome that’s akin to a wildfire blazing through a forest, indiscriminately killing everything in its path. Many species will be affected, but the species that survive in the aftermath of it may be different compared to those who were present before. 

Put simply, antibiotics can kill many bacteria in the body which is good when you have an infection, but can also lead to a loss of specific bacteria in the gut that help protect us from type 2 diabetes. These bacteria can be replenished, but that doesn’t always happen (likely owing to the combination of antibiotic use along with other factors listed here). 



Chronic stress can have many different effects on our health and is often associated with changes in diet and exercise behavior. 

And increases in chronic stress are associated with changes in the microbiome. 

One possible reason for this is that stress causes the body to enter a survival mode when it anticipates tough times ahead. It knows it will need energy and responds by releasing an arsenal of hormones that help to boost blood sugar levels and increase immune cell activity. 

Some of these hormones are released into the gut where they affect bacterial cell growth as well, acting to suppress growth and prevent activity in the gut. 

Each of these responses alters the gut microbiome and, in turn, can change which type of bacteria are able to survive and thrive.  


With age comes many physiological changes, including changes in the gut microbiome. As we age from infants to young adults, our gut microbiomes go through significant changes—likely due to changes in diet, exercise habits, and hormones13

While the differences in the gut microbiomes are most prominent when comparing infants to adults, our gut microbiome can continue to evolve as we age out of young adulthood and into other phases of life. 

It’s likely no secret that a person’s diet and exercise habits can change as they get older. Sometimes this is due to injuries or a lack of time. Stress, too, can play an important role in shaping both our habits and our microbiome. 

Age can also lead to health conditions that require medication. These medications can have varied effects on the gut microenvironment, leading to new conditions that may favor one bacterial species over another.

In short, age brings with it a number of changing environmental factors that can then affect the gut microbiome.

Circadian rhythm

Genetics, environment, and more

We have limited our conversation here to a few of the main factors that have been studied. This list isn’t exhaustive, though, as there are several other influential factors that are believed to affect the gut microbiome. 

The full list of factors is both diverse and growing, but they all share similar features: 

Most things that affect your gut microbiome do so by changing the microenvironment of the gut (such as mutations in the DNA that cause different nutrients to be present in the gut mucus layer16), or else changing the types of bacteria that are introduced to the gut (new species might be introduced when traveling to foreign places). 

In short, your gut microbiome is a complex environment and, like all environments, is always changing. 

How can you increase these strains in your own microbiome?

Fortunately, there are steps you can take to increase the beneficial strains of bacteria in your gut microbiome. 

Boosting the beneficial bacteria in your gut can be done through a combination of increasing the fiber, emphasizing soluble, content in your diet, forming routine exercise habits, and re-introducing key strains of bacteria through the use of probiotics. 

The right nutrition

Bacteria strains that are believed to help protect us from type 2 diabetes can be nurtured and grown with a diet that includes soluble fiber-rich foods. This includes foods such as:

  • Beans and legumes (black beans, kidney beans, pintos, chickpeas, white beans, and lentils)
  • Whole fruits and vegetables
  • Nuts such as walnuts, almonds, and peanuts
  • Whole grain pasta, cereal, and oats
  • Flax seeds

    Adding in prebiotics, such as inulin, also help. Inulin is a type of complex carbohydrate that can promote beneficial bacteria in the gut15. Foods rich with inulin include:

    • Leeks
    • Onions
    • Wheat
    • Asparagus
    • Garlic
    • Chicory

    Adding these foods to your diet can help ensure that there is a consistent food source for the beneficial bacteria. Be mindful to speak with your healthcare provider about adding these foods to your current eating plan. It’s important to add fiber slowly to your diet. 

    However, while the food source is important, it is also important to cultivate the gut microenvironment to be favorable for these bacteria. 


    Exercise appears to play an important role in shaping the gut microbiome.

    People who exercise more tend to have more beneficial bacteria represented in their gut microbiome. 

    Exercise can be particularly helpful for people with type 2 diabetes for a number of reasons that go beyond the gut microbiome. For instance, routine exercise can help reduce A1C levels.

    The right probiotics

    As mentioned earlier, the gut microbiome is a complex ecosystem that involves harsh competition between species. To help the species that protect us from type 2 diabetes survive, it’s important to give them a consistent food source (fiber for instance) and to make the environment as favorable to their survival as possible. 

    Forming an environment where these bacteria can thrive, however, may not be successful if the bacteria are already gone. This is where probiotics can be extremely helpful. 

    There are many probiotics in the market, each directed towards a specific set of conditions. With so many out there, it can be difficult to know what is the best probiotic supplement for people with type 2 diabetes

    Generally speaking, you should look for a probiotic that is backed by clinical evidence demonstrating efficacy in type 2 diabetes. This will likely include a combination of bacteria that help to increase butyrate production.

    Some probiotics will also include inulin as a starter food for the bacteria; this is to help the bacteria hit the ground running, so to speak. 

    Glucose Control is one such probiotic. This medical probiotic provides 3 different species of bacteria that are known to boost butyrate levels and are often missing in people with type 2 diabetes. It also includes Akkermansia muciniphila to help strengthen the gut barrier. Glucose Control contains inulin as well to encourage rapid growth of these bacterial species. 

    In a double-blind clinical study, it was shown that people with type 2 diabetes taking metformin experienced a larger decrease in their blood A1C levels when taking Glucose Control relative to people who had not taken it.17

    Final Thoughts

    When we think about health and disease, the bacteria residing deep within our gut microbiome are often overlooked. 

    But the past few decades have revealed just how important the microbiome is. It’s a rich ecosystem teaming with life; and, like all ecosystems, it needs to be cared for. 

    We can care for our microbiome by forming routine exercise habits, reducing stress where possible, and by adding fiber and probiotics to our diet. 

    When we do these things, we favor the growth and survival of bacteria that help protect us from many different conditions, even type 2 diabetes. 

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    2. Tai, Ningwen et al. “The role of gut microbiota in the development of type 1, type 2 diabetes mellitus and obesity.” Reviews in endocrine & metabolic disorders vol. 16,1 (2015): 55-65. doi:10.1007/s11154-015-9309-0 https://pubmed.ncbi.nlm.nih.gov/25619480/ 
    3. Ortega, Miguel A et al. “Type 2 Diabetes Mellitus Associated with Obesity (Diabesity). The Central Role of Gut Microbiota and Its Translational Applications.” Nutrients vol. 12,9 2749. 9 Sep. 2020, doi:10.3390/nu12092749 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7551493/ 
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    6. Madsen, Mette Simone Aae et al. “Metabolic and gut microbiome changes following GLP-1 or dual GLP-1/GLP-2 receptor agonist treatment in diet-induced obese mice.” Scientific reports vol. 9,1 15582. 30 Oct. 2019, doi:10.1038/s41598-019-52103-x https://www.nature.com/articles/s41598-019-52103-x 
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    8. Boets, Eef et al. “Systemic availability and metabolism of colonic-derived short-chain fatty acids in healthy subjects: a stable isotope study.” The Journal of physiology vol. 595,2 (2017): 541-555. doi:10.1113/JP272613 https://pubmed.ncbi.nlm.nih.gov/27510655/ 
    9. Xu, Yu, et al. “Function of Akkermansia muciniphila in Obesity: Interactions With Lipid Metabolism, Immune Response and Gut Systems.” Frontiers in Microbiology, vol. 11, 2020, doi:10.3389/fmicb.2020.00219. https://www.frontiersin.org/articles/10.3389/fmicb.2020.00219/full 
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    Before you consider any of these gut microbiome dietary solutions, talk to your healthcare provider. 
    The FDA has not approved or evaluated these statements. Pendulum products are not intended to diagnose, treat, cure, or prevent any diseases. Results may vary.

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