What is dysbiosis?

As you read this, trillions of bacteria and other microorganisms are living in the warmth of your gut.

Collectively known as your gut microbiome, these microscopic beings are vital for good health. 

And conversely, your health can be affected if these bacteria aren’t in a state of balance. This imbalance is known as dysbiosis.

Below, we’ll describe what dysbiosis is. We’ll also explain why it might happen, how it relates to specific health conditions, and how it's treated.

What is dysbiosis?

In a nutshell, dysbiosis means an unbalanced microbiome. That could be the microbiome of your skin, mouth, or anywhere else bacteria live. 

In this article, we’ll focus on gut microbiome dysbiosis.

We should mention that there’s no official criteria for dysbiosis. Because everyone’s gut microbiome is different, scientists are still figuring out what’s “good” and “bad.”

The picture is growing clearer, though. For instance, ZOE’s own research has identified 15 species of bacteria associated with good health outcomes and 15 related to poorer outcomes.

Still, we have a lot to learn about our essential bacterial guests and what happens when they’re out of balance.

What changes in dysbiosis?

Most people always have “good” and “bad” bacteria in their guts, and maintaining a peaceful balance is important for health. 

A healthy balance is called eubiosis, and when that balance is upset in some way, it’s dysbiosis. 

The healthy order in your gut can be upset to produce dysbiosis in three main ways:

  1. a loss of “good” gut bacteria

  2. too many “bad” gut bugs

  3. reduced diversity

Often, two or three of these can happen at the same time. 

What can cause dysbiosis?

Scientists are still getting to the bottom of it, but they have identified some factors that can lead to this imbalance. We’ll cover a few below.

The first and perhaps least surprising factor is what you eat.

The Western diet

Researchers have shown that people with a Western diet have very different gut microbiomes from people who live off the land in more traditional societies. 

People with a Western diet have fewer gut bacteria that produce short-chain fatty acids (SCFAs).

SCFAs play important roles throughout your body, and one of their top jobs is nourishing the lining of your gut. We’ll meet them a few times throughout this article.

One SCFA called butyrate crops up particularly frequently. It seems to block “bad” gut bacteria from getting a foothold, while supporting the growth of “good” bacteria. 

So, butyrate might be important in preventing dysbiosis and stabilizing the gut microbiome.


One of your gut microbiome’s favorite nutrients is fiber. It’s the fuel that these bacteria need to thrive. 

Scientists have shown that people who eat more fiber have more diverse gut bacteria, which is a good sign of a healthy gut microbiome. They also have more species that produce butyrate.

On the other hand, people who eat the least fiber are likelier to have a less diverse population of gut bacteria.

And this links back to the Western diet, which is particularly low in fiber, compared with more traditional diets.


There’s evidence that genes play a part in dysbiosis, too. Many that scientists have identified so far are associated with inflammatory bowel disease (IBD).

IBD is an umbrella term for bowel conditions that involve chronic inflammation.

The two most common are Crohn's disease and ulcerative colitis. And we’ll talk more about these conditions later.

One gene called NOD2 plays a part in your immune response. Among other things, it helps prevent “bad” bugs from settling in your gut.

In this way, it helps maintain stability and protect against dysbiosis.

However, some people have variants of the NOD2 gene that simply don’t work.

People with these versions have an increased risk of developing dysbiosis. Once dysbiosis begins, it causes inflammation, which might then lead to Crohn’s disease.


Because antibiotics are excellent at killing bacteria, they've saved countless lives. But for the same reason, they can cause havoc in your gut microbiome.

For instance, broad-spectrum antibiotics are useful because they kill a wide range of bacteria. 

This is great for treating infections when doctors don't know which microbe is to blame. But this broad action means that many of your “good” gut bacteria are also in the firing line.

Dysbiosis associated with antibiotics can involve reduced diversity and a reduced ability to fight off “bad” gut bugs.

However, if you’re taking antibiotics, make sure you take them as your doctor prescribed. They’re still essential, lifesaving medicines. 

And once your course has finished, you might want to help support your gut microbiome’s regeneration with a gut-healthy diet or perhaps probiotics.

Anything else?

We don’t know all of the risk factors for dysbiosis, but a list is slowly forming. And some of the relationships are complex.

For instance, psychological stress might affect the balance of your gut microbiome. And in turn, dysbiosis might play a part in developing mental health conditions.

Returning to what we eat, evidence from animal studies suggests that a diet high in meat proteins and fat might be associated with dysbiosis.

Plus, diets high in some forms of carbohydrates are linked to dysbiosis, as are artificial sweeteners.

Finally, environmental chemicals, like pesticide residues, can upset your gut microbiome’s state of balance. After all, many of these compounds are designed to kill bacteria.

Thanks to the complex relationship between your gut bugs and you, there are probably many other factors waiting to be discovered.

Next, we’ll look at some health conditions that have intimate ties to dysbiosis.


Over the years, scientists have hunted for a bacterial cause of IBD.

Although a few bacteria seemed like they might fit the bill, including Escheria coli and Clostridium difficile, studies produced conflicting results.

Scientists now think that rather than just one species causing IBD, a more general dysbiosis might be to blame.

A review of dysbiosis studies identified specific changes in the gut microbiomes of people with IBD. 

Microbiome changes in IBD

There’s often a loss of gut microbiome diversity in people with IBD. This particularly involves species of Firmicutes and Bacteroides, which are usually the most abundant bacteria in your gut.

Scientists have also found increased numbers of Ruminococcus gnavus, one of the 15 “bad” bugs that ZOE’s research identified.

And they've noted decreases in certain species, like Faecalibacterium prausnitzii, which we’ll return to in a moment.

As it stands, experts are still trying to figure out whether dysbiosis causes IBD or whether IBD causes dysbiosis. The old chicken-or-egg question.

However, growing evidence suggests that dysbiosis might directly cause IBD. And scientists have some theories about how it might trigger the condition.

Butyrate again

As we mentioned, studies have shown that people with IBD have reductions in F. prausnitzii bacteria. These bacteria produce an SCFA called butyrate, which is vital for maintaining a healthy gut wall.

So, if the bacteria become scarce and the gut wall becomes less stable, that might play a part in triggering IBD symptoms. 

Scientists still need to determine whether IBD causes dysbiosis or vice versa. 

And the relationship could run both ways: Dysbiosis might cause IBD, while other factors associated with IBD might drive changes in the gut microbiome. 

A role in obesity?

People with obesity tend to have less diverse gut microbiomes — one sign of dysbiosis. They also tend to have less Bacteroidetes and more Firmicutes bacteria.

Experts are still figuring out whether dysbiosis might cause obesity or whether factors associated with obesity, like changes in diet, might cause dysbiosis.

There's some evidence that dysbiosis might cause obesity.

For example, scientists have shown that when you transfer the gut microbiome of an obese mouse into a mouse with a moderate weight, it becomes obese.

Other studies looked at a similar relationship in humans. Researchers took gut bacteria from "lean" participants and transplanted the bacteria into participants with obesity and insulin resistance.

After 6 weeks, the recipients’ insulin sensitivity improved. 

Back to SCFAs

Experts have some theories about how dysbiosis might cause obesity. As with IBD, one theory involves SCFAs.

People with obesity tend to have fewer gut bacteria that produce SCFAs, like butyrate. And SCFAs might stop fat from accumulating as adipose tissue, which we also call body fat.

So, if fewer gut bugs are producing SCFAs, more fat might accumulate, contributing to weight gain.

Colon cancer

Risk factors for colon cancer include IBD, obesity, and a diet high in fat and protein.

As these factors are also associated with dysbiosis, some experts think that there may be a link between gut microbiome dysbiosis and colon cancer.

Researchers have found a wide range of gut microbiome changes associated with colon cancer. Among these changes is a reduction in species that produce the SCFA butyrate. 

And you might remember that butyrate helps nourish the lining of your gut — the tissue that turns cancerous in cases of colon cancer.

One animal study helps demonstrate the complexity of the links between cancer, dysbiosis, and other factors.

The researchers used mice with a particular susceptibility to colon cancer. When the team fed them a high-fat diet, their gut microbiomes changed. This shift in gut bacteria was linked to a weakened gut immune response and increased tumor growth.

When they gave butyrate to these animals, their immune systems recovered, and tumor growth slowed. So once again, butyrate seems important.

Next, the scientists took poop samples from the high-fat diet mice that had developed tumors. Then, they transferred the poop into healthy mice. These mice then started to grow tumors.

As with IBD and obesity, the links are complex. Scientists are figuring it out, but there’s likely an interaction between dysbiosis, diet, the immune system, cancer, and other factors.

Treating dysbiosis

The best approach depends on the cause of the imbalance. For instance, if it's caused by a medication, your doctor might ask you to stop the treatment for a while or try a different drug.

Meanwhile, there’s growing interest in fecal transplants. In this procedure, doctors transfer gut bacteria from a healthy donor into a patient’s colon. 

Research has shown that this technique is effective for treating C. difficile infections and restoring diversity to the gut microbiome.

And experts believe that this type of transplant might help address gut dysbiosis from other causes.

However, understanding in which situations fecal transplants are helpful and safe requires more research.

The round-up

Dysbiosis is a general imbalance of your gut microbiome. It can involve a loss of diversity, increased numbers of “bad” gut bacteria, and reduced numbers of “good” bacteria.

We know some of the factors that can help generate dysbiosis, including diet, genetics, stress, and medications. But there are probably many others.

Dysbiosis is linked with a range of conditions, including IBD, obesity, and colon cancer. But we don’t fully understand how these relationships work.

As for treatment, fecal transplants seem promising, but many questions remain.

If you’re worried that you may have dysbiosis, speak with a doctor. And if you’re interested in supporting your gut microbiome, read our guide to improving gut health.


An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. (2006). https://pubmed.ncbi.nlm.nih.gov/17183312/ 

Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease. Nature. (2001). https://pubmed.ncbi.nlm.nih.gov/11385576/ 

Butyrate reduces high-fat diet-induced metabolic alterations, hepatic steatosis and pancreatic beta cell and intestinal barrier dysfunctions in prediabetic mice. Experimental Biology and Medicine. (2017). https://journals.sagepub.com/doi/abs/10.1177/1535370217708188 

Current understanding of dysbiosis in disease in human and animal models. Inflammatory Bowel Diseases. (2016). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4838534/ 

Decreased dietary fiber intake and structural alteration of gut microbiota in patients with advanced colorectal adenoma. The American Journal of Clinical Nutrition. (2013). https://pubmed.ncbi.nlm.nih.gov/23553152/ 

Dietary carbohydrate constituents related to gut dysbiosis and health. Microorganisms. (2020). https://www.mdpi.com/2076-2607/8/3/427 

Dysbiosis: A review highlighting obesity and inflammatory bowel disease. Journal of Clinical Gastroenterology. (2015). https://journals.lww.com/jcge/Abstract/2015/11001/Dysbiosis__A_Review_Highlighting_Obesity_and.7.aspx 

Effects of antibiotics on gut microbiota. Digestive Diseases. (2016). https://pubmed.ncbi.nlm.nih.gov/27028893/  

Functional impacts of the intestinal microbiome in the pathogenesis of inflammatory bowel disease. Inflammatory Bowel Diseases. (2015). https://academic.oup.com/ibdjournal/article/21/1/139/4604250 

High-fat-diet-mediated dysbiosis promotes intestinal carcinogenesis independently of obesity. Nature. (2014). https://www.nature.com/articles/nature13398 

High-meat-protein high-fat diet induced dysbiosis of gut microbiota and tryptophan metabolism in Wistar rats. Journal of Agricultural and Food Chemistry. (2020). https://pubs.acs.org/doi/abs/10.1021/acs.jafc.0c00245 

Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. PNAS. (2010). https://pubmed.ncbi.nlm.nih.gov/20679230/ 

Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals. Nature Medicine. (2021). https://www.nature.com/articles/s41591-020-01183-8 

Nod2: A key regulator linking microbiota to intestinal mucosal immunity. Journal of Molecular Medicine. (2012). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3263373/ 

Nod2 is required for the regulation of commensal microbiota in the intestine. PNAS. (2009). https://pubmed.ncbi.nlm.nih.gov/19805227/ 

Pros and cons: Is faecal microbiota transplantation a safe and efficient treatment option for gut dysbiosis? Allergy. (2021). https://onlinelibrary.wiley.com/doi/full/10.1111/all.14750 

Structural & functional consequences of chronic psychosocial stress on the microbiome & host. Psychoneuroendocrinology. (2015). https://www.sciencedirect.com/science/article/abs/pii/S0306453015009348 

The impact of Western diet and nutrients on the microbiota and immune response at mucosal interfaces. Frontiers in Immunology. (2017). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5532387/

The microbiome as a novel paradigm in studying stress and mental health. American Psychologist. (2017). https://psycnet.apa.org/doiLanding?doi=10.1037%2Famp0000058 

The role of butyrate in attenuating pathobiont-induced hyperinflammation. Immune Network. (2020). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7192831/ 

The vexed relationship between Clostridium difficile and inflammatory bowel disease: An assessment of carriage in an outpatient setting among patients in remission. American Journal of Gastroenterology. (2009). https://pubmed.ncbi.nlm.nih.gov/19319128/ 

Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome. Gastroenterology. (2012). https://www.gastrojournal.org/article/S0016-5085(12)00892-X/fulltext  

What is inflammatory bowel disease (IBD)? (2022). https://www.cdc.gov/ibd/what-is-IBD.htm