What is Gut Dysbiosis? (Plus Associated Conditions)

If you’ve ever suffered with digestive problems like cramping, constipation, diarrhea or grumbly gas, you’ll know just how debilitating they can be. Not to mention embarrassing!

And while it’s obvious these issues arise from your belly, have you ever wondered if your acne, chronic fatigue, or anxiety have something to do with your gut too?

As a naturopath, my clients often wonder how these seemingly separate conditions are connected. 

  • Digestive distress + brain fog … or 
  • Bloating + anxiety … or
  • Constipation + chronic acne … or 
  • Diarrohea + exhaustion … the list goes on!

And quite often a number of these symptoms arise together!

I treat so many people who are silently suffering with both digestive and non-digestive problems. Symptoms they’ve been led to believe are completely unrelated. It’s so common that it’s often predictable. 

But how are they related, you ask? … The answer is deceivingly simple.

Gut dysbiosis.

In this article, you’ll learn how your gut and your body are connected, what gut dysbiosis is (and what it’s not), the signs and symptoms of gut dysbiosis, its causes, tests that work and general treatment options.

Let’s get started!

What Is Gut Dysbiosis?

Gut dysbiosis simply means there is a microbial imbalance in your gut. Most often within different populations of bacteria (as these are the most abundant) but other microbes like yeasts can become imbalanced.

There are a number of ways that dysbiosis can occur:

  • When you lose beneficial bacteria in your gut – with antibiotics, chemicals, dietary choices etc.
  • Gastro or infections from food poisoning or parasites may allow pathogenic bacteria to increase
  • You have low diversity 
  • Chronic stress is a common cause 
  • And so many MANY more…
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The majority of bacteria in your gut are actually “beneficial bacteria”, meaning that they will not cause you any harm and are of benefit to your health.


Some of these are called probiotic bacteria – there are also plenty that haven’t earned this title but are definitely still beneficial.

There are also many groups of the bacteria that need to be kept in balance by a thriving community of beneficial bacteria – and they will not cause harm. However, if their populations increase substantially they can cause problems.

This situation is called gut dysbiosis.

It’s All About Balance (and Diversity)

A healthy and highly diverse gut will often house more than 1,000 different species of bacteria – living symbiotically in a fluid state of balance.

Along with balance (something we can see from your gut testing results), diversity is also a key indicator of gut health. This important diversity metric is included in all our comprehensive gut testing programs.

For most of our clients struggling with gut issues, we commonly see diversity scores in the range of the low 200’s up to 600-ish…with the balance tipped toward (or very much all the way) into dysbiosis.


When in balance, our extensive community of bacteria work together in a complex and highly evolved microbial ecosystem.

They use the food we provide, to exchange and excrete metabolites between each other. Keeping one another in balance by default and contributing to our health and wellbeing in the process.

And an important part of this symbiosis is that we also benefit from their by-products and interactions too.

Our gut bacteria perform so many beneficial functions:

  • They help you maintain a healthy metabolism
  • Breakdown and digest your food 
  • Make vitamins, minerals, and other beneficial nutrients
  • Maintain the integrity of the lining of your gut 
  • Excrete the revered gut powerhouses SCFAs (short-chain fatty acids) 
  • And so much more….
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Ultimately the silent activities of your gut bacteria are so important in our overall health that they’ve been recognized as an ‘organ’. And so, it makes sense that you consider this thriving microbial organ along with your heart health, brain function, or physical fitness.

For example, let’s say you decided you want to develop your physical fitness… what would you do? You’d include activities that you knew worked toward this goal.

You would change your habits to positively affect fitness – like limiting overeating poor quality foods, becoming mindful of sedentary practices, signing up to a gym or taking a yoga class and so on.

In a similar way, this process is not that much different for gut health. You need to do more of what brings you closer to your goal and less of what takes you farther away.

And gratefully, with the advent of gut microbiome testing – we have a pretty clear idea of what those things are.

  1. You need to focus on building diversity within your gut microbiome – diversity brings a greater variety of nutrients and metabolites that you need
  2. Within this diversity you need to foster a healthy balance – in favour of beneficial microbes rather than detrimental species (we talk about 
  3. To be aware that everything you do impacts your microbes –  because your gut microbiome is an organ and is connected with your lifestyle and choices – especially everyday food and diet decisions

So in concert with being an organ, bacterial metabolites play a crucial role in communication between our other organs.  Communicating with everything from your immune system, your hormones and even your brain.

When we look at it this way, it makes perfect sense that when your gut bacteria are out-of-whack the consequences are certainly far-reaching.

Gut Dysbiosis Symptoms And Signs

It’s also because of this interconnectivity, gut dysbiosis causes a huge range of effects and a similarly huge range of signs and symptoms.

Including (but certainly not limited to) the following:

  • Constipation
  • Cramping
  • Diarrhoea
  • Heartburn
  • Gas
  • Bloating
  • Food allergies, intolerance or sensitivities
  • Inflammation and inflammatory conditions
  • Aching joints
  • Acne
  • Skin conditions, rashes, dermatitis etc.
  • Psoriasis, eczema
  • Chronic fatigue
  • Difficulty concentrating, brain fog
  • Anxiety
  • Depression
  • Migraine
  • Hormonal disturbances
  • Candida overgrowth
  • Reduced immune function
  • Irritable Bowel Syndrome (IBS) and symptoms
  • Allergies
  • Asthma 
  • Autoimmune conditions
  • Headaches
  • Memory loss
  • Nutritional/vitamin deficiencies
  • … and the list goes on …

But there is a common thread. Reduction of gut lining integrity.

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Dysbiosis is known to both cause and contribute to intestinal permeability. Often called “leaky gut”, this inflammatory process refers to the loss of function of our vital gut protection barriers in the gut lining.

I’ve covered leaky gut in-depth in Do You Have Leaky Gut? (Plus Warning Signs To Look For) if you are interested in learning more.

When the gut becomes leaky antigenic substances like toxins, bacteria and food-breakdown products can enter your bloodstream. Which triggers your immune system and results in the variety of symptoms we mentioned such as nutrient malabsorption, autoimmune responses, brain fog, and fatigue etc.

It really is a very long list – and it’s growing! 

Consequently, there’s an equally large list of conditions that have dysbiosis connections.

Conditions That Have Been Linked To Gut Dysbiosis

The following list are just some of the enormous list of conditions that were once thought to be stand-alone illness – but have been linked to gut dysbiosis. 

It may surprise you to see how many of these are non-gut-related!

Research has uncovered so much about how gut dysbiosis affects our health – but in many cases there is still uncertainty around which came first. The condition or the dysbiosis. 

But what is now being more accepted, is how our modern lifestyles, medical interventions and just about everything can influence our gut balance.

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Potential Causes Of Gut Dysbiosis

If you have gut dysbiosis, it could be as a result of any number of one of the following potential factors. And often these occur in combination to create a hostile environment for beneficial bacteria.

#1 Taking antibiotics, antibacterial supplements and medications

Did you know that taking antibiotics for just a short period of time actually shifts your gut to an unbalanced state of being in the long-term? In fact, you can be in a state of dysbiosis for months or even years!

Research has shown that taking antibiotics such as metronidazole and omeprazole affects upwards of 30% of your microbiome makeup and this can last up to 4 years.

Clindamycin is another devastating culprit.

Specifically, when you take antibiotics you reduce the number and diversity of bacteria in your gut. Why does this matter?

As we said earlier, the less diverse your microbiome is, you have reduced supply of the nutrients and metabolites they produce. But also your immune system becomes compromised as 70-80% of your immune cells call your gut home!

Tip: Be cautious with antibiotic use as much as possible. Sometimes they are definitely absolutely necessary. If you must take an antibiotic, AFTER you’ve finished your course of antibiotics, take a high quality probiotic to help re-populate your gut.

#2 High intake of sugars, refined starch, processed foods, and food additives e.g. artificial sweeteners and preservatives

What we eat feeds our microbes. And sugars, refined starch, processed foods and many additives selectively feed non-beneficial bacteria.

With every mouthful of sugary drinks, poor-quality sweets and ultra-processed packet foods you contribute to dysbiosis – even if only short-term. When these habits become an everyday habit, dysbiosis becomes normal.

And if you thought the new wave of artificial sweeteners were safe, think again…

Sucralose (Splenda) for instance, has been ‘reported’ to be safe because most of it is not absorbed or metabolized in our bodies. But what about that microbial organ? 

Animal research has shown that sucralose affects the makeup of bacteria in the gut. Sucralose has also been shown to increase the amount of inflammation-causing products (toxins) secreted by the gut bacteria. Other artificial sweeteners have also been shown to cause gut dysbiosis.

Tip: Limit your intake of refined sugar, flours, processed foods and artificial sweeteners. 

#3 Exposure to harmful chemicals and toxins

We are constantly exposed to chemicals. From our drinking water to the plastic microwave food containers we reuse. These unwanted substances not only harm our cells but can also be very harmful to our gut microbiome.

A major cause is through ingestion of foods treated with highly toxic pesticides and herbicides. Fruit, vegetables and grains grown conventionally are coated in chemicals many times during their growth. 

One of the most widely used pesticides, chlorpyrifos has been shown to increase the concentration of bad bacteria in the gut. Though chlorpyrifos is no longer commonly used in the States and Europe, it is still commonly used in other parts of the world. So, if you are consuming produce from other parts of the world, make sure you wash it thoroughly!

Tip: If you can, eat locally and organically! By eating locally and organically, you not only decrease your chances of ingesting harmful chemicals, you increase your nutrient intake by eating produce that is at its peak nutritionally!

#4 Drinking too much alcohol

Studies show that drinking too much alcohol increases the number of predominantly non-beneficial bacteria like Proteobacteria and Fusobacterium in your gut. Notably, Proteobacteria and Fusobacterium have been linked to inflammation in the body.

Not to mention the myriad of detrimental liver, brain and nervous system effects alcohol induces.

Tip: Limit your alcohol intake. If you already have gut dysbiosis related to drinking too much alcohol, take a prebiotic as research suggests that this may help improve your gut microbiome.

#5 Poor oral hygiene

Not taking care of your teeth properly may not only lead to tooth decay and gum disease, it may also result in gut dysbiosis! Studies have found that periodontal  or gum disease is dysbiosis of the oral microbiome! The harmful bacteria and parasites which have been associated with gum disease also lead to a change in the gut microbiome and inflammation of the fatty tissue and liver!

Tip: Make sure you brush your teeth twice daily. You could also try swishing your mouth with extra virgin coconut oil as research has found that swishing your mouth with extra virgin coconut oil for about 10 to 20 minutes, is as effective as chlorhexidine mouthwash in reducing gum disease-promoting bacteria.

#6 Elevated levels of stress


You probably already realize that your brain affects your stomach. For instance, when you just think about eating, your brain sends signals to produce digestive juices. Well, the connection goes both ways!

Your gut actually sends signals to your brain when it is in trouble. As a result, when you have a problem with your gut as occurs with gut dysbiosis, non-digestive symptoms such as anxiety can occur. Truly amazing!

Stress is similarly a huge culprit when it comes to gut health. One of the chemicals released when you are under a lot of stress is norepinephrine. Research has shown that norepinephrine released during surgery (a form of stress) increases the production of the bad bacteria Pseudomonas aeruginosa which can contribute to gut dysbiosis and potentially infection. In addition, norepinephrine causes other non-beneficial bacteria to multiply or become more potent.

Tip: If you are under a lot of stress engage in relaxation techniques such as meditation and deep breathing exercises to assist you in managing stress. We wrote a whole article on this topic you can check out titled… Gut-Brain Connection and How it Affects Your Mood.

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Testing For Gut Dysbiosis

So beyond symptom spotting, how can you tell if you have gut dysbiosis?

It’s actually easier than you may have thought.

A simple faecal test gives you a picture of the number of good and “bad” bacteria in your gut.

Gut Microbiome Testing

This is a comprehensive gut microbiome profiling test I use with clients. Advanced DNA technology is used to isolate the bacterial genes that come from the gut bacteria in your sample.

This test gives us a clear picture of the exact percentage and ratio of different species and important groups of bacteria in your gut. Experienced practitioners can then interpret this information into a practical plan. With my clients, I develop a personalised plan in conjunction with both their testing results, any recent blood work I feel necessary, their conditions, and of course their most prevalent symptoms needs. If you’re ready to change your health for the better you can learn about the gut microbiome programs we offer here.

I also want to clear up some confusion and make mention of feaces or stool tests that are commonly used by a GP. I’m often asked what the difference is – basically your GP will order a pathology stool test that only looks for a handful of bacteria, parasites, or helminths that are known gut pathogens. Things like Salmonella, Campylobacter, Shigella, etc., and typical parasites like Giardia, Dientamoeba etc. which can be very helpful when you have an acute case of gastro.

But for more chronic conditions, gut microbiome profiling gives information on bacterial pathogens too but also includes the majority of the 1000 species of bacteria living in your gut.

Additionally, it offers important information above their relative abundance (how many of them there are) and includes the hundreds of beneficial and symbiotic species that a standard pathology analysis will not provide.

In short Gut Microbiome Testing offers a more comprehensive look at who is living in your gut and how they are coexisting together.

It’s a mainstay in my testing regime with good reason.

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How to Help Manage Dysbiosis 

Now that you know what gut dysbiosis is and what causes it, you may be wondering how you can tackle it.

There are a number of beneficial protocols that I recommend for my clients based on their personal results and their conditions/symptoms. I commonly prescribe (where required) a unique combination of targeted high-quality practitioner-only herbal and nutritional medicines, high-strength probiotics, species specific dietary modifications and holistic lifestyle suggestions.

But here I will only outline simple practical support to begin to manage dysbiosis as it’s most beneficial for you, and your microbiome that you work with an experienced practitioner to pin-point your specific problem with guidance. 

  1. Include Fermented Foods: Eating fermented foods can be a helpful step toward gut health. Not only do they include naturally occuring probiotic bacteria but new research suggests fermented foods also carry ready-to-go post-biotics like SCFAs and other beneficial bacterial metabolites. And most importantly you’re also eating the very food they need to continue to survive in your gut.

    Try our Quick and Easy Rainbow Kimchi or Fermented Jalapenos with Lime in your diet.
  2. Eat More Fibre and Resistant Starch: Your beneficial gut bacteria need fibre to survive. By getting more fibre to where it’s needed, you’ll help build up your beneficial gut bacteria community and reap the beneficial metabolite benefits.

    A few examples of fiber-rich foods include starchy tubers, vegetables, nuts, seeds, legumes and fruit.

    Read What is Resistant Starch? (and why your diet needs more) and The Ultimate Guide to Prebiotics A-Z Guide (plus 31 of the most common prebiotics) to learn more.
  3. Consider a Probiotic Supplement: Investing in a high-quality probiotic supplement in order to increase the number of good bacteria in your gut can be beneficial if you are lacking in those specific species or strains.

    As part of our Gut Testing Program packages these probiotic bacteria are included in your report. And we offer tailored advice around which species would benefit you the most.

    To learn more about probiotics and their functions read Probiotics: How to Choose the Best One For You (Inc. 22 common species).

  4. Avoid highly processed foods: Are you a processed food junkie? If so, your eating habits could be contributing to gut dysbiosis. Processed foods typically contain a significant quantity of refined carbohydrates, sugars, fats and artificial additives which as we know, feed non-beneficial or “bad” bacteria.

    A wholefood plant-predominant diet not only ensures you get a variety of prebiotic fibres and polyphenol-rich plant compounds for your gut bugs – it also naturally limits processed food intake.

    And believe it or not as your gut bugs change with your diet, so too will your tastebuds. As this happens, takeaway or processed foods don’t actually taste the same as you remember.

    If you’re interested in taking this further our Gut Heal & Nourish online program walks you through how to change your eating habits and lifestyle choices for better gut health. It‘s designed to help you understand gut health from the inside out and how to shift your life to reflect this knowledge.
  5. Avoid a high-fat,low-fibre diet: The ketogenic diet with its high proportion of fats is all the rage now for weight loss and I have worked with many clients who have definitely not felt better on it. So despite the seemingly radical weight-loss claims it may not be a good idea for your gut microbiome!

    Many species of non-beneficial bacteria love fat so being on a ketogenic diet may not be a good idea especially if you have gut dysbiosis. Studies have shown the keto diet to reduce some beneficial bacterial groups like Firmicutes and Bifidobacteria while increasing the less-beneficial Bacteroidetes and rotten-egg gas producing Desulfovibrio spp.

    A ketogenic diet does however also increase the powerful gut protector Akkermanisa and can be a powerful protocol for specific health goals, but it is important to understand exactly what your food choices are doing to your gut.

    Read How to Improve Gut Health Naturally: The Ultimate Guide if you want more actionable tips and a deeper look at the science.
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To Recap

Gut dysbiosis is an imbalance in the bacterial community in your gut. It can result in a number of digestive and non-digestive signs and symptoms including constipation, diarrhoea, anxiety, and depression. Additionally, gut dysbiosis is linked to a huge number of conditions including Crohn’s disease, type 2 diabetes, and colorectal cancer to name a few.

And it may be caused by a number of factors including drinking too much alcohol, taking antibiotics and poor dental hygiene. The most accurate and comprehensive way to know if you have gut dysbiosis is a Gut Microbiome Test

If you suspect you have gut dysbiosis we can certainly help you to organize testing through one of our Gut Microbiome Testing programs.

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