The 7 Causes Of Digestive Problems

The 7 Causes Of Digestion Problems

Are you suffering from digestive problems but not getting answers?

There are many causes of digestive problems and the key to long term treatment is understanding the underlying cause.

I see so many clients who have lots of tests with their doctor, only to be told everything is fine, or you just have IBS and have to deal with it. Has this happened to you?

This article is going to describe the different causes of digestion issues, this is important as it is the first step to getting your health back on track. Also what is the best way to test your digestion.

However there is always a cause of your digestion problem, and determining what the cause is, rather than just treating symptoms, can help you get your digestion back on track.

Key Takeaways

The primary causes of digestive problems include low stomach acid, Small Intestinal Bacterial Overgrowth (SIBO), infections, dysbiosis, food intolerances and allergies, increased intestinal permeability, and Inflammatory Bowel Disease (IBD). Understanding these triggers is essential for addressing gut health issues effectively.

The Common Causes Of Digestive Problems

Problems with your digestive tract can cause many other health problems, as Hippocrates said many years ago “all disease begins in the gut” and modern research shows that he is right.

This can include hormone issues, mood problems, skin, autoimmune and the list goes on, basically, any health problem can be made worse if your digestion is out of balance.

There are many different symptoms to tell you that there is something wrong with your digestive tract, this includes constipation, diarrhea, reflux/ heartburn, bloating, gas and pain.

If the symptoms are bad enough you may be referred to get a colonoscopy, this is just to check that you do not have cancer, pre-cancerous polyps or inflammatory bowel disease …. if you are clear of all of these (and most people are) you are told that you just have IBS, which is irritable bowel syndrome (and just put up with it).

Let’s take a brief look at the 7 causes of digestive problems and in some follow-up articles I will go into more detail. These are not in order of importance, and you may have one or more of these causes of digestive problems.

How Hypochlorydia Causes Digestive Problems

Number one - low stomach acid.

Hypochlorydia is low stomach acid. The stomach produces hydrochloric acid which is essential for the breakdown of food in the stomach, the absorption of nutrients and to protect against pathogens.

If the stomach is not producing enough stomach acid this can have a flow on effect and cause issues with bile production and pancreatic enzymes. This can lead to symptoms such as acid reflux, nausea, heartburn, indigestion, burping, gas and pain.

The medical treatment for these symptoms is acid lowering drugs like Losec, Pariet, and Somac. While they can treat the symptoms, they do not address the cause of the problem and end up causing a lot of long term health issues, as well as increasing the risk of other gut pathologies.

It is often thought that symptoms like reflux and heartburn are caused by excess stomach acid but this is not always the case.

Low stomach acid leads to bacterial overgrowth (SIBO), the bacteria produces gases like hydrogen and methane which put pressure on the oesophageal sphincter muscle causing it to relax.

 The acid from the stomach can move into the oesophagus because of this pressure …. you don’t need much stomach acid for this to happen.

Low stomach acid is a common cause of digestive problems in the elderly, yet many are given PPI medications to treat the symptoms.

Small Intestinal Bacterial Overgrowth (SIBO)

Number two - SIBO

It is estimated that 80% of IBS symptoms are caused by SIBO, yet most doctors know very little about it and rarely test for it.

This is because a lot of the research into SIBO has been done over the past 20 years and most doctors don't have time to keep up with the latest research.

There should be a lot of bacteria in the large intestine (trillions!!!) but very little in the small intestine, SIBO occurs when some of the bacteria from the large intestine moves into the small intestine and then starts to take over.

Hypochlorydia or low stomach acid can be a cause as this leads to carbohydrate malabsorption which is the primary “food” for the bacteria. Other causes of SIBO include antibiotics, poor diet, infections, and constipation.

SIBO can cause depression/ anxiety, vitamin and mineral deficiencies, malabsorption issues, intestinal permeability due to damage to the intestines. As well as many digestive symptoms like constipation, diarrhea, reflux, bloating, gas and pain.

SIBO is associated with many chronic illnesses, too many to list here, and if you have chronic health problems and digestive issues then you should be tested for SIBO.

Diagnosis of SIBO is via a breathe test which measures the hydrogen and methane gases that the bacteria produce.

Of all the causes of digestive problems SIBO is number one!

Or another option which I recommend is the Food Marble Aire 2 device, this is your own personal SIBO testing device that you can use many times over. I find this to be a better solution than a one-off SIBO test.

Anyone can buy the Food Marble device but to do a formal SIBO test you need to be connected to a practitioner who has an account with Food Marble.

If your interested in this, and getting a discount on the device email to ask how you can connect with us to do the SIBO testing and get the discount.

The 7 Causes Of Digestive Problems 1

Parasite and Bacterial Infections Cause Digestion Problems

Number three - Infections

Before doing a SIBO test I would consider doing a stool test to rule out other gut infections, plus assessing intestinal health markers.

Gut infections like Giardia, Blastocystis hominis, Dientamoeba Fragilis, Helicobacter pylori, Klebsiella and Salmonella are another major causes of digestive problems.

These types of infections can produce acute pain and diarrhea, but also cause low-grade chronic symptoms that come and go with the life cycle of the infection.

As well as digestive symptoms chronic infections can cause fatigue, muscle aches, mood changes, brain fog, sleep issues and skin problems. I recommend getting tested for parasite or bacterial infections if you have chronic health problems, even if you think your digestion is ok.

The best way to test for these types of infections is with the Vibrant Wellness Gut Zoomer Test OR the G.I Map stool test

Not sure where to start, or if you need this type of testing, then schedule a consultation and I can help you with previous test results or see if you need more testing, or if we can help you with a treatment plan based on symptoms.

Dysbiosis and Fungal Overgrowth - Causes of Digestive Problems

Number four - dysbiosis

Dysbiosis is when there is an imbalance of gut bacteria in the gastrointestinal tract. We have around 100 trillion bacteria in our gut, many of them beneficial and essential to our survival, and some of them not.

This is known as the gut microbiome.

Dysbiosis can be an overgrowth of the wrong type of bacteria, or it can be not enough of the beneficial bacteria, or missing key bacteria species.

Knowing what type of dysbiosis you have can help guide the best way to treat, the Gut Zoomer test is the best option for this - especially when combined with the Wheat Zoomer test which also assesses leaky gut.

Candida overgrowth is a good example of what happens if you have dysbiosis, candida is normally found in small amounts in the gut but due to poor diet, antibiotics, stress and other infections this can lead to an imbalance in our good bacteria which allows candida to thrive.

High candida will cause many digestion and other systemic symptoms, especially fatigue and neurological symptoms.

Dysbiosis does not just affect Candida, but it can also lead to overgrowth of other bacteria like Klebsiella that are normally present in the intestinal tract and only cause problems when there is too many.

Dysbiosis and Candida can be identified with a stool test or an Organic Acids test. The Organic Acid test is a more sensitive test for candida overgrowth compared to the stool test.

If you were going to choose one test to assess gut health I would choose the Gut Zoomer stool test, but the Organic Acids test does give extra information on nutrients, energy production as well as candidia.

Food Intolerances and Food Allergies

Number five - food intolerances and allergies

Food intolerances and food allergies are the next possible causes of digestive problems. This includes celiac disease which is an allergy to gluten, and despite the severity of symptoms that celiac disease can cause, many people have an undiagnosed celiac disease.

The standard test for celiac is not very good so even if the test says you do not have celiac disease it is a good idea to do a 30-day gluten free period to see how your symptoms respond.

Or do an advanced test for celiac and wheat sensitivity like the Vibrant Wellness Wheat Zoomer, this test also assesses for leaky gut.

Other digestion problems like SIBO, hypochlorydia and intestinal permeability can cause food intolerances, and once you address these cause often you can re-introduce the problem foods again …. this is especially true if the food intolerances occurred late in life.

Food intolerance can be hard to identify because sometimes symptoms occur hours or even days after eating a particular food. Food intolerances can cause many digestive symptoms as well as fatigue, nutritional deficiencies, skin problems, headaches and many other common symptoms.

To test for food intolerances there are a couple of different options, the cheapest and sometimes the most effective option is an elimination diet, these can be great for identifying trigger foods but can be difficult to stick to.

The Vibrant Wellness Food Sensitivity Complete assesses for 209 foods and 57 common food additives. Most tests don't measure the food additives and this is important as they are a common cause of health problems.

This test measures IgG which is a marker for sensitivity, and also IgA which is a marker for food allergies. If you have an IgA reaction the food will likely need to be avoided 100%.

Intestinal Permeability

Number six - Intestinal Permeability

Intestinal Permeability or “leaky gut” was for a long time dismissed as being a real condition by the mainstream medical practitioners, but with more advanced testing over the past 20 years, it is not only recognized as a real condition but one of the biggest areas of research.

Along with the gut microbiome, this is now a leading area of research in medicine as intestinal permeability can lead to autoimmune conditions (all autoimmune conditions are associated with leaky gut), cause neurological problems, skin issues like psoriasis and eczema as well as many other common symptoms.

Intestinal permeability means that the intestinal wall becomes more permeable so that larger toxins that should be eliminated are allowed to get through the intestinal wall into the bloodstream.

The intestinal wall should be selectively permeable to allow nutrients from the food we eat to get into our body, but if the intestinal wall becomes damaged then other toxins can enter and circulate through the blood to other parts of the body.

Causes of Intestinal Permeability are similar to other causes of digestion problems and these include alcohol, stress, SIBO, NSAID’s, pathogens and other medications.

Tests like the Vibrant Wellness Gut Zoomer combined with the Wheat Zoomer will help to identify if you have leaky gut, and what the underlying cause may be for you.

Inflammatory Bowel Disease (IBD)

Number seven - Inflammatory Bowel Disease

Inflammatory bowel disease or IBD for short should not be confused with IBS, as IBD is a much more serious condition. The two most common forms of IBD are Crohn’s disease and Ulcerative Colitis, this is an autoimmune condition where your body’s own immune system is attacking itself.

IBD is diagnosed with a colonoscopy, and a stool test like the Vibrant Wellness Gut Zoomer or G.I Map test can also show markers indicating IBD.

The standard treatment is immune-suppressing drugs and surgery though there is a lot of nutritional, herbal and dietary changes that can be made to improve this condition.

Faecal transplants have also been shown to be helpful with treating IBD, which shows that is it connected to the health of the gut bacteria. Now there is an option in the U.S for oral FMT treatments with Thaenabiotic


A healthy digestion is a key to good health so it is important to address any digestive issues, and the first step is identifying the cause.

Depending on your signs and symptoms the best place to start would be with a stool test to identify if there are any parasites or bacterial infections (or any other gut issues) and do a test for SIBO to see if there are any small intestine bacteria infections.

It is important to identify if there are any infections as a first step otherwise you may improve digestive health by correcting hypochlorydia or intestinal permeability, but you are not going to get to the root cause of the problem, and the symptoms will keep returning.

A wide range of functional pathology testing is available through Planet Naturopath, these tests can be done anywhere in Australia, the U.S and many parts of the world.

Recommended Tests For Identifying The Cause Of Digestive Problems

Gut Zoomer

Vibrant Wellness Gut Zoomer

The Gut Zoomer assesses bacteria, yeast, viruses, and parasites in the gut microbiome, alongside relevant digestive and inflammatory markers. The panel measures hundreds of species of microbes at once, providing the most comprehensive digestive health test on the market. 

Gut Zoomer + Wheat Zoomer

Gut Zoomer + Wheat Zoomer

Everything in the Gut Zoomer plus if you suspect you have wheat sensitivity, multiple food sensitivities, intestinal permeability, autoimmune disorders, or chronic inflammation, you may benefit from Wheat Zoomer panel

Food Sensitivity Complete

Food Sensitivity Complete

The Food Sensitivity Complete bundle assesses the most common foods and food additives available, with 209 foods and 57 food additives tested. Non-food-based additives include difficult to detect ingredients such as preservatives, artificial sweeteners, emulsifiers, food dyes, and even pesticides

Organic Acids test kit

Organic Acids Test

The Organic Acids Test detects the organic acids in urine that are byproducts of daily cellular metabolism. The panel can accurately identify conditions associated with genetic disorders, nutrient deficiencies, intestinal dysbiosis and detoxification.

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