5 Common Causes of Digestion Problems


The Paleo diet has many success stories of people improving digestion problems, losing excess weight, improving energy levels, skin conditions going away and symptoms like gas, bloating and constipation improving within weeks of transitioning to a paleo diet.

However not everyone gets these benefits and it is possible that it is your digestive system that is the cause behind these problems. Once you address the cause and not just focus on the symptoms, you will start seeing long lasting benefits.

5 common causes of digestion problems

1. Diet

People often have less bloating, gas, diarrhea, constipation and reflux when following a paleo diet because it cuts out the gluten containing foods and dairy – both of these can be big triggers for digestion symptoms. However if you have been following a paleo diet for at least a month, and you are still experiencing digestion symptoms there maybe other foods that are the problem.

The first thing that I would look at are gluten and dairy as these are always the prime suspects. While you might have been following a paleo diet 80-90% of the time, if you are still including just a little bit of these foods, this can cause problems in sensitive individuals. While I don’t think everyone has to follow a strict paleo diet 100% of the time, to identify food sensitivities it is necessary to cut these foods out 100% for at least a month.

Eggs and nuts are some of my favorite foods and I usually eat them everyday but they are not for everyone. While some people have obvious allergies to these foods, other people can be sensitive to them which can lead to vague digestion symptoms. The best way is to eliminate them 100% for a month and see what difference this makes. If you also have an autoimmune condition then following an autoimmune paleo diet for at least a month would be your best option.

Eating lots of vegetables is an essential part of a healthy paleo diet, but there are certain vegetables that are high in FODMAPS and not easily digested by some people. For an excellent article explaining what they are check out this FODMAPS article. The FODMAP diet is not a forever diet and once you address the underlying digestion issues then you will often be able to tolerate these foods again.

2. Dysbiosis

Symbiosis translates to living in harmony and dysbiosis is the opposite. Dysbiosis in your large intestine is when you have an imbalance in your good and bad bacteria. This can lead to many digestion symptoms as well as other chronic health problems.

Dysbiosis can be caused by antibiotics, poor diet, stress and infections and can lead to many symptoms like gas, bloating, diarrhea and constipation. A colonoscopy will not reveal that anything is wrong and often people are just told that they have IBS, but that is just a collection of symptoms and not the cause of the problem.

Dysbiosis can lead to a leaky gut and this is how it can cause many diverse chronic health problems like autoimmune conditions, skin problems, depression and mood disorders, chronic fatigue and arthritis. Dysbiosis can be treated with a digestive repair program which will help to eliminate pathogens and restore the good bacteria using prebiotics and probiotics.

Your signs and symptoms can often help to diagnose dysbiosis but the best way is through a comprehensive stool analysis. This will reveal many things about your digestion including how much good bacteria you have, as well as how much bad bacteria, parasites and yeast that you have in your digestion that are causing these issues.

3. Low Stomach Acid

Low stomach acid can cause many common digestion symptoms like gas, bloating, nausea, reflux and heartburn. These symptoms are often treated by acid lowering drugs like Losec, Nexium and Pariet which are some of the most commonly prescribed drugs in the world. Unfortunately these drugs only address the symptoms and not the cause and after taking them for a while they are often ineffective.

Side effects of low stomach acid, and acid lowering drugs is a reduced ability to absorb minerals such as iron, zinc, calcium and copper, along with the vitamins B12 and Folate. This can have many health consequences and addressing the underlying cause should be the priority.

Many things can affect stomach acid production including stress, vitamin and mineral deficiencies and it naturally lowers as we get older.

4. Bacteria and Parasite infections

Acute parasitic and bacterial infections often cause pain, diarrhea and gas which can last for days or weeks. Some people make a full recovery after this time, but many people I see say that there digestion problems have been there ever since they picked up an infection. With chronic infections the digestion symptoms are often mild but there could also be systemic symptoms like fatigue, brain fog, depression and aching joints.

Parasite and bacterial infections can often be hard to diagnose with a standard stool test that the doctor does, but thanks to advances in technology you can now get a special stool tests that measures the DNA of a pathogen and is a lot more accurate.

Even if a parasite has been cleared from the body it can cause a lot of inflammation and damage to the intestinal wall that will need to be repaired before a full recovery is made.

Helicobacter pylori is another type of bacterial infection that lives in the stomach wall, this can cause a range of symptoms including pain, reflux and eventually stomach ulcers.

5. Stress

In my last article Hormones could be the cause of your health problems I wrote about how stress can affect many aspects of our health by disrupting our hormones. Well stress can have a significant impact on our digestion too.

I have already mentioned how stress can affect stomach acid production which is vital for a healthy digestive system but stress can also have a significant impact on our secretory IgA levels (SIgA). This is like a protective film on the digestive tract that helps to protect the mucous membrane of our intestines. If this protective mechanism breaks down it can be another trigger for leaky gut. It can be also why some people will start reacting to foods that previously they have had no problems with.

An adrenal saliva stress test can help to identify how well your body is responding to stress and help to determine a clear treatment plan.


The good news about these causes of digestion problems is that you can fix them. Addressing the diet and low stomach acid can sometimes bring about rapid improvements to your health but some of the other causes can take several months to fix. The key is to identify the cause, find the right diet for you and take the right supplements to get you back to feeling great.

To find out more about this and other topics visit my website and see my bio and web links below. I can also help you with your health concerns via online consultation.

Michael Smith

Michael Smith is a Naturopath and Functional Medicine Practitioner at Planet Naturopath. Specializing in hormonal disorders, adrenal, thyroid and digestive function, Michael works with clients form the chronically ill to athletes wanting to improve performance. Consultations are available via Skype or phone.

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