The causes of depression and poor gut health


Antibiotics are great modern healers. But as I said  in the opening pages they are like an atomic bomb to your colon. They kill the enemy (bad bugs) but they also take a lot of innocents out as well. The more antibiotics you have had and the younger you are when you first had them, the potential damage to your gut increases. Good news though, it's mostly repairable.

Obviously, everyone that takes antibiotics does not get depression. I suspect a lot of the luck in this is your starting position, as in how good your gut was to start with. There must be many other factors.

The point is, who cares? You are here because you are trying to solve the problem that you now have. I am not saying don’t take antibiotics. If your doctor recommends them – take them. Just use them when you really need them. My doc once said to me that with the ‘flu or cold if you take antibiotics you will probably get better in two weeks, but if you take nothing, then it will last about 14 days!


There are plenty more experts on the internet cleverer and with more information on these subjects but I will just give you the bare bones.

Just to hammer home the above point on antibiotics, unless you have an organic vegan diet you are likely to pick up doses of antibiotics in your food supply. Almost all corn and soy grown in the USA has residues of glyphosate (Roundup) in it. Roundup is an antibiotic. You don’t have to live in the USA to find products with US corn and soy in them.

The modern food supply (depending where you live) also includes many GMOs (Genetically Modified Organisms) and many modified products like for example hydrogenated vegetable oils, canola oil and margarine.

Grass fed beef has a much higher Omega 3 content (Healthy fat) than grain fed beef.

Farmed salmon is not the same as wild caught salmon.

How old is that juicy apple you are eating? Is it 1 week, 1 month or 6 months old?

There is simply too much sugar in the modern diet and too much wheat or corn or non-nutritious rice.

Pasteurising of milk changes the proteins and the digestibility of the milk and homogenisation is probably even worse. 

Almost all cheese consumed today is processed cheese.

Wheat of today is nothing like the wheat that our grandparents ate.

All these factors affect your gut health, and your mental health. 

See also Psuedo Foods versus Real Foods >>


We kill bacteria today everywhere we find it, usually with chemicals. These chemicals kill off our exposure to harmless and often beneficial bacteria. Overwhelmingly, we live in urban areas and don’t touch nature or the soil. We generally shower too much and generally use more chemicals on our skins. We apply sunscreens as we have been taught to do and have learned that lesson well. We are fully clothed and shoed, so we limit our exposure to environmental bacteria. 

Fresh food is kept in refrigerators where it slowly loses its nutrients. Old methods of food preservation like lacto fermentation are rare but becoming more popular.

Most of us urban dwellers are not in touch with nature often enough.

See also Nature's Probiotics >>


No doubt running tap water and working sewers were two of the greatest lifesaving inventions of the modern era. It’s the chlorine (and if applicable to you, the fluoride) residues in the water that kill your gut bacteria. Chlorine and Fluoride are designed to kill bacteria and chlorine is absolutely necessary in modern urban areas. By the time you receive the water the chlorine has done its job, now you want it gone. When you heat it in your tea and coffee it’s even worse because it becomes more active. When you get in a hot shower the same happens on your skin.


I do not recommend stopping or not starting any drug prescribed by a doctor or any over-the-counter medications you feel are working for you.

All drugs have side effects. Many drugs disrupt the natural systems in the body. But worse is that some drugs cause depression. Just to give you an example, I never take paracetamol (eg Panadol, Tylenol, acetaminophen). Neither does my wife. We have independently come to the conclusion that it causes us depressive like symptoms, although these go away quickly when the drug is stopped.

I had a similar experience with Celebrex (an anti-inflammatory) I took briefly to help with sciatica. It didn’t help with the sciatica but it did interfere with my gut and make me unhappy/depressed. It was temporary and ceased after stopping the medication. I only took it for a week.


This is probably the number one thing that “causes” depression, and perhaps some anxiety, but it is not what causes depression and anxiety to persist. We all get down when life throws us something painful, stressful or worrying to deal with. Usually that passes - it’s when it persists that it becomes depression. Often these difficult life events are the trigger for depression, but it is because of all the other factors mentioned above that you don’t recover. It’s sort of like life and happiness are not about what happens to you but how you deal with it.

Don’t be ashamed of depression - you are not guilty for it. No one intentionally sets out to get depression or anxiety. It is something that happens to you like getting a cold or the 'flu.

Right, what do we do about it.

Hippocrates is recognised as the father of modern medicine and said “all disease begins in the gut”.

Well the solution is simple, fix the gut and you will fix the disease. Your depression is not in your head, even though it feels like it. Your depression stems from your gut (your colon).

Now, if your diet consists of organically grown vegetables and meat, you drink plenty of clean water and don’t take prescription or non-prescription medicine and don’t drink too much alcohol AND your bowel movements are regular (daily), well formed, a good colour and easy to pass, and you still have depression then I probably can’t help you.

For everyone else which I expect is everyone still reading, read on and I will give you the solution that worked for me and many people I know that I have helped.

To be fair there are a couple of other “causes” of depression that in my view are important but fewer in numbers. I will loosely call them Pyoluria and MTHFR. I will discuss them later but my belief is that they have the same root cause (gut health) or can also be alleviated by the same pathway.

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