How We Wrecked Our Guts

Last modified on November 19th, 2019

There is great deal of evidence to show that our guts used to be in a much healthier state decades ago. For example, the Hadza in Africa, one of the last ‘hunter-gatherer’ species on the planet, appear to have 300% more bacteria in their guts than we do. It seems that over time we have lost many of these bacteria, and whatever functions they once provided.

In terms of gut health, one metric that’s often used is diversity. Similar to the environment, it’s often thought that the health of any ecosystem is related to the number of species in it and their relative abundance. Harmony is basically where you have a lot of species, with a mostly equal membership. If any one species starts to take over and populate excessively, it endangers the entire ecosystem.

This is similar to the gut microbiota. Any overgrowth of a particular species can tend to cause problems for the health of the entire individual. Likewise, certain species seem to be protective against ailments like diabetes and obesity – a person generally doesn’t want to lose them.

The Danger of Antibiotics

When I was a child, my mother would take me to the doctor’s office when I was sick. They would perform a bunch of tests, sometimes putting cotton swabs in my nose or throat, and then wait a few days to see what I was infected with. If it was something treatable, often I would get a prescription for an antibiotic and take it home. The key difference back then was they often wanted to know what the bacterial infection was before prescribing the antibiotic. Nowadays most doctors simply prescribe broad-spectrum antibiotics, which are mostly non-specific with regards to the bacteria they tend to kill.

There’s no question that antibiotics save lives. But nowadays doctors are pretty eager to prescribe them, and patients have been trained to basically ask for them whenever there is an issue. The body has an amazing ability to heal itself and fight off disease, but most of us don’t want to go through that process and instead simply opt to take antibiotics whenever we are ill.

The problem is that antibiotics have a massive detrimental effect on the gut microbiota. In one study I read, one course of antibiotics caused persistent changes in the gut for over two years. Some species can be totally eliminated by antibiotics, and never return. Over time this has led to a gradually declining gut microbiota in North America, one that’s getting further and further from our Hadza counterparts in Africa.

I would never tell someone not to take antibiotics, but for myself I actively avoid them whenever I can. The last time I had any antibiotics was a few years ago when I had a surgery, and my gut health has never looked better. If I got really sick, I wouldn’t hesitate to take antibiotics. But for the average cold or periodic infection, I personally steer clear of them myself.


Another aspect of gut health that is causing damage is the preferential shift to c-section deliveries in many countries. There are two problems with this.

First, there’s growing evidence that a child acquires its initial microbiota from its mother during delivery through the birth canal. C-section babies, since they don’t pass through the birth canal, instead end up with a microbiota that resembles the bacteria on the walls and equipment in the hospital, one that looks nothing like what a typical healthy microbiota is supposed to represent.

The second issue is that during a c-section antibiotics are usually administered, which has the effect of further damaging the microbiota of the mother and baby, depending on the timing of the antibiotics.

While there are many medically justified reasons to have a c-section childbirth over a natural birth, the trend in many countries to do it primarily for convenience or cosmetic reasons is increasing.

Breast Feeding

There’s a long line of research that shows that breastfed babies are generally healthier than ones fed formula. This seems to be the case as well in terms of the gut microbiota. In fact, there are certain elements in breast milk that can only be consumed by certain bacteria in the gut – without them they would pass right through the body. So this shows at some level that breast milk has evolved to not only feed the baby, but the baby’s microbiota as well.

Excessive Cleanliness

Another aspect which is hurting our gut microbiota is our excessive cleanliness. There are antibiotics unfortunately in many places now, and most people probably aren’t aware of them. For example, some toothpastes have ingredients in them that effectively act like antibiotics. Those hand sanitizers that many people use also are good at wiping away bacteria on our hands, many of which may be beneficial to the body. The chlorine and chloramine in our water also kills bacteria in the body.

Research has shown that children who grow up on farms have improved health in general, and one theory about why this is rests in the fact that they are exposed to far more germs and bacteria than kids off the farm. This causes the immune system to be far stronger, and seems to show that they can fend off more pathogens and diseases. So our excessive fear of being dirty may be causing our immune systems to be weaker.

Research has shown that in families with dogs, they not only have a healthier microbiota but also the microbiota of family members are more similar to each other. So Fido the dog is not only an important companion, but he’s helping to transfer beneficial bacteria (through licking and being outside) throughout the house.

So in terms of gut health, what does all of this mean? I can’t instruct others on what to do as these are personal decisions, but for me I avoid hand sanitizers (nothing wrong with a little water) and antibiotics whenever I can. I haven’t quite found the perfect solution to removing chlorine/chloramine from water, but I am actively looking for a good solution. But in general, I try to avoid anything that I think will hurt my microbiota.

In the next newsletter (sign-up here!), I’ll talk about some common ways you can improve your gut health, primarily through what you are eating! We’ll discuss fibre (digestible and non-digestible) and the new term, Microbiota Accessible Carbohydrates (MAC).