Our vanishing microbiome and what we can do about it

Steps we can all take today to build a better microbiome for tomorrow

We are not fully human. In fact we are more microbe than we are human. The bacteria, viruses, fungi, parasites and archaea that live on us and within us have evolved with us. They make us who we are. They are us, and they are astonishingly brilliant. The microbes in our gut protect us from infections, digest the food that we can’t, make vitamins for us and produce other beneficial chemicals that we need but can’t manufacture on our own. They can help control our weight, our mood and how we age. They are so important to us that human breast milk has evolved over the millennia to contain both bacterial species (probiotics) to line the baby’s gut and some substances purely to feed these vital microbes (prebiotics).

But we are witnessing a mass extinction event. The bacteria and other microbes in the gut that we collectively call the microbiome are under threat. This is one of the greatest current challenges facing human health and I’m going to explain to you why it’s happening, and what we can do about it. 

In order to understand this issue properly, I need to explain what the gut microbiome actually is … Let’s dive straight in.

Introducing Your Gut and the Gut Microbiome

It's worth clarifying that the gut, also called the gastrointestinal or digestive tract, is technically the entire pathway that runs from the mouth to the anus, meaning that the gut microbiome consists of the vast collection of microscopic flora and fauna (and their genes) that live in the mouth, oesophagus, stomach, small intestine and colon. That said, 95% of the gut microbiome is found in the large intestine.

There are other microbiomes throughout the body, including the skin microbiome and the reproductive tract microbiome. Each microbiome is vitally important to the organ in which it is located. The gut microbiome, however, has been found to be crucial to every other organ in the body as well. It’s depletion (known as a loss of microbial diversity or as dysbiosis) comes with a host of medical problems which I’ll cover later.

The origins for establishing gut health interventions as a medical treatment can be traced back to the 4^th Century and the Chinese physician Ge Hong’s yellow soup remedy for treating diarrhoea. A key ingredient of this medicinal broth was the stool from a healthy person. This is believed to be one of the earliest references to what is now known as FMT  (faecal microbiota transplantation or “stool transplant”) a current life saving treatment where healthy donor poo is transplanted to someone suffering from a severe infection in the bowel. 

Many of the ground-breaking microbiome research techniques and new discoveries we see in headline-grabbing stories today, find their origins in the 2007 launch of the Human Microbiome Project. Here are the top eight fascinating things that have been uncovered through this project and others like it:

1. The human microbiome is considered by many to be a newly discovered organ. At a combined weight of 2kg, it is heavier than your heart and lungs combined. 

2. The gut microbiome alone consists of around 100 trillion microbes, which is a higher number than all the actual human mammalian cells in the body. 

3. Because the gut microbiome consists of thousands of different species all with different genes, humans are actually composed of far more microbial genes than human ones (around 3 million, compared to the 23,000 genes in the human genome).

4. The gut’s own nervous system, the enteric nervous system, has 500 million nerve cells, more than our central nervous system.

5. 70% of our immune cells are now understood to reside in the gut, highlighted by research linking the condition of our gut to the overall strength of our immune system and to the development of allergic and autoimmune conditions.

6. Over 90% of serotonin, often called the body’s ‘happy’ chemical, is produced in the gut, which has helped to establish the link between mood, mental health and the health of the gut microbiome. 

7. Fibre is a type of carbohydrate that the body cannot actually break down by itself. Thankfully, Bifidobacteria, a vital ‘good’ gut bacteria, does digest fibre for us. Their good work results in a beneficial cascade of important compounds for us, such as short-chain fatty acids (SCFAs) which have tremendous health benefits.

8. Each person’s gut microbiome is completely unique to them and results from a number of factors that include: what we inherited from our parents; how we were born (canal birth or caesarean); where we were raised geographically (city or countryside; global north or global south); and what we eat and even who we eat it with.

So what is going wrong with our microbes, and with our health?

The inexorable rise in cases of gut disorders that my colleagues and I are seeing in our clinics is mirrored in other areas of health too. Obesity, allergies, inflammation, cancer, depression and anxiety are also on the rise and are all linked to poor gut health. So why are gut disorders rising? In short, because we are treating our gut microbes badly. Just as modern lifestyles are damaging the rainforests through deforestation, and we see a disappearance of some species and reductions in many more, so modern diets and other factors are causing a disappearance of some species of our gut microbes and reductions in many others.

So what specifically is happening in the gut when these species are depleted? Here are just a few of the ways in which loss of gut microbial diversity can have a negative impact on us:

• If a species has beneficial effects for us, and we reduce its number, then we lose out on those beneficial effects.

• Large populations of good bacteria usually crowd out harmful (or pathogenic) ones and help maintain the integrity of the gut as a barrier - this protection is lost with reduced diversity.

• Good microbes make substances that support other good microbes, so a reduction in one helpful species can have knock on effects.

We’ll explore how our gut microbes protect us and the mechanisms by which damage to them harms us in more detail in a future article.

What are we doing that is so detrimental to our microbes?

The most obvious harm comes from junk food, also called ultra processed foods (UPFs). This modern, convenience-oriented Western diet is low in fibre; over-dependent on red and processed meat products; contains few fruits, vegetables or whole grains; involves the widespread use of antibiotics in animal farming; and risks from free radicals related to plastic packaging in the food chain. Sadly, there is incontrovertible evidence that high intake of UPFs is associated with the development of cancer and with poor cancer outcomes. Unfortunately, we are eating more UPFs than ever before, with over half of the calories consumed in the USA, UK, Canada and Australia coming from junk food. This is an impending health crisis which can and must be averted.

Overuse of antibiotics in the worried well and in the food industry is also culpable. This is a complex issue because antibiotics are arguably the greatest medical invention of the 20th century. They have saved millions of lives since they became widely available in the 1940s and underuse of antibiotics is also dangerous, because late treatment of sepsis is associated with higher risk of death.

Several of the other determinants of how an individual's gut microbiome are being affected are sensitive topics of discussion. These include: mode of birthing delivery; breastfeeding versus formula and exposure to antibiotics early in life. It is important to stress that there are often strong medical, societal and personal factors at play.

As humans, we have autonomy to make decisions about behaviours that impact upon our own health. If our behaviours adversely affects others, though, there are societal, medical or legal pressures to avoid them. But surely my gut health and microbial diversity are my business and don’t impact others?  Unfortunately, and amazingly, this isn’t the case. The UPF diet and other sequelae of modernisation have led to a vast reduction of the gut microbes in the Western world. This is a legacy that is being handed down to our offspring.

Gut microbes are transmitted between people, with greatest transmission being between couples and between parents and their children. This transmission helps maintain high levels of diversity in our guts. A fascinating study showed that mice whose microbiome was fed a fibre poor diet experienced a loss of microbial species that transferred to the next generation of mice. Whilst microbial loss was reversible to some degree when first generation offspring were fed a high fibre diet, this reversibility was lost over the generations, and the temporary microbial loss became a permanent extinction from this line. 

This corroborates other evidence that suggests that we are witnessing an extinction of gut microbes from our bodies as individuals and as whole societies. To return to the rainforest analogy, just as we want to avoid the deforestation tipping point for the Amazon, where the destruction becomes too widespread and the rainforest degrades to a Savannah, so we want to avoid the microbiome tipping point where reduced gut microbial diversity can no longer support a healthy human being. We don’t want to rob our future generations of the opportunity of having a diverse and healthy gut microbiome and the many known, and as yet undiscovered, health advantages that come with that.

Steps we can all take today to build a better microbiome for tomorrow 

So, is all lost?

Absolutely not. There is great hope.

Now that the issue of dysbiosis and microbial extinction has been identified we can take steps to solve it. Humans are very good at problem solving (just think of the CFC crisis of the 1990s). We certainly don’t have all of the answers at the moment, but we do know enough to get started. We know that our gut microbiota can start to heal if it is treated well. For instance, we can see positive changes in the gut microbiome after just 2 days on a healthier diet.

3 of the most important things that you could do today for your gut would be to:

1. Increase your fibre intake (this NHS advice sheet gives an example meal plan).

2. Reduce the UPFs in your diet (here is a handy guide).

3. Take some exercise outside - the combination of exercise and connecting to the great outdoors (together with the improved food choices that we usually make after exercising) will turbocharge your gut microbiome.

Future newsletters will cover specific dietary and other lifestyle steps to improve your microbiome health in greater detail.

In addition to individual change, collective action is underway as well. Consider the Microbiota Vault. Established “to conserve long-term health for humanity”, this is akin to a seed bank – but for gut bacteria - like the ecological versions at London’s Kew Gardens and Svalbard in Norway which aim to preserve billions of wild plant seeds in the event any are lost now to future generations. 

Gut microbial health drives the wellbeing and vitality of our entire body and mind. As a society, we may have lost our way in this regard, but we are understanding more and more about why, so can make improvements to rectify these mistakes now. 

These weekly newsletters will help educate and inform you about your gut microbiome and digestive health – and give you simple steps on how to eat better, feel better and live better. For us. And for future generations.

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Dr Philip Hendy

The Better Gut Doctor

Medical Disclaimer:

Although I’m a doctor, I can’t replace your registered doctor. As such, the information in this newsletter is for information purposes only. It is not intended to be a substitute for medical advice, diagnosis or treatment. Always seek the advice of your qualified healthcare provider for any medical conditions, and never disregard professional medical advice because of information you have found in this newsletter.