Healthier Gut Microbiome, Healthier Life

In my previous article, I wrote about the practise of Shinrin-yoku and how cultures of the past have seen our existence as being intimately linked with that of nature’s existence. In this article, I will be exploring another way in which our lives are mutualistic with nature, only this time on a microscopic level, inside our bodies.


What makes a person a person? In thinking about this question, the phrase “you are what you eat” comes to mind; if you eat poorly, and eat foods with little nutritional content, then the quality of your health will be poor in return. This seems like a concept most people could agree upon. However, when you try to understand why this is the case, it becomes apparent that a ‘person’ is not just one organism, but instead a ‘holobiont’; a whole community of microorganisms which work together with their host to ensure both survive. Moreover, it’s believed people harbour more bacterial cells in their body than they do human cells, speaking volumes to the importance of understanding this relationship between humans and microbes.


This article will explore the concept of a gut microbiome, how a dysfunctional microbiome is implicated in a variety of diseases, and the importance of diet in promoting a healthy gut flora.

Understanding the Gut Microbiome

Élie Metchnikoff

The concept of a microbiome, or an ecosystem of microorganisms acting in relation to each other and to their environment, is a relatively recent development in scientific understanding. Beginning in the mid-to-late 1800s, Pasteur, Koch, Metchnikoff, and Escherich all recognised the potential for human-microbe interactions, including beneficial ones from bacteria naturally found on and within the body. Around the same time, Winogradsky demonstrated how multiple bacteria may work together in natural environments in the process of nitrogen fixation. These works are often seen as progenitors for the modern idea of microbiomes. Once the understanding of genetics and genetic technology developed, we began to gain a much deeper appreciation of the nature and relationships these microorganisms have with each other and with the body. Some noteworthy works of late include  Lederberg’s Nobel Prize-winning work on bacterial gene transfer and Doré’s genetic analyses of gut bacteria.


We now recognise that our digestive system is home to a plethora of bacteria, taking refuge in the relatively safe environment of our bodies very shortly after our birth, feeding off the foodstuffs that we consume. Many of these have evolved mechanisms to allow our bodies to tolerate their presence, such as the stimulation of regulatory immune cells that prevent inflammation that might otherwise arise. The different ways in which gut flora interacts with human bodies is still being understood, but already studies suggest the bacteria in our gut can affect gene expression, inflammation and signalling within the nervous system.


A yellow-billed oxpecker eating mites from an animal’s back

Furthermore, the presence of these bacteria can provide a benefit to us as living organisms. Just as oxpecker birds will cleanse buffalo of ticks and mites which might be a detriment to a buffalo’s health, bacteria in turn can improve our digestive capabilities by converting otherwise inedible compounds into useful nutrients. For example, a number of gut bacteria can convert fibre into short chain fatty acids, which can then be used in the metabolism of carbohydrates and lipids. They may even impact on our mood through regulating the serotonin used in back-and-forth signalling between the brain and gut, which, given the rates of mental health conditions in our modern day societies, makes understanding this link even more vital.

Disease as an Imbalance of Microbiomes

While microbiomes can be beneficial when in ‘eubiosis’, where the ecosystem is in equilibrium, a failure to maintain healthy bacteria in our body’s microbiomes can contribute to a whole host of diseases. In my native field of dentistry, it is well recognised that gum disease should be seen as an imbalance within the bacterial populations of the mouth, whereby factors such as smoking, poor saliva quality and diet can encourage tissue-damaging bacteria to ‘take over’ from many of the bacteria you would typically expect to see within oral microbial communities.


This kind of imbalance, or dysbiosis, can also occur in gut microbiomes. Healthy gut microbiomes will typically exhibit a wide range of different bacterial species, including Lactobacillus species, Bifidobacterium bifidum and Bacteriodes species. Conversely, poor gut microbiomes typically show a lower range of diversity. Those living in highly urban, socioeconomically deprived places, or those with little fibre intake, exhibit far less diversity in their gut microbiome.


By being both disconnected from nature, reducing contact with bacteria that would otherwise help build our disease tolerance, and by not having access to healthy, organic foods, this leads to dysbiotic gut ecosystem. And just like with gum disease, this unregulated state has been implicated in a wide range of diseases, including cardiovascular disease, inflammatory bowel conditions, rheumatoid arthritis, colorectal cancer, obesity, and diabetes to name a select few. Moreover, even some of the persisting conditions following COVID-19 infections have been associated with dysregulation of the gut microbiota.

Prebiotics, Probiotics and Diet

“Let food be thy medicine and medicine be thy food”

While the mechanisms leading to microbial dysbiosis are not fully understood, it perhaps comes as no surprise that what we consume is a major determining factor for the health of our gut microbiomes. Some of the things we eat, such as artificial sweeteners, have been shown to encourage increases in the numbers of Enterobacteriaceae present, with adverse effects on blood glucose levels as a result.


Other foods, however, may actively promote a healthy gut microbiome. These are generally classed into two groups: prebiotics and probiotics. The latter of these terms is likely the one most readers are familiar with, referring to foods which harbour significant quantities of beneficial microorganisms. They exist in many cultures around the world, particularly in fermented foods like yoghurt, kimchi and sauerkraut, although it is only in the past hundred years or so that scientists like Metchnikoff have theorised benefits of consuming bacteria like Lactobacillus in yoghurt. As an added benefit, many fermented foods, such as sauerkraut, are also high in Vitamin K2, which has important roles in managing calcium levels in blood and synergistic effects with Vitamin D.


Prebiotics, on the other hand, see much less attention in the public eye. First defined in 1995, these are non-human-digestible substances that encourage the growth of beneficial microorganisms in the gut. Dietary fibres, such as those found in pulses, wholegrains, and vegetables, are fermented by bacteria into molecules useful in stabilising blood glucose. Polyphenols, found in berries, spices and tea, have been linked to gut immune responses and management of metabolic processes.


Organic vegetables

Pre- and probiotics are by no means the only diet-related route towards encouraging a favourable gut microbiome. Eating organic and foraged foods might be one way of promoting a healthy gut flora, as pesticides and herbicides have not killed off potentially beneficial bacteria on food. Additionally, traces of such herbicides are not ingested either, which might otherwise have harmful effects on gut microbial communities and their hosts. Similarly, highly processed foods are far less likely to contain both the pre- and probiotics that would benefit the gut ecosystem. The idea of probiotic-based supplements is also being actively explored, but that topic really deserves an article of its own.

Final Thoughts to Digest

Of course, foods are not the only things we consume that can impact on gut microbiomes. Research is beginning to recognise the ability of antibiotics in driving dysbiosis in the gut. While we intend for antibiotics to kill off specific pathogens that cause disease, many of them also act to kill the healthy gut flora that gives us resistance to disease. This is precisely how Clostridioides difficile infections occur; a destruction of the resident microorganisms allows C. difficile to take over, leading to a range of illnesses and, in some cases, death. Combined with the rise in antimicrobial resistance, there is a clear need to re-think our approach in how we manage disease, and whether our decisions are further driving dysbiosis within our bodies’ microbiomes. We are not just treating one organism when we manage disease, we are treating a ‘holobiont’, with more microorganisms than human cells that have evolved alongside us, for the benefit of both of us.

While our understanding of the gut microbiome is still growing, it’s becoming clearer by the day that we should be thinking about ourselves and our health as being in harmony with the natural world. You are indeed what you eat, in some ways quite literally, through the microorganisms in our food that can go on to take residence in our gut microbiomes. Maybe it is time for all of us to take a greater look at our diets and ask the question “Is this right for me and for my health?”, and I think that, if we do, we may begin turning the goodness that we eat into goodness in the world around us.

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Disclaimer: Over To The Youth is a community of conscious individuals. The content reflects the lens of its individual creator rather than the community as a whole.

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