Gut microbes: our friends not our foes

There is such a thing as ‘good’ microbes. Just ask your gut.

Photo by Artem Bryzgalov on Unsplash

You’d be forgiven for thinking that all biological entities, invisible to the human eye were our enemies. After all, it isn’t just viruses, like Covid-19, that have devastated our planet – bacterial diseases, such as tuberculosis, are still major problems too. However, there are some that are on our side.

In fact, our bodies are home to a whole host of “friendly” microbes –  trillions of them! They are found all over us, from inside our mouths, to on our skin. The area that has been of most interest, however, is the gut, where the population, collectively known as the gut microbiota (GM), reside. Similar to our organs, the development of the GM is highly dynamic during the first years of life, as different species colonize at different rates, and at different times. Once past this phase, the GM remains relatively stable throughout the rest of life, and is mainly composed of anaerobic bacteria, which can thrive in environments with limited oxygen.

The relationship between the GM and our gut is described as either mutualistic or commensal. This means that the microbes will use the nutrients, which they get from us, as fuel to drive their activity, which is either beneficial to our health (mutualistic), or has no effect (commensal). Given the diversity of this population (which also harbours fungi and even some viruses), the GM is a jack-of-all-trades.

 These microbes primarily work by producing chemicals called metabolites. The types of metabolites are vast, and their functions are even broader. These molecules can affect various systems within the body, from our immune system and physical health, to the nervous system and our mental health. Through these chemical signals and building blocks, the GM plays a crucial role in maintaining healthy gut function, and helps to protect us from harm, such as against infection from nasty, disease-causing pathogens, like C.difficile.

The gut microbiota is like a fierce guard dog: if we take care of it, then it will help take care of us. But if we can’t…then things can turn sour. Unhealthy lifestyle habits and underlying medical conditions are just some of the reasons for how the delicate balance between these microbial  sub-populations can be disturbed. This imbalance is known as dysbiosis, and can transform harmless residents, such as the Candida Albicans fungi, into dangerous pathogens, which are responsible for troublesome infections, like candidiasis. The manifestation of bacterial GM residents, like E.coli, has also been seen in conditions, such as colorectal cancer, with their metabolites being used for the wrong reasons. Assessing the balance within the GM has therefore been touted as a potential diagnostic strategy for gut-related conditions.

Diets, high in fat and processed foods, can lead to inflammatory GM species dominating. This can potentially lead to inflammatory problems of the bowel. However, maintaining a sufficient level of dietary fibre will help preserve species diversity. This will further maintain healthy digestion. (Figure created with Biorender by author)

So how can we keep the GM on our side? As highlighted before, our lifestyle plays a big part - most notably what we eat. It has been shown that adopting a diet, which is heavy on protein and processed foods, leads to reduced diversity of the GM, when compared to plant-based diets, which are rich in fibre. The nutrients, which are abstracted from fruits and vegetables, are  converted into key metabolites by the GM. These include short-chain fatty acids (SCFA), such as butyrate and propionate, which have known anti-inflammatory and immunoregulatory properties. On the flipside, high-fat diets can encourage the overgrowth of potentially inflammatory GM species, which may contribute to the onset of metabolic conditions, like obesity and type-2 diabetes. 

Even the decisions that are made during infancy, like between being breast-fed or having powdered milk, can impact the GM. Breast milk contains beneficial natural molecules, such as the human milk oligosaccharide (HMO) and the immunoglobulin A (IgA) antibody. These compounds assist species, such as Bifidobacterium, for gut colonization, early on in life. Improper colonization, during infancy, has been shown to increase our susceptibility to autoimmune disorders, like asthma, later on in life.

However, the GM is not just affected by our diets. Long-term use of drugs, such as the acid-reducing proton-pump inhibitors, can also disrupt the harmony within the GM. This has led to the search for more ‘natural’ therapies, which can work alongside the GM. Popular examples include probiotics (containing live, GM-complementing micro-organisms) and prebiotics (containing GM-associated nutrients). These products are now commonplace amongst healthy food stores on the high streets.                  

The possibilities appear to be endless with the microbiota, and we have barely scratched the surface. Nevertheless, GM research is now growing faster than ever before, as more and more scientists realise the importance that these microbes have on our health and wellbeing. Perhaps we should think twice, when we next order a take-out, or reach for the meds.