The Gut Microbiome: Our Symbiotic Relationship

There is growing interest and research to understand how the gut microbiome affects our physiology and health. The complexity and vastness of our gut microbiome means pinpointing exactly how this occurs is difficult and likely to be due to a combination of factors. As a relatively new area of focus within health, human nutrition and physiology research, the scientific evidence is gradually emerging which is helping to address the abundance of misconceptions, pseudoscience and miracle treatments promoted to members of the general public. While this misinformation is widespread, a considerable portion has its origins in social media and so-called ‘internet influencers,’ many of whom have no formal nutrition training or qualifications.

Composition of the gut microbiome

From the moment we are born, microorganisms (e.g., bacteria, fungi, parasites) begin to occupy various parts of our bodies. As we reach adulthood, it is believed that we have as many bacterial cells within our bodies as we do human cells. Most of these bacteria reside within the gastrointestinal (GI) tract and the majority of them live in the large intestine where they are collectively referred to as the ‘gut microbiota’. Due to the large number of bacterial cells and species in the gut, a single person’s microbial composition in their gut is as unique as a fingerprint (although it is ever changing). It is near impossible to be able to define what constitutes a healthy level of microorganisms and species because of the large individual variations that exist. For simplicity however, the most common bacterial phyla (a taxonomic rank that groups bacterial species based on similar genetic characteristics) are:

• Firmicutes*
• Bacteroidetes*
• Proteobacteria
• Actinobacteria
• Verrucomicrobia

*Generally account for ~90% of gut microbiome community. (Rinninella et al, 2019).

Multiple factors, such as diet, genetics, environment, age, ethnicity and drug usage influence the composition of a person’s gut microbiome, physiology and overall health. This is why giving people overly specific recommendations to improve their gut microbiome (e.g., certain supplements, diets, etc) is unlikely to be effective.  Put simply, everybody’s needs are vastly different and ever-changing.

Evolution of the gut microbiome

Over the course of millions of years of evolution, we humans and the bacteria residing within our gut microbiome have generally developed a positive symbiotic relationship with other aspects of our physiology. We provide a stable environment and food supply and in return, the bacteria digest this food (e.g., fibre) to produce important products known as metabolites, which subsequently influence the physiological state of the gut and ultimately, whole-body physiology.

Changes in the human diet over the last two centuries in particular, have reduced our fibre intake, especially in more recent years where our consumption of processed and sterile foods has increased dramatically. The consequence of this dietary shift has resulted in a greater number of so-called ‘negative health outcomes’ and conditions, many of which are associated with the gut environment. Whilst the reasons for these negative health outcomes are complex and multifactorial, altered gut microbiome composition and metabolism have been cited as potential contributing factors (González Olmo et al, 2021).

The gut microbiome and human physiology

The gut microbiome can affect many cells (e.g., immune cells, GI cells), tissues (e.g., liver, lungs, brain) and physiological systems (e.g., immune, respiratory, appetite) throughout the body, mostly due to the production of metabolites.  The effects of these metabolites  can be positive (e.g., lowering inflammation) or negative (e.g., cardiovascular events) depending on the specific metabolites produced, and their concentration.

Short-chain fatty acids (SCFAs) are commonly acknowledged as “positive” metabolites that the gut microbiome produces. There is growing evidence of their ability to help reduce inflammation, improve immune system functions, affect appetite and assist in lowering the negative symptoms associated with GI conditions (e.g., Crohn’s disease). Secondary bile acids are another group of metabolites produced by the gut microbiome that have been associated with improving insulin sensitivity and lowering hyperglycaemia. Additionally, these positive metabolites play a key role in maintaining the strength of the intestinal cell wall. A weak intestinal cell wall (as a result of low positive metabolite production) can increase the risk of “leaky gut” where pathogens (e.g., disease causing bacteria) and other waste products can be transferred to circulating blood from the GI tract where they can potentially lead to a range of illnesses and conditions (e.g., type 1 diabetes mellitus).

Negative metabolite production (e.g., ammonia, Trimethylamine, etc) or the low production of positive metabolites have been associated with increasing the risk of multiple conditions, such as liver disease and chronic inflammation (Christovich & Luo, 2022; Gomaa, 2020; Koh et al, 2016).

A healthy gut microbiome

As has been stated already, defining what a healthy gut microbiome composition should be, or advising people to consume specific foods or a supplements to use will have varying effects from person to person because their needs will be very different. However, broadly speaking, a healthy gut microbiome is one that will mostly consist of bacterial species that can produce beneficial metabolites such as SCFAs and will have no presence of disease-causing bacterial species (e.g., Salmonella).

To achieve and maintain a healthy gut microbiome, it is recommended that a diverse bacterial community is promoted. Many bacterial species can produce positive metabolites (e.g., SCFAs), therefore the more species present, the more chance of positive metabolites being produced. A diverse range of bacteria within the gut can be achieved via the consumption of a balanced and well-rounded diet consisting of adequate amounts of fibre, fruit and vegetables which are the main food sources for gut bacteria. The overconsumption of processed foods, very high-protein low-carbohydrate diets, excessive alcohol, the intake of medication (e.g., antibiotics) and exposure to toxins (e.g., from smoking) have all been suggested to lower diversity of the gut microbiome and potentially increase the risk of negative health outcomes associated with the gut.

There is evidence of a relationship between performing exercise and the gut microbiome. Active people tend to have a more diverse gut microbiome and presence of “good” bacteria compared to more sedentary populations. However, it is not clear how much influence exercising itself has on the gut microbiome. Some research has shown that performing exercise can directly alter the gut microbiome composition, but it is important to remember that a combination of lifestyle choices are likely to be needed to have meaningful impacts for our health. Athletic and active people generally adopt healthier lifestyle choices such as balanced diets, reduced alcohol consumption and lower likelihood of smoking, which can all contribute to healthy gut microbiome communities. Therefore, the relationship between active people and a healthier gut microbiome may be due to having healthier lifestyle choices in the first place that reduce illnesses and diseases make performing regular exercise easier and more enjoyable. (Van Hul et al, 2024).

Probiotics and the gut microbiome

Most generally healthy people are unlikely to “need” additional strategies beyond a balanced diet, regular exercise and not smoking, including limiting exposure to other toxins, to have a healthy gut microbiome. However, for some, especially those with digestive conditions (e.g., IBS), constant environmental/geographical changes (e.g., regular international travel), those using prescription medication (e.g., antibiotics) and/or who have other health conditions/diseases (e.g., type 2 diabetes mellitus) that impact the gut microbiome negatively, additive/supplemental strategies may be required.

At this junction, it’s important to underline that promoting or endorsing supplements is not something that any nutrition coach or personal trainer should be doing. Only Registered Nutritionists and Dieticians ought to be promoting nutritional supplements like these, and this would normally be in response to a series of comprehensive and clinical test(s).

One of the most common additive strategies is the consumption of probiotics. Probiotic consumption refers to ingesting products containing ‘live’ bacterial strains that are suggested to be of benefit to our health, mostly via gut microbiome activity. Probiotics can be consumed as food or drink (e.g., Sourdough bread, yoghurt, fermented milk, etc) and are readily available from many food and nutrition retailers. Additionally, the supplement industry is flooded with probiotic powders, pills and shots, all of which are claiming to improve your gut health further increasing our access to probiotics. Read our supplement article to find out more about the lack of regulation for nutrition supplements: A Tough Pill to Swallow. 

It is beyond the scope of this article to provide any comprehensive insight into probiotics because a full article would be needed just to scrape the surface of this complex and ever-changing landscape. However, if you are considering using a probiotic, there are a few things you will definitely want to consider:

• It might not work for you.
• It might not work at all.
• It might “work” via placebo effects or other habits you adopt alongside (e.g., exercising more, healthier diet).

Side note: These points are relevant for many supplements, not just probiotics!

Not all probiotic supplements are equal

While there can be no doubt that are some reputable supplement manufacturers that  invest in rigorous scientific research to carefully select bacterial strains, determine effective doses, and develop transparent marketing campaigns, a significant number do not, so it is worth baring this in mind when considering supplements, especially probiotics! Consequently, directly applying findings from scientific studies to real-world scenarios becomes challenging.

Again, it is important to remember that supplements do not undergo the same testing and approval processes that medicines do, meaning it is easy and quick to sell products that do not really work, as long as they do not cause any significant harm. Where probiotics are concerned, the most common example of this is whether the so-called ‘live bacteria’ actually reach the large intestine (where they are meant to work) in the first place.

Each type of bacterial species needs specific conditions to survive. The journey from product development in a factory to the large intestine following consumption, involves everchanging and highly variable environments such as temperatures, acidity and contact with other substances (e.g., saliva). If bacterial species are not delivered in appropriately coated pill capsules/substances, they will likely die when reaching the stomach due to the high acidity. Consequently they do not get to the large intestine and have no effect whatsoever on the gut environment. Additionally, consuming probiotics is only the first part of the process. If the bacteria from probiotic supplements does reach the gut microbiome alive, the consumer will still need to eat the right foods (e.g., balanced diet, high fibre, fruit and vegetables) to produce the beneficial metabolites  necessary to improve gut health (Han et al, 2021; NHS, 2022).

Summary

Due to our symbiotic relationship with our gut microbiome that has been developed over millions of years of evolution, it is unsurprising that it plays such an important role in our overall health and wellbeing. However, this is a field of research where there is still a lot of  unknowns, which is why it is incredibly difficult to understand exactly how these complex  mechanisms occur. For this reason, there are many treatments and supplements readily available that are suggested to improve our gut health. For most healthy people, although they are unlikely to cause any harm, there is also a strong likelihood that they simply aren’t necessary, and/or they will be ineffective. The most effective way to promote a diverse gut microbiome community is to consume a balanced and varied diet, complete regular exercise, limiting alcohol consumption, avoiding non-essential/non-prescribed antibiotics, and limit exposure to other toxins (e.g., cigarette smoke). These are generally simple and achievable strategies that most people can employ to develop and maintain a “healthy gut microbiome.”

References

Christovich, A., & Luo, X. M. (2022). Gut Microbiota, Leaky Gut, and Autoimmune Diseases. Frontiers in Immunology, 13.

Gomaa, E. Z. (2020). Human gut microbiota/microbiome in health and diseases: a review. Antonie van Leeuwenhoek, 113(12), 2019–2040.

González Olmo, B. M., Butler, M. J., & Barrientos, R. M. (2021). Evolution of the Human Diet and Its Impact on Gut Microbiota, Immune Responses, and Brain Health. Nutrients, 13(1), 196.

Han, S., Lu, Y., Xie, J., Fei, Y., Zheng, G., Wang, Z., Liu, J., Lv, L., Ling, Z., Berglund, B., Yao, M., & Li, L. (2021). Probiotic Gastrointestinal Transit and Colonization After Oral Administration: A Long Journey. Frontiers in Cellular and Infection Microbiology, 11.

Koh, A., De Vadder, F., Kovatcheva-Datchary, P., & Bäckhed, F. (2016). From dietary fiber to host physiology: Short-chain fatty acids as key bacterial metabolites. In Cell (Vol. 165, Issue 6, pp. 1332–1345).

NHS. Probiotics. (2022).

Rinninella, E., Raoul, P., Cintoni, M., Franceschi, F., Miggiano, G. A. D., Gasbarrini, A., & Mele, M. C. (2019). What is the Healthy Gut Microbiota Composition? A Changing Ecosystem across Age, Environment, Diet, and Diseases. Microorganisms, 7(1), 14.

Van Hul, M., Cani, P. D., Petitfils, C., De Vos, W. M., Tilg, H., & El-Omar, E. M. (2024). What defines a healthy gut microbiome? Gut, 73(11), 1893–1908.