Microbiome describes the constitution of microorganisms in an environment, specifically in this discussion we are referring to the gut microbiome, constituting the stomach, small and large intestine. Bacteria and small amounts of fungal species may exist, yet viruses are not natural inhabitants of the gut except in circumstances of gastroenteritis and viral illness.

Minimal bacteria thrive in the high acidity environment of the stomach and proximal end of the small intestine, but gut flora thrive at the distal end of the small intestine, throughout the large intestine and particularly in the colonic area. The only bacteria that thrive in high acidity environments include helicobacter pylori, the bacterium known to be responsible for stomach ulcers and other gastrointestinal inflammation. 500 to 1000 species of bacteria exist in the human microbiome at any one time. Previous research until now has been conscription and sequencing, and taxonomy of the species. Now we can investigate mechanistic involvement in health and disease.

The microbiome provide useful processes such as the production of vitamins, fat storing hormones, buffer ions and undigested compounds, allow for fermentation of certain food groups and also to prevent the overgrowth of harmful strains. It is much more prudent to view the microbiome as a form of organ and endocrine organ due to its massive role in nervous system, endocrine and immune responses

It is thought that the microbiome develops as early as in the intrauterine environment, with the passage through the birth canal as a baby leading to intake through the skin of bacteria and yeasts. It is controversial whether bacteria are present in the foetus or whether they are sterile, and due to ethical reasons, this has only been studied in rodents. Once in the world, human touch, breastmilk and food allow the intake of more species which eventually inhabit the gut of the infant. Breast-fed infants have more Bifidobacterium which are more beneficial than the enterobacterium found in formula. It appears the prebiotic nature of natural breast milk nourishes and provides factors for growth of already present bacteria.

Children by the age of 5 may have had many cases of gastroenteritis due to a reduced capacity for immunity, meaning a large variation occurs in the constituency of the microbiome over the years. In adults, our diet, stress, sleep schedule, weather, environment, genetics, mood, sex life and even preference for certain foods influence our microbiome, which is receptive to change in as little as days to weeks. The use of antibiotics frivolously in the past has more recently been disregarded and reconsidered due to the damage it causes to gut flora, killing all bacteria indiscriminately, ensuring even your beneficial species are eradicated. This can lead to possession of the environment by negative strains which can cause health outcomes which are most undesirable. Even a simple caesarean section reduces the transmission of bacteria from mother to baby and increases the risk for type 1 diabetes, metabolic diseases and even depression. There may be a role in vaginal birth providing vectors for health bacteria to thrive in the infant which are otherwise vacant with birth interventions.

Overgrowth of the small intestinal bacteria due to changes in stomach acidity can promote gastrointestinal conditions with bloating, diarrhoea and fatigue, but these are just the tip of the iceberg for microbiome disruption. Cancer, diabetes, depression and other major health disorders are thought to stem partly due to reductions in microbial diversity in the flora, as well as the propensity for individuals to respond to treatment. Microbial agents have a large role to play in the acquisition in autoimmune diseases due to the proximal nature of the intestinal folds with vessels and lymphatic nodules, ensuring that interplay between microbiota and immune systems cause systemic changes. It is thought that the presence of certain species of bacteria promote changes in cell signalling and cytokine release, causing chains of expression in genetics and transcription within other bodily cells causing a cascade of change. This can lead to over-expression of a gene which can disrupt the synthesis of proteins, leading to cancer. Even a lack of exposure to certain bacterial strains can influence the digestion of and production of short chain fatty acids which can cause immune changes and influence the development of breathing conditions like asthma. We should not view our stomach and intestines as distant and only for food – this in the next 50 years will be fundamental area where most scientific advancements will be centred through. 

Even on our page Nutritionally Fit we have a vast array of opinions and diets people follow, often with animosity to those who follow something different. But if one sequenced our microbiota from a stool sample, they would be completely different. This may explain why some people can get great results on a high carbohydrate diet, whereas others thrive on ketogenic style diets – there is an insurmountable role that the microbiome plays in the digestion of material and even the storage of fat, and we must express diligence in blanketing our recommendations to others.

This area is still very much unravelling, but it has been known for years that the GI tract is its own entity, innervated to the central nervous system through the vagal nerve, known as the ‘enteric nervous system’. This two-way interaction allows the brain to relay signals to the gut, but also provides feedback in the opposite direction, meaning the gut can very much affect the brain. Although anecdotal, the actual sense of ‘gut feelings’ in life and situation where you can somatically judge whether a decision is good or bad, or feeling about a person actually ring in to be true. 

What’s more, the enteric nervous system is lined with serotonin receptors which is a molecule responsible for happiness, feelings of pleasure, satiety and motivation. In individuals with conditions like IBS, sometimes a down regulation of serotonin affects the movement of the gut and causes dysfunction, which is relayed to the brain and may cause feelings of anxiety. Even if you don’t have this condition, you may relate to feelings before races or big events where your bathroom habits change – this is your anxiety and nerves directly affecting the normal peristalsis in your gut.

It is thought that the gut flora affects mood and behaviour significantly, but as yet the research is still being conductive to understand how and why, yet promising rodent studies have found difference in mood behaviour between microbially sterile and bacterial supplemented models. These murine studies have been upscaled to involve healthy human volunteers, who once supplemented with certain probiotics, have changes in lobe specificity and operation when seen under technology like an MRI. The gut-brain axis involves a two-way communication feedback loop, suggesting an enormous interaction of the gastrointestinal tract with the rest of the body. This is a area that is going to be hot for some time.

The microbiome is under specific investigation with more impetus placed into human studies with athletic performance. It appears significant exercise from rest may promote low level inflammation in the hours following exercise, yet on a regular basis can influence the composition of the gut microbiome through expression of mediating compounds which reduce inflammation. Exercise modulates the immune response in many chronic diseases by reducing systemic inflammation and downregulates the inflammatory cell signallers called cytokines. In one study, elite rugby players had higher faecal strains of metabolome associated strains which indicate higher muscle turnover and cardiorespiratory fitness, including a compelling link between aerobic fitness and the microbiome make up. 

It is as yet unknown the extent to which diet affects the microbiome constitution purely in athletes, and randomised controlled trials may need to be issued. Is it the exercise which changes the microbiome, or is their microbiome more health because of their typical athlete diet? Would be interesting to look at different diets in the athletes (fat adapted, high carb) and look at variations. Your body generally selects for the most beneficial strains of bacteria to support its homeostasis, except in periods and states of disrepair. 

As aforementioned, strenuous prolonged exercise like ironman and century rides increase intestinal permeability (the amount of water which can travel into large intestine). Likewise, blood is redistributed away from the gastrointestinal tract for respiration, and thus the gut is left in a relatively ischaemic state, compromising the function and increasing the concentration of inflammatory cytokines in the area. This often leads to diarrhoea, stomach pain and dehydration in individuals who do not recover properly or who are not habituated to the level of exercise. However, this is less of a concern for those who have exercised for a long time, as adaptation has occurred, and exercise will promote a decrease in inflammation. 

In another study, differences in composition of intestinal microbiome in athletes was responsible for 20% of the variation of VO2 max. In other words, those who had the highest VO2 max had an increased diversity of certain species of bacteria. This was after dietary differences and genetic components were excluded, suggesting that the action of exercise in promoting greater autonomic control through the vagal nerve at rest has positive effects on the gut function. More beneficial bacteria however are associated with protein intake, which is often elevated in athletes with recovery ambition. Thus, no conclusive evidence has been published, yet there seems to be a missing link in the ability to deduce conclusions. Was it exercise that caused a beneficial microbiome composition, or do athletes simply eat better with more antioxidant foods and probiotic supplements? 

Take in foods high in bacterial diversity – vegetables, but also probiotic supplements like kefir are great. Kombucha is another popular one. Even getting regular sleep, staying relaxed through meditation and maybe even exercising less can have a great impact on your microbiome constitution. IF you have stomach cramps and GI distress after hard races, it may be worth supplementing with probiotic supplements to see whether this reduces symptoms, yet it may take longer to ameliorate conditions like disease. Going forward,using initiatives like Fitness Genes, individuals will be able to understand more about their disease risk and athletic performance. The future will involve personalised individual healthcare, and supplementation of strains of microbiota to support health outcomes and physical performance. Screening the microbiome composition can be used to alter the diversity in individuals with disease to see whether this affects their health outcomes. 

Spokes Nutritionist Jess’s Top Tips For Mastering Your Gut Microbiome:


POLYPHENOLS act as a prebiotic-type substance, meaning that they increase the amount of healthy bacteria in the gut, such as Lactobacillus and Bifidobacteria strains - all berries, teas - green tea, (Resveratrol grapes and red wine - in small amounts ;)), cocoa, apples, pomegranate.. 

PROBIOTICS, feed good bacteria - bananas, apples, Blueberries, apple cider vinegar, onions and garlic, Jerusalem artichokes, broccoli...

- Kefir. Can be dairy or simply water kefir. Available to buy in supermarkets and brands such as Yeo Valley sell kefir now. You can buy starters called SCOBYs (Symbiotic Culture Of Bacteria and Yeasts) from health shops if you want to make it yourself.
- Kombucha. This fizzy, often flavoured drink is also likely to be in most large supermarkets. Equinox or Rude Health are nice brands.
- Kimchi (Koreans national dish) made from salad and fermented veg - sold in Wagamamas if you want to try initially!
- Sauerkraut - fermented cabbage basically. Ideally make at home to ensure lots of lovely bacteria are present 

I haven’t added yogurt to the list above as most yogurt is pasteurised. This means the bacteria is killed off (good and bad), so unless it states ‘unpasteurised’ its not going to have much probiotic goodness. 


Sugar and processed foods encourage bad bacteria growth, especially candida (fungi) in the case of sugar. 

Unnecessary antibiotics (ideal to look into root cause of immune problems, and consider using probiotics after a course of antibiotics to repopulate the gut) 

Other medications, proton pump inhibitors and antacids also disrupt the micro biome balance

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