Our amazing gut microbiome – what is it and what happens when it goes awry?

Courtesy of MetaHit website
Courtesy of MetaHit website

Our microbiome is the name for the microbes that live on our body and some people think that the microbiome is our forgotten organ. Over the last few years our knowledge of what our microbiome is has increased through the Human Microbiome Project (USA) and the Metagenomics of the Human Intestinal Tract (metaHIT) project (Europe) specifically researching the digestive system microflora. Research has also been instigated to look at the way these microbes interact with our immune system and the implications that alterations to our microbiome has our health and well-being. This also has implications of how you think of yourself – do you consider at all that you are a home for microbes that do provide tangible benefits, some of which are still possibly to be discovered? We live in a synergistic way with our microbiota so both them & us gain benefit from this relationship, so it is worthwhile considering this aspect of ourselves when we choose our lifestyle and diet.

The microbes that live with us have over 400-1000 species depending on which research is viewed. As this blog is all about the digestive system we will focus on this area – we have approximately 100 trillion microbes in our large bowel, that number is very difficult to comprehend, but it is 10 times the number of cells we have in our bodies. For an average man of 70 Kg, 2kg (or 3 percent) of his body weight will be due to his microbiota. Throughout the digestive tract the numbers are as follows, in our mouth anywhere between 20 – 100 billion this is a difficult area to measure the population level, because it does tend to vary with levels of mouth hygiene. Our stomach has a much reduced level of 10-1000 per ml, this is as a result of the acid produced by the stomach, it is a more difficult environment, some microbes have developed complex strategies to make the stomach a home, H Pylori is one such bacteria and this is a pathogenic bacteria causing ulcers. Our small intestine is a more favourable environment, due to its neutral pH, but again numbers are small 10,000 – 10 million. The large bowel is where all the action takes place, 70% of the bodies microbes are found within the large bowel.

Our gut microbes provide us with vitamins examples such as vitamin K, B vitamins biotin & folate, through the bacterial fermentation of the fibre sources in our diet. This process also produces substances such as short chain fatty acids (SCFA) such as butyrate, the cells lining the digestive tract use SCFA as an energy source and butyrate is a beneficial SCFA, which has been implicated in helping to have a good gut barrier function and also protective against colon cancer for example. Chemicals produced by our commensal gut bacteria act to kill off pathogenic bacteria and our ‘good’ bacteria compete for nutrition, through competitive exclusion, so there is definitely benefits to having safety in numbers of our ‘good’ bacteria. Our microbes have a role to play in our developing immune system and the barrier function of the digestive tract.


A new born baby is exposed to the microbiome of it’s mother during birth and it has been found that vaginal birth compared with c-section changes the types of digestive system microbes – c-section babies have higher numbers of the microbes that are found on the skin. Exclusive breast feeding also populates the digestive system, it is known that breast feeding protects the infant, lowering the risk of diarrhoea & vomiting, constipation, developing obesity, type 2 diabetes, allergy and atopy. It is not always possible for women to breast feed but as a society we should be promoting breastfeeding and making it easier for women who can, to be able to do so. The microbiome then changes around the time of weaning to the first three years of life so what we eat also changes the population too. Infancy is also an important time for the developing immune system and also new exposures to our environment and this has lead to the ‘old friends’ theory.

The ‘old friends’ theory has overtaken the hygiene hypothesis as a concept for the changes in our microbiome in early years and the implications this has for our future risk of disease development. It hypothesizes that regular exposures to human, environmental and animal microbiota during the development of the immune system is essential, as these microbes interact and regulate the immune system, keeping it in balance. In recent years changes to our lifestyles and exposures to our environment have inadvertently reduced our exposure to our microbial ‘friends’. Lack of exposure to the right kinds, doses and diversity of microbes is implicated in affecting long term health – it is known that children who live on farms have a lower level of allergic disease for example, but more research is needed.

Schematic representation of theories behind IBD development (2)

Changes to the microbiota have been implicated in obesity, malnutrition, cardiovascular disease, diabetes and the digestive conditions such as irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD). For Crohn’s and colitis it is hypothesized that it is a genetic variability in the innate immune response that predisposes the risk of developing these diseases. For IBS it is known that a lower number of lactobacillus and bifidobacteria and generally a reduction in number of species of the microbiome is present. Previous acute gastrointestinal inflammation has been established as a major risk factor for the development of post-infectious IBS (IBS-PI) and a significant body of evidence has emerged in support of microscopic inflammation as a primary factor in the pathophysiology of IBS without necessarily a clinical history of infection. Therefore is an altered gut microbiome a subgroup of patients with IBS? However we also know that people do change their diet in an effort to ameliorate symptoms – so is it changes to gut function in IBS or changes in the diet resulting in microbiota changes in the large bowel? There is still some uncertainty needing further research with this complex area. More also needs to be researched with respect of our dietary choices and how this changes our commensal populations. With particular respect to alterations in macro-nutrient components in our diet and the possible implications that malnutrition and obesity states have an associated alteration in the microbiome and what effect this has on health & disease.

What is certain however is much more is likely to be discovered about our interactions with our microbiota and how those interactions protect us from long term medical conditions, plus this information may lead to new treatment possibilities for the diseases implicated in an altered microbiome. It is a really exciting time for the understanding of the microbiota and I for one will keep looking at the published studies to see what new developments arise in this fascinating area – will you join me?

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I am a state registered dietitian. My speciality is dietary treatment of gut disorders such as irritable bowel syndrome, crohns disease, ulcerative colitis, coeliac disease, lactose & fructose malabsorption and multiple food intolerances. I have had lots of experience in other areas of dietetics and I wished to start this blog to spread the word about evidence based dietary treatments and dispel much of the quackery that is common with these diseases. All information on this site is of a general nature and is based on UK based treatments and guidelines. Please see your healthcare practitioner should you need more country specific information.

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