You’ve probably all heard of the the gut microbiome (the collection of microorganisms living in the digestive tract) and you may be aware of the effects that it can have on the health of your digestive system. But are you aware of how it can influence the health of many other bodily systems?

In a 70 kg human, there are approximately 38 trillion bacteria within our gut – that’s 38,000,000,000,000 (38 with twelve zeros after it) (1). This means that there are more bacterial cells in the body than human cells. It’s starting to come to light that these bacteria not only play a vital role in the maintenance of a healthy digestive tract, but that dysbiosis (an imbalance or maladaptation of the bacteria) can cause a vast array of other health conditions.

Let’s start by looking how they influence the health of the digestive tract.


What makes up the gut microbiome?

The microorganisms that make up the microbiome include bacteria, viruses, fungi and, sorry to say it, parasites. Most of these organisms inhabit the large intestine, with a much smaller amount making their home in the small intestine. A normal gut microbiome is hard to define, as it varies from population to population around the world. The microbiome of indigenous hunter-gatherer populations share bacterial families with other traditional societies, that are all but missing from the microbiomes of industrialised populations. There are observed seasonal shifts in bacterial species and diversity (2). The microbiome also varies with sex and age. What we do know however is that a greater diversity in the microbiome is linked to better health. Lower diversity is considered a marker of dysbiosis and has been found in obesity, autoimmune diseases and cardiometabolic conditions.

However, there is a common “core” of bacteria which inhabit most people’s digestive system. Bacteroides and Firmicutes make up approximately 90% of the categories present in the distal gut (4). Bacteria can be:

    • Commensal – those that normally live in the gut
    • Pathogenic – those that cause disease, such as Salmonella.
    • Opportunistic – those usually present at low levels, but multiply to potentially cause problems when beneficial bacteria levels are low

Viruses can live in harmony with the bacteria of the gut (5) or cause infection (such as norovirus, the “winter vomiting bug”). Fungi are usually present in small amounts within the digestive tract, but can proliferate to cause problems with antibiotic use or if people consume a high amount of carbohydrates. 


Human Digestive System Anatomy


Functions of the gut microbiome – within the gut

A healthy gut microbiome plays important roles in producing important fatty acids, vitamin synthesis, gastrointestinal motility and maintaining the barrier function of the gut. 

Short chain fatty acids (SFCAs)

These are produced by gut bacteria and control the pH of the bowel. An optimal pH controls the growth of pathogenic organisms and helps with the absorption of nutrients. Other roles of SFCAs include:

    • Maintaining the barrier function of the tight junctions.
    • Participation in lipid and glucose metabolism in the liver.
    • Production of gut hormones.
    • Appetite control.
    • Controlling inflammation.
    • Protection against the formation of colorectal cancer (6).

Vitamin Synthesis

A healthy gut microbiome plays a role in Vitamin K2, folate and thiamine synthesis. Vitamin K2 is important in maintaining cardiovascular health, skin appearance and strengthening bones. Folate is important for DNA synthesis and cell division, while thiamine helps carbohydrate  metabolism, muscle contractions and the conduction of nerve signals.

Gastrointestinal motility

This is a two way relationship here, with a disrupted microbiome having an effect on motility and motility issues having an effect on the microbiome. Dysmotility predisposes to an increase in colonic bacteria in the small intestine and the development of SIBO (Small Intestinal Bacterial Overgrowth) as a complication.

Barrier function of the gut

The microbes of the gut help maintain a healthy intestinal lining and help maintain the barrier function of the gut. This is by targeting and changing the expression and distribution of tight junction proteins (7). Tight junctions regulate the intestinal barrier function, keeping out the things that shouldn’t normally be absorbed. When the barrier system malfunctions and permeability becomes inappropriate, this is called leaky gut , or intestinal permeability.


A person making a heart shape with their hands, held over their abdomen.

Functions of the gut microbiome – outside the gut

Research has steadily been emerging that the gut microbiome has an effect on many organ systems and tissues elsewhere in the body.

The Brain

The gut-brain axis is no longer the realm of alternative health practitioners. Mainstream medicine is starting to recognise the very real associations between gut microbiome disruptions and neurological or psychiatric disorders. These include:

    • Autism (8, 9, 10, 11, 12)
    • Parkinson’s disease (13)
    • Alzheimer’s disease (14)
    • Anxiety and depression (15)

Importantly for the future, the gut microbiota may be a modifiable factor modulating the development or pathogenesis of neuropsychiatric conditions (16). Future research is expected to assess whether modulation of the gut microbiota and its functions has any effect in improving mental health.

The Cardiovascular System

Heart disease is still one of the leading causes of death worldwide and is the leading cause of death of males in the UK. There is emerging evidence that the gut microbiome may play a significant role in atherosclerosis, coronary artery disease and myocardial infarction (17). Structural component of microbiota such as lipopolysaccharides (LPS) and pro-inflammatory peptidoglycans can trigger numerous downstream signalling processes within blood vessels, particularly when gut wall barrier function is impaired. 

Gut microbiota can also have an impact via bioactive metabolites that can affect distal organs directly or indirectly, through a number of pathways, including the trimethylamine N-oxide (TMAO) pathway and the short chain fatty acid (SFCA) pathway. Trimethylamine production from gut microbes and subsequent modification to TMAO has emerged as a strong microbiome-mediated risk factor for cardiovascular disease. TMAO is associated with enhanced atherosclerosis and thrombosis in vitro and in vivo. SCFAs can play an important role in regulating metabolic health and reducing cardiovascular disease risk.

Atherosclerotic plaques contain bacterial DNA, and the bacterial taxa observed in these plaques were also present in the gut of the same individuals.


Various factors are involved in the development of Type 1 Diabetes, including diet, genome, and gut microbiota. Some have reported reduced microbial diversity in children with islet autoimmunity before progression to diabetes, compared with healthy controls (18). The gut microbiome has also been implicated in the development in Type 2 Diabetes (19), with a reduction in butyrate producing species in people with Type 2 Diabetes. 


An elevation in the ratio of Firmicutes to Bacteroidetes has been linked with a greater risk of being obese or overweight (20). Dysbiosis can lead to obesity by increasing the amount of calories that are absorbed from a person’s food intake. Other mechanisms dysbiosis promotes obesity are by the development of leaky gut which can cause systemic inflammation, by increasing appetite and by impairing mechanisms of satiety or fullness after eating. (21)

Thyroid disorders

Changes in the gut microbiome have been associated with hyperthyroidism (22). The mechanism through which this can occur is by the sustained release of LPS into the bloodstream. LPS has been demonstrated to inhibit the enzyme iodothyronine deiodinase, which converts thyroxine (T4) into the more active thyroid hormone triiodothyronine (T3). LPS has also been shown to reduce the expression of thyroid hormone receptors, which have effects on all cells in the body.


As you can see from this article, a healthy gut microbiome is not just essential for a healthy digestive system, but also a crucial component for good overall health too. Hippocrates was on the right track by saying “all disease begins in the gut”. Diet, managing your stress and exercise all play vital roles in maintaining a healthy gut microbiome. Evidence is starting to emerge of the effects that the gut microbiome composition has on organs systems distant to the gut and the list is growing all the time. It will be interesting to see how future research addresses modulation of the gut microbiome and how this impacts the development of diseases, that are becoming increasingly common in the industrialised world.

If you would like to know more about your own microbiome, get tested for dysbiosis, or improve your overall gut health, you can make an appointment to see me by clicking here.



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