The Gut Microbiome

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The gut microbiome is the collection of microorganisms, including bacteria, viruses, fungi, and protozoa, that live in the human digestive tract. These microorganisms play an important role in maintaining overall health by aiding in digestion, synthesizing vitamins/nutrients, and interacting with the immune system.

The gut microbiome may as well be its own organ. It weighs over 1kg and contributes to more biochemical reactions than the liver. It forms a major part of our immune system, moves food through the intestines, synthesises nutrients from our food, impacts our mood and dampens inflammation. Beneficial bacteria in the gut microbiome are responsible for producing ‘postbiotics’ like butyrate and other short chain fatty acids which keep the gut wall strong, reduce inflammation and keep the gut slightly acidic to prevent infections.

Beneficial species include Bifidobacterium, Lactobacillus, Faecalibacterium prausnitzii, Akkermansia municiphila and Roseburia to name a few.

Opportunistic bacteria are those that live in the gut microbiome but can overgrow when the pH of the gut is too high. These species include Streptococcus, Enterococcus faecalis and Enterococcus faecium, Escherichia coli and Clostridium.

Small Intestine Bacterial Overgrowth refers to an over abundance of bacteria in the small bowel which can produce upper gastrointestinal symptoms like reflux, indigestion, gas or bloating. It commnly occurs with IBS and can lead to diarrhoea or constipation. Species that produce methane gas can lead to constipation, including Methanobrevibacter smithii. On the other hand, species that produce hydrogen can lead to diarrhoea such as Klebsellia pneumoniae, Desulfovibrio, Pseudomonas aeruginosa and Staphylococcus species. Yeast like Candida albicans can also overgrow in the small intestine, leading to diarrhoea or IBS symptoms.

Many conditions are now linked with changes in the composition of the gut microbiome. For example IBS, Crohn’s disease, obesity, depression, chronic fatigue are linked with certain microbial signatures. Often with these conditions there is a deficiency of beneficial bacteria and an abundance of opportunistic bacteria, or the presence of endotoxin producing bacteria combined with increased leaky gut or intestinal permeability. Many auto-immune conditions have also been linked with an increased incidence of leaky gut, which is directly related to imbalanced in the gut microbiome.

What is the gut microbiome? 

The gut microbiome is the collection of microorganisms, including bacteria, viruses, fungi, and protozoa, that live in the human digestive tract. These microorganisms play an important role in maintaining overall health by aiding in digestion, synthesizing vitamins/nutrients, and interacting with the immune system.

The term microbiota refers specifically to the collection of microorganisms that live in a particular environment, such as the gut. It is essentially the same as the microbiome, but microbiota is a more specific term that refers only to the microorganisms themselves, rather than including their genetic material and surrounding environment.

The gut microbiota plays an important role in maintaining a healthy gut, and disruptions to the gut microbiota have been linked to a wide range of health conditions, including inflammatory bowel disease, obesity, and mental health disorders. Maintaining a healthy gut microbiota can be achieved through a balanced and diverse diet, the use of probiotics and prebiotics, regular exercise and reduced stress.

How can the gut microbiome protect against or contribute to inflammation?

The answer is: leaky gut & endotoxins

Leaky gut and the gut microbiome

Leaky gut, also known as intestinal permeability, is a condition that refers to increased permeability or “leakiness” of the lining of the small intestine. Normally, the lining of the intestines acts as a barrier, controlling what substances are allowed to pass from the intestine into the bloodstream. It selectively absorbs nutrients and prevents harmful substances, bacteria, and toxins from entering the bloodstream.

In the case of leaky gut, the intestinal lining becomes compromised, and the tight junctions between the cells that make up the intestinal wall become loose, allowing larger molecules, undigested food particles, bacteria, and toxins to pass through and enter the bloodstream. This can trigger an immune response as the body recognizes these substances as foreign invaders. 

Butyrate is the antidote for leaky gut. It is one of the very important short chain fatty acids produced by beneficial bacteria in the gut. It is a natural byproduct of their fermentation of foods. Some examples of butyrate producing species include Faecalibacterium prausnitziiRoseburia species and Eubacterium rectale. Out of all the short chain fatty acids, butyrate is used as the main fuel source used by the cells that line the intestinal wall, called enterocytes. Butyrate is like oxygen to them. 

Low levels of butyrate are typically seen in chronic inflammatory bowel conditions like Crohn’s or colitis but it can also occur with Coeliac disease, cancer, chronic fatigue and individuals who have had very aggressive antibiotic therapy. The cause of low butyrate is having depleted levels of the bacteria that produce it. Those bacterial species rely on a certain diet for them to continue flourishing. This is why long term low FODMAP diets often lead to severe depletion of Faecalibacterium, and therefore butyrate. 


Endotoxins are toxic molecules that are produced by certain types of bacteria in the gut. They are known to cause leaky gut and subsequent inflammation throughout the body. Gram-negative bacteria have an outer membrane that contains a molecule called lipopolysaccharide (LPS). LPS is a component of the bacterial cell wall and is released when the bacteria die or are destroyed. 

The LPS molecule contains a lipid portion that anchors it to the bacterial outer membrane and a polysaccharide portion that projects outward. It is this polysaccharide portion that is responsible for the toxic effects of LPS.

In the gut, Gram-negative bacteria are able to survive by forming colonies in the intestinal lining or biofilms that protect them from the immune system. However, when these bacteria die or are destroyed, they release their endotoxins, which can cause damage to the body.

What is Small Intestine Bacterial Overgrowth (SIBO)?

SIBO is a commonly diagnosed gastrointestinal disorder involving the gut microbiome. It refers to an excess and imbalance of bacteria in the small intestine. Upper GIT symptoms include reflux, nausea, unexplained vomiting or indigestion that begins quickly after eating. Lower GIT symptoms, such as abdominal bloating, distention, diarrhoea and gas formation overlap with other functional disorders like IBS. In fact, many studies have shown that a significant percentage of IBS sufferers also have SIBO.

SIBO can be either hydrogen dominant (where bacterial species produce hydrogen leading to diarrhoea) or methane dominant (where methane gas is produced that slows colonic transit time = constipation). Species commonly found with SIBO include Pseudomonas aeruginosa, Escherichia coli, Staphylococcus species, Klebsiella pneumoniae, Streptococcus species, Enterococcus faecalis, and Enterococcus faecium.

Irritable Bowel Syndrome

Irritable bowel syndrome (IBS) is a common functional gastrointestinal disorder that is characterized by chronic abdominal pain, bloating, and changes in bowel habits. The exact cause of IBS is not fully understood, but it is thought to involve a complex interplay between genetic, environmental, and lifestyle factors.

One factor that may contribute to the development of IBS is dysbiosis, which refers to an imbalance in the gut microbiota. Dysbiosis can occur as a result of a variety of factors, including antibiotic use, a poor diet, stress, and other environmental factors.

Studies have shown that individuals with IBS often have alterations in their gut microbiota compared to healthy individuals, including a decrease in beneficial bacteria such as Bifidobacterium and an increase in potentially harmful bacteria such as Enterobacteriaceae. These changes in the gut microbiota have been linked to the symptoms of IBS, including abdominal pain, bloating, and altered bowel habits.

Additionally, research suggests that the gut-brain axis, which involves communication between the gut and the central nervous system, may also play a role in the development of IBS. Dysbiosis can disrupt the gut-brain axis, leading to changes in gut motility, sensitivity, and other functions that contribute to the symptoms of IBS.

Treatment of IBS may involve strategies to rebalance the gut microbiota, such as the use of probiotics, prebiotics, and dietary changes. Other strategies, such as stress reduction and the use of medications to manage symptoms, may also be effective for some individuals with IBS.

Studies have shown that individuals with IBS may have lower levels of Faecalibacterium prausnitzii in their gut microbiota compared to healthy individuals. It’s important to note that dysbiosis in IBS is not necessarily characterized by the presence or absence of specific bacterial species, but rather by an overall disruption of the balance of the gut microbiota. While some bacterial species may be more commonly associated with IBS or dysbiosis, the specific composition of the gut microbiota can vary widely between individuals and may change over time.

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