The gut microbiome & disease

The human gut microbiome holds over 100 trillion microorganisms, including bacteria, viruses, fungi and protozoa. Majority of these microogranisms are commensal with the intestinal tract.

Some definitions


Microogranisms - are microscopic organisms, e.g. bacteria, virus, fungus.

Microbiota - are the microorganisms of a particular environment.

Microbiome - refers to the combined genetic material of the microorganisms found in a particular environment.

Commensal - the relationship between organisms, where one benefits and the other receives no benefit, but also no harm.

The gut bacteria 


The predominant bacterial groups found in the gut microbiome include Firmicutes (gram positive) and Bacteroidetes (gram negative).

They mostly live in the large intestine.

Microbiome functions


The biomass of the gut microbiome make up anywhere from 1 to 3 kilograms. These microbes contribute to our health through a number of functions, including:

  • Biosynthesis of vitamins and essential amino acids

  • Generation of beneficial metabolic byproducts (e.g. butyrate)

  • Feeding our intestinal cell lining (epithelial cells)

  • Strengthening our gut lining (mucosal) barrier

  • Providing both local intestinal immunity and systemic (whole body) immunity

Diet & the microbiome


An acute change in diet, for example one that is strictly plant-based or animal-based, alters the composition of the gut microbiota within 24 hours of making the diet changes.

For example, it has been found that the gut microbiome in animals fed a high-sugar or high fat diet are more prone to circadian rhythm disruption (altered sleep), which in turn may have implications for inflammatory diseases.

Further to this...

Disease & the microbiome


A number of studies looking at the composition and role of the gut microbiome have uncovered associations with a number of disease states, including obesity, type 2 diabetes, arthritis, atherosclerosis, inflammatory bowel disease (IBD) and dermatitis.


People with IBD commonly have less bacterial diversity as well as lower numbers of Firmicutes and Bacteroides. This in turn may contribute to reduced amounts of butyrate, a by-product of microbiota fermentation that it believed to have anti-inflammatory effects in the gut. Furthermore, it has also been found that different bacteria may mediate intestinal inflammation and Crohn’s disease (IBD) activity. It has also been found that certain enzymes found in higher concentrations in IBD microbiomes are more frequently involved in membrane transport, contributing to unwanted materials getting into the individuals system. 

Type 2 Diabetes

It has been found in people with type 2 diabetes that their gut microbiotia have different functional characteristics, including boosted membrane transport of sugars and branched-chain amino acids, decreased bacterial chemotaxis, decreased butyrate synthesis and decreased metabolism of vitamins. Further demonstrating an association between the gut microbiome and disease states.


Obesity has been characterized by an altered ratio of Bacteroides to Firmicutes, with a greater relative abundance of Firmicutes. Furthermore, it has been shown that those with obesity may contain certain (and more) microbiota that have an increased capacity to harvest extra energy (calories) from the diet. For more on this, click here.


Atherosclerosis is a disease in which plaques (made up of fat and other substances) build up in the artery walls and over time narrow these blood vessels, restricting blood flow. This condition has also been linked to the gut microbiome through the enhanced metabolism of products that produce pro-atherogenic compounds.

Disease, the microbiome & more plants


Based on the above, we can see that the microbiome is associated with various disease states. Considering we have the opportunity to influence our microbiome through diet and lifestyle choices, it is paramount we focus on better gut health.

Eat more plants, eat more fibre and avoid unhealthy habits.