An introduction to the microbiome


60-second summary

  • The microbiota is the variety of microbes present that may be found in several places around the body such as skin gut and vagina
  • The relationship between us and many of our gut microbes is mutualistic which means that both sides benefit
  • Immune cells have pattern recognition receptors which can identify pathogen associated molecular patterns present on pathogens.
  • The term “good microbe” is subjective because the same microbe can be anti and proinflammatory in different diseases

What is the microbiota?

Your microbiota is the collection of organisms living in harmony with your own cells. Their genes, outnumbering your own 100 to 1, are called the microbiome. [1]

Gene– sequence of DNA coding for a particular protein

Microbes can be found in a variety of bodily areas such as the skin, conjunctiva (lining of inside of eyelids), gut, bladder, vagina, placenta, uterus, lung, oral cavity and biliary tract.

But what type of microbes are present?

Aside from commonly known bacteria other organisms include fungi, archaea and viruses.

Archaea-a type of single celled organism. Note each human has an average of 37.2 trillion cells!

The 4 main categories or so called phyla of bacteria in the gut are- Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria of which some are pathogenic.

Pathogenic– a microorganism with the potential to causes disease

For instance bacteria in residing in the mouth such as Actinomyces viscosus may contribute to tooth decay by secreting acid which dissolves tooth enamel. In the gut too, certain types of bacteria have been associated with disease such as an increased proportion of the Firmicutes microbe, which has been associated to the development of obesity.

Microbiome and disease?

Dysbiosis– imbalances between different communities gut microbes

Dysbiosis is a key contributing factor to not only the development of diseases affecting the gastrointestinal tract but also neurological and psychological conditions. This is a phenomenon known as co morbidity and evidence has shown that people with depression and anxiety often also have diseases such as inflammatory bowel disease (IBD) and Crohn’s disease.

Crohn’s disease– chronic condition where the lining of the gut is inflammed

In terms of anxiety, it has also been shown that mice raised in environments free of any microorganisms tend to have higher stress levels and portray cognitive deficits. Establishment of a varied gut microbiome from birth is essential and is influenced by a variety of factors including maternal genetics, stress levels and type of birth: babies born by cesarean section typically show to have more pathogenic bacteria such as Escherichia coli. With a lower proportion of beneficial bacteria, it is not frivolous to link a deficient microbiota to the fact that C section born babies are 5 times more likely to develop allergies than their vaginally born counterparts.

These microbes have a special relationship with us as their hosts- a mutualistic one. It used to be thought that the relationship was mostly commensal, meaning that one side benefits and the other neither gains or loses anything. Yet evidence points towards mutualistic friendship, with both sides benefitting. Bacteria are given a habitat and energy supply through our diet and we are provided with a variety of metabolites and chemicals such as Vitamin K, essential for health.

Distinguishing good and bad microbes

In a healthy individual it is crucial for the body to distinguish the beneficial from the harmful microbes and this is regulated by the innate immune system.[2]

Innate immune system– Mechanisms you are born with giving you non specific protection against pathogens

On these cells you may find receptors called pattern recognition receptors which can recognise cellular structures on unwanted bacteria (such as flagellin, a protein common in certain bacteria forming a tail like structure called the flagellum). These cellular structures are collectively called pathogen associated molecular patterns (PAMPs).

When the receptors detect these PAMPs they initiate a variety of responses to try and eliminate the harmful microorganism.[3] One example is the release of a molecule called Interlukin 8 which encourages the recruitment of other immune related cells to destroy the pathogen. [4] Therefore in a healthy individual only pathogenic bacteria will be targeted.

But do our ‘good’ microbes always stay good?

In a recent study in Yale university on individuals with antiphospholipid syndrome scientists found an association between an apparently ‘good’ microbe- Roseburia intestinalis, and inflammation.

Antiphospholipid syndrome- disorder where the body’s immune system destroys a type of protein essential in blood thinning without which a person is at risk of blood clotting.

Experiments in mice even showed that this microbe could trigger the disease implying that a microorganism protecting from one disease may simultaneously induce another. [5]

All in all microbes microbes play a huge role in our health; disease causing or not, they influence our metabolism, mood and longevity.

[1] The Psychobiotic revolution, Scott C. Anderson

[2] BMJ. (2018). Role of gut microbiota in nutrition and health. [online] Available at: [Accessed 5 Jul. 2019].

[3] BMJ. (2018). Human gut microbiome: hopes, threats and promises. [online] Available at: [Accessed 5 Jul. 2019].

[4] Wikipedia. (2019). Interlukin 8. [online] Available at: [Accessed 5 Jul. 2019].

[5] New scientist. (2019). A severe autoimmune condition may be triggered by ‘good’ gut bacteria. [online] Available at: [Accessed 5 Jul. 2019].

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