Microbiome – The “Second Human Genome”

There are so many microbes that live in the human body, about 100 trillion, that they comprise 2% of the person’s total body weight.  Over 1300 different bacterial species have  been identified in the human body and form the human microbiome.  The bacterial population varies from person to person and is as unique as a fingerprint.  Diet, environment, genes and early exposure to microbes are all thought to affect the individual microbiome.  However, researchers still do not know what makes a given person’s microbiome better or worse.

Our understanding of the role of the “good” bacteria in the body is increasing rapidly with genetic sequencing and computational modelling.  These bacteria, which can be difficult to grow in the laboratory as many are sensitive to oxygen, can now be identified and are now known to have an important part in human health and diseases.

IMG_8446Most of these microbes live in the gut.  They are involved in many bodily functions from homeostasis, training the immune system to recognise friend from foe, digestion and production of essential vitamins, pathogen resistance, mental health to diseases such as obesity, diabetes, Inflammatory Bowel Disease (IBD), Irritable Bowel Syndrome (IBS) and allergies.  The human microbiome is dynamic over a person’s lifetime, altering both in numbers and species diversity.  It also varies with geographical location, for example the microbiome of children in Malawi and Venezuela contains more riboflavin-producing microbes than that of North Americans.

The microbiome greatly increases the human genome of about 23,000 genes, to around 3 million.  This has an important nutritional role.  Carbohydrates that cannot be broken down by the human digestive system are dealt with by the microbiome, for example gut bacteria produce an enzyme that is better at extracting nutrition from the mother’s milk.

The variability of the human microbiome may be useful in treating conditions where antibiotics are failing.  Treatments that get rid of disease or improve health by changing the microbiome from one that is unbalanced to one that is effective against pathogens could be valuable.  Antibiotic-resistant infections are estimated to cause 700,000 deaths each year worldwide and it’s estimated will rise to 10 million by 2050.  As antibiotics kill all the bacteria in the gut, both the pathogens and the naturally occurring bacteria, they can leave patients more vulnerable to bacteria that are resistant to the antibiotic.  These bacteria will repopulate the gut faster leading to further health problems.  One such bacterium is Clostridium difficile which causes abdominal pain, diarrhoea, dehydration and fever, and kills over 29,000 people each year in US.  The bacterial imbalance can be readjusted by adding a sample of gut bacteria from a healthy individual to the sick person.

In cancer patients doctors are realising that preserving a sample of the patient’s microbiome before harsh treatments such as radiotherapy and chemotherapy can enhance recovery time.  Once the cancer treatments are finished, the patient can receive an inoculum of their own stored microbiome to reestablish the equilibrium of bacteria in their gut.

The study of the human microbiome is still in its infancy and further research with larger groups of individuals is needed.  This should begin to reveal how patterns in the composition of the microbiome is associated with health.  Already we are seeing that a more diverse microbiome seems to be related to better health and this can be directly controlled by our diet.


Schmidt C.  2015.  Mental health may depend on creature in the gut.  Scientific American


Browne HP et al.  2016.  Culturing of “unculturable” human microbiota reveals novel taxa and extensive sporulation.  Nature 533, 543-546.

The Review on Antimicrobial Resistance. 2016. http://amr-review.org (accessed 2 June 2016)

Me, myself, us. The Economist

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