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The microbiome: What does it mean?

The definition of ‘microbiome’ is a community of microorganisms. This includes bacteria, fungi, yeasts and archaea, that inhabit a particular environment.

The gut microbiome has received lots of attention in recent years as scientists discover more and more ways in which it benefits various aspects of human health. The microorganisms in our gut support digestion, provide the body with nutrients and vitamins, ensure that our immune system remains intact and strive to achieve a healthy balance within the body overall.

In addition to the gut microbiome, there are several vast communities of microorganisms inhabiting other areas of the human body, such as the sinus cavities, skin and urogenital tract. These different microbiomes differ greatly from each other and the microorganisms present are different in each.


More often than not, when people talk about ‘the microbiome’, they are referring to the gut microbiome, as this huge population of microbes is the most researched, and arguably has the most profound influence over our health. Tens of trillions of microbes make up the gut microbiome, including over a thousand different species of bacteria. The weight of this vast living colony is as much as 2kg, making it one of the heaviest ‘organs’ in the body.

Scientists state that bacterial DNA rivals the amount of human DNA in our bodies, but whereas the DNA making up the human ‘genome’ is fixed from birth, this ‘second genome’ (made up from bacterial DNA) is open to external influence and change; i.e. the bacteria in our bodies can be affected by a number of factors. It is hoped that in the future we will be able to manipulate this DNA in order to control or even prevent chronic diseases.

The role of the microbiome

It is thought that the reason the human body tolerates such a huge amount of microorganisms making us their ‘home’ is that these microbes, in return, perform many different beneficial functions for us. The list of known functions is long and growing all the time as more and more research is carried out in to the microbiome. Here are just a few of them:

  • Digestion: beneficial strains of bacteria living in the intestines produce different enzymes (a type of protein) that help us to digest and break down our food.
  • Energy levels: certain strains of bacteria are capable of making B-vitamins, which are known to help with our energy.
  • Immunity: 70% of our immune system is located in the gut, allowing for direct interaction between the microbiota and our immune cells. Healthcare practitioners can read more about the gut and immunity here.
  • Skin health: friendly bacteria produce beneficial substances in the body, as opposed to the toxins produced by pathogenic (bad) bacteria which can contribute to poor skin. Therefore, an unhealthy gut can be reflected in our face.

Dysbiosis: When things go wrong

It is said that ‘health begins in the gut’. It is certainly true that when we look after the ‘friendly’ bacteria living in our intestines, we reap many rewards, including improved digestion. However, many different lifestyle factors have been shown to have a negative impact on our guts. This means maintaining a healthy balance of microbes in the gut can be a bit of a challenge at times.
The name given to an imbalance of gut bacteria is dysbiosis, and the following are all factors that can contribute to this:

  • Taking antibiotics
  • A high-sugar diet
  • Processed foods
  • A low-fibre diet
  • Stress
  • Ageing
  • Certain medications, including the contraceptive pill, NSAIDs and HRT

    Certain lifestyle factors can lead to a decrease in friendly bacteria, causing dysbiosis

Correcting dysbiosis

Given that the microbes living in our gut are fragile and susceptible to damage, it is important that we know how to actively encourage their growth and proliferation, as well as simply preventing their losses. In addition to avoiding the factors listed above where possible, it is also a good idea to consume a number of different sources of prebiotic fibre.

Prebiotics are the preferred ‘food source’ for our probiotic colonies, allowing them to flourish, and are found in many different fruits and vegetables, including: bananas, artichokes, onions and garlic.

The future of the microbiome

Much research is being done into the microbiome that will hopefully enable scientists to know exactly how to manipulate the microbes in the gut to elicit positive changes in our health. Centres of excellence that are leading the way in to this research include Reading University, Cork University and Stanford University.

Our gut microflora has been shown to impact on many areas of our health, and links have been made between dysbiosis in the gut and numerous different diseases and health symptoms. These health conditions might be fairly obvious in some cases, such as IBS and colic in infants, or in other cases, their links to gut health may be much less obvious, as in the case of mental health disorders, allergies or even neurological disorders.

It appears that the gut microbiome impacts not only our physical health, but also our emotional health and our mood. This discovery has led to the emergence of the term: ‘The gut-brain axis’, which describes the two-way relationship between gut health and our mood and emotions.

The Microbiome Project

In 2008 eminent scientists from four different medical centres in the U.S established the Human Microbiome Project, which set out to ‘further our understanding of how the microbiome impacts human health and disease’. The ultimate goal of this project is to establish whether there is a core healthy microbiome seen in the guts of well individuals. It is already known that the exact composition of the intestinal microbiome differs hugely between individuals, and that our gut microbiome is said to be as unique to us as our fingerprint.

However, scientists now believe that one third of the total number of species of bacteria may be common to most people, opening up the possibility for ‘mapping’ this percentage of the microbial population, and looking for anomalies present in different diseases and health conditions.
So, it's clear to see that our microbiome plays an enormous role in overall health, so we hope this article has helped you to understand this fascinating system a little bit better.

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