What is the microbiome

The human microbiome is the community of bacteria (microbes) that lives in and on our bodies – on our skin and in our mouths, respiratory tract, gastrointestinal tract and genito-urinary tract.

These bacteria express genes and mean that as humans, we are made up of both human and microbial cells, which define the structure and function of our body. It is so important in fact, that without our microbiome, it is likely that we would not survive beyond five years of age.

The gut microbiome

As part of the overall human microbiome, each of us has around 100,000 billion viable bacteria living in our intestines, comprising over 1,000 different species and more than 5,000 strains. These microbes weigh around 1.5 kg in total and are referred to collectively as the gut microbiome.

95% of the gut microbiome is in the large intestine, with only around 50g (weight) of the microbiome residing in the small intestine.
The gut microbiome is also referred to as the gut bacteria, gut microbes, gut microorganisms, gut microbiota, gut microflora, gut flora and the intestinal bacteria.
Although we all have similar bacteria, everybody has their own individual microbiome, influenced by diet, environment, genetics and early exposure to microbes.

And, just as not all bacteria are bad, our gut bacteria are not all good either. We all carry strains of bacteria that might be considered to be ‘bad’, but balance between the good and the bad microbes is the key to a healthy microbiome. A healthy diet and lifestyle are both key to supporting this balance, as medications (particularly antibiotics), alcohol, sugar and other unhealthy choices will all have an effect and potentially enable the over-growth of the unfriendly microbes.

When does the gut microbiome become established?

The microbiome is established immediately when we are born – at birth, the baby acquires his or her first microbial bacteria from the environment it is born into. For babies born vaginally, the first colonisation is from their mother’s vaginal, skin and rectal bacteria. For those born via caesarean section, these bacteria come from skin and the hospital environment.

A few hours following birth, a mucosal layer starts to form on the baby’s GI tract to act as a barrier to prevent pathogens from crossing into the gut. This mucosal layer is where the beneficial bacteria colonise, helping to reinforce the barrier and support immunity.
The development of the baby’s microbiome is then influenced by diet. Breast milk contains the mother’s bacteria and prebiotic oligosaccharides, which are the fibres that feed the bacteria and help them to colonise as part of the baby’s microbiome.

If the baby is formula fed, he or she will not receive the ‘mammary microbiota’, although many formula milks now contain prebiotic fibre, which helps to feed the existing bacteria in the baby’s microbiome.
When the baby is weaned onto solid foods, the microbiome development will continue based upon the foods that are introduced. Fruits and vegetables help provide prebiotics, which feed the good bacteria and help them to grown, and plain yoghurt and fermented foods contain probiotic bacteria, which can support the development of the microbiome in these early years.

Microbiome life stages

Being in the womb is part of the microbiome life stage journey

In utero (womb)

Maternal microbiota

Becoming a newborn is part of the microbiome life stage journey


Maternal transmission
Vaginal delivery
Caesarean section delivery
Pre-term delivery

Becoming an infant is part of the microbiome life stage journey


Breast feeding
Geographical location
Family environment
Milk consumption
Solid food introduction

Becoming a toddler or child is part of the microbiome life stage journey


Full adult diet
Microbiome formed

Becoming an adult is part of the microbiome life stage journey


Full adult diet

Microbiome life stage

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What does the gut microbiome do?

The gut microbiome is made up of specific kinds of micro-organisms that complement each other and their host (person), fulfilling various functions that depend on the species of bacteria. Some bacteria synthesise (produce) vitamins and neurotransmitters, others support digestion and/or absorption of nutrients and some support the immune system.

The bacteria also help to support the function of the mucous membrane (mucosa) that covers the inside surface (wall) of our intestines. The microbes form part of this mucosa as they move through the body and help form a protective barrier to defend against toxins and bad bacteria.

As a result of the many different functions of the gut bacteria, an imbalance of unhealthy and healthy microbes in the intestines has also now been shown to affect health in general.

Can the bacteria in the gut microbiome change over time?

The intestinal microbiome acquires adult characteristics and is fully formed by three years of age. This process is driven by genetic factors and the intake of major food groups by this age. Breast feeding and a diet full of vegetables and fibre will help with the development of a healthy microbiome, whilst an excessive intake of sugar in these early years will potentially lead to the growth of a less diverse microbiome.

Whilst the basic structure of our microbiome is established by three years of age, the specific composition will change almost daily throughout our lives. Bacteria forms around half of the faecal mass (poop) we excrete every day and replenishing this bacteria with friendly species depends upon what we eat and drink and any medications and supplements we take on a daily basis.

Like the rest of our body, our gut bacteria is designed to reset back to its ‘normal’ structure following any challenges, such as illness or medications, but vegetables and a healthy diet are required to enable this to happen.

Before refrigeration was invented, we ate lots of fermented and cultured foods (such as sauerkraut and pickled vegetables), which gave us an ongoing supply of friendly bacteria and help to maintain balance in the microbiome. Today’s diet lacks these foods and, whilst they are once again becoming more popular, good bacteria supplements have been developed to help provide additional bacteria to enhance our modern diets.

Microbiome fascinating facts

The gut microbiome

Each of us has around 100,000 billion live bacteria living in our intestines.

Probiotics & Antibiotics

Research has shown that taking friendly bacteria (probiotics) alongside antibiotics can help to maintain a healthy balance of the bacteria in the gut.

Should I take probiotics with food?

If live bacteria supplements are not taken alongside food, 90-95% of the bacteria will die in the stomach acid.

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