What is a microbiome?

by | Nov 13, 2023 | gut health and digestion

A human body contains trillions of cells.  Yet most of these cells are not actually human cells, but microbial.  Some estimates suggest that we may in fact be only 10% human! The remainder being mostly bacteria, yeasts and other microbes – our microbiota. In fact, even if these figures are over estimated the collective genetic material of the microbiota – otherwise known as the microbiome – certainly outnumber or own genes many times and therefore have a massive influence on our health and wellbeing.

A microbiota with larger numbers of species is believed to be healthier for the host. Most microbes inhabit the digestive tract, especially the colon. They also cover the skin surface.  Every person, has a unique combination of microbes. Even identical twins have different microbiomes.

Despite the modern obsession with cleanliness. Most of the microbes that we encounter are not harmful. Most of them are harmless, others are beneficial and some are even vital for our health.

We acquire our first microbes during birth, from our mother. If we are breast fed our mother’s milk provides a further source of microbes. The breast milk even includes food for the microbes. This encourages establishment of a healthy microbial colony in our digestive tract.

As we grow, exposure to the world around us results in the addition of new bacterial species. The gut microbiota continues to develop, until we are about two years of age. After this it can remain fairly constant throughout life unless disrupted by outside influences. After the community is established, new species have to compete with the resident microbes. If the microbiome is healthy then new species will struggle to gain a foothold. Pathogenic species may exist in healthy people but are kept in check by other species and cause no harm.

Beneficial microbial species help us in many ways. They help us to digest our food and can influence our appetites and metabolism. They also produce vitamins for us and help to regulate our immune systems. With a healthy gut microbiome we are more likely to enjoy a sharp, clear mind. Other benefits include better sleep and a sense of well being.

Things that affect our microbiome include dietary changes, our environment, and certain medications. These can all influence the numbers and diversity of the microbiome. And this can lead to an imbalance between beneficial and pathogenic bacteria.

Evidence is growing that an imbalanced microbiome may be linked to a leaky gut and chronic disease.  Associated conditions include irritable bowel syndrome, inflammatory bowel disease, type 2 diabetes and obesity.

Research also shows that we can promote a healthy microbiome. We can eat the right foods and take certain supplements where necessary. Probiotics are live beneficial bacteria that can multiply in our gut. Probiotic supplements tend to contain a small number of bacterial species, in high number. Prebiotics are the foods that nourish and encourage the proliferation of the beneficial bacteria. Prebiotics are also available as supplements.


Regular consumption of fermented foods can help to establish a diverse population of bacteria. Fermented foods include sauerkraut, kimchi, certain cheeses, kombucha tea, kefir and live yoghurt. While a diet rich in vegetables and fruits help to sustain a healthy microbiome.

Read more about this in the series of posts about optimising gut health and digestion.  Starting with Optimise your digestive health


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