By Dr Duane Mellor RD PhD

Microbiome – What Does it Mean?

Microbiome literally means a small naturally occurring community of flora and fauna, so it is the bacteria, yeast and other microscopic lifeforms which live in an environment. When we talk about microbiome relating to human health, often we refer to the gut microbiome which is the bacteria and other microorganisms that live inside our digestive tract. Most of this lives in our colon, and if the balance of these organisms can influence our health in a positive way. However, it is not only the colon where bacteria can live in our digestive tract, sometime some bacteria can live and make home in the harsh environment of our acidic stomach. Often this can lead to an increased risk of stomach ulcers, more recently these highly specialised bacteria, Helicobacter pylori can colonise their stomach without any ill effects.

Elsewhere in our bodies we have different microbiomes on our skin and in the vagina, but it might be more surprising to know that we also have a microbiome living on the surface of our eye and in our lungs. The type of numbers of bacteria varies between these different parts of our body, but why are they there?

Well, all these parts of our bodies represent surfaces that in some way or other are external surfaces, where all the potential disease-causing microorganisms that exist in our environment may potentially find a way into our bodies and possibly cause ill health and disease. So,  all the tiny bumps and crevices that these bugs may find a home, are probably best occupied by bacteria and other microbes which do not cause disease, and ideally interact with our body to benefit our health.

Where do the bacteria in the body come from?

Before we are born our body is effectively sterile, if we are born by Caesarean section our body will be exposed to very different numbers and types of bacteria than if we were born vaginally. This has led to the observation that individuals born by Caesarean section tend to have a less healthy gut microbiome. This has been associated with increased risk of a number of health issues, including an increased risk of being overweight. After being born, being breastfed also helps to develop a healthy gut microbiome, as the increased skin contact and the breastmilk itself helps to encourage the baby’s microbiome to establish and thrive. It is not therefore surprising that a baby’s gut microbiome can be similar to that of their mothers.

Then as we grow a combination of diet and our environment helps to develop a healthy, mixed and robust microbiome, with respect to our skin that means not overusing harsh soaps and chemicals on our skin, and with respect to our digestive tract eating a varied diet containing lots of fibre rich plants, including vegetables, beans, peas, lentils, nuts and seeds. However, sometimes there are times when our microbiome changes, the most common reason being ill health and the use of antibiotics which due to how they work they can kill a number of bacteria all over our bodies. In this case it can be useful to try and replace the bacteria in our bodies, and especially our colon. This can be done to some extent by the use of fermented foods, especially live yoghurt or perhaps in a more targeted way by providing a probiotic (live bacteria supplement). If you are planning to choose a friendly bacteria supplement then it is important to check which bacteria it contains, the number of bacteria it contains and that it is formulated in a way that supports these bacteria to get past the acid of the stomach and the bile of the small intestine and safely find their way to our colon. It is not just people following antibiotics who may benefit from Good bacteria, some people with bloating or even individuals at risk of respiratory tract infections have been shown in studies to benefit by reduced severity of symptoms from live culture supplements.

So, when it comes to our bodies, we are really not a zoo but almost a planet of different environments and ecosystems which support a variety of microscopic organisms. Most of the attention focuses on bacteria, especially in our gut where we hear that more Lactobacillus and Bifidobacteria are a good thing. But across the other surfaces of our body’s different types of bacteria along with other microbes such as yeasts, make their home and help prevent potential pathogens from taking hold. With some of these organisms interacting with our bodies by making compounds that may nourish the cells they are living next to as happens in the gut, or produce their own antimicrobials which not only protects the bacteria itself but can help ward off diseases that can afflict us!


Due to the European Food Safety Authority (EFSA) rulings regarding the use of the terminology “probiotics”, herein probiotics are referred to as live cultures, good bacteria supplements, friendly bacteria supplements.’