Are we cleaning our way out of health?

Coronavirus has made us all more conscious of our hygiene. We wash our hands more often, usually with antibacterial soaps, we sanitise our hands regularly with alcohol gel, we avoid situations where we come into contact with people and quickly pull out our alcohol gel when we touch anything outside our homes.

Even inside our homes we are more conscious of our hygiene, spraying antibacterial cleaners around liberally and sanitising anything that arrives in the post.

Whilst this has proven to be a reasonable strategy against covid, what might living in such a sanitary world be doing to us?

We each have 37 trillion microorganisms (microbes) in our bodies which make up our microbiome (ecosystem).

We have a different set of microbes on our skin, in our mouths, ears, noses and guts and even microbes in our bloodstream and organs. These microbes are extremely important to us. They help us to produce hormones and vitamins, they perform vital immune and metabolic functions and protect the integrity of our membranes and gut wall as well as many more roles that we are only just discovering. Without these vital, friendly microbes we would quickly succumb to infection and die.

Our microbiome is unique to each of us – much like a fingerprint. We get some of these friendly microbes from our mothers when we are born by vaginal delivery and others through close contact with family members and friends.

We also get friendly microbes from our environment – the food we eat, the pets we have, our exposure to other people, animals, soil, air and surfaces. The jobs we do can affect our microbiome – with organic gardeners having a great diversity.

Microbiome health

The health of our microbiome is measured by its diversity ie the variety of good microbes. It’s through this diversity that we maintain some of the most important metabolic and immunological functions in our bodies. Our microbes even play a big role in maintaining our mood and reducing our anxiety. If we improve the diversity of species of these friendly microbes in our bodies we can help prevent disease and maintain our health.

A dysbiotic microbiome on the other hand is one which lacks the diversity of microbes to maintain a healthy balance between the helpful microbes and the harmful ones. This can lead to harmful microbes taking over and maintenance of normal function can be disrupted.

This can progress to a breakdown of the structure of the gut wall – leaky gut – which allows harmful pathogens to penetrate into the bloodstream. This process has been implicated in many diseases.

Gut dysbiosis is seen in patients with chronic conditions such as obesity, IBS, inflammatory bowel disease, diabetes, ischaemic heart disease, autoimmune disease, depression, anxiety, cancers and more.

Dysbiosis and Covid-19

A recent article in the BMJ has even shown dysbiosis is strongly associated with people who have severe coronavirus symptoms and long covid – the more severe the symptoms the more dysbiotic the gut.

Dysbiosis can be caused by a modern diet high in fat, sugar and white carbs. It’s also associated with antibiotic use, certain drugs, such as PPIs and NSAIDS, lack of sleep, alcohol and stress.

There is also a notable difference between rural and urban microbiomes. Living in the countryside exposes us to a greater variety of friendly microbes which complement our ecosystems.

It has long been recognised that people brought up in rural environments have less incidence of allergies and atopic disease which is thought to be due to the protective effect of this more diverse ecosystem. Every day we touch, inhale and ingest microbes which support our healthy ecosystems.

Those of us living in the city were already more at risk of having a less diverse microbiome but with all the measures we have taken in the fight against coronavirus we are further reducing our exposure to these helpful critters.

If we want to kill coronavirus we need only wash our hands with plain soap to break down the lipid cell wall of the virus. Plain soap is not as damaging to our friendly microbes. In fact studies have demonstrated significant changes to our friendly microbes when using antibacterial soaps which persist for two weeks on stopping them.

Antibacterial soaps also leak into our water supply and our environment so affect the microbes we are in contact with around us. Destroying these helpful organisms can allow more aggressive pathogenic microbes to take their place. With the rise in antibiotic resistant pathogenic organisms this is concerning.

So what can we do to prevent our own ecosystems from crumbling during a pandemic?


Firstly we should ensure that we eat a wide variety of plants in our diet – greater than 30 varieties of fruit, vegetables, seeds, nuts, whole grains, herbs and spices per week. This may sound a bit daunting but by making soups and salads and having at least three vegetables with every meal it’s not so hard.

Seeds and nuts can be added to dishes or sprinkled over yogurt or cereals. Organic produce has even more helpful microbes, especially when we eat the skin of the fruit or veg.

Consider boosting your healthy microbes with a dose of probiotics, eg yogurt, kefir, sauerkraut, kim chi etc. Try to consume this daily to keep the levels of these bacteria topped up. Try to cut out processed foods, sugary foods and fatty fast foods which encourage more harmful bacteria to thrive.

Cut down on meat especially red meat and processed meats such as sausages, ham, burgers etc as these also encourage more harmful microbes and lead to more inflammation in our gut. Finally, eating a greater quantity of fibrous food – wholegrains, fruit and veg, feeds our healthy microbes and encourages them to thrive.


We should consider moving away from using antibacterial soap and use plain soap instead and try to only use alcohol gels when out of our homes in places where there is a coronavirus risk.

Perhaps we could be less hygienic in our homes, use plain soap or water for cleaning surfaces, wear your shoes around your house and consider having a pet – dogs and cats help to expand our microbial communities in a positive way.

The great outdoors

More time in nature – doing gardening, walking, playing in the mud with your kids, is really beneficial to our ecosystems. We shouldn’t be scared to get muddy, allowing our children to play in dirt is possibly one of the best things we can do for them.

Start with small changes

Whilst all this advice may seem hard to achieve, even small changes can bring about some improvement in your gut health so start small like cutting out processed foods or spending more time out walking and build from there.

It can take a bit of time for your gut to adapt to changes in diet especially big increases in dietary fibre so a gradual change may be more easy to stomach!

I believe we have a better chance of emerging from this pandemic healthy if we maintain a good relationship with our microbes. We must nurture and develop our own ecosystems and whilst we take measures to protect against harmful viruses and bacteria, we mustn’t forget to protect the microbes that are looking after us.

Dr Sheena Fraser is a GP based in Glasgow and a member of the British Society of Lifestyle Medicine

Further Reading