Our friend Julia moved to a small free-range pig and poultry farm when her first child, Jedd, was a preschooler. When her second baby was born she would strap him on her back so that she could go to the chicken coop to pick up eggs. Jedd would chase the chickens and a couple of times she even caught him chewing on something he had picked up from the ground.At first, all of this caused Julia to freak out. Yet once she realised that Jedd wasn’t getting sick from these encounters with the chickens, she relaxed a bit. Her second child, Jacob, followed suit and got dirty on the farm. Her early worries that her children were going to contract diseases from all this messiness dissipated, and she was pleased to see that they remained healthy.

Was Julia being an irresponsible parent — or might we all have something to learn from her example?

For most of the past century we have considered microbes bad news, and for good reason; they cause disease, pandemics and death. Most human communities have experienced the benefits of medical advances such as antibiotics, vaccines and sterilisation, which have radically reduced the number and severity of infections that we suffer. Dying from a microbial infection is a very rare event in the western world.

Unfortunately, this progress has come with a price, as news reports have been telling us for some years. Our anti-microbe mission has been accompanied, in industrialised countries, by an explosion in the prevalence of chronic non-infectious diseases and disorders. Diabetes, allergies, asthma, inflammatory bowel diseases, autoimmune diseases, autism, obesity and certain types of cancer are at an all-time high. The incidence of some of these disorders is doubling every ten years, and they are starting to appear sooner in life, often in childhood.

All of these diseases have a genetic component, but their alarming growth cannot be explained by genetics alone. Recent studies find a direct link between the presence and absence of certain bacteria and all of the chronic diseases mentioned above. It turns out that the microbes within us are much more than quiet residents; they are an inherent part of our physiology, and altering them leads to disease.

Our own 2015 study (published in the journal Science Translational Medicine) found, for example, that three-month-olds who had four particular microbes in their faeces were much less likely to get asthma later in life. When those four microbes were introduced into mice, they protected against experimentally induced asthma, showing for the first time that alterations in gut microbes can drive the development of the disease. Laboratory experiments also have found that obese mice lose weight when they get a transfer of gut microbes from lean mice (the reverse holds true as well, with lean mice growing fat after a transfer from obese mice).

The practical upshot of all this research is clear: our health depends to a large degree on maintaining a robust and diverse community of microorganisms in our bodies — and establishing good gut health as children is especially important.

Epidemiological research shows that children who are exposed to dogs early in life have a decreased risk of developing asthma and allergies

During the first few months of life the microbe community in our bodies is considerably less established and stable than later in life. Any drastic changes to it have a much higher chance of permanently altering our microbiota (as specialists call this world of tiny organisms within us) and our long-term health.

From the moment we are born we begin getting colonised by bacteria, which kick-start a series of fundamental biological processes, including the development of our immune system. Before birth the lining of our gut is full of immature immune cells. When bacteria move in, the immune cells react to them, changing and multiplying. They even move to other parts of the body to train other cells with the information they have acquired from these intruders. If deprived of this interaction, the immune system remains sloppy and immature, unable to fight off diseases properly.

Scientists haven’t figured out exactly how microbes do this at the molecular level, but we do know that most bacteria will teach these immune cells to tolerate them, whereas some bacteria — the pathogens that cause diseases — prompt strong resistance. The result is to make the intestine a relatively controlled and harmonious place.

Another fundamental function of microbes is to aid the regulation of our metabolism. Like other animals, humans obtain energy from food that is digested and absorbed in the intestines. Besides helping us to digest certain foods that the intestines can’t handle on their own, bacteria produce compounds that help to define how we use or store energy in our bodies. New research also shows that our microbiota plays an important role in neurological development and even in the health of our blood vessels.

Most of this knowledge is still relatively new and many pieces of the puzzle remain unsolved, but protecting the initial developmental stages of our microbiota clearly has a significant impact on our health.

Inflammatory diseases (such as asthma, allergies and inflammatory bowel disease) and metabolic diseases (such as obesity and diabetes) are characterised by alterations in our immune system and our metabolic regulation. Knowing what we do now about the role of the microbiota, it is not surprising that these diseases are being diagnosed in more children. They are, to a great extent, a consequence of relatively recent changes in our lifestyle — modern diet, oversanitisation, excessive use of antibiotics — that have altered the specific microbes that affect our metabolism early on. We urgently need to find ways to modify our behaviour so that our microbes can function properly.

Never before in human history have children grown up so cleanly, and our diets have lost many of the elements most crucial to the health of our guts. We have become bad hosts to our microbes.
Extracted from Let Them Eat Dirt: Saving Your Child from an Oversanitised World by B Brett Finlay and Marie-Claire Arrieta (Windmill, £12.99)

Boost your immune system: 6 things you can do

Eat a varied diet
Seventy-five per cent of the world’s food comes from only twelve plant species and five animal species. Amazingly, just three species — rice, corn, and wheat — account for 60 per cent of the calories that humans obtain from plants.

Given how well bacteria respond to diet, eating a variety of foods is most likely the best way to increase microbial diversity. The first two to three years of life are the optimal time to promote a diverse microbiota through diet. Offer children a variety of grains, including oats, rice, barley and quinoa. It’s also important to offer whole grains instead of refined ones. The western diet is extremely low in fibre, and refined grains contain very little of it.

Take antibiotics only when you need them
This week all 193 United Nations member states met to discuss the future of antibiotics in relation to the fight against antibiotic resistance and superbugs.

In response to our massive use of antibiotics, microbes have spread resistance genes like wildfire to other microbes, with antibiotics providing a strong selection pressure (live or die). We now see massive microbial resistance to all leading antibiotics that are used extensively, with resistance arising within a year or two, often making the drug obsolete within three to five years.

Multiple courses of antibiotics in the first year of life lead to a significant increase in asthma, because they affect the microbes involved in ensuring a healthy maturation of the immune system.

Get a dog
Epidemiological research shows that children who are exposed to dogs early in life have a decreased risk of developing asthma and allergies.

Studies have found that exposure to a dog during pregnancy or before the age of one decreases the risk of developing eczema by 30 per cent. In several other studies the presence of a dog is also associated with a reduced risk of asthma, decreasing the risk by about 20 per cent.

Go outside more
Children spend half as much time outside as they did 20 years ago; children aged 8 to 18 spend a daily average of 7 hours and 38 minutes using entertainment media.

They are growing up mainly exposed to indoor microbes, such as the ones growing on their computer keyboards. For millions of years children had grown up exposed to a substantial number of outdoor microbes, and this connection has been broken in the past couple of generations — which coincides with the time it has taken for western lifestyle diseases to skyrocket.

Don’t be too clean
Our modern societies have never been so clean. Babies and children are prevented from following their innate nature to get dirty, so they’re being shielded from the microbial exposure that’s essential for their development.

Handwashing is the best hygienic practice to prevent contracting and spreading infectious diseases. That said, children do not need to wash their hands all day long. Handwashing should occur before eating; after using the toilet; after being in contact with someone sick, or, if the child is sick, before they touch other people; after touching rubbish or food that is decomposing; after touching animal waste or farm animals; or after being in places frequented by many people (eg, public transport).

When out in a green space allow your children to touch anything they want (except animal waste), including dirt, mud, trees etc. And let them stay dirty until it’s time to eat.

Don’t use antibacterial soap or gel sanitisers
It’s best to avoid antibacterial soap. A US Food and Drug Administration (FDA) committee found that antibacterial soaps provide no benefits over regular soap and water. Plain soap and water is enough, and an alternative sanitiser (such as a gel sanitiser) should be applied only if there isn’t a potable source of running water and soap.

A common antibacterial chemical used in soap, called triclosan, has been shown to alter hormone regulation in animals, and it might contribute to the development of antibiotic resistance in bacteria.