It is hard to know if the rash of headlines about allergy epidemics is real or hype. Over the past few weeks, anyone reading a variety of quality newspapers would have found themselves thoroughly perplexed.

Last week our news pages quoted a study from the National Research Centre for Environmental Health in Munich saying that children lessen their risk of being sensitive to allergens if they grow up with a dog. Professor Joachim Heinrich and colleagues found that children raised with a dog had fewer allergy markers, such as antibodies to pollen, house-dust mites, cat and dog dander and mould spores. He told the European Respiratory Journal that a dog's presence in early childhood encourages the immune system to develop less sensitivity to allergies such as asthma, eczema and hay fever.

But earlier reports from researchers at Portsmouth University claimed that the incidence of food hypersensitivity - which embraces allergy and intolerance - has not changed in the past 20 years. And they added that parents were too quick to put their children's gripes down to food allergies; people are worrying unduly.

On the letters page of The Times, however, a group of allergists and scientists claimed that we are “in the midst of an allergy epidemic, with about 20 million children and adult allergy sufferers in the UK”.

So what is the truth? There is an idea called the “Hygiene Theory”, or “Hygiene Hypothesis”, which considers whether modern life has become too clean; that in our increasingly sanitised, antibacterial and deodorised age, children's immune systems are not exposed to enough germs to develop normally. According to the market research firm Mintel, Britons spent £612 million on bathing products in 2005; in 2011, the estimated figure will be £709 million.

We have certainly declared war on germs, but has it come at a price? The incidence of certain illnesses - asthma, eczema and respiratory allergy and autoimmune diseases such as arthritis and multiple sclerosis - has soared. Britain now tops the asthma league in Europe. Scientists are still searching for a reason. One clue is that these illnesses afflict only the developed world; they are rare or non-existent in poorer, dirtier countries (where, admittedly, more harmful diseases such as cholera and typhoid are prevalent).

There are other clues: children in bigger families are less likely than those in smaller ones to suffer allergies. One theory is that they are exposed through siblings to more childhood infections, which benefits health. Likewise for children who, while babies, were brought up with household pets or on farms; they are less prone to animal allergies.

What do all these factors have in common? Germs. Siblings, pets and poor neighbourhoods carry them in abundance. That has led to the idea that the sterility of modern urban life is making us ill. A recent book, Good Germs, Bad Germs, by Jessica Snyder Sachs, explores the idea that modern medicine and sanitation has expunged harmless germs along with the bad, and that these harmless microbes are responsible for protecting against allergy. Some scientists argue that we should restore some germs to their rightful place - back inside us.

The Hygiene Hypothesis, formulated by the epidemiologist David Strachan about 20 years ago, argued that children's immune systems were not being sufficiently challenged - because of falling family size and increasingly sterile homes - to learn how to fend off diseases. The result was that once harmless invaders, such as cat hair, triggered immune overreactions (this is what constitutes an allergy). In the late Nineties, the evidence for Strachan's hunch was snowballing: kids in daycare showed lower rates of asthma than infants kept at home, suggesting that immunity might be conferred by early contact with other children.

But in recent years there has been a backlash against the Hygiene Hypothesis, especially from experts on infectious diseases. They worry be-cause the hygiene hypothesis lulls people into thinking that poor hygiene is OK, or beneficial, when the opposite is true. Poor hygiene allows bad germs to flourish, and the prevalence of gastrointestinal infections and MRSA, along with norovirus, show we should not drop our guard.

Professor Sally Bloomfield, an expert on infectious diseases at the London School of Hygiene and Tropical Medicine, is one who finds the persistence of Strachan's unproven thesis counterproductive. “When we have unacceptable levels of gastrointestinal disease, norovirus - and Sars and a possibile flu pandemic - the idea that hygiene is unnatural is frightening. We need to support cleanliness and hygiene. I still find people who think it's proven that we are too clean. We must dispel this.”

How has this error come about? Bloomfield says that while exposure to microbes seemed pivotal in the prevention of allergies, Strachan went farther, suggesting that it was disease-causing microbes (pathogens) that offered protection: “He made the link between exposure to infection and protection from allergy, but it could be benign microbes, rather than disease-causing ones, that are providing protection. It could be that as we've improved water and food, knocked out the benign bacteria along with the pathogens. Or it could be nothing to do with microbes.”

Bloomfield is a member of the International Scientific Forum on Home Hygiene, which suggested several years ago that the Hygiene Hypothesis be renamed the Microbial Exposure Hypothesis. It would convey the growing conviction that it is our modern relationship with microbes, rather than extra cleanliness, that is making us ill. Scientists are warming to the idea that the benign microbes colonising our guts and skin, rather than full-blown diseases, defend against allergy. A recent study published in the Journal of Allergy and Clinical Immunology showed that British, Swedish and Italian newborn babies with a narrow range of bacteria in their stools are more likely to have developed eczema at 18 months than newborns with a wider range of bacteria (researchers, from Lund University, Sweden, speculate that antibiotics given during delivery might be killing off beneficial bacteria).

Another way of smuggling “good” microbes back into the body is to consume probiotic yoghurt drinks or fruit juices. These products contain so-called friendly bacteria. But the science on whether they improve health remains contradictory.

And that's the rub: we don't yet know if extreme hygiene has propelled the rise of allergies. What we do know, to our cost, is that a lack of cleanliness is leading to an explosion in preventable, transmissible infections at home and in hospitals.

Searching for the good microbes in your gut

Scientific attention is now focusing on the gut, home to benign microbes that have colonised human beings throughout our history. For every one of your own cells, there are ten microbial cells. Most moved in on you just after birth, evading your immature immune system and then setting up permanent residence. Scientists have a scant knowledge of these teeming creatures; they do not know if the microbes in your body are anything like the ones in mine.

The mystery attached to microbes has inspired the Human Microbiome Project, akin to the Human Genome Project. This huge undertaking - to catalogue the microbes that live on and inside humans and work out how they affect our health - began last year, funded by the National Institutes of Health in America.

Explore Health

• Expert Advice

• Health Features

• Mental Health

• Alternative Medicine

• Child Health

• Health Club