Over the past few years, it has become clear that far from being our foes, many bacteria and parasites can act as our body’s caretakers, guarding us from the nastier intruders and fine-tuning our immune system.  This has prompted some to suggest abandoning soap altogether: being too clean, they say, may actually make us less healthy, leading to an increased rate of diseases like hay fever, asthma and food allergies.  But is it now time to ditch this theory? That’s the message of an expert panel convened by the UK’s Royal Society of Public Health (RSPH) and the International Scientific Forum on Home Hygiene.  Not washing only undermines efforts to combat infections at a time of increased antibiotic resistance and susceptibility to infectious disease, but blasting every household surface with disinfectant isn’t helpful either. We need to tend our ‘microbiome’, but there are safer and more effective ways of doing so than wallowing in dirt.  Walk into the household aisle of any supermarket or grocery store and you’ll be confronted with a wall of cleansing products, soaps and hand gels each promising to eliminate the bacteria and viruses responsible for infections like flu and E. coli. At the same time, growing awareness of the microbiome and the role it plays in human health has prompted a backlash by some of those that study it – including suggestions that we might be healthier if we stopped washing our hands.  But the new paper, published in a special issue of Perspective in Public Health this month, dubbed “The Hygiene Misnomer” argues that neither approach is correct. Instead, we need to adopt a framework of ‘targeted hygiene’: measures that reduce the transmission of harmful organisms, while simultaneously allowing beneficial bacteria to thrive.  “People think the problem is we’re too clean, but hygiene is not a state: it’s what we do in the times and places that matter,” says Sally Bloomfield, honorary professor at the London School of Hygiene and Tropical Medicine and lead author of the paper. In other words, “it’s not about having a clean room; it’s about what we do in that room.”  Our exposure to microorganisms is being limited by antibiotics, modern diets, and the urban lifestyle  Their intervention follows a RSPH conference in February, at which immunologists, microbiologists, allergists and public health experts gathered to review strategies for tackling the issues of allergies and infectious diseases in light of our increased understanding of the microbiome – the ecosystem of organisms living within and upon us.  “The real point is that our exposure to microorganisms is being limited by antibiotics, modern diets, and the urban lifestyle, rather than by what the public understands as home hygiene,” says co-author Graham Rook, emeritus professor of medical microbiology at University College London. “We do not need to stop washing our hands.”  Many people assume that allergies are the price we must pay for our freedom from infections like measles. This ‘hygiene hypothesis’ was first put forward in 1989 by Professor David Strachan, an epidemiologist at St George's Hospital in Tooting, south London. He had been wrestling with the paradox that despite the availability of clean drinking water, childhood vaccinations and sanitation – all of which had cut infectious killers like typhoid and cholera – allergies seemed to be on the increase. Noting that children with fewer older siblings had higher rates of hay fever, he suggested that exposure to common childhood infections might serve to train up the immune system; in their absence it would be tipped towards a more inflammatory state, in which immune cells overreacted to everyday substances like pollen or egg.  Over time, this message has become simplified to ‘being too hygienic is making us ill’. But there are other problems with the hygiene hypothesis too. For one thing, a closer look at the data suggests that the reported spikes in hay fever, asthma and food allergy have occurred at different points over the past 120 years – all somewhat later than the big advances in water chlorination, sanitation and hygiene. This suggests that a variety of factors may have been at play. Further studies have also contradicted the proposed link between childhood illness and allergy  “We’ve had massive changes over the last century in terms of how we live our lives, the amount of time we spend inside and outside – and how we spend that time outdoors; we’re mostly clean and wearing shoes, as opposed to covered in grime, barefooted and with different organisms living on us,” says co-author Paul Turner, an allergist and paediatric immunologist at Imperial College London. “It’s very hard, and I think misleading, to say it’s down to one particular thing.”  The current best guess is that it’s not colds, measles and other infectious diseases that nurture a healthy immune system, but “old friends” that were with us when the human immune system was evolving, such as environmental microbes and parasitic worms – things it’s hard to acquire in towns and cities. Combined with factors like increased pollution and exposure to non-native pollens, their absence increases the risk of allergic disease.  The immune system in the current environment is like a car that's out of tune  “The immune system in the current environment is like a car that's out of tune. It's not running efficiently; it’s too inflamed; but it also lacks the fine-tuned specificity which an immune system should have,” says William Parker, who researches gut biology at Duke University in North Carolina, and authored a separate commentary in the special issue. “It’s like having a police force with only hand grenades.”  David Dowling, a research fellow in paediatrics, at Childrens Hospital Boston, agrees. "The hypothesis of hygiene, as put forward in the late 1980’s, had a subtle but fatal flaw: it did not contemplate the fact that, while exposure to some microbial organisms may be bad and leads to infection, exposure to other microbial organisms in our environment may be beneficial in ways yet to be understood," he says. "In short, it all boils down to the idea of maximising appropriate exposure. But there is little evidence that appropriate exposure includes the need for pathogenic infection."  What’s needed are strategies to boost our exposure to beneficial microbes, whilst at the same time reducing our exposure to the ones that cause disease. But embracing dirt and failing to wash our hands is not the answer. Indeed, infectious intestinal diseases such as campylobacter are currently 43% percent higher than they were in the 1990s. Antibiotic resistance is also on the increase, while an ageing population means more people are susceptible to infectious illness.  Targeted hygiene is one solution. “It means you can be as tidy or dirty as you like in your day-to-day activities, but you need to make sure you are hygienically clean at the times and the places that matter,” says Bloomfield. These include immediately cleaning hands and kitchen surfaces that have come into contact with raw meat (particularly chicken); covering your hands and mouth (or using a tissue), if you cough or sneeze - and then washing your hands and disposing of the tissue; not only washing your hands after visiting the bathroom, but regularly disinfecting the toilet seat, flush, taps and bathroom handles.  At the same time, the panel recommends a number of measures to boost exposure to beneficial microbes, particularly during early childhood. “Data are now strong enough to encourage changes such as encouraging natural childbirth, physical interaction between siblings and non-siblings, more sport and other outdoor activities (including babies in prams) and less time spent indoors, and reduced antibiotic consumption,” they write.  Our diet is also looking increasingly important, adds Rook. “Fibre and polyphenols (present in red wine and fruit and vegetables) seem to help maintain the diversity of our gut microbiota, whereas if we take diets deficient in these things, diversity decreases, and some important species become extinct,” he says.  The bugs living upon and within us are part of the rich tapestry that makes us human. It seems we really are stronger together.  Linda Geddes is a freelance writer in Bristol and the author of Bumpology: The Myth-busting Pregnancy Book for Curious Parents-to-be.  Join 600,000+ Future fans by liking us on Facebook, or follow us on Twitter, Google+, LinkedIn and Instagram. If you liked this story, sign up for the weekly bbc.com features newsletter, called “If You Only Read 6 Things This Week”. A handpicked selection of stories from BBC Future, Earth, Culture, Capital, Travel and Autos, delivered to your inbox every Friday.
Friendly bugs can protect our health - but the answer is not to abandon hygiene. There are now many more effective ways to nurture your 'microbiome'.