Are We Too Clean?

You may have heard the idea that if we exposed our kids to more dirt, got rid of antibacterial cleaning products and our obsession with hygiene everyone would be far healthier.

Studies have linked asthma and other respiratory problems to cleaning products.

In addition many allergies and autoimmune conditions are on the increase and it seems this isn’t just down to to increased awareness or surveillance.

But is also true that vaccination, improvements in sanitation, diet and lifestyle have transformed life expectancy and diminished the risks posed by what were ‘killer’ bugs a generation or two ago. And if we’re unlucky there are still antibiotics that work. Just.

But we all know correlation isn’t necessarily causation so is there a causal link between ‘too much’ cleanliness and the increase in allergies, immune and other disorders?

Clean vs Hygienic

Let’s clear up the first problem right away: ‘cleanliness’ and ‘hygiene’ are not the same but are often conflated. There’s a huge difference between kids getting dirty when they interact with each other or their environment and kids not washing their hands after visiting the lavatory, before eating food or after farm visits. This was demonstrated again recently with another petting farm-related E. coli outbreak and I had a go at that at the time.

Many people don’t understand the difference between ‘honest’ dirt and situations that can really get you sick – as manifested in those who are paranoid about ‘germs’ in the house but have no issue with handing their kids sweets immediately after touching farm animals at petting zoos.

The key purpose of good hygiene is to reduce exposure to harmful germs, not all of them – that’s impossible. We are less likely to die of infectious diseases than our ancestors or to suffer parasites like intestinal worms and it’s been suggested a hygienic environment fails to give our immune system the exercise it needs, resulting in the rise in – say – asthma.

But were ‘too much cleanliness’ the sole cause of asthma in children we’d expect to see it across all backgrounds rather than disproportionately in impoverished inner cities, or where pollution levels tend to be higher.

And don’t forget genetics, diet, stress and multiple other influences all affect susceptibility too. Also you just need to look at any hand washing survey and you’ll realise most people aren’t ‘too clean’ – quite the opposite.

As ever, it’s complicated. No evidence supports the idea that reducing modern practices of cleanliness and hygiene would have any impact on rates of chronic inflammatory or allergic disorders but there is a heap of evidence that it would increase the risks of infectious diseases.

Also Our Microbial Overlords are omnipresent and no amount of cleaning will get rid of them. Clean them off and they’re back in a heartbeat. But fortunately most of them don’t give a shit about us – which is why hygiene is all about keeping those that do at bay.

The Hygiene Hypothesis

The data are suggestive that lack of exposure to Our Microbial Overlords and increased risk of allergies and autoimmune disorders are somehow linked. The basis for this was first proposed about 25 years ago when an inverse correlation between hay fever and the number of older siblings was observed in a study of over 17,000 British children born in 1958.

It became known as the Hygiene Hypothesis and many claim asthma and allergies are on the increase (especially in our kids) because we keep everything just too damn clean nowadays. But it’s not that simple.

There are variations on this theme such as the ‘Old Friends’ hypothesis – that we require the organisms we were exposed to during the Stone Age when our immune systems were evolving. And if we re-introduce exposure to these ‘old friends’ the incidence of allergies and other chronic inflammatory diseases that plague modern society will decrease.

This is a bit simplistic for me; we have co-evolved with Our Microbial Overlords and like the Paleo Diet this idea seems predicated on two principal fallacies; that evolution stopped millennia ago (Spoiler Alert: it didn’t and hasn’t), and that the troglodyte lifestyle was some sort of golden age free of infection, cancer, heart disease and many more ‘modern’ diseases. That this is Utter, Utter Bollocks (µ²B) is evidenced – inter alia – by the sub-30 Paleo life expectancy and the inefficiency of probiotics for prevention or treatment of allergies, inflammatory or autoimmune illness.

Many forget that it’s not just the many harmful organisms like cholera, smallpox and stuff we have vaccines for; we are still constantly exposed to millions of innocuous microorganisms of one flavour or another and we don’t even notice; our body recognises any marauders and the immune system sorts them out.

Add to that our ‘normal flora’ (the billions of microorganisms we carry on and in us) and you quickly realise we are not alone; we might be born germ-free but it only takes 48 hours or so to pick up our own ‘fingerprint’ of similar but slightly different bacterial species we then carry for life.

The Evidence

The decrease in overall infection rates in the West is now being mirrored in developing countries – as is an increase in both autoimmune and allergic disorders. But there’s more: other epidemiological data is also suggestive, in particular migration studies looking at people migrating from low-incidence to high incidence areas and some animal studies. Remember this all started with the presence of one or more older siblings being protective against later development of hay fever and asthma – but it’s also true of MS and Type 1 diabetes (the autoimmune one you get early in life).

It’s also been shown attendance at nursery during the first 6 months of life lowers risk of atopic dermatitis and asthma later, and children born to mothers who were exposed to bugs found in dairy farms were less likely to develop allergies. None of these necessarily proves a causal link between infections and immune disorders but it is the case that changes in the makeup of Our Microbial Overlords and some diseases are linked, and a particularly good example is inflammatory bowel diseases.

The Gut Microbiota

The hundred million million bacteria that rapidly colonise our gut immediately after we’re born are vital in shaping our immune system, and in many autoimmune diseases our microbiota also seems to modulate the immune response. For example the biodiversity of the faecal microbiota of patients with Crohn’s disease has been shown to be diminished.

There are plenty of other examples of our gut microbiota moulding us. For example, fat people have more firmicutes and fewer bacteroidetes than thin folks. A more striking claim for links between our microbiome and human health has to do with the brain. It has been known for a long time that people with autism generally have intestinal problems as well, and that these are often coupled with abnormal microbiomes. In particular, their gut flora is rich in the clostridia. This may be crucial to their condition.

Clostridia kill other bacteria to compete for their niches with chemicals called phenols (carbolic acid, the first antiseptic, is one such). But phenols are poisonous to human cells too, and thus have to be neutralised. This is done by throwing sulphate at them. So having too many clostridia producing too many phenols will deplete the body’s reserves of sulphur. And sulphur is needed for other things—including brain development. If an unusual microbiome leads to the gut needing extra sulphur the brain may pay the price by developing abnormally.

The microbiome also makes vitamins, notably B2, B12, K and folic acid. It is, moreover, capable of adjusting its output to suit its host’s needs and diet. The microbiomes of babies make more folic acid than do those of adults. And microbiomes in vitamin-hungry places like Malawi and rural Venezuela turn out more of these chemicals than do those in the guts of North Americans. Cool or what?

OK, back to immune-related matters. A Firmicute called Faecalibacterium prautsnitzii is particularly depleted in IBD and animal tests have shown the anti-inflammatories it secretes are effective in treating IBD. Bacteroides fragilis has also been shown to be protective. While the evidence for the role of Our Microbial Overlords in IBD is supportive, in other allergic and immunosuppressive diseases the data is weak.


Parasitic infections are very different to those cause by bacteria and viruses. Parasitic infections have been pretty much eradicated in European countries since about the end of World War II just as inflammatory diseases and allergies have increased. It’s been shown Schistosoma (a blood fluke) infections have a strong protective effect against inflammation, hookworms such as Necator also seem to be protective against asthma. But Ascaris (a worm) and Trichuris (a nematode) have no effect. Eh?

Helper T Cells

Our immune system comprises specific and non-specific mechanisms to deal with microbial and other challenges that has evolved over millennia. So it’s messy.

A particular class of white blood cell called Helper T cells (CD4s to those in the biz) form part of the incredibly complex web of many different components that contribute to the immune response.

  • Th1 T cells respond to pathogens like bacteria and some viruses. They produce inflammatory cytokines, interferon and tumour necrosis factors that are play a part in cell-mediated immunity.
  • Th2 cells respond to multicellular parasites like worms. They produce different cytokines to Th1s and like all immunology it’s messy and it’s complicated – which is unsurprising given our immune systems co-evolved over millions of years with Our Microbial Overlords and with other stuff like parasitic worms. Amongst other things Th2s are involved in producing allergic reactions (contributing to IgE production) and also contribute to a woman’s ability to tolerate (immunologically-speaking) a foetus – which is a foreign object that could otherwise be rejected.

To try to simplify, Th1 causes inflammation and Th2 partially suppress that inflammation. The Th1 and Th2 pathways can down-regulate each other and some have argued that our lower microbial burden in early childhood means we don’t have a strong Th1-biased immunity which pushes us towards a Th2 phenotype which is what predisposes us to allergic disorders.

Except that many autoimmune diseases are Th1 cell-mediated. That’s as simple as I can make it, at least. Told you immunology was complicated…

What's the Answer?

Our Microbial Overlords, parasitic worms, all sorts of allergies and autoimmune diseases are all part of a complex interaction between us, our environment and the non-human cells in our bodies that outnumber our own tenfold. And that’s not including viruses.

People are already looking at worm therapy as a treatment for Crohn’s Disease and I’ve already mentioned stool replacement therapy. There may well be treatments for Type 1 diabetes and all sorts of allergies in the future based on understanding how those interactions work – but we are a long way from that right now.

What I think we can be certain of is a whole new World of Woo will soon overwhelm us based on mutant and science-free variations of such modalities with the Woo Warriors using this as another reason for promoting probiotics and all their other crap.

In another post I covered fears that vaccines might overwhelm a child’s immune system – but it could be that the immune system is not being exercised enough and increased challenge by Our Microbial Overlords and other parasites might make allergies and autoimmune diseases less likely in later life.

But that doesn’t mean deliberately exposing children to harmful bugs will make them any healthier.

Don’t forget that infectious diseases still kill far too many people and hygiene is one of the cornerstones of containing these threats – along with vaccination, sanitation and other public health measures. As I’ve already said, people need to understand the difference between ‘clean’ and ‘hygienic’.

For example any think you’re more likely to pick up an infection in a dirty hospital than a clean one – this actually isn’t the case because interventions like hand hygiene totally eclipse environmental cleanliness in terms of risk. Basically if the staff don’t observe proper hand hygiene it doesn’t matter how clean or dirty the hospital is, patients will pick up preventable infections.

All the interventions above make it more likely our kids will survive into old age in spite of those determined to bring back plague and pestilence – it’s not just the antivaccine nutters; Our Microbial Overlords reprogramme many organisms to do dumb stuff in their service and I would be entirely unsurprised if this is also the case for dumb-arsed ‘alternative’ health suggestions like drinking sewage.

And I’ll give Tapeworm Therapy a miss for now, thanks.