Sweeping Away the Hygiene Hypothesis: New Perspective on Human Microbiome and Allergy/Infection Prevention
Written By Microbiome Plus+

Sweeping Away the Hygiene Hypothesis: New Perspective on Human Microbiome and Allergy/Infection Prevention

According to the hygiene hypothesis, the lack of exposure to germs and bugs in early childhood robs the immune system of its power to resist diseases, especially allergic diseases, making your child more susceptible to such diseases. This notion, first devised by a physician named Dr. Strachan in 1989, has long been widely accepted. [1]
However, the scientists of the 21st are now debunking the concept of the so-called “hygiene hypothesis.” [2] Due to the drastically rising rates of infectious and allergic diseases, it is now believed that hygiene plays a vital role in early life. This is very much unlike the hygiene hypothesis where people assumed that exposing a child to germs is important for developing a strong immune system. This indicates that people have been so convinced by the misleading concept of hygiene hypothesis (not being too clean) that they have been exposing their children to all kinds of microbes since early life, which has resulted in significant negative health outcomes and a profound increase in health burden.

Factors that indicate a failure of the Hygiene Hypothesis

A drastic rise in allergic diseases and altered microbial exposure

Scientists relate the immune system at birth to computer hardware that doesn’t have enough data. However, more data needs to be delivered during the early years of life, via contact with microbes from other humans and nature. But what if this data is not sufficient enough or wrong? The immune system would go haywire and start attacking not only the harmful germs that trigger infections but also harmless agents such as pollen, dust, and food allergens giving rise to allergic diseases. [2] Over the last century, there has been a prominent trend in allergic diseases like eczema, hay fever, and food allergies worldwide, with the highest trend in Western countries. [3]

The upsurge in allergic diseases is due to a limited exposure to healthy bacteria rather than reduced infection in early childhood — that is contrary to the notion of hygiene or the “not too clean” hypothesis.

We, humans, are both bacteria and human with the ratio between the two inhabitants approaching 1:1 in our bodies. Trillions of microbes reside on and within us, making the forgotten organ, “the human microbiome” vital for our health and other organs.

Various factors upset the human microbial balance, which in turn, drives allergic diseases. For instance, we know that exposure to antibiotics disrupts the gut microbiota.

Our microbiome starts to shape soon after we take the first birth. Babies born through vaginal delivery acquire more beneficial bacteria from their mother’s vagina than babies born via Caesarean section that are at risk of developing allergies. Likewise, breastfed babies are likely to carry more good bugs than their bottle-fed counterparts with the latter being more prone to allergies.

An upsurge in food poisoning

Another factor that debunks the myth of the hygiene hypothesis is the dramatic rise in clinical cases of food poisoning. A UK study revealed around 17 million cases each year, which is a pretty high figure. [4 These high rates are because people have been so much into this”hygiene hypothesis” thing that they no longer work out the healthy habits into their routine.

Clostridium difficile infection is now contracted from the environment

difficileis a harmful bug, which when infects your gut — leads to severe diarrhea and dehydration. Until now, C. difficileinfection was mostly contracted in hospital settings. However, it is now becoming apparent that several other potential sources in nature, such as water, farm animals or pets, and food greatly put you at risk of catching this infection. [2] Hence, it’s not the clean but the unclean atmosphere that may cause this harmful bug to contaminate your intestines.
Maintaining hygiene and keeping clean
Evidence shows that practicing proper hygiene by washing hands frequently with soap and water can limit the spread of airborne infections, particularly colds and flu as well as food-and-waterborne infections. [5] There are no antibiotics for respiratory and intestinal viral infections. Hence, prevention through hygiene is worth a pound of cure here.

Wrapping up

It is thus obvious that the hygiene hypothesis is now a serious bone of contention and the opposite idea is what better underscores the rising cases of allergic diseases. Strategies like having natural childbirth, breastfeeding, diet, use of probiotics, outdoor activities, and using antibiotics only when needed could help restore the microbiome and possibly cut down the risks of allergic health issues.


  1. Strachan DP. Family size, infection and atopy: the first decade of the “hygiene hypothesis”. Thorax. 2000;55 Suppl 1(Suppl 1):S2-10.
  2. Bloomfield SF, Rook GA, Scott EA, Shanahan F, Stanwell-Smith R, Turner P. Time to abandon the hygiene hypothesis: new perspectives on allergic disease, the human microbiome, infectious disease prevention and the role of targeted hygiene. Perspect Public Health. 2016;136(4):213-24.
  3. Prescott SL, Pawankar R, Allen KJ et al. A global survey of changing patterns of food allergy burden in children. World Allergy Organ J. 2013 4;6(1):21. doi: 10.1186/1939-4551-6-21.
  4. Tam CG, Larose T, O’Brien SJ. Costed extension to the Second Study of Infectious Intestinal Disease in the Community: Identifying the proportion of foodborne disease in the UK and attributing foodborne disease by food commodity. Food Standards Agency, 2014. Available online at: http://www.food.gov.uk
  5. Little P, Stuart B, Hobbs FD et al. An internet-delivered handwashing intervention to modify influenza-like illness and respiratory infection transmission (PRIMIT): a primary care randomised trial. Lancet. 2015 Oct 24;386(10004):1631-9. doi: 10.1016/S0140-6736(15)60127-1.
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