The Hygiene Hypothesis

Some call it the five-second rule, some extend that to five minutes, and some don’t care. This is the amount of time people are comfortable with picking up and eating food that has dropped to the floor. Of course, a lot depends on which floor and how confident one is that some insidious microbes are not lurking on its surface.

There is no question that sanitation is one of the main determinants of the good health that we enjoy in developed countries. Removal of waste and rubbish minimizes opportunities for the spread of diseases and, along with good nutrition and exercise, is arguably more important to health maintenance than the important advances in medical care for those already ill. However, has our modern obsession with cleanliness gone way too far? There is mounting evidence that it has.

The hygiene hypothesis states that dissociation between people and potential allergens and foreign substances early in life can profoundly affect people’s abilities to deal with these challenges in later life. Isolation from all the filthiness of the world is unnatural and is just not the environmental condition in which humans evolved.

What else could explain the relatively recent proliferation of food allergies, asthma, autism, rheumatoid arthritis, lupus, and a host of other autoimmune diseases? Perhaps the hygiene hypothesis offers an explanation.

Research has shown that children exposed to pets and bacteria early in life have reduced allergic sensitivity to environmental allergens [1]. Furthermore, it has recently been recommended that young children should be exposed early to peanut products to forestall the development of peanut allergies later in childhood [2], [3].

Studies of the microbiome, the panoply of microbes that inhabit our bodies at ten times the number of human cells, demonstrate amazing characteristics. Gut bacteria, for instance, play a very important role in health maintenance. The variety of gut biota in healthy, nonobese people is different from the biota in obese individuals. Studies from mice show that replacing microbes in obese mice with microbes from thin mice causes the obese mice to reduce weight to healthier levels. People with irritable bowel syndrome have been shown to be helped by enemas containing stools from healthy people, presumably replacing their faulty microbiomes with those from healthy individuals.

All living beings require information legacies to act as templates for future generations. We have come to recognize the genetic code built into each of us as just such a legacy. Nevertheless, our genes are not the only information legacy that we have. Our microbiomes also contain information to guide the present and future generations, and as these are passed from older generations to younger ones, the information that they convey to our bodies is important for our well-being [4].

Gut biota are not always good, and not always bad; a balance of numbers is the most beneficial. Helicobacter pylori, for instance, a normal stomach microbe, has been identified as a major cause of gastric ulcers and some cancers. However, removing H. pylori from the stomach with antibiotic use can result in gastric hyperacidity. H. pylori produces large amounts of urease, which breaks down the urea present in the stomach to carbon dioxide and ammonia. The ammonia, which is basic, then neutralizes stomach acid.

Let’s not forget the microbes inhabiting our skin. Staphylococcus aureus, the infamous cause of staph infections, is normally present on the skin, but is held in check by all the other microbes living there, all vying for the same space and resources that allow them to live. This situation is called competitive inhibition, where all microbes compete with each other.

Microbes in the gut may profoundly affect mood and psychological well-being. Although research along this line has been limited to tests with mice thus far, the evidence is accumulating that personality traits are at least partially determined by the gut microbiome. Anxiety, depression, and even autism may be treatable with certain types of microbes, called psychobiotics [5].

Is the rise in autism also a consequence of hygienic behavior? Certain research results would say it’s possible. Tests in mice have shown that abnormal gut microbiomes can lead to autistic traits, and these traits of inattention to others and communication difficulties could be reversed when the mice were given certain microbes that restored normal gut microbiota [5]–[7].

Sterilization is especially important in hospitals, where pathogenic microbes of all kinds may be found. Yet, even with the meticulous care of hospital sterilization, infections acquired in U.S. hospitals kill an estimated 75,000 people each year [8]. This is more than the number of deaths from breast cancer and human immunodeficiency virus infection and acquired immune deficiency syndrome combined. Removal of pathogenic microbes in hospitals also removes beneficial microbes as collateral damage, and that offers great opportunities for recolonization by dangerous microbes.

Microbes are passed to us naturally starting with vaginal births, sucking breasts, and intimate skin-to-skin contacts. Microbes from the environment are passed to our insides from our hands and respiratory systems. Some of these microbes are beneficial, some are benign, and some are harmful, but all are part of the walking ecosystems that we represent.

We are not meant to be born by cesarean section, we are not meant to take antibiotics for every little disease, and we are not meant to disinfect our hands and every surface they contact repeatedly. We are not meant to use sterilizer sprays and antimicrobial paints, surfaces, clothing, and other products. We are meant to have our immune systems challenged by invaders and we are meant to be assisted by other tiny creatures in that endeavor. Our germs have evolved with us and we need them. There are times when we need some other help to restore our health, but we cannot maintain our health by living a germ-free life. As Jack Gilbert of Argonne National Labs has said, “Hygiene is good, sterility may not be” [8].


  1. S. V. Lynch, R. A. Wood, H. Boushey, L. B Bacharier, G. R. Bloomberg, M. Kattan, G. T. O’Connor, M. T. Sandel, A. Calatroni, E. Matsui, C. C. Johnson, H. Lynn, C. M. Visness, K. F. Jaffee, P. J. Gergen, D. R. Gold, R. J. Wright, K. Fujimura, M. Rauch, W. W. Busse, and J. E. Gern, “Effects of early-life exposure to allergens
    and bacteria on recurrent wheeze and atopy in urban children,” J. Allergy Clin. Immunol. vol. 134, no. 3, pp. 593–601, Sept. 2014.
  2. K. Anagnostou, S. Islam, Y. King, L. Foley, L. Pasea, S. Bond, C. Palmer, J. Deighton, P. Ewan, and A. Clark, “Assessing the efficacy of oral immunotherapy for the desensitisation of peanut allergy in children (STOP II): A phase 2 randomised controlled trial,” Lancet, vol. 383, no. 9925, pp. 1297–1304, 12 Apr. 2014.
  3. G. Du Toit, G. Roberts, P. H. Sayre, H. T. Bahnson, S. Radulovic, A. F. Santos, H. A. Brough, D. Phippard, M. Basting, M. Feeney, V. Turcanu, M. L. Sever, M. G. Lorenzo, M. Plaut, and G. Lack, “Randomized trial of peanut consumption in infants at risk for peanut allergy,” N. Engl. J. Med. vol. 372, pp. 803–813, 26 Feb. 2015.
  4. A. T. Johnson, Biology for Engineers. Boca Raton, FL: Taylor and Francis, 2011.
  5. C. Schmidt, “Thinking from the gut,” Sci. Amer. vol. 312, no. 3, pp. S13–S15, Mar. 2015.
  6. J. L. Benach, E. Li, and M. M. McGovern, “A microbial association with autism,” MBio, vol. 3, no. 1, pp. 9–12, 14 Feb. 2012.
  7. J. G. Mulle, W. G. Sharp, and J. F. Cubells, “The gut microbiome: A new Frontier in autism research,” Curr. Psychiatry Rep., vol. 15, no. 2, p. 337, Feb. 2013.
  8. R. Patel, “Bugged,” Pop. Sci. vol. 287, no. 2, pp. 40–45, Aug. 2015.

  • Brian Lingard

    interesting comment on what is today extremely relevant. Our children are today exposed to a plethora of antibacterial: sprays:cleaners:hand washes etc. What will be the outcome for them? the balance between good hygiene practice and over-use of antibacterial products is a precarious one lets hope we get it right. As a family Doctor said to my own Mother many years ago ‘ your children need to eat a little dirt they are too clean.’

  • therealmccoys

    This article relates well to the reality we one with the environment, and when one is segregated from the environment they suffer.