Balancing Hygiene and Microbiome Health: Daycare and Household Cleaners



While deep cleaning may be okay and necessary in certain circumstances, antimicrobial compounds don’t distinguish between beneficial and unfriendly bacteria, and their overuse may have unintended effects on our microbiome.

How much should we clean our home?

Something called the hygiene hypothesis may provide clues.

The hygiene hypothesis was first proposed in 1989 by a scientist who observed that children from households with larger families had a reduced risk of hay fever [1]. This scientist deduced that the reduction in allergy in these households was due to an increased amount of bacteria present in the environment from older siblings [2]. Essentially, he was saying that the cleaner we are the more allergic we will be.

Since then, our knowledge has greatly expanded. We’ve come to realize that early exposure to a variety of microbes -such as those found in pets, farm animals, and the outdoors- during infancy plays a crucial role in reducing the risk of developing allergic diseases [3]. Instead, frequent use of harsh household cleaners is one of the factors that can negatively impact the microbial diversity that greatly benefits our gut microbiome [4], [5].

Keep reading to learn more about potential dangerous effects of using common household cleaners and daycare cleaning practices that you should be aware of.

Household cleaning products

Common harsh chemicals in household cleaners are bleach, MIPA-borate, and ammonium hydroxide. All of which may have negative effects on our health.

Here are some examples:

  • Bleach may increase the risk of non-allergic asthma for the person applying it [6], [7].
  • MIPA-Borate is suspected to interfere with natural hormone balance [8].
  • Ammonium hydroxide can cause nose and throat irritation and possibly respiratory irritation if used above the recommended concentration posted on the bottle [9].
  • Some studies suggest that the use of harsh household cleaners during pregnancy may make the baby more prone to suffer wheezing [10], [11]. The same could happen when children are directly exposed to these products [4], [5]. 
  • One study linked the use of harsh household cleaners to obesity in children [12].

Luckily, eco-friendly cleaning products are just as effective as bleach against unfriendly bacteria such as Escherichia coli and Staphylococcus aureus [13], [14].

These household cleaning products have less impact on individual health and the environment than conventional ones. Instead of containing potentially harmful chemicals, they contain natural ingredients like vinegar, baking soda, and essential oils. Bio-enzymatic cleaners are made of harmless bacteria that like to digest chemical and organic waste.

Ideally, an eco-friendly cleaner should be/have:

  • Biodegradable
  • Nontoxic
  • Free of harsh chemicals like phosphates, chlorine and hypochlorite
  • Dye-free
  • Natural fragrances
  • A label with a complete list of active and inactive ingredients

Our recommendation on household cleaning products 

  • Prefer eco-friendly products for everyday cleaning. These will be effective against common kitchen bacteria such as Salmonella and Campylobacter which can leave you running for the bathroom clutching your stomach. Eco-friendly, non-toxic cleansers can safely clean your counters without disrupting the balance of bacteria in the gut.
  • Another alternative could be a DIY cleaner containing 10% acetic acid (vinegar) and 1.5% citric acid [15].
  • While probiotic or enzyme cleaners are good for general household cleaning and for the environment, they are not disinfectants and therefore will not eliminate the coronavirus. Harsher cleaning products may still be useful for highly touched surfaces which may have been contacted by strangers such as doorbells and door handles during the course of the pandemic.
  • When using disinfectants, it is recommended to leave them to act on the cleaned surface until it dries and then rinse with water, because disinfectants can persist for a long period of time and may cause unintentional exposure to hazardous chemicals.
  • If you must dine out, it would be a good idea to wipe down surfaces like the table and high chair with a natural non-toxic wipe just to remove any excess chemicals that may linger after the sanitization process taken by staff.
  • Check the Environmental Working Group (EWG) web page, where you can search for household cleaning products and their potentially dangerous effects.

Daycare cleaning practices

With the pandemic, daycare centers and schools had to close. In order to re-open, they had to comply with strict cleaning guidelines and schedules. These may include disinfecting toys and games that babies/toddlers might put in their mouths and regularly using products containing bleach or other potentially harmful ingredients to clean toilets and sinks.

And also, a strict schedule of hand washing for all children attending daycare. The problem is that too much hand washing done inappropriately may have some negative consequences.

Here’s what happened in Denmark: To prevent the transmission of coronavirus, the Danish Health Authorities issued hygiene guidelines for children attending daycare centers. Children were instructed to wash their hands for 45 to 60 seconds with water and soap at least every 2 hours and also upon arrival at daycare, before and after meals, after toilet visits, after coughing/sneezing in the hand, and whenever hands were visibly dirty.

That’s a lot of hand washing. 

What happened? Such an intense regimen produced a marked increase in hand eczema in children [16]. In light of these events, there were new revised guidelines that included the use of a moisturizing lipid-rich cream after hand washing.

Here is how to correctly wash hands:

  • Use lukewarm water to wet the hands before applying the soap.
  • Apply enough soap to make foam that covers both hands.
  • Rub hand while singing “Happy Birthday” twice. This will ensure you thoroughly clean your hand for about 20 seconds.
  • Make sure to get into tricky spots, like in between your fingers.
  • Rinse hands well free of soap.
  • Dry hands gently after washing.
  • Use a moisturizing cream following hand washing or as frequently as possible.

Our recommendation on daycare cleaning

It’s a good idea to be aware of the cleaning practices conducted at daycare centers or schools and know what your child is exposed to. 

Daycare centers and schools usually provide a guide detailing cleaning procedures, but if there is no such guide, ask about what products are being used to clean, how often and at what times of the day.

Best practices daycare centers/schools should follow when cleaning include:

  • Harsh disinfectants and cleaning sprays should be preferably applied in the afternoon once the day has finished, not in the morning before the day starts. Definitely not while children are present.
  • Windows and doors should be kept open for appropriate ventilation while and after cleaning, unless there is an appropriate mechanical ventilation system.
  • Cleaning products have to be diluted correctly. Applying the undiluted product won’t be more effective, it will be dangerous.

Some products require rinsing with water after their application [17].


[1] M. Scudellari, “News Feature: Cleaning up the hygiene hypothesis,” Proc. Natl. Acad. Sci. U. S. A., vol. 114, no. 7, pp. 1433–1436, Feb. 2017, doi: 10.1073/pnas.1700688114.

[2] D. P. Strachan, “Hay fever, hygiene, and household size,” BMJ, vol. 299, no. 6710, pp. 1259–1260, Nov. 1989, doi: 10.1136/bmj.299.6710.1259.

[3] K. Lee-Sarwar, “The farm-like effect: Rural exposures in early life, the microbiome, and asthma,” J. Allergy Clin. Immunol., vol. 148, no. 1, pp. 89–90, Jul. 2021, doi: 10.1016/j.jaci.2021.04.020.

[4] J. Parks et al., “Association of use of cleaning products with respiratory health in a Canadian birth cohort,” CMAJ Can. Med. Assoc. J. J. Assoc. Medicale Can., vol. 192, no. 7, pp. E154–E161, Feb. 2020, doi: 10.1503/cmaj.190819.

[5] O. Mikeš, M. Vrbová, J. Klánová, P. Čupr, J. Švancara, and H. Pikhart, “Early-life exposure to household chemicals and wheezing in children,” Sci. Total Environ., vol. 663, pp. 418–425, May 2019, doi: 10.1016/j.scitotenv.2019.01.254.

[6] B. Matulonga et al., “Women using bleach for home cleaning are at increased risk of non-allergic asthma,” Respir. Med., vol. 117, pp. 264–271, Aug. 2016, doi: 10.1016/j.rmed.2016.06.019.

[7] K. W. Whitworth, B. Berumen-Flucker, G. L. Delclos, S. Fragoso, C. Mata, and D. Gimeno Ruiz de Porras, “Job hazards and respiratory symptoms in Hispanic female domestic cleaners,” Arch. Environ. Occup. Health, vol. 75, no. 2, pp. 70–74, 2020, doi: 10.1080/19338244.2019.1606774.

[8] “EWG’s Guide to Healthy Cleaning | MIPA-BORATE | Substance.” (accessed Dec. 20, 2021).

[9] M. J. Fedoruk, R. Bronstein, and B. D. Kerger, “Ammonia exposure and hazard assessment for selected household cleaning product uses,” J. Expo. Anal. Environ. Epidemiol., vol. 15, no. 6, pp. 534–544, Nov. 2005, doi: 10.1038/sj.jea.7500431.

[10] J. Henderson, A. Sherriff, A. Farrow, and J. G. Ayres, “Household chemicals, persistent wheezing and lung function: effect modification by atopy?,” Eur. Respir. J., vol. 31, no. 3, pp. 547–554, Mar. 2008, doi: 10.1183/09031936.00086807.

[11] L. Casas et al., “The use of household cleaning products during pregnancy and lower respiratory tract infections and wheezing during early life,” Int. J. Public Health, vol. 58, no. 5, pp. 757–764, Oct. 2013, doi: 10.1007/s00038-012-0417-2.

[12] M. H. Tun et al., “Postnatal exposure to household disinfectants, infant gut microbiota and subsequent risk of overweight in children,” CMAJ Can. Med. Assoc. J. J. Assoc. Medicale Can., vol. 190, no. 37, pp. E1097–E1107, Sep. 2018, doi: 10.1503/cmaj.170809.

[13] N. Goodyear, N. Brouillette, K. Tenaglia, R. Gore, and J. Marshall, “The effectiveness of three home products in cleaning and disinfection of Staphylococcus aureus and Escherichia coli on home environmental surfaces,” J. Appl. Microbiol., vol. 119, no. 5, pp. 1245–1252, Nov. 2015, doi: 10.1111/jam.12935.

[14] N. Goodyear et al., “Cleaning and disinfection in home care: A comparison of 2 commercial products with potentially different consequences for respiratory health,” Am. J. Infect. Control, vol. 46, no. 4, pp. 410–416, Apr. 2018, doi: 10.1016/j.ajic.2017.09.033.

[15] M.-K. Zinn and D. Bockmühl, “Did granny know best? Evaluating the antibacterial, antifungal and antiviral efficacy of acetic acid for home care procedures,” BMC Microbiol., vol. 20, no. 1, p. 265, Aug. 2020, doi: 10.1186/s12866-020-01948-8.

[16] A. B. Simonsen, I. F. Ruge, A. S. Quaade, J. D. Johansen, J. P. Thyssen, and C. Zachariae, “Increased occurrence of hand eczema in young children following the Danish hand hygiene recommendations during the COVID-19 pandemic,” Contact Dermatitis, vol. 84, no. 3, pp. 144–152, Mar. 2021, doi: 10.1111/cod.13727.

[17] W. Wei, J. Boumier, G. Wyart, O. Ramalho, and C. Mandin, “Cleaning practices and cleaning products in nurseries and schools: to what extent can they impact indoor air quality?,” Indoor Air, vol. 26, no. 4, pp. 517–525, Aug. 2016, doi: 10.1111/ina.12236.