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Spring Cleaning With Your Microbiome in Mind

Have you considered how the antimicrobial products you’re using to scrub your home affect your microbiome? We’re digging into the dos and don’ts of cleaning with the help of Dr. Cezmi Akdis, immunologist, director of the Swiss Institute of Allergy and Asthma Research, and Seed Scientific Advisor.

5 minutes

15 Citations

Spring is in full swing. If you’re ready for some good old-fashioned spring cleaning, consider this: How do the products you’re using to scour and scrub your home affect your microbiome? 

The sharp increase in rates of autoimmune and allergic disorders over the course of the 20th century has led some researchers to look to our environments for answers. How might the spaces we call home impact certain aspects of our health, including our microbiomes and epithelial barriers (the protective cellular layers that line the surfaces of the skin, respiratory tract, and gut)?

One theory—the Microbiome Depletion or “Lost Friends” theory—proposes that a loss of “good” bacteria in homes and surroundings (due in large part to our attempts to eradicate the “bad” bacteria with antimicrobial agents like bleach and antibiotics) could be disrupting the early development of our microbiomes. This has major implications for immune system function, as early microbes play a critical role in the development and training of our immune cells. The reduction of “good bacteria” also means less ongoing exposure to a wide range of microbes as we age. A microbially diverse environment, however, is important to maintain a diverse, balanced microbiome throughout life (a key indicator of human health). In fact, study after study has shown that many of the most pernicious noncommunicable diseases—including asthma and inflammatory bowel disease—are linked to disruptions of the microbiome.1-3 

Our efforts to get rid of bacteria have had other consequences, too. In addition to indiscriminately targeting both “bad” and “good” bacteria, many of the compounds included in common cleaning agents simultaneously have been shown to disrupt our epithelial barriers. This allows pathogens and other unwanted substances to enter our bodies and trigger inflammatory immune responses.4 The Epithelial Barrier Theory, proposed by Dr. Cezmi Akdis (immunologist, director of the Swiss Institute of Allergy and Asthma Research, and Seed Scientific Advisor), posits that this damage to our epithelial barriers, along with a loss of microbial biodiversity, underlies the rise in autoimmune and allergic disorders.5

So, what to do about that bottle of all-purpose cleaner? With the help of Dr. Akdis, we’re looking at how best to mitigate these disruptions and promote a microbiome-nurturing home.

If I Really Want to Protect My Health, Should I Never Clean My House? 

Not quite. First, it’s important to note the difference between cleaning or tidying and sanitizing or disinfecting. Cleaning your home—wiping down high-touch surfaces, clearing away food waste, using some elbow grease in the bathroom—is necessary to keep your home safe for you, your roommates or family, and your pets. Sanitizing or disinfecting, on the other hand—using the kind of industrial-strength cleaners that are common in medical settings and which became increasingly popular during the pandemic—generally isn’t necessary in a private home, and could be doing more harm than good. 

Consider much maligned dust, for example. House dust has actually been found to be a reservoir of microbial communities that modulate the human microbiome. One review suggested that exposure to higher amounts of allergen and house dust may actually protect against, and potentially alleviate, genetic allergies—however, this is significantly dependent on the bacterial species present in the household dust.6 

While it’s impossible to identify the specific microbial content of our household dust just by looking at it, the message here is that a bit of dust won’t hurt you—and, in fact, it might just help. While there may be times when more thorough cleaning is necessary (certain pathogens such as norovirus, for example, are resistant to anything but bleach; food prep areas where raw meats or eggs are present should be cleaned to avoid salmonella), in most homes and at most times of the year, cleaning doesn’t need to be fastidious or aggressive to be effective. 

Which Ingredients Should I Avoid When I’m Buying Household Cleaning Supplies? 

“Natural,” “clean,” and “green” are marketing buzzwords, but there is little to no regulation around when and how these terms can be used. Even products that might be labeled eco-friendly can include ingredients that stress your microbiome.  

Dr. Akdis is especially wary of ingredients that can cause stress or damage to the epithelial barrier. That’s because intact skin and mucosal barriers are crucial in protecting host tissues from infections, pollutants, and allergens, and a defective epithelial barrier has been linked to a range of autoimmune diseases, from inflammatory bowel disease to asthma.7 One study, for example, showed that women who frequently used bleach while cleaning were more likely to suffer from non-allergic asthma and common cough.8

Common epithelial barrier disruptors in household cleaning products include:

  • Anionic detergents and surfactants such as sodium dodecyl sulfate (SDS), sodium lauryl sulfate (SLS), sodium lauryl ether sulfate (SLES), and ammonium lauryl sulfate (ALS).
  • Non-ionic surfactants such as alcohol ethoxylates. 
  • Mild amphoteric surfactants such as cocamidopropyl betaine.
  • Formaldehyde 
  • Parabens, which are used as preservatives and can mimic hormones in the body.
  • Chlorine
  • Triclosan, an antimicrobial agent.
  • Artificial fragrances, which may contain phthalates that can interfere with the endocrine system.

As for what to use instead? Dr. Akdis cleans all surfaces in his home with a mix of vinegar, baking soda, and water. For carpet cleaning, he recommends sprinkling baking soda on the carpet and allowing it to sit before vacuuming. 

What Can I Do to Protect My Health While Cleaning?

Dr. Akdis recommends avoiding harsh all-purpose cleaners or those that include bleach when you can. If you do choose to use these kinds of cleansers, wearing gloves to protect your skin and ensuring proper ventilation while cleaning are measures that can help limit exposure to any harmful compounds contained within these products.

As for laundry and dish detergents, Dr. Akdis’ team has conducted research showing that many commercial detergents leave behind residues on items like mattresses, pillows, and clothing, that contain barrier-damaging compounds that are easily inhaled.9 The best way to avoid these? 

  • Look for detergents without alcohol ethoxylates or surfactants, as both are shown to be epithelial disruptors  
  • Use less than half the recommended amount of detergent to minimize toxic load
  • Avoid rinse-aid and fabric softeners, both of which contain chemicals that remain on clothing and dishes after washing
  • Incorporate an additional rinse cycle in dishwashers and laundry machines to lessen the amount of detergent residue left on clothing and dishes

Is There Anything I Can Do to Make My Home More Supportive of My Microbiome? What About Probiotic Cleaners? 

The recent increase in interest in how the microbiome affects overall health (good!) has led to a proliferation of products that claim to contain probiotics for wellness (less good). This includes everything from breakfast cereals to toilet bowl cleansers. While a few recent studies have shown that cleansers made with specific bacterial strains are successful at fighting certain pathogens in hospital and dental settings, it’s difficult to know whether commercially available “probiotic” cleaners contain these particular living strains in the necessary quantities.10,11 

However, there are simple ways you can make your home more microbiome-friendly: 

  • Nurture your house plants. Just one cm3 of soil contains as many microbes as there are humans in the world, so treat yourself to a new potted fern or herb garden.12 One study found that touching soil or plants, such as during gardening, temporarily increases diversity of the skin microbiome.13 
  • Adopt a pet. Studies show that children growing up in homes with dogs are at lower risk of developing allergic diseases, likely due to the increased exposure to microbial diversity.14 
  • Open your windows. One study of indoor spaces showed that homes where windows were frequently opened had fewer gram-negative (i.e., antibiotic resistant) bacteria, and that naturally vented areas had better diversity of overall microbes.15



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