How the Home Microbiome Impacts Health (& How to Improve It)

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The home microbiome. How it impacts health and how to improve it.
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Thanks to a bunch of recent research, most of us have at least a passing familiarity with our gut microbiomes and how much the bacteria in our bodies impact our lives.

We even now understand that our skin has a microbiome and so does our mouth. But what science is just starting to reveal and understand is that our daily environment also hosts a diverse population of bacteria and our daily interaction with this greatly influences our bodily microbiome as well.

In short, our outer world impacts our inner microbial world… and vice versa. This microbial environment is diverse and may even help protect us from disease… as long as we don’t bleach it to death!

What is a Home Microbiome?

Our homes have a rich and diverse microbial environment. We can now test microbes in the home and environment and start to understand them. While many people are familiar with “germs” and dangerous pathogens, all of the beneficial strains are often not as well understood.

A swab of the indoor door trim of homes around the country revealed “more than sixty-three thousand species of fungi and a hundred and sixteen thousand species of bacteria.” This includes many beneficial species of bacteria, leading researchers to believe that our environmental microbiome works synergistically with us and may even help protect us from harmful bacteria.

Factors like pets, access to outdoors, and houseplants all changed the microbial environment in a home.

Why the Home Microbiome is So Important

This microbial environment develops in reaction to us and our microbes but also in response to the outside factors that come in contact with our environment, including pets, pesticides, chemical cleaners, and so much more.

I’ve written before about how kids (and adults) need dirt, but it turns out that “dirt” in our home environment is important too. We know, for instance that children who are exposed to pets at an early age have up to a 13% reduced risk of asthma. Even more startling, Amish children and children who grow up on farms show a more diverse microbiome. They also have a 50+% reduced risk of developing allergies and autoimmune conditions.

We also know that the reverse is true and that, for instance, cell phones can be more contaminated that toilet seats. And the air-blowers in public bathrooms spew harmful bacteria all over. Toilet seats and pillow cases, it turns out, have very similar microbial patterns.

This microbiome interacts with us and us with it all day everyday. Since we now spend more time indoors than outdoors and indoor air can be much more polluted, perhaps its time to give the home microbiome more than a passing thought.

Factors That Harm the Home Microbiome

So we know that pets and exposure to the bacteria on a farm can improve the microbial environment. Unfortunately, some factors can harm the home microbiome as well:


Modern homes are more likely to harbor mold because they are well-insulated and have materials like wood and paper where mold can easily grow. Toxic mold metabolites can cause skin and lung irritation and even DNA damage. There is no safe level and many of us are exposed without even knowing it.

Mold also causes an imbalance of the bacterial environment in a home and makes it easier for harmful bacteria to grow.

Antibacterial Products

You’d think with hundreds of thousands of fungi and bacteria in our environments, using antibacterial products would be a good thing, but it turns out the opposite is true.

Research shows that plain ol’ soap and water is just as effective as antibacterial products, and possibly much safer too! Exposure to antibacterial soaps can alter our skin and gut microbiome. Since we also now know that the body’s microbiome affects gene expression, this is a really big deal!

In the same way, the use of antibacterial and disinfecting products in the home can change the home microbiome. As research reveals more and more about our daily interaction with microbes, understanding and using safe cleaning products becomes increasingly important.


Studies show that pesticide exposure changes the microbiome of the body, and this is true of the home microbiome as well. Yet many people spray pesticides on and around the home on a regular basis.

How does it get in the house? Ever wear shoes inside? Even if we don’t spray our yards, studies show wearing shoes in the house can track in many unsavory elements from when we were out and about during the day.

How to Improve the Home Microbiome

Enough with the bad news! Now, let’s talk about some simple and practical steps we can all take to support the home microbiome:

Add Good Bacteria to the Environment

Especially if we are starting with known factors that harm the home microbiome like mold, pesticides, or strong use of antibacterial products, it can make sense to start by adding beneficial probiotics to your home. I personally did this when we recently moved to a new home where I knew pesticides were used.

What I do: I used Homebiotic spray all over our house before we moved in and use it once a month or so to keep the microbial environment optimized. This spray is specifically designed (and lab-tested) to reduce mold growth and improve the bacterial environment in a home.

Take Off Shoes Inside (& Outside Too)

Many countries have a firm tradition of removing shoes before entering a home. Turns out that there are some good health reasons for this too, especially depending on where you live. Think about this: we walk around all day outside and likely on grass sprayed with herbicides and pesticides. When we wear shoes inside, all of these things get tracked into the home and onto the floors where our children and pets play.

What I do: Not every outdoor environment is harmful. As a general rule, we remove shoes because we’ve worn them to stores or in public places that are likely to be contaminated. We also make an effort to go barefoot outside in our own yard (that we do not spray with pesticides or fertilizers) to get the benefit of the beneficial soil bacteria.

Use Natural Cleaning Products

Antibacterial cleaners and disinfectants kill even the beneficial bacteria in the home environment and alter the microbiome. Of course, we all need to keep our homes clean… and this is where natural cleaners come in. Natural cleaners like natural soaps and water are effective enough to clean big messes when needed but don’t have a long-term negative effect on the home microbiome.

What I do: I personally use Branch Basics for almost all of my cleaning including laundry, bathrooms, and even as a natural body soap. I also keep these DIY disinfecting wipes on hand for wiping down counters after preparing raw meat or if one of the kids gets sick.

Avoid Pesticides and Antibacterial Products

With so many natural alternatives, it is now easy to avoid pesticides and harsh antibacterials. One important first step is even free: just don’t buy the bad stuff to begin with!

What I do: I use diatomaceous earth instead of harsh pesticides in our home. I also choose or make my own natural cleaners and avoid antibacterial products. This homemade hand soap is a good place to start.

Be More Bacterial Yourself

We affect and are affected by our microbial environment so the more beneficial bacteria we host, the more our environment has as well. More on this below, but some good ways to increase your own beneficial bacteria are through probiotic-rich foods, exposure to healthy soil-based organisms, and using only natural soaps.

What I do: I make sure I spend time in the garden, which is great for a variety of reasons. (Studies show that gardeners live longer!) We also consume probiotic-rich foods, like sauerkraut, and use natural soaps like castile soap and Branch Basics on skin.

Adopt Some House Plants

Adding a few well-chosen plants to your home is a great way to boost good bacteria. Plants (and the dirt they live in) come with a wide variety of viruses and bacteria and over 99% of these are harmless or beneficial.

What I do: Adding even just one houseplant per room is a great way to alter the home microbiome. Check out this list of the most beneficial houseplants that have the added benefit of helping purify indoor air.

Or Even Adopt a Pet

As mentioned above, having a pet in the home is correlated with a reduced risk of asthma and allergies in children. It is a big commitment, but adopting a dog or cat is a great way to improve your bacterial environment. (And a great way to save a pet in need as well).

What I do: We have a cat and a dog (and had hamsters at one point too).

Only Sanitize When Truly Necessary

Another totally free step… just avoid the disinfectants and sanitizers, at least most of the time. Regular household messes don’t actually warrant the big guns. In most cases, the disinfectants themselves are much more harmful than anything they are designed to kill. In fact, even toilets aren’t as dangerous as you’d think. The bacteria from feces has to be swallowed to cause infection. (Most are organism-specific so dogs and cats are generally even safe drinking out of the toilet — though I wouldn’t recommend it).

When you do disinfect, start with hydrogen peroxide. It kills viruses, bacteria, and fungi and is the safest natural disinfectant around.

What I do: 95% of the time I just use natural cleaners and water for household cleaning. In the rare cases I need more serious disinfecting, I just use hydrogen peroxide. Make sure to keep it in an opaque dark-colored spray bottle. Spray only shared items and exposed surfaces, not the whole house.

Consider an Air Filter for Particulate Pollution

In most cases, adding some house plants and switching to natural cleaners is enough to improve the home microbiome. In areas with a lot of pollution or homes with smoke or mold damage, a really high quality air filter is a great addition. This also helps with pet hair and dust.

What I do: We have several Air Doctor air filters in our home to catch particulate pollution and also airborne viruses. They filter down to 0.003 microns, making them ultra-HEPA and great when needed.

What is your home microbiome like? Do you take any of these steps? Share below!

Katie Wells Avatar

About Katie Wells

Katie Wells, CTNC, MCHC, Founder of Wellness Mama and Co-founder of Wellnesse, has a background in research, journalism, and nutrition. As a mom of six, she turned to research and took health into her own hands to find answers to her health problems. is the culmination of her thousands of hours of research and all posts are medically reviewed and verified by the Wellness Mama research team. Katie is also the author of the bestselling books The Wellness Mama Cookbook and The Wellness Mama 5-Step Lifestyle Detox.


13 responses to “How the Home Microbiome Impacts Health (& How to Improve It)”

  1. Claude Avatar

    Hi, do you know if you could make your own probiotic spray, using distilled water and a probiotic capsule, if that is really all the ingredients in the Homebiotics product? Thanks

  2. Leslie Avatar

    How would you clean a shower that is prone to mildew even thought we leave the door open to let the shower dry. OR how would you clean Jacuzzi jets? I will do everything natural except those two and I can’t find anything that will clean it well.

  3. Mara Avatar

    Wow! thank you for all these great tips! I’ve never thought of my homes “microbiome” but it totally makes sense.
    I’ve been able to stop using harmful chemicals in our home with some awesome towels.
    Keep the great content coming 😀

  4. Molly Avatar

    I enjoyed this post – thank you! I do wonder, though, what you recommend for getting rid of mold (say, on window frames in an old house)? I’ve used bleach-water in the past (at a former apartment), but wonder if there’s a less toxic formula that would eradicate the mold as well or better. Something that includes essential oils, perhaps?

  5. Nic Avatar

    I seen a service that is specifically for this. The process essentially “resets” your home biome with high levels of ozone gas and an inoculation of “Effective Microorganisms”. The ozone mimics the same process that creates lightning (the smell after a storm is actually ozone gas). It destroys viruses and bacteria, mold spores, mycotoxins, dust mites, odors, VOC’s… the list is long. The EM then has the ability to populate your indoor environment and provide powerful competition to any harmful microbes that may be introduced from outside. The EM also works to eliminate toxins including residual mycotoxins. I’ve seen nothing but positive results from this process.

  6. Emma Avatar

    I’ve become much more aware of my body’s microbiome lately and it is thanking me for the effort. So I want to extend this to my home to make it healthy as well.

    I use far too many chemicals round my home and really want to reduce this.

    Thanks for these wonderful tips. I am going to start putting them into practice.

  7. Kathleen Avatar

    Hmm. I’ve been thinking about my house biome… the child I’ve had since we no longer have a dog and since I started making sourdough has been my first (of 5) to have problems with thrush. I have been wondering if I tipped the balance of bacteria versus yeast (even beneficial type with the sourdough cultures constantly being fed) in my home to make this little one more susceptible. Wish I had before-and-after swabbed my own home to verify. Thanks for the post, Katie!

  8. Jenya Avatar

    I make ” bio enzymes” , by fermenting fruit peels in lightly sugary water for 3 months. I add them into water for cleaning and mopping.

  9. Leslie Avatar

    Karie, I’ve been following you daily for years. What an excellent article. So very important for this day we live in. I am printing it out to study it. Thank you!

  10. Motto Avatar

    Excellent article. Never over clean your environment influenced by many advertisement, like kill s 99.9% bacteria.
    We need to live with them as we cannot live in an industrial “clean-room” kind of environment.

  11. OMAR Avatar

    The cultures that took off their shoes before entering a home had the right idea but they weren’t fully conscious of completely eliminating cross contamination from every angle. I mean, what’s the point of not tracking in harmful bacteria from the outer world through your shoes if you’re not giving the same treatment to your hands and other areas? This is why I disagree with those that advise to not sanitize often or thinking that you’re going to take care of harmful bacteria you’ve contracted transdermally by orally taking in more probiotics. You’ve got to nip it the bad bacteria in the bud and sanitize after coming into contact with doorknobs, shopping carts, gas pumps, items that have had contact with the floor, shaking hands etc. Plus the fact that we have the devil’s bacteria in the air through chemtrails, you’d be insane to not sanititze often.

  12. Helene Avatar

    We take off our shoes for the old-fashioned reason of … dirt. We don’t want dirt tracked all over the house from outside. The cultures that removed their shoes were very ahead of us!

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