Clean Living

Our Top 5 Favorite Microbe-Friendly Household Cleaning Products

Our Top 5 Favorite Microbe-Friendly Household Cleaning Products

There’s nothing better than a beautifully clean home. It’s a sanctuary, your space away from the world, and of course, a place for you and your family to come together and make memories that last a lifetime.

There’s just one problem…most of the cleaners on the market are actually quite bad for your home’s microbiome. That’s right, your home has an ecosystem of bacteria just like your body does, and it has a direct effect on your health. Unfortunately, many of our overzealous cleaning habits are devastating to our indoor ecology, with harsh chemicals and antibacterial products destroying both helpful and inhospitable bacteria indiscriminately. No wonder it’s so hard to stay healthy!

The results can be devastating: without a balanced indoor microbiome, your own microbiome can suffer, as underexposure to beneficial bacteria can affect your body via your skin microbiome, your immune function, and even the air you breathe. And if you’ve got kids, it’s especially problematic. You see, kids’ immune systems are still developing as they grow into adulthood, and they need to interact with a wide variety of microbes for their immune systems to learn how to respond appropriately to all kinds of stimuli.

The good news is, there are more microbe-friendly natural cleaning products on the market than ever, and you can simply swap them out for your old, chemical-laden cleaners. Whether you're wiping down the counter, need a natural laundry detergent that won't drive your skin crazy, or just want the easiest way to clean without decimating your family’s microbiomes, we've got you covered with our top choices for non-toxic, microbe-friendly cleaning products.

How to Get That Green Clean (Without Killing Your Microbial Allies)

1. Aunt Fannie's

Aunt Fannie’s got its start when founder Mat realized that his son’s mood swings and immune function challenges had their roots in their well-intentioned, but ultimately harmful, overcleaning of their house.

When he started looking into the “natural” cleaners they were using, he realized that they weren’t so natural after all, and so he set out to make his own. What started as a simple mission to help his son feel his best resulted in an impressive line-up of microbe-friendly products made from whole, food-based ingredients to keep your home—and your body—clean and microbially diverse. Oh, and did we mention that every single one of their cleaning products has earned an "A" from Environmental Working Group?

2. Molly's Suds

What you put on your body is just as important as what you put in it––the gut-brain-skin axis means that the health of your skin microbes has a direct, significant impact on the rest of your microbiome. And this goes double for those of us with little ones around! Their sensitive skin and still-developing immune systems simply can’t handle the harsh chemicals found even in so many “gentle” or “baby-safe” cleansers.

Molly’s Suds beautifully sidesteps this problem by using safe, food-grade ingredients for a truly effective clean that doesn’t compromise you or your little ones’ health. What's more, by allowing your natural flora to do their work on your skin, it also contributes to your home's microbiome. You see, the microbiome goes both ways: you pick up bacteria from the surfaces around you, and you also shed skin cells and bacteria as you move around your home. The more friendly bacteria on your skin, the more you can contribute to your home's ecosystem!

3. Airbiotics

We often don’t really think about the quality of our air until it becomes noticeably bad––but the air in your home contains a mix of bacteria, VOCs, and toxins from cleaning and building products. What’s more, most modern construction techniques don't allow buildings to “breathe.” While creating airtight seals is great for saving energy, it can create an undesirable stew of indoor pollution. (Just think about that stale, still smell that a room gets if you seal it up for a while and you’ll start to get the idea.)

Airbiotics cleaning products are a great way to keep your indoor microbiome fresh while also taking care of potential issues like dust mites and pet dander. Made with probiotics, these surface cleaners remove the biofilm that acts as a food source for unwanted bacteria, making it difficult for them to colonize surfaces (and from there your air supply), helping restore balance to your indoor microbiome and keeping your home smelling great without the use of potentially toxic perfumes or synthetics.

4. Branch Basics

If you’re into minimalism, Branch Basics is the brand for you. With just one concentrate that works for everything––and we do mean everything, from produce to laundry to grout––it’s a great solution for those who like to keep things simple. Even better, it’s not going to do a number on your indoor microbiome. (After all, if you’re going to be putting something all over your home, you want to make sure it’s safe for the whole family!) With no VOCs, toxins, synthetic preservatives, or pollutants, it’s created with a “first, do no harm” mentality that keeps your home safe for all its inhabitants—big, small, and microscopic.

5. Seventh Generation

A classic for a reason, Seventh Generation offers a wide range of home cleaning products, as well as personal care products that are specifically designed to go easy on sensitive skin. By using botanical ingredients like thymol (rather than artificial chemicals) to address unwanted bacteria, they give you all the clean you want without doing a number on your home's beneficial bacteria. We’re especially big fans of the way they list all their ingredients on the label so you can see exactly what you’re getting, and their dedication to explaining the science behind those ingredients. But our favorite part might just be their blog, where they regularly dole out tips for mindful, microbe-conscious cleaning.

With all they're up against, our microbes need all the help they can get––so the next time you're stocking up on cleaning products, make sure to keep your friendly flora in mind and use effective, responsible products like these. All the clean, without compromising your microbial health? That's the ultimate win-win!


Rachel Allen is a writer at Hyperbiotics who's absolutely obsessed with learning about how our bodies work. She's fascinated by the latest research on bacteria and the role they play in health, and loves to help others learn about how probiotics can help the body get back in balance. For more ideas on how you can benefit from the power of probiotics and live healthier days, be sure to subscribe to our newsletter. To learn more about how a healthy microbiome can enrich your life, subscribe to our newsletter.