Good Bacteria Guide: Why Too Clean Isn't Healthy

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Think all bacteria is bad? Think again! In this Guide to Good Bacteria, we share the dangers of over-sanitation and how being too clean can lead to many serious diseases and infections, including gut problems and immune disorders. Discover five tips on how to boost health, digestion, and immunity by increasing your exposure to the right kind of good bacteria (bonus: you'll likely even lose weight!). 

Think all bacteria is bad? Think again! In this Guide to Good Bacteria, we share the dangers of over-sanitation and how being too clean can lead to many serious diseases and infections, including gut problems and immune disorders. Discover five tips on how to boost health, digestion, and immunity by increasing your exposure to the right kind of good bacteria (bonus: you'll likely even lose weight!). 

This post is sponsored by Mother Dirt. All thoughts and opinions are my own. Thank you for supporting the brands that make it possible for Root + Revel to provide free content and healthy living inspiration.

Are you someone who washes your hands excessively throughout the day, or carries around hand sanitizer wherever you go?

Are you someone who can't stand for your kids to be outside in the dirt, washes your produce like it's your job, or obsessively cleans your house (potentially even with hazardous substances like bleach) to be sure things are sterilized?

Whether you're an obsessively clean germaphobe or not, over-sanitation in our modern world is actually a bigger problem than you probably think… for ALL of us.

Even if you're not a clean freak, it's more than likely that your exposure to good bacteria has been limited with modern life–and this poses a big problem.


Most of us are living remarkably germ-free lives compared to our ancestors, yet becoming sick more and more often.

Studies have suggested that early life exposure to microbes (i.e. germs) is an important determinant of adulthood sensitivity to allergic and autoimmune diseases, including hay fever, asthma, Irritable Bowel Syndrome (IBS), Leaky Gut, Celiac Disease, Depression, ADHD and a whole lot more. (source; source)

This means, the less you're exposed to a variety of good bacterias at a young age, the more likely your chances are to develop these serious conditions.

Although many of us have been led to believe that all germs are potentially dangerous–and that the cleaner our diets, bodies and environments stay, the better–there's actually a fine line.

As it turns out, our culture's obsession with sterilization is, in many cases, a detriment vs. a benefit. Dirty is good, there is such a thing as too clean. Really!

But let's back up.

What is good bacteria, anyway?

RELATED:  Embrace Bacteria for Better Skin with Mother Dirt

Think all bacteria is bad? Think again! In this Guide to Good Bacteria, we share the dangers of oversanitation and sterility and how this can lead to many serious diseases that we see plaguing our world. Find out five tips for how to boost your health and immunity by increasing your exposure to good bacteria. 


About 100 trillion bacteria, both good and bad, live inside your digestive system. Collectively, they're known as the gut microbiota or the “microbiome”.

Within those trillions of gut bacteria are about 1,000 different species, represented by some 5,000 distinct bacterial strains. In fact, the human body has nearly 10 times the amount of bacterial cells as it does human cells. (source)

We'll get into a detailed post next month all about the microbiome, but for now, it's enough to know that our gut/microbiome plays a HUGE role in our health (from digestion to skin, immunity and thyroid, mood and anxiety, metabolism, etc.)–one we are uncovering more and more about each day.

RELATED:  Get to Know Your Gut: What Are Probiotics?

In recent years, cutting-edge science and research has begun to look more closely at how this enormous system of organisms influences–and even improves–health conditions, from heart disease to arthritis to cancer.

The main factors that affect your personal microbial mix are age, diet, environment, genes and medications.

Everyone's gut microbiome is unique, but there are certain combinations and collections of bacteria that are found in healthy individuals, and initial research findings suggest gut bacteria may be the key to preventing or treating a whole bunch of diseases. (source)

In total layman's terms, helpful or “good” bacteria is anything that keeps your gut healthy, like probiotics. These organisms fight pathogenic or “bad” bacteria, help regenerate cells, produce vitamins, break down our food and more. (source)

Thus, without good bacteria, our bodies can't thrive. Herein lies the inherent problem: with an overly sterilized environment, we kill not just the bad but ALSO the good bacteria.

In fact, we need exposure to BOTH good and bad bacteria to build up our resilience against illnesses.

Think about it: as a species, we have evolved with numerous types of microbes for millions of years and, as a result, have learned to successfully adapt to those most prevalent in our environments and food supply. (source)

From the time we are born, our bodies’ natural defense mechanisms are actually made stronger as we come into contact with an array of microbes.

It's the same premise behind the flu shot: when you get the flu shot, you're actually receiving a small amount of the influenza virus itself. In theory, it's just enough that your body can recognize this bacteria as not being a threat, so that when you are actually exposed to the flu later on, your body thinks it's no big deal, doesn't overreact and uses its good bacteria to fight off those bad bacteria.

RELATED:  5 Ways to Strengthen Your Immune System

When our immune system lacks practice fighting bacteria and viruses, perhaps from an overly sanitary/clean lifestyle, another part of our immune system becomes too powerful and overreacts. This can manifest as an allergic reaction to harmless substances, like pollen, certain foods (hello nut allergies!) or other substances.

Moral of the story: it’s crucial to understand that exposure to certain germs and bacteria is not inherently bad, as it actually helps our bodies fight off bad bacteria and disease in the long run.

For more information on this topic of good bacteria–especially if you're interested in Leaky Gut–check out the book Eat Dirt by Dr. Josh Axe.

In it he explains how what we regard as modern “improvements” to our food supply–including refrigeration, sanitation, and modified grains–have damaged our intestinal health, and that it’s essential to get a little “dirty” in our daily lives in order to support our gut bacteria and prevent Leaky Gut Syndrome and other digestive disorders.

Think all bacteria is bad? Think again! In this Guide to Good Bacteria, we share the dangers of oversanitation and sterility and how this can lead to many serious diseases that we see plaguing our world. Find out five tips for how to boost your health and immunity by increasing your exposure to good bacteria. 


Ironically, parents try to keep infants and young children protected from bacteria, yet microbial exposure during the earliest periods of life seems to be the most important for long-term immunity.

It's no coincidence that, as we've started reducing our children's exposure to the quantity and variety of bacterias, we've seen more chronic illnesses, inflammation, allergies and the like than ever before.

A study published in the journal Science done by researchers at Brigham and Women’s Hospital in Boston shows that when mice are exposed to an increased number of bacteria (especially from a very young age), they develop a normalized immune system and wind up becoming more capable of warding off future health problems compared to mice who are kept in an oversanitized environment. (source)

RELATED:  How To Heal Leaky Gut + Cure IBS Naturally

But it's not just mice. In the late 1990s Dr. Erika Von Mutius, a health researcher, compared the rates of allergies and asthma in East and West Germany. She found that children in the polluted, dirtier and less healthful areas of East Germany had LOWER allergic reactions and fewer cases of asthma than children in the West, with its cleaner and more modern environment.

How can this be? One explanation is that the children in the poorer cities were exposed to more bacteria, meaning that their immune systems developed more tolerance for the irritants that cause asthma. These children were also around other children more often, coming from larger families and being in daycare, which also increases exposure to microbes. (source)

It's one of the reasons that I plan to use gentle cleansers on my babe when he arrives in September, not to mention limiting his exposure to antibiotics and products that wipe out all bacteria (like bleach), putting him on infant probiotics right away and exposing him to lots of other kids in daycare.


This all begs the question: how can we keep our gut happy and increase good bacteria?

Don't worry–we've got ya covered with these helpful tips!


By now, you've likely heard about the importance of taking a daily probiotic to nourish your gut. For a complete guide to probiotics, check out this post.

RELATED:  How to Get Probiotics from Food: Vegan Probiotic Yogurt

But did you know that the human body fights diseases NOT just through the gut microflora and immune system, but also through the skin layer?

After all, your skin is your biggest organ and what you put on your skin gets directly absorbed into your body. In fact, many people don't know that your skin also has its own microbiome that relies on good bacteria to help us be healthy.

Just like we've oversterilized our internal bodies, we've done the same with our skin through antibacterial washes and gels, antibiotics (topical and ingested), and exposure to other harsh substances in toiletries, makeup and our everyday environments that have continually been damaging the skin microbiome.

This prevents the skin biome from performing it’s crucial role, likely leaving the skin more susceptible to a variety of problems.

That's why I was so excited when I discovered Mother Dirt a couple years ago because they created a line of preservative-free, hypoallergenic products all bursting with good bacteria! Cool, right?

Their products–which include a face and body mist, cleanser, moisturizer and shampoo–help restore and maintain good bacteria on your skin and hair.

While great for anyone to achieve and maintain proper balance, these products are especially supportive if you have skin blotchiness or redness, acne, dry, oily or sensitive skin, or skin infections. Their products have been proven to improve skin appearance within 2-4 weeks! (source; source)

Mother Dirt is having a birthday sale from July 7 -9, 2018, with 25% OFF on the entire store, so stock up now! You can also buy it here on Amazon.


There are so many dangers of overtaking antibiotics (I recommend this article from Dr. Axe for more info).

Overusing antibiotics can wipe out both good and bad bacteria in the gut, so only take them when absolutely necessary. (source) This is especially important when it comes to babies and children, as the impact of antibiotics at a young age may have lifelong impacts.

Instead of being quick to ask for antibiotics to fight viral ailments like the common cold, check out natural remedies and other solutions. If you do get prescribed an antibiotic, ask your doctor if you really need it, what is the shortest treatment course, and whether there are alternative methods.

And if you must take antibiotics, be sure to also supplement with probiotics heavily while you're on the medication. My favorite is Seed’s Daily Synbiotic–go here to use the code ROOTANDREVEL to get 15% off your first month! A synbiotic is a combination of probiotics and prebiotics–prebiotics are a special form of dietary fiber that act as a fertilizer for the good bacteria in your gut, and this supplement is backed by legit science. Read more about it here.

RELATED:  4 Myths About Probiotic Supplements


Bacteria are living organisms that need to eat. A real food-based, varied, balanced diet rich in fiber is good for the bacteria living in your gut and encourages a diverse ecosystem. (source)

Here are some of top foods that nourish your good bacteria:

  • Naturally fermented and probiotic rich foods: sauerkraut, pickles, miso, certain types of yogurt, kefir, cultured veggies, apple cider vinegar and kombucha
  • Allergy-fighting and gut-building prebiotic rich foods: onions, asparagus, raw chicory root, raw Jerusalem artichokes and dandelion greens (source)
  • Natural antibacterial foods: raw garlic, onions, mushrooms, turmeric, echinacea, manuka honey, oregano oil, colloidal silver (source)
  • Gut healing Bone broth (get our homemade recipe here or stick to healthy convenience with Kettle & Fire's organic bone broths–get 15% off your order here with the code RRHQ15!)
  • Raw, local honey and bee pollen: this has been shown to help prevent allergies and exposes you to beneficial organisms and enzymes native to your environment

Another tip: don't overly clean your produce. Assuming you buy organic–and particularly when it's from a local source like at a farmers market–ingesting a little local soil can actually be a good thing! (source)

RELATED:  How to Get Probiotics from Food: Vegan Probiotic Yogurt


When it comes to cleaning products, soaps, moisturizers and pretty much anything you're putting on your body or using in your home, it's time go natural. Mainstream products contain harsh chemicals that deplete your skin and gut microbiome as they're absorbed through the skin in varying degrees and, once inside your body, they may upset your delicate microbial balance. Be sure to avoid antibacterial soaps, too. (source)

According to the EWG, some of the big ones to watch out for in cleaning products are formaldehyde (sometimes called formalin), 1,4-Dioxane, borax and boric acid, Diethylene glycol monomethyl ether, sulfuric acid, ethanolamine and more. These chemicals aren’t selective; again, they kill both the good probiotic organisms along with the bad.

If you still use bleach (sodium hypochlorite), I beg you to reconsider: bleach is not only a known asthmagen that causes severe skin burns and eye damage, but is riddled with impurities like chloroform and chlorine that can cause reproductive toxicity, damage to organs, and even cancer.

In relationship to gut health, researchers are now looking into how white blood cells, called neutrophils, are releasing uncontrolled secretions of bleach at the sites of chronic inflammation. The cells send this not only to the bad bacteria, but onward, which can start damaging the body's own proteins. (source)

For personal care products, here are just a handful of toxic ingredients to look for that can have the same effects: triclosan and triclocarban, oxybenzone, fragrance, butylated hydroxyanisole (BHA), parabens, phthalates and a whole lot more. (source)

Definitely check out our posts on 5 Cancer-Causing Toxic Chemicals to Avoid in Everyday Products and The 10 Most Toxic Skincare Ingredients to Avoid.

Of course, we're all about non-toxic living here at R+R, so look through our plentiful DIY cleaning and DIY beauty recipes where you won't miss any of that gunk–promise!

If you're not a do-it-yourselfer, there are tons of great non-toxic cleaning and personal care products on the market.

In fact, there are even some probiotic cleaning products now that support the elimination of harmful bacteria, while keeping the good! Check out Homebiotic, where each spray adds billions of naturally-occurring beneficial probiotics to the environment. It's safe for kids and pets, is clinically proven to inhibit mold growth and can be used on all surfaces. Pretty amazing! 

Also look into P2, a natural probiotic for deep cleaning–it's more powerful than bleach and disinfectants with no chemicals. It's a great all-purpose cleaner, while also being perfect for traveling (c'mon, you know you wanna spritz your hotel comforter and airplane seat that millions of others have sat on!).

RELATED:  Savvy Swaps: Toxic Cleaning Products


As we've established, because our biomes are shaped by our natural environment, modern urban living has made it difficult for us to re-establish or maintain beneficial bacteria that we’d be regularly exposed to in nature.

Getting outside supports our health for so many reasons. When it comes to good bacteria, it's helpful because you’re exposed to natural molds, bacteria and fungus–plus you get more vitamin D from the sun which is great for your skin and overall health.

RELATED:  The Best Natural Sunscreen Brands

So, my friends, it's safe to say that bacteria is the new black! 😉

Let us know in the comments below how you're going to be a healthy trendsetter and support the health of your family and friends by embracing good bacteria. 

Photo Credit: Heidi Geldhauser

Disclaimer: This post includes affiliate links, and I will earn a commission if you purchase through these links. Please note that I’ve linked to these products purely because I recommend them and they are from companies I trust.

4 thoughts on “Good Bacteria Guide: Why Too Clean Isn't Healthy”

  1. This is SO interesting! Love all the facts. I just got a probiotic cleaning spray and can’t wait to test it out. I also love Mother Dirt and think their mist has really improved my skin.

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