3 Ways You May Be Sabotaging Your Gut Microbiome

3 Ways You May Be Sabotaging Your Gut Microbiome

We know that the gut is the root of all health. We know the steps to take to improve gut health, but it’s easy to overlook these (seemingly unrelated) areas of everyday life that dramatically impact gut health.

In fact, you can be doing everything right in your gut-healing protocol, but if you’re still doing these 3 things, you’re not going to experience the healing you’re looking for.

Related: How to Tell if Your Gut Is the Cause of Your Health Issues

It’s easy to assume that our gut microbiome is impacted solely by what we eat and things we consume internally (like supplements and probiotics).

However, there’s more to it than that. There are several areas of health that dramatically impact our gut microbiome:

Oral Microbiome

1. Using products that disrupt your oral microbiome

Just like we have a gut microbiome, we also have an entire microbiome inside the mouth. There are about 700 species present in the human oral cavity. These are viral, bacterial, and fungal species. Like the gut microbiome, we need balance in the oral microbiome.

It’s safe to say that our oral microbiome is equally as important as our gut microbiome, as it directly impacts the health of our gut. Oral health plays a key role in systemic inflammation, which is why individuals with chronic diseases related to inflammation, have issues with oral health.

If your oral health is suffering, so will your gut and ultimately your immune system. Plaque, for example, houses many species of bacteria and creates systemic inflammation if not removed.

We know that antibiotics kill both harmful bacteria and beneficial bacteria, leading to additional health problems. Similarly, using antiseptic and antibacterial mouthwash kills beneficial bacteria in the mouth, which we absolutely need for oral health.

Toss your mainstream mouthwash. If it’s unopened, return it. I’m serious. It’s doing MUCH more harm than good.

Avoid mainstream toothpaste which often contains triclosan and other harmful ingredients that destroy our oral microbiome.

What you can use instead:

If your oral health is really in trouble and you know it’s causing systemic issues, you may consider taking a chewable probiotic that is designed specifically to repopulate the beneficial bacteria in the mouth.

Skin Microbiome

2. Using antibacterial products that disrupt your skin microbiome

Did you know that we have an entire microbiome of organisms that live on the surface of our skin? Just like we have an oral and gut microbiome, there are thousands of microbes on our skin that are living, breathing, and reproducing. They impact our immune system (as the ‘gut-skin axis’ communicates with our immune system via lymph nodes), protect us from infection, determine how we respond to allergies, and much more.

The microbiome living on our skin (our largest organ) plays an important role in overall health.

Here’s where the problem lies: our culture encourages and often requires constant and relentless use of damaging antibacterial products. These products are not safe. They destroy the beneficial bacteria that we need on our skin.

When we constantly use antibacterial products such as hand sanitizers and alkalizing conventional hand/body soaps, we’re causing skin dysbiosis, which contributes to skin issues such as psoriasis, acne, eczema, dermatitis, yeast & fungal skin infections, compromised wound healing, and more.

How you can protect your skin microbiome:

  • Don’t be afraid of dirt (plant some flowers or play with your kids in the dirt – it’s good for your health)
  • Apply coconut oil topically (Coconut oil is antiviral, antifungal, etc!)
  • Avoid taking too many showers (unless your child is visibly dirty or smells, don’t bathe him/her every day)
  • Avoid toxic antibacterial soaps, sanitizers, laundry detergents, and household products (these destroy healthy skin flora!)
  • Use gut-friendly hand soap, skincare products, and safe laundry detergent (code healthfullyhannah saves you at checkout)
  • Use prebiotic skincare (this is my favorite!) that is a ‘superfood’ for the beneficial bacteria on the skin. (Code “healthfullyhannah” saves you 15% on all Aleavia products!)
  • Topical probiotics may also be used depending on your skin issue
  • Sweat regularly

In addition to protecting gut health, many people see dramatic improvements in skin conditions like acne, eczema, psoriasis, and more when they stop using harsh, synthetic antibacterial products.

If you’re serious about healing your gut, you can work with me one-on-one through Gut Health Reset, right here:

I'm ready for my personalized gut-healing protocol

Mental/Emotional Health

3. Holding on to Stress, Fear, and Anxiety

Stress, fear, anxiety, depression, and negative self-image play a large role in gut health. You already know exactly what is meant by the phrase: “The gut is our second brain”. You might have a ‘gut-feeling’ or ‘feel butterflies in your stomach’ when you get nervous. These are normal (even healthy) in the right circumstances, but when stress, fear, anxiety, and negative self-image issues become chronic struggles that we face on a daily, ongoing basis, our gut becomes compromised.

Many of my clients with Irritable Bowel Syndrome, for example, admit that when they are stressed or anxious their symptoms are greatly magnified, and when they reduce stress they see noticeable improvements. Another example is that individuals who suffer with autoimmune conditions often struggle with self-image issues. This is not a coincidence. These are great examples of how stress affects gut health.

Cortisol (our stress hormone) weakens the immune system. Norepinephrine and epinephrine affect our gut microbiome as they allow harmful bacteria to flourish, and reduce healthy gut species.

Your thoughts change your gut microbiome. Choose wisely.

(This also works the other way. Your gut bacteria impact your thoughts, since our mood hormones rely on a balanced microbiome)

When you’re stressed, your body kicks into sympathetic mode (the “fight or flight” mode that prepares you to fight or run.) When your body is in this state of heightened stress and awareness, it’s not allowing you to do two things: digest/absorb nutrients or reproduce.

In other words, when you are under extreme stress, you will not be able to absorb the nutrients from the food you’re eating and you won’t be able to conceive. It makes perfect sense if you think about it: if you’re being chased by a bear or are in the middle of a famine, it wouldn’t be a good time to grow a baby 😉

In fact, the chemical reaction that takes place under this type of stress diminishes the good bacteria in our gut microbiome, slows our metabolism, weakens our immune system and contributes to chronic inflammation.

It goes without saying that finding a way to reduce stress is essential to being truly healthy. You can be eating real, nutrient-dense food all day every day, but if you’re stressed to the limit, you’re not going to be healthy because you won’t be absorbing the nutrients from the food you’re eating.

Try some different stress-relieving methods. Find what works for you. Whether it’s prayer or meditation, affirmations, yoga or stretching, doing an inversion (like shoulder stand, headstand, or handstand) journaling, reading & listening to music, exercising, spending time in nature, using flower remedies, or maybe just being still & quiet. Experiment with different methods until you find what makes a difference in your stress level.

Related Post: 7 Powerful Stress-Relieving Yoga Poses
Did any of this information surprise you? Share below!


Hannah Smith

Hannah is the founder and health educator at Healthfully Hannah, empowering women to live healthfully through science-based, step-by-step guidance. Read Hannah’s personal health journey that led her to discover the power of Functional Medicine and Nutrition. Feel free to send Hannah a message here.


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  1. Although I’ve been focused on creating a more natural lifestyle, I didn’t even think about how more products really effect our natural microbiomes. Absolutely loved this post, Hannah!