Healing the Gut Microbiome

Digestion is essential for healing the gut microbiome. With over 39 trillion bacteria inhabiting the body, you are more bacteria than human cells. These 39 trillion bacteria, give or take a few trillion bacteria make up 1-3% of our body mass but they affect our immunity, well-being, hormone metabolism, memory, detoxification, and nutrient assimilation to name a few.

Beneficial Bacteria from the Birth Canal

We obtain our microbes initially from our mother. When we came shooting out the birth canal we were baptized in bacteria from our mom to enable us to withstand the outside world. Unfortunately, for those born by caesarean section, the likelihood of developing allergies, asthma, celiac disease, and obesity is higher because they did not get to go through the bacterial baptism that was their mother’s birth canal.

The baptism of bacteria through the vaginal canal is essential for aiding digestion and fending off pathogens.

A 2020 study from the Center for Celiac Research and Treatment at Mass General Hospital revealed that cesarean delivery, antibiotics at birth, and formula feeding causes changes in the microbiome of infants linked to inflammatory conditions and immune system dysfunction.

Antibiotics, being formula fed, being born via cesarean delivery are not an automatic sentence to a life of autoimmunity. Thankfully our body is fearfully and wonderfully made.

When we give our body health promoting inputs, it can overcome massive obstacles and perform magnificently. If you were put on soy milk formula at 4-6 months like myself, you want to be more diligent in supporting your gut flora via excellent lifestyle habits. For more information on how to structure your eating routine, check this post.

Antibiotics and Gut Flora

One round of antibiotics can destroy 90% of our gut flora. Considering that many people have been on 10-20 rounds over their lifetime, the impact is immense. As antibiotic exposure increases the risk of obesity, cardiovascular disease and autoimmunity does as well. It is vital that after going through a round of antibiotics that you replenish beneficial flora and shore up the mucin layer which protects our intestinal membranes.

Thankfully research and patient experience is moving at breakneck speed and we have more knowledge on how to heal the gut, rebalance flora and heal leaky gut.

We now know that even our food preferences and our appetite are related to the balance of flora in our gut.

Get this, even the amount of pleasure we receive from particular foods is affected by the bacteria balance in our digestive tract.

Healing leaky gut, consuming probiotics, fermented foods, changing your dietary routine from whole foods to processed foods or vice versa, can actually change the food preferences you have beyond just a desire to be healthy.

How I Destroyed My Gut Bacteria

I was a candy and ice cream addict growing up. Especially between the ages of about 10-15. Whether it was Swedish fish, sour patch kids, Cocoa Pebbles, Red Vines licorice, deep dish pizzas, chocolate ice cream before bed, I was eating junk food every chance I got. All the while, I was experiencing stomach pain that would leave me doubled over on the couch after meals. I had no desire for meat or vegetables, but I had plenty of desire for cinnamon sugar toast and pancakes loaded with syrup. You can hear my health accumulation story here.

Fast forward to my current life and I have no desire for those ultra-processed pseudo foods manufactured to create addicted humans. It didn’t happen over night but over about a four year time frame, I went from multiple servings of sweets per day, to no sweets, and not only that, my body started craving vegetables, fruit, meat, sweet potatoes, eggs, avocados.

I know it may seem like an insurmountable mountain, but when we shift our microbiome, we shift our desires, and it becomes much easier to make the choices we want to make related to our health.

We can heal our gut microbiome through proper inputs and change the trajectory of our health. Our microbiome has the power to promote a state of health and healing throughout our body when we support it with life-giving foods.

Have you experienced issues with your gut? I’d love to hear about it in the comments below.


Leonard, Maureen M et al. “Multi-omics analysis reveals the influence of genetic and environmental risk factors on developing gut microbiota in infants at risk of celiac disease.” Microbiome vol. 8,1 130. 11 Sep. 2020, doi:10.1186/s40168-020-00906-w

de Wouters d’Oplinter, Alice et al. “Gut microbes participate in food preference alterations during obesity.” Gut microbes vol. 13,1 (2021): 1959242. doi:10.1080/19490976.2021.1959242

de Wouters d’Oplinter, Alice et al. “Gut microbes and food reward: From the gut to the brain.” Frontiers in neuroscience vol. 16 947240. 25 Jul. 2022, doi:10.3389/fnins.2022.947240

Chris Dall. “Two studies tie early antibiotic exposure to increased obesity risk”. CIDRAP News, 31 Oct 2018

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