The 411 on the Microbiome

There is an evolutionary theory suggesting the first living cells on the planet needed a place to reside in for protection. So, they created humans to be their safe haven. While I don’t believe this 100%, I do find it captivating to consider.

I love telling my patients that we are more microbial than human. Because we have more bacteria cells than actual human cells. To say that the microbiome is important is an understatement. The more science reveals correlations between microbiome composition and disease, the more it validates that cliché Hippocrates’s quote:

“All disease begins in the gut.”

What is the microbiome?

The term microbiome refers to the world of trillions of bacteria (among other creatures) that inhabit our bodies. The microbiome is as individualized as a fingerprint – unique to you. The bacteria predominantly reside in your colon (AKA large intestine). However, there was a time that you did not have a microbiome; you were a clean slate.

For one thing, back when you were a fetus in mom’s belly, you were germ-free. Everything changed the moment you entered the world. As you left your mom’s body, you received your first dose of bacteria. This single moment determined the foundation of your microbiome. If you were a vaginal birth, the bacteria in the vaginal canal inoculated your little face. If you were a c-section, you likely collected hospital-acquired bacteria.

Babies that are born c-section have a higher risk of developing a multitude of medical conditions (including asthma and obesity). Indeed this is due to missing the first dose of germs from the vaginal canal. Don’t be alarmed if you were born c-section, though. It is necessary to keep in mind your mode of delivery so you can take preventative actions.

The next determinant that developed your microbiome is breastmilk. Breastmilk contains a prebiotic called human milk oligosaccharide (HMO). Evidently this prebiotic fiber feeds your infant microbiota so they may flourish and grow as you do. Again, don’t be too distressed if you were not breastfed – this was not in your control (as you were only an infant). And most baby formulas contain the HMO prebiotic. However, some studies show that breastfed vs. formula-fed humans have different microbiomes.

Probiotics vs. Prebiotics

You may have a bottle of probiotics in your supplement cabinet. You may have heard probiotics improve gut health – this is true. Probiotics are beneficial bacteria that can help build a healthy microbiome. But probiotics aren’t only found in tiny capsules. You can get probiotics from food too. Anything fermented (even wine) will contain beneficial bacteria.

Dietary probiotics:

• Yogurt
• Kefir
• Kimchi
• Tempeh
• Sauerkraut
• Kombucha
• Sourdough bread
• Pickles

You can even find a type of probiotic called soil-based organisms (SBOs) on your garden vegetables. If you have a dog, this is another way to obtain SBOs. (I’ve heard of a doctor that recommends his patients get a dog – not only are dogs a great companion, but dog owners have been shown to have healthier microbiomes).

Probiotics supplements alone won’t drastically change your health, especially if you depend on the little capsule to act as a magic pill. Taking a probiotic supplement is like adding one cup of water to a bathtub each day.

Probiotics are only half the gut health equation. These guys are alive and need fuel to reproduce and proliferate (which is the primary driver of any life-form with DNA: to reproduce and proliferate).

The other half of the equation are prebiotics. You can think of prebiotics as the food for the probiotics. Prebiotics are a type of fiber that can be fermented by the microbiota. Fiber is found in every plant food: vegetables, fruits, beans, nuts, and seeds. There are different types of fiber that I will not bore you with. Just know that fiber is essential because it feeds your bacteria.

Humans are missing an enzyme to breakdown fiber. This results in an undigested food mass traveling through the small intestine to the large intestine (where food remains for 2-3 days before it is excreted while you sit on your throne.) Once fiber meets the bacteria in the colon, the feasting begins—bacteria breakdown and ferment the fiber. Bacteria create healthful byproducts during this fermentation/feasting process. It’s a symbiotic relationship – we feed them, and they make short-chain fatty acids (among other things) that feed our intestinal cells.

Dietary Prebiotics

• Banana (the greener the better)
• Oatmeal (ditch the instant oats)
• Onions
• Garlic
• Leeks
• Strawberries
• Asparagus
• Jerusalem artichoke
• Apple

Particularly, prebiotic fibers will best promote a healthy microbiome; though, all plant foods are beneficial. Next time you cook a meal, remember that you are eating for “two”.

There is a Tanzanian tribe that eats 100-150 grams of fiber per day. Gastrointestinal diseases and obesity are practically nonexistent there. It is believed to do with their high fiber diet creating a diverse microbiome.

What happens when you don’t eat fiber?

Things can go very wrong if we don’t feed our bacteria. Exhibit A: The United States of America (obesity rates >30%). The majority of Americans aren’t eating enough fiber. The current fiber intake recommendation is 28-38 grams per day. Most people are only eating about 15 grams. Is it possible that the rise in obesity and other health problems is partly due to the havoc going on in the microbiome?

Technically the hallowed part of your colon is “outside” of your body. Our incredible body has developed a layer of protection from the outside world, called the mucosa membrane. This mucous membrane is crucial for gastrointestinal and immune health.

A diet low in fiber can result in a decreased protective layer. If you don’t feed your bugs, they will feast on what’s there: your mucous membrane. Studies have found that a low fiber diet will result in an eroded mucus later, resulting in our intestinal cells being exposed to the “outside” environment of the microbiome. If there are harmful bacteria present and no mucus barrier, things can go wrong…

Besides an eroded mucus barrier, dysbiosis can occur. Dysbiosis is the term used to describe an imbalanced microbiome (more bad bacteria than good bacteria). There is an extensive list of conditions associated with dysbiosis.

Dysbiosis Associated Conditions:

Autoimmune disease
Bacterial vaginosis (BV)
Bloating
Celiac/gluten sensitivity
Chronic fatigue syndrome (CFS)
Depression
Diabetes
Food allergies and sensitivities
Food cravings
Inflammatory bowel disease (IBD)
Irritable bowel syndrome (IBS)
Leaky gut (AKA intestinal permeability)
Multiple sclerosis
Obesity
Parasites
Sinitis
Skin conditions (acne, rosacea, eczema)
Small intestinal bacterial overgrowth (SIBO)
Thyroid disease
Weight gain
Yeast infection
Yeast overgrowth

Dietary habits that can cause dysbiosis:

• A low-fiber diet
• Excess, refined sugar
• Artificial sweeteners (especially aspartame found in diet coke)
• Hydrogenated and trans fat
• High-protein (animal products) diet
• Highly processed food

Other factors that can negatively impact your microbiome:

• Alcohol
• Antibiotic use (especially frequent antibiotic use)
• Inadequate sleep
• Stress
• Other medications (NSAIDs, PPIs, opioids)

Steps to start nourishing your microbiome

1. Increase your fiber intake to 28-38 grams daily (and be sure to increase water as you increase fiber) – Tips to increase fiber here.
2. Eat dietary probiotics – Or trial a probiotic supplement (but make sure you are still eating prebiotic fibers!)
3. Get enough sleep each night (7-9 hours)
4. Manage stress through breathwork, prayer/meditation, or journaling
5. Avoid eating late at night and consider a Circadian Cycle Fast (eating window sunrise to sunset)

A fiber-rich diet feeds the good gut bacteria. When we feed these beneficial bacteria, they produce short-chain fatty acids that provide energy for our intestinal cells. Our nourished intestinal cells make mucous adding on to the barrier. It is a wonderful process.

Eat Fiber -> fiber feeds gut bacteria -> bacteria make short-chain fatty acids (SCFA) -> SCFA nourish the intestinal cells -> intestinal cells produce mucous -> mucous membrane protects our intestinal cells -> healthy gut 🙂

Remember that you are not alone. You have trillions of little organisms that do a lot of good for you. You are always eating for two.

If you want to learn more, I recommend reading The Good Gut – check it out my book list!

Need a gut health starter recommendation? Trial a one-month gut health starter with a nourishing prebiotic and high quality probiotic: Here.