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  • Writer's pictureOlivia Borer

The Gut Microbiome

As promised, my plan for the next few blog posts is to take some of the amazing information I took in over my time at Roots, the NTA Conference in Portland, and translate it into several new blog posts brimming with information. Today’s topic? The gut microbiome.

My favorite speaker of the weekend was likely Sarah Ballantyne, who I’ve been following since I first was introduced to the paleo/holistic health world five years ago. She is a biochemist by trade (she has her PhD in it!), but now works as what she calls a “communicator” to take high level scientific information and bring it to the masses. Her blog is and she also is co-host of an amazing podcast The Paleo View.

Sarah’s talk on the microbiome was something very special to me, as gut issues and dysfunction have been one of the two main issues I’ve been dealing with for several years now. Her talk gave me numerous concrete takeaway steps to help improve my gut health, and I am so excited to dive in and get started building a new protocol!

As I begin my post on the gut microbiome, however, I realize I need to take a step back and explain what that actually is.

The gut microbiome is basically the gut bacteria that live in our digestive tract (mostly the large intestine) and aid in EVERY aspect of our health through the numerous (and sometimes still unknown) functions that they do on a daily basis. The gut microbiome has been in place to do certain things our bodies didn’t evolve to do, as well as aid in digestion, produce neuroactive compounds (aka neurotransmitters like serotonin), and regulate the gut barrier integrity. I’ve talked about the gut barrier before, but basically it is a lining that protects our digestive organs from the rest of the body, two aspects of our bodies that should NEVER mix, but because of our poor health in society today, we see this happening more often than not, leading to what we call intestinal permeability or leaky gut.

The most important aspect when it comes to the health of our gut microbiome (and thereby the rest of our ENTIRE body), is diversity. We need a diverse array of beneficial bacteria to help our body digest and assimilate food and nutrients properly, as well as support all other aspects of our health (thyroid, brain, etc). When we have good gut diversity, our bodies function normally. When we don’t have diversity and instead have too little beneficial flora or an overgrowth of pathogenic bacteria, we instead have dysbiosis, which is linked to EVERY CHRONIC DISEASE.

Read that last sentence again. If you don’t take care of your gut, we can literally trace your poor gut health back to every chronic disease. These diseases include, but aren’t limited to: Type II diabetes, cardiovascular disease, Alzheimer’s, dementia, Hashimoto’s or other thyroid issues, arthritis (including Rheumatoid Arthritis), IBD, and so much more. So if you have a family history of these diseases or are struggling with them currently, you MUST take a look at your gut health. It is a non-negotiable.

When it comes to supporting the gut microbiome, there are several areas to consider.


We all have heard how fiber is important and that we need to get 25 grams or more in per day, but what we don’t realize is that this information is too basic and way outdated. Instead, we need more fiber than not from a variety of fruits and vegetables (aka plants) NOT fiber supplements or packaged foods with added fiber (Fiber One bars anyone?). This is NOT the same as eating fiber from real, whole foods in our diet which, coincidently, also come along with a ton of beneficial vitamins and minerals to help support our gut as well.

Fiber is the structural component of plants (think of the strings in celery), and there are several types of fibers. I won’t bore you with those names and types, but know this: it is important to get a variety of vegetables and fruit to get a variety of different types of fiber to support all aspects of your microbiome. We also want to make sure these plants are in their whole forms and not juiced where they lose a good portion of the beneficial fiber.

We may have also heard the myth that grains are loaded with beneficial fiber, but honestly that simply isn’t true. While yes, some grains have fiber, we can’t always access that fiber and the nutrients in those grains because our bodies were not meant to break down those foods properly. Instead, they do more harm than good to our gut microbiome and gut lining, especially when they contain gluten and added sugars.


Phytochemicals (biologically active chemicals in plants) are a class of polyphenols (micronutrients we get from foods) that are so important to the gut microbiome as they can act as prebiotics (food) to the beneficial probiotics (good bacteria) in our gut, as well as support gut diversity and prevent the bad strains of bacteria from growing. We can find these beneficial phytochemicals in foods like green tea, onions, apples, and berries.

Vitamin D

We all know how important vitamin D is, but this time of year especially it is critical because a deficiency in vitamin D leads to a shift towards pathogenic bacteria and less diversity in the gut. This time of year, it’s hard to get outside in the sun, so supplementation might be necessary until you can spend more time outside in the spring, summer, and fall.


10% of the protein we eat is not absorbed by the body, but actually feeds our gut bacteria because we need the amino acids found in protein to support our gut bacteria (which are made from protein too!). Studies have shown that fish protein, followed by chicken and beef/pork proteins are best for the gut microbiome. Casein (dairy) and soy are terrible for the gut microbiome, which is why I typically recommend avoiding them.

Fat Intake

We need a balance of omega 3:omega 6 fatty acids in our diet to help keep inflammation at bay and thereby support the health of the gut microbiome. Omega 6 fatty acids are pretty easy to get in our diet, especially if we eat a lot of toxic vegetable oils or lots of nuts and seeds and very little seafood. Instead, focusing on high quality fats like extra virgin olive oil, avocado oil, some raw or dry roasted nuts, and plenty of fatty fish can help keep omega 3:omega 6 levels balanced at a 1:1 or 1:2-4 ratio (rather than 1:50 like most Americans).

Toxins – Foods and Other Factors to Avoid

I’ve mentioned some of the foods that are beneficial for the gut microbiome, but what needs to be made clear are the foods and toxins that are NOT beneficial. These include alcohol, excess sugar/starch, artificial sweeteners high saturated fat (more than 15% of calories per day, not a bit deal to still use some coconut oil and REAL butter!), omega 6 fatty acids in excess, emulsifiers (additives to hold foods together), gluten, dairy, and digestive enzyme inhibiters (basically grains and other foods the body can’t digest properly).

Toxins that should be avoided include antibiotics, long-term drug usage, heavy metals, industrial pollutants, unfiltered water, and other toxic chemicals floating around in our environment.


Stress suppressed the growth of good gut bacteria, and what’s curious is that stress does this in a unique pattern depending on the person. This has likely been the biggest impactor of my own personal gut health journey, especially after so many years undereating, eating a Standard American Diet, and/or overtraining.


WE NEED TO SLEEP MORE. That’s all I’m going to say.


There definitely is a nice bell curve when it comes to exercise and the gut microbiome. Too little and too much exercise are not great (I know the latter so well…), but right in the middle is movement every day (not necessarily exercise every day, but movement) and avoiding intense, prolonged periods of exercise (aka running all the time and HIIT classes every day). Instead, walking and basic strength training are the best ways to go

Whew – what a ton of information! Basically, it boils down to this: eat plenty of vegetables and fruits loaded with fiber, manage stress, sleep, move your body, get outside, and eat an otherwise PFC balanced diet focused on quality protein and fats.

The gut microbiome might seem like a far-away concept you don’t need to worry about, but trust me when I say it is critical, no matter what age you are (but especially if you are having kids or about to start – we didn’t even have time to jump into that topic today!).

Xoxo Olivia

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