How to Naturally Improve Your Gut Health

Gut health is essential for good health. As our gut is the gatekeeper for the food and water that fuel our organic existence, this may seem obvious.

Nevertheless, digestion alone isn’t what makes a gut healthy.
In the past, we thought disease had something to do with genetic expression, but now we see that it has everything to do with the bugs that live inside of us.
Mental and psychological disorders are in large part a result of gastrointestinal problems.
In recent years, we have learned that serotonin (a neurotransmitter responsible for many of our behaviors, moods, sleep cycles, libido, appetite, and so on) is largely produced in our gut with the aid of our diverse gut microbiome.
There are over 10,000 types of bacteria in the human gut. Microorganisms in the gut continue to be a mystery to scientists.
There are thousands of bacteria added every few years, and that list is not exclusive to bacteria. Furthermore, viruses and fungi live in our bodies, although less is known about how they affect our health.
The hundred trillion bacteria in the body of an adult human outnumber our own cells 10:1.
They contain about 4 million distinct functioning bacterial genes, with more than 95% of them located in the large intestine. I highlighted the word functioning so you didn’t miss it. Yes, the genes from microorganisms are influencing the day-to-day biological nuances that are happening inside of us.
According to the Human Genome Project, there are more bacterial genes modulating our daily bodily functions than human ones!
We are very much in the infancy stage of our understanding of the human microbiome as it relates to health. One thing we all agree on is the microorganisms living inside our gut have the ability to “well oil” the machine. Have an overgrowth in the wrong species, and we become very, very sick.

The influence of our microbiome can change our immune response, turning a normal day into a complete disaster when we encounter commonplace foods like peanuts.
They have the capacity to synthesize chemicals that affect our sleep cycles and stress response.
They provide us with an extra-intestinal barrier against pathogenic bacteria and assist in digestion by converting foods that would not otherwise be absorbed into bioavailable energy sources.
Our health has everything to do with our microbiome.
This is great news for us because we now have hope!
We no longer have to fear things outside of our control such as our familial genes. We can influence our health by protecting our gut with a diverse microbiome.
Our next quest then is to understand what are the building blocks of an optimal microbiome. But before we can do that, we need to know the warning signs that we are colonized by some not-so-friendly microorganisms.

Symptoms of Bad Bacteria in the Gut

Our gut balance can be easily thrown off by poor diet choices, stress, lack of sleep, antibiotic overuse, and all kinds of environmental influences (we will get more into the specifics of this later).
When our system is negatively influenced by an outside source, it can trigger one species to take over. The process is coined small intestine bacterial overgrowth (SIBO).
Symptoms of SIBO can be subtle or much more alarming. Your symptoms will depend on the type of bacteria present and how their metabolites (their waste products) affect your own tissue.
Most of the time, SIBO is related to the overgrowth of a gram-negative coliform, such as Escherichia coli, Enterococcus spp., Klebsiella pneumonia, or Proteus mirabilis species.
While most of the time, the symptoms you may experience with this overgrowth will be mild, (things like bloating, gas, abdominal discomfort, and diarrhea) it is possible to experience more concerning things like weight loss (I wouldn’t mind that part), anemia and malnourishment leading to a serious vitamin deficiency.
The frequency and severity of your symptoms can reflect both the degree of bacterial overgrowth along the extent of inflammation they are causing.
Here are some general symptoms that may alert you of SIBO:

  • Bloating
  • Abdominal pain
  • Abdominal firmness
  • Diarrhea
  • Fatigue not relieved by sleep
  • Generalized weakness
  • Unexplained weight loss or gain
  • Depression/anxiety
  • Headaches

Gut inflammation: here’s what is happening

What all this talk about bad bacterial or lack of microbiome diversity boils down to, is gut inflammation.
Gut inflammation also called the endotoxic response, is defined as a rapid physiological response by the body after being exposed to a lipopolysaccharide substance (fancy name for a fat molecule) present in the outer membrane of gram-negative bacteria.
Normally, our body would protect itself bypassing things like unfriendly microorganisms, undigested food particles, and toxins right through us, excreted as a stool. When inflammation is present, the lining of our intestines becomes damaged. Subsequently, harmful things are able to leak through our gut and into our bloodstream.
Inflammation is not just happening to those who have been diagnosed with a crippling intestinal disease like Crohn’s and Ulcerative Colitis.
It could be happening to you and you may not realize it. One study done on 80 healthy college students of normal weight showed that over half of them had a massive inflammatory response to food.
When you experience unproductive inflammation it has devastating effects on human health.
The normal process of inflammation has a set endpoint once the source of the inflammation has been eliminated. Afterward, your body will begin to heal.
In a situation like a leaky gut, the cause of the inflammation continues to infiltrate the blood so the inflammation never stops.
Long-term inflammation increases the odds of developing cardiovascular diseases, liver disease, cancer, diabetes, dementia, and obesity.
At the risk of beating a dead horse… inflammation is pretty much bad news!
At this point, you may be wondering, “Oh my goodness, do I need to get tested for SIBO and inflammation?”
The answer is, not really. In fact, most of the tests we have for SIBO aren’t that reliable.
If you do want to know if your body is in an active inflammatory process, you could visit a functional medicine physician or ask your family doctor to run a C-reactive protein (CRP), Tumor Necrosis Factor Alpha (TNF-a), Interleukin-1 beta (IL-1β), Interleukin-6 (IL-6), Interleukin-8 (IL-8). 
Keep in mind this test will cost a pretty penny.

If you are truly struggling and want to better understand your own unique microbiome and how it influences you, you should check out the company Viome. They offer a home-based test which you will mail off and receive all kinds of personalized information on how your microbiome is influencing your health.
They also give nutritional advice based on your specific needs.
The next part of this post will contain tips on how to eat for a healthy gut and how to improve gut health naturally.
It doesn’t matter whether or not your inflammatory markers are off the chain. We should all be protecting our gut in the same way.
These tips are applicable if your gut is healthy or if it is sick. And the focus of this advice will be on simplicity because let’s face it, we don’t need life to be more complicated than it already is!

A Simple Healthy Gut Diet Plan

When it comes to nutrition, I have never been a fan of fad diets. I know right now everyone is focused on things like fasting, the Keto diet, and Whole 30.
You aren’t going to get any recommendations for fad diets in this plan.
When it comes to eating for a healthy gut, we need to think back to what our ancestors were doing and a time before big food corporations were spraying our agriculture with chemicals that none of us can pronounce (hint: glyphosate).
Back then we were hunters. We didn’t necessarily kill animals every single day for our dinner. Meat causes gut inflammation and it shouldn’t be eaten on a daily basis.
We were gatherers, eating a diverse amount of plants that were available to us according to season. We weren’t eating tomatoes in January.
So how does this relate to us in our modern city life?
I can describe a healthy gut diet in a few simple adjectives. Local, seasonal, unprocessed, and for the sake of keeping up with present-day vernacular, organic.
Let’s look at each of these individually.


Local food sourced from small farms is better for your health. That might comes as a bold statement but here are a few reasons why this is true.
Local foods don’t have to travel the distance to reach your plate. This means it is allowed to ripen on the vine.
Produce allowed to ripen on the vine is much more nutritionally diverse and superior than food that was picked green.
The best local food you can eat is from your personal backyard garden. Not only will you have complete control over the growing and harvesting process, but the experience of digging around in the dirt will enrich your microbiome.
You don’t have to turn up your entire backyard and take up farming! Just doing something as simple as having potted fresh herbs and greens will substantially contribute to your microbiome.
Don’t rinse anything off before eating either!


What does it mean to eat seasonally? Well, it will depend on the area that you live but think about what is growing outside in your current climate.
If it is summer then you will have the chance to eat a diverse amount of ripe produce at the peak of its nutritional value.
If it is the middle of fall, think about eating things like squash, cabbage, and dark greens.
Wintertime is great to eat root vegetables.
By eating seasonally, you allow your microbiome to change seasonally. This triggers a change in the genetic expression inside your body.
Obviously eating seasonally does not mean that you starve yourself during the winter.
But you can get creative in consuming food that is preserved in different ways.
For example, in the winter you can eat more frozen fruit. Frozen fruit was allowed to ripen on the vine and then stuck in the freezer. It will be more nutrient-dense than fresh strawberries in the winter.
Eating for a healthy gut ultimately means more time in the kitchen. In modern culture, life is moving as such a fast pace. We often don’t make time to do simple things like cooking our own food.
This is a tragedy because cooking your own food can be a way to bring peace to your soul.
I guess that’s why they call it soul food!
If you don’t have time to cook every day then you could start meal prepping. Meal prepping simply involves taking one day to plan out a week’s worth of meals. You then cook a lot of food at once and eat it throughout the week.
Another tip to eat less processed is to look at the ingredients on a label. You can find a variety of packaged snacks that contain minimal ingredients and still align with your intentions to heal your gut naturally.


All of the previous nutritional advice is valid. But one of the most important things when eating to heal your gut is to avoid synthetic fertilizers, pesticides, and herbicides.
You cannot wash these chemicals off of food. They integrate on a cellular level of the food and are the number one way we are exposed to toxins.
Exposure to pesticides can have both short-term and long-lasting effects, and they definitely disrupt your microbiome
One of the biggest hesitancies when buying organic food is of course the price. It’s hard to part with 6 dollars for a basket of organic blueberries when you can get them for half the price buying conventional.
feature for organic dry goods. Buying 5 things a month saves you 15% so it’s a great way to keep pantry foods like peanut butter and healthy snacks stocked.
As much as it stinks to pay extra money for food, you will end up saving more in medical bills in the long run by protecting your health.
Another aspect of eating organic involves the quality of meat you are getting. Conventionally raised animals are given tons of antibiotics and treated extremely inhumanely.
It is not within the scope of this post to get into the specifics of how the meat industry abuses animals (although It is absolutely devastating).
However, if you are eating an animal that spent its entire short life full of fear and suffering, the stress hormones circulating through its body will most certainly negatively alter your microbiome.
When eating meat, less is more.
Lean meat, eggs from free-range hens, and wild-caught fish are great sources of protein to eat 5 days a week. Red meat should be eaten minimally and always be pasture-raised.

Probiotics and Gut Health

 probiotic industry is huge these days. With so much research coming out about the connection between the gut and natural health, it’s not surprising.

Everyone is looking to capitalize on this new trend.
I must admit I was completely uninformed when I started taking a probiotic supplement.
I started supplementing after I was given IV antibiotics in the hospital during the birth of my son.
I subsequently developed recurrent yeast infections and started having so much abdominal bloating.
Many of the probiotics I tried didn’t seem to help at all. I found out later that the way most probiotics are processed makes them completely unviable once they reach the human gut.
The process of encapsulating probiotics involves growing different strains of bacteria in separate mediums. They are then spun to remove their liquid food (also called prebiotic), freeze-dried, crushed, and when combined with the other cultures in the capsule.
In this process, you have taken microbes that aren’t used to living with each other away from their food source and dropped them into a harsh environment like the stomach.
The reality is that none of them survive to reach our lower intestines.
One company I recently found, uses non-GMO, organic sugar molasses to grow 11 different species in harmony together.
The pH of this bottle is around 3.5. The human stomach has a pH anywhere from 1.5-3.5.
It is much more likely for this product to survive past your stomach and thus be able to set up camp inside your intestines and do some good work.

Are probiotics really necessary?

That is a great question and one that I still ponder upon.
How does dosing our gut with large amounts of a few species really affect us? We are supposed to be made up of a diverse ecosystem involving thousands of species right?
The truth is, we don’t really know yet. This is an exciting time and new research is being published every single day.
I have personally read testimonies of people experiencing an amazing healing from things like eczema, allergies, and ADD using a liquid probiotic.
Then again, our ancestors have been fermenting food for centuries so there is definitely something to the probiotic theory.
I am way more excited about the prospect of healing from amplifying something in nature versus anything the pharmaceutical industry has to offer!
How to Improve Gut Health Naturally
So far we have covered a lot but I didn’t want to leave you without giving a few more quick tips for taking care of your gut health on a daily basis.
There are numerous nutritional and healing benefits to drinking a daily cup of bone broth. There is a reason they call it chicken soup for the soul!
Another thing you can do is start your day with a morning detox drink.
Of course, getting enough sleep and minimizing toxic stress is essential for any true healing process. There are so many strategies to do this such as setting a daily schedule, meditation, and working on controlling your thoughts.
If you can, limit your caffeine and alcohol intake.
If you do drink, go for a glass of red wine over a beer. The flavonoids in red wine actually contribute to your health!
Eat more coconut oil and extra virgin olive oil over other vegetable oils. Most vegetable oils have high levels of omega-6 fatty acids. A little omega-6 is good for you but too much can actually cause oxidative stress (aka inflammation!).
Get some form of exercise at least 3 days a week. The more the merrier when it comes to exercise. This can be as simple as a brisk walk.
Get outside in nature. Go to the beach, a state park, the mountains, or even the woods near your neighborhood. Getting out in nature helps to diversify your microbiome.
Stop using antimicrobial hand sanitizers. Not only are these gels filled to the brim with chemicals that easily absorb but you are killing your natural skin microbiome. Plain soap and water is enough when you are out in public.