Beyond Probiotics: 3 Incredible Tools for Healing the Gut Biome

If you follow my articles, you may already know I didn’t get into gut health purely from a place of passion. While I was already into biohacking and deep health science years ago, I really became an expert on the subject as a way to heal myself when I became sick for almost two years.

I never had stomach problems, and my symptoms were primarily mental, including panic attacks, deep anxiety, fatigue, and inability to exercise without mental repercussions (a common trait of chronic fatigue syndrome).

Only when I had a deep diagnostic lab panel done did I finally find something officially wrong. Everything up until then had showed perfect numbers, despite how I felt.

Well, in case you haven’t guessed, the first lab result I got showed that the issue was related to my gut. I had severe gut dysbiosis, an imbalance of bad bacteria, yet I had never experienced stomach or gastrointestinal issues.

In this article, I’ll share with you three of the most powerful gut healing methods I know. These incredible tools helped me immensely and go far beyond the abilities of the average probiotic.

With that in mind, we’ll still briefly cover probiotics, as they really are a good tool for gut health.

So without delay, let’s get started.

Inside our digestive tract lies an ecosystem of bacteria that functions in synchronization with our human biology. This ecosystem, known as the gut microbiome or gut biome, aids in digestion, fights disease, and even affects our mood and emotions. However, we’ve only begun to realize how important it is in the past 5 to 10 years.

How important are we talking? Let’s put things in perspective: You have approximately 23,000 human genes influencing your biology. Your gut biome, if it is healthy, has closer to 3.3 million genes, all of which influence you. That number is staggering, and research supports the idea that the gut biome may be one of the most foundational elements of our health—period.

Specifically, dysfunction in the gut microbiome has been associated with obesity, diabetes, cancer, chronic disease, heart disease, liver disease, and even severe mental conditions such as schizophrenia, bipolar disorder, and autism. Furthermore, the state of your gut biome is so inextricably linked to your mental state that the relationship between the two has even been labeled the “gut-brain axis.”

Probiotics, which are supplements consisting of “good” bacteria for the gut biome, have shown efficacy in addressing mood symptoms such as anxiety and depression.

If you’ve already heard of probiotics, I’m not surprised. These supplements have become the go-to method for helping the gut. However, in truth, they are one of the least impactful methods available for this purpose. The gut biome is incredibly complex, and there are now many different approaches to maintaining it, several of which are magnitudes more powerful than your average probiotic.

Though I aim in this guide to go beyond probiotics, I want to take some time to address them. They are, after all, the most popular way of dealing with gut health, and I’d be remiss to leave them out.

Now, to be clear, when I say “probiotics,” I mean probiotic supplements, not probiotic foods. Probiotic foods are fermented foods that contain a wide variety of bacteria strains, usually in much larger numbers than are found in a probiotic supplement, a pill that contains millions or billions of copies of a few strains of bacteria.

The efficacy of probiotic supplements is questionable, but probiotics are usually well tolerated by the human body, so they are unlikely to cause any harm. Depending on what kind of probiotic you use, it may not be helping much, but it’s also not likely to be hurting you.

One of the biggest reasons why many probiotics aren’t very effective is that they only contain a small number of different strains of bacteria, whereas the human gut contains thousands of different strains when healthy.

With all of this in mind, there is only one probiotic supplement I regularly use, but I’ll tell you about two other options as well.

I first heard about the P3-OM probiotic on the Ben Greenfield Fitness Podcast, which is my personal go-to source for all things biohacking, health, and fitness. This blend is a patented probiotic that contains a strain of bacteria known as L. plantarum that is particularly effective at eliminating gut pathogens. In layman’s terms, it kills bad bacteria and fungal infections in your gut by populating it with this strain.

P3-OM also combines well with a good digestive enzyme supplement, and BiOptimizers has my favorite for that as well. Digestive enzymes can benefit fitness by supporting amino acid absorption, and the P3-OM probiotic also has this effect.

Now, I’m not saying that this is the only good probiotic out there. I just believe that if you use a probiotic, you should stick with one from a very reputable company with great reviews. When in doubt, stick with probiotics that are made by doctors or are used by functional medical practitioners and gut health experts. Speaking of that, I’ll turn to my next recommendation.

Dr. Michael Ruscio is a prominent expert on gut health and the author of Healthy Gut, Healthy You, the most in-depth material on gut health that I’ve found. His Soil-Based Probiotic uses bacteria strains often found in soil. Soil is where humans typically come into contact with many of the bacteria that form our biome.

Children who grow up on farms are exposed to a wide variety of bacteria through their environment, and research has shown that they display greater resistance than other children to conditions such as asthma.

While I haven’t used the Soil-Based Probiotic personally, I consider Dr. Ruscio to be a reliable source for gut health products. Not only does he really know his stuff, but he cares deeply about clinical relevance and research.

While probiotic foods are not the focus this article, they are an awesome tool and worth mentioning. Probiotic foods are an improvement over probiotic supplements in two ways: they offer greater strain variety, and they contain a larger number of bacteria.

First, probiotic foods are created by fermenting food, and the bacteria strains that grow in them come from the air. This results in much greater variety of strains compared to those found in most probiotic supplements.

Second, probiotic supplements contain millions or billions of colony-forming units (CFUs) at best. The therapeutic dosage for a probiotic is 10 billion CFUs. Let’s say for the sake of argument that your daily probiotic has exactly this amount (in fact, most are lower).

Kimchi, a popular form of fermented cabbage, often contains 1 billion CFUs per gram. That means that 10 grams of kimchi is equivalent to the therapeutic dose. Ten grams isn’t much; as a regular kimchi eater, I usually consume 5 or 10 times more than that on a daily basis. This means that comparatively, I get five times the probiotic benefit from kimchi than I would if I were taking a daily probiotic, and with greater bacterial variety.

There are tons of probiotic foods out there, but some of the most popular are:

Of these foods, kimchi is my favorite. Low in calories but very tasty and filling, it’s a good starting point when it comes to fermented foods. You can even toss it in with your cooking, such as when pan-grilling steaks, to add some great spice and a vegetable feel.

Now that you have at least a basic understanding of probiotics, let’s look at the three tools that helped me heal my own gut biome.

Lactobasillus reuteri (say that five times fast!) is a bacterial strain found in our gut biome. L. reuteri is unique in that it occupies our upper intestine. (Most of the strains in our gut biome occupy our lower intestine.) It is one of the few bacteria native to our gut, and it can be found in the digestive systems of many vertebrate animals.

This little bacteria is great for our health, providing a host of benefits. It boosts the immune system by lowering inflammatory cytokines and improving T-cell function. It heals “leaky gut” by repairing the holes in the gut lining that cause this condition, and it kills pathogenic “bad” bacteria by creating antimicrobial compounds. In short, L. reuteri basically addresses every major component of gut health except for colonization of new “good” bacteria (other than L. reuteri itself).

It also has one particularly unique benefit: It boosts the neuropeptide oxytocin. Does that name sound familiar? It should. Oxytocin is often referred to as the “love hormone,” because our bodies release it when we hug, kiss, partake in other romantic activities, or even play with our dog.

Feeling cuddly is all well and good, but the benefits of oxytocin go far beyond this:

And that’s not all. L. reuteri has even more benefits, including:

Hopefully I’ve convinced you that L. reuteri is good stuff, so here’s how you can get it: make yogurt.

You can, of course, take L. reuteri in pill form, but these supplements contain far less of the strain than you’ll get from making yogurt out of it. Plus, L. reuteri yogurt is thick, creamy, and borderline cheese-like. Honestly, it’s delicious, and it’s not that hard to make. Here’s what you’ll need:

To make the yogurt, crush the L. reuteri tablets into fine powder using a mortar and pestle or two spoons. Blend the 6 tablespoons of Inulin into the half and half, milk, or cream using a stick blender. I prefer to use half and half or thicker dairy products in order to render a more solid, less runny end product. Mix the 10 crushed tablets of L. reuteri into the blend using a fork.

Move the mixture to an oven-safe container and use a yogurt maker, food dehydrator, or other similar device to “cook” the mixture at 100 degrees Fahrenheit for 36 hours.

Don’t have a yogurt maker? No worries; you can use your oven. Open the door and turn the oven on to 250 degrees for a minute or two. You’ll know it’s ready to use when you place your hand inside the oven and it feels like a hot summer day. Turn the oven off, put your mixture inside, and close the door. Then, every four hours, open the door and turn the oven on until the inside once again feels like a hot summer day. This should take about a minute at 250 degrees. If you’re worried about it getting too hot, use a meat thermometer to check that the yogurt mixture is between 95 and 115 degrees.

Once your yogurt is finished, you can make new batches by using a few tablespoons of yogurt from the first batch instead of the crushed Biogaia tablets. Subsequent batches are usually thicker.

Important note: At 120 degrees or higher, L. reuteri dies off rapidly. This is usually a bigger problem with yogurt makers, as many of them are inconsistent and don’t let you set a temperature. If you use such a device, it’s best to find something that has a manual temperature control, and to use a thermometer to make sure it is accurate.

My experience: I first tried L. reuteri while in a “stalemate” with my chronic disease. I’d been improving for some time but had spent a month or so feeling stuck with some anxiety and fatigue.

After taking this bacteria, I experienced two profound effects. First, I saw a great reduction in food cravings. L. reuteri yogurt really is amazing for curbing hunger, and it’s a great addition to a keto diet when you’re trying to avoid carbs, as it clears cravings as well.

Second, I just felt happier. I got my energy back, and my lingering fatigue and anxiety died down, but mainly I just felt happy. This is likely because of L. reuteri’s oxytocin-boosting effects, but it surprised me nevertheless.

You can make L. reuteri yogurt without dairy by using coconut milk or cream, but the process is a bit more involved.

First, you may need to get a dehydrator or high-end yogurt maker, as coconut milk ferments closer to 115 degrees Fahrenheit—dangerously close to the 120 degrees at which L. reuteri starts to die off.

Second, you will need more ingredients. With milk products, L. reuteri ferments by consuming the lactose sugars found in dairy. For coconut yogurt, we need to add this sugar ourselves.

We’ve still got a lot of article left and two more methods for healing your gut that I want to address, so instead of detailing how to make the coconut version of L. reuteri yogurt, I’ll direct you to my favorite recipe, which is courtesy of a forum member named Daphne at undoctored.com and includes detailed instructions for making her version of this yogurt.

Okay, “lignite extracts” are the technical term for the next product we’re going to discuss. However, here’s an easier way to think about it: it’s dirt water. We’ll come back to this idea in a bit.

Restore is a product developed by one of the few triple-board-certified physicians in the country, Dr. Zach Bush, whose recent research has been on cellular communication (as in communication by bacteria and human cells, not telecommunication) and redox signaling.

Redox signaling is a process of oxidation and reduction that occurs at the most basic levels of biology, literally involving the transporting of electrons, and forms a communication network—not for our cells, but for our mitochondria. Mitochondria are the energy sources of cells in both bacteria and human cells, and are one of the oldest living mechanisms on the planet.

How is this relevant to gut health? Well, basically, redox signaling is involved in your gut biome’s bacteria communicating and coordinating with each other. If bad bacteria are increasing or certain cells are malfunctioning, “communication” within mitochondria can trigger processes to fix these problems, such as killing malfunctioning cells or making new ones.

This is deep and complicated biology, but all you really need to know is that this communication structure exists at the most basic level of biology, and that it can become compromised.

In the gut, this compromised signaling seems to be involved with the deterioration of tight junctions between cells, which causes holes in the intestinal wall and leads to the condition known as leaky gut.

This brings us to lignite extracts, a fancy term for materials present in the soil (read: dirt). In soil, bacteria communicate using redox signaling through the materials present there. Basically, it’s a place where we can study and replicate redox signaling.

With the right ratios and blend, solutions of these lignite, or soil, extracts are able to restore redox signaling for the bacteria in our gut. In turn, this repairs cells’ tight junctions, allowing cellular communication to be restored.

This is cutting-edge stuff, and there’s not a ton of research about these products. As far as I know, there are only two products on the market that address redox signaling. The first, ASEA, is sold by a network marketing company and targets the mitochondria. The second, Restore, is Zach Bush’s product, and it targets the gut biome and restores tight junctions between cells.

Both of these products, but especially Restore, were paramount in my efforts to regain my health when I was fighting the effects of HPA-axis disregulation, a state of overdrive fight-or-flight response brought on by too much stress (in my case, overtraining).

What is so powerful about a tool that focuses on redox signaling is that by addressing the most foundational levels of biology, you can effectively improve the entire biological system above them.

For me, the effect of this approach was so strong that for some time I couldn’t use ASEA because I had detox reactions to it. I couldn’t tolerate it until I was about halfway through a multiple-month heavy-metal detox program called True Cellular Detox.

Restore, on the other hand, turned off anxiety and panic feelings and allowed me to not only start working full-time for the first time in months, but to travel to Roanoke for an outdoor educator academic conference despite having been bedridden mere weeks prior.

This isn’t medical advice, and if you have medical issues, then work with a physician to resolve them. However, Restore is safe and, considering that most of us have gut health problems of some kind, it’s a great idea for most of us.

And yes: most of the good research on this product comes from the people who make it, and there is the possibility of biased or skewed data. However, I was helped greatly by Restore, and if it works the way its makers claim it does, then it’s truly one of the best things you can take for your gut biome and long-term health as a whole.

Furthermore, I’ve also listened to several interviews with Dr. Bush, and it’s always been my feeling that he is a man of intelligence. His explanations of the science behind Restore are clear and make sense, and he seems to truly want to make people healthier.

For example, his team has applied for a grant from the National Institute of Diabetes and Digestive and Kidney Diseases for further double-blind research with the goal of making Restore a widely available and clinically relevant product. As far as I can tell, they would love for other parties to research their product, but in the meantime, since this science is new, they’ve been doing it themselves.

You can get Restore on Amazon and from the company’s website.

The following is a list of resources for learning more about Restore via research and interviews of Dr. Bush, including a clinical trial and the aforementioned clinical grant application:

So far we’ve discussed the importance of increasing the bacteria in our gut. Most of the methods we’ve talked about are used to increase good bacteria in our biome. However, much of the clinical data show another side to gut health: the need to reduce bacteria in the gut biome. This is because many people’s gut health problems stem from bacterial overgrowth, which you can think of as stubborn colonies of pathogenic “bad” bacteria.

But wait, don’t we want to avoid killing bacteria in our gut? Isn’t the goal to increase biodiversity and the content of our gut biome? Yes, in the long run, but think of your biome like a garden. Pathogenic bad bacteria are like weeds that prevent diversity and cause problems, while otherwise good bacteria can become overgrown. Addressing bacterial overgrowth is like pulling the “weeds” of bad bacteria and trimming the “hedges” of overgrown good bacteria.

Here comes the elemental diet, a hypo-allergenic, liquid diet that behaves like a long-term “fast” that starves pathogenic gut bacteria. Research examining the benefits of gut biome diversity has shown that simple fasts increase biodiversity and the prevalence of good bacteria. Elemental diets simply speed up this process by allowing you to “fast” for much longer, up to three weeks for some people, by consuming food in its elemental form.

Before we get into the details of elemental diets, I want to take a moment to address the idea of dietary fiber. I’ve been hearing that fiber is good for the digestive system for as long as I can remember, but elemental diets and fasting are fiber-free, so what gives?

First of all, fasting is a metabolic state that we entered more often in ancient times than we do now. Even if fiber really is good for the gut, our biome may simply have adapted in response to these periods of fasting, which we can think of as a sort of reset button.

Second, I think fiber isn’t as important as people believe. Dr. Michael Ruscio (who I mentioned earlier in this article) mentions in his book Healthy Gut, Healthy You that the only benefit of fiber supported by strong research is its protection against digestive or colorectal cancers. Even then, he points out that there is a ton of other data implying that fiber intake has no positive benefit for these conditions.

The 55 studies, meta-analyses, and academic papers he uses to back up his argument can be found at location 3243 of the Kindle edition of the book, at the end of chapter 10.

I’m not here to tell you fiber is bad for you or good for you. I’m just saying that I don’t think it’s a relevant concern when it comes to long fasts or the elemental diet.

Earlier I mentioned that elemental diets involve consuming food in its elemental form. This simply means food that is already broken down into a digested form. For example, when you digest protein, your body breaks it down into amino acids. Therefore, the “elemental” form of protein is amino acids.

The foods consumed in these diets used to have to be made at home, but nowadays, they are offered premade by multiple sources, including prescription-quality elemental diets such as Vivonex Plus.

This option has been well studied and works well, but the taste is difficult for some to get past. This brings us to a second type of antimicrobial diet: the semi-elemental diet.

Semi-elemental diets, also known as polymeric diets, are very similar to elemental diets except that their ingredients are not 100 percent digested. This makes them generally more filling and palatable. In theory, a full elemental diet would be more effective due to smaller particle size, but clinical studies do not show this to be the case. Semi-elemental diets appear to work just as well as elemental diets—and they taste good too.

These diets are primarily used for the purpose of fighting bacterial overgrowth, but what does that mean clinically? Here are some specific conditions the elemental diet has been used for:

Small intestinal bacterial overgrowth (SIBO): In a 2004 study, a 14-day elemental diet normalized SIBO breath test results in 80 percent of a 93-patient population, and 63 percent experienced a reduction in symptoms of irritable bowel syndrome (IBS).

Crohn’s and ulcerative colitis: Many studies show that elemental diets are equally as effective as anti-inflammatory drugs and corticosteroids in treating Crohn’s and inflammatory bowel disease, although some studies show them to be less effective. If avoiding drugs is important to you, you can try an elemental diet, and if that isn’t enough, then you could try corticosteroids.

Weight loss: There has been little to no research on weight loss and the elemental diet, but in Healthy Gut, Healthy You, Dr. Ruscio notes that his patients tend to improve their weight problems in proportion to the degree to which the elemental diet heals their gut (Chapter 18, loc. 6381). One clinical study also shows positive weight changes in individuals who used a semi-elemental diet to treat Crohn’s.

Celiac disease: The elemental diet has been shown to repair intestinal damage and reduce symptoms in those with celiac disease (an extreme reaction to gluten in wheat) in cases in which a gluten-free diet did not.

The elemental diet can be a powerful tool for gut healing for many of the most stubborn conditions. In this article, I’m simply interested in the fact that it heals the gut, which by extension results in health improvements ranging from weight loss to improved focus to better mood.

This is a more powerful tool than the previous methods I’ve addressed, and in the words of a great philosopher, with great power comes great responsibility. Before you start an elemental diet, it is worth knowing when to use it and when not to use it.

This is really just about asking yourself if you are doing the elemental diet casually, like I do, for performance boosts, or to fight specific issues with the help of a clinician.

First things first: If you are not working with a clinician and doing lab work, then you should only do the elemental diet for four days at a maximum.

Here’s the thing: elemental diets can be maintained for up to three weeks in proportion with the severity of your gut health problems if you are working with a medical professional. They operate by starving bad bacteria in your gut and trimming overgrowths of good bacteria.

However, if you don’t have much bad bacteria, a long elemental diet could be the wrong tool for the job, and furthermore, three weeks on a diet that is essentially a modified fast could have other negative impacts.

This is why I suggest that you only follow the diet for a maximum of four days if you are just looking for performance improvements and are not working with a clinician.

My reasoning is that many people can perform a four-day fast, and an elemental diet is just like a fast plus nutrients. Many people experiment with fasting without doctor supervision and without issue for periods of up to four days.

Caveat: If you have severe health issues, you should always work with a clinician before doing a multiple-day fast, elemental diet, or anything similar.

Assuming, however, that you are a healthy individual who is simply seeking to improve your body and mind, a four-day fast is hardly extreme. Furthermore, you’ll be getting nutrients as part of an elemental diet. This diet isn’t intended to starve you—just the bad bacteria in your gut. Consequently, it’s generally easier than a straight fast. And if you find you’re having a hard time, then just stop. Go back to eating normally, and come back again later with supervision and a purpose.

Last, it’s good practice to think of the elemental diet as a one-time reset. You don’t need to do it all the time. This is what I did, and I experienced less inflammation and fewer GI problems when I ate “cheat” foods like grain, dairy, or candy. I also haven’t felt a return of these issues despite having done the diet months ago.

If you feel that you still have some gut health issues or other areas you want to improve that you think could be related to gut health, then do another two- to four-day reset in one to three months, or do some testing and work with a clinician for a one- to three-week elemental diet.

As I said, I’ve only done the elemental diet one time, and I noticed major improvements in my energy, focus, and sensitivity to “cheat” foods. I may do another in two to three months, but for now, I still feel like I’m in an improved health space without it. Furthermore, I use other gut-healing techniques and eat a good diet, so it should be harder for bacteria overgrowths to reform in my gut.

Gut health is a big topic, and I wanted to provide you with information about three powerful tools that many are unaware of. However, there is much, much more you can learn and do to improve your gut health. From learning more about the gut-brain connection to discovering how diet influences the biome, there is an absolute ton we didn’t cover today.

This is why I’d like to humbly suggest checking out another article on Better Humans by another great health coach: Maria Cross, MSc. Her article “Heal Your Gut, Heal Your Mind” goes into depth on how the gut affects our health, including mental conditions like depression.

She further includes information on the many factors involved in our gut health, such as diet, allergens, and even stress, as well as how you can diagnose gut health problems using testing.

The only quick add-on I’ll include is that the best gut health testing available that I am aware of is Viome by Naveen Jain, a billionaire philanthropist who owns multiple companies, including Moon Express, which is the first private company in the world to gain permission to land on the moon from the U.S. government. Viome is an equally impressive company dedicated to helping solve the world’s health problems, and Naveen’s team and the equipment behind this project are unparalleled.

My journey to both heal and become my best self has involved many different therapies and trial-and-error methods. From long-term heavy-metal detox to a ketogenic diet to photobiomodulation and light therapy, I’ve done a ton of different things.

Of all the things I’ve tried, gut healing has been a constant help, and each of the methods I’ve discussed here was paramount to my improvement. In fact, Restore, the product I recommend in method 2, was the first thing that allowed me to start working full-time after almost six months of feeling too tired and anxious to do so.

Health and performance are complex and multifactorial issues. However, by addressing the foundations of health, we can usually improve everything else. So far, I know of little else that is more foundational than our gut biome.

Whether you have issues you’d like to improve, such as lack of energy, focus problems, or mood instability, or you’re already a top performer and are just looking for an edge, I think addressing gut health may be the best and most important place to start.

As always, thank you for the support, and I hope this article proves valuable guidance for your personal health and performance journey.

Beyond Probiotics: 3 Incredible Tools for Healing the Gut Biome

Research & References of Beyond Probiotics: 3 Incredible Tools for Healing the Gut Biome|A&C Accounting And Tax Services
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