7 Surprising Ways to Improve Your Microbiome

Episode Summary

In this episode of the Empowered Nutrition Podcast, we dive deep into the importance of the microbiome for overall health. We tackle common misconceptions about what impacts the microbiome and offer evidence-based recommendations for optimizing gut health. We also explore the factors that harm the microbiome and underscore the significance of making informed dietary choices.

Episode Highlights

1. Introduction to the Microbiome:
   • Understanding the importance of the microbiome for overall health.
   • Common misconceptions about microbiome health.
2. Connections Between Microbiome and Health:
   • The role of the microbiome in metabolic health, mood, and hormonal balance.
   • How an impaired microbiome can lead to systemic inflammation and chronic diseases.
3. Probiotics and Fiber:
   • Limitations of probiotics in changing the microbiome long-term.
   • The importance of fiber, but why it alone may not restore microbiome diversity.
4. Effective Ways to Improve Microbiome Health:
   • The significant impact of fermented foods on microbiome diversity.
   • Key findings from the Sonenberg study on fiber vs. fermented foods.
   • Benefits of prebiotics and specific polyphenols for gut health.
   • The role of berberine in improving metabolic health and the gut microbiome.
5. Harmful Factors for the Microbiome:
   • Four categories of food additives that impair gut health:
     1. Emulsifiers
     2. Artificial sweeteners
     3. Food colorings
     4. Nanoparticles
6. Practical Tips for a Healthy Microbiome:
   • Incorporating fermented foods into the diet.
   • Avoiding food additives that harm gut health.
   • Understanding the broader impact of diet on systemic inflammation and chronic diseases.

Resources Mentioned

• Study: Wastyk, H. C., Fragiadakis, G. K., Perelman, D., Dahan, D., Merrill, B. D., Yu, F. B., Topf, M., Gonzalez, C. G., Van Treuren, W., Han, S., Robinson, J. L., Elias, J. E., Sonnenburg, E. D., Gardner, C. D., & Sonnenburg, J. L. (2021). Gut-microbiota-targeted diets modulate human immune status. Cell, 184(16), 4137–4153.e14. https://doi.org/10.1016/j.cell.2021.06.019 
• Common Fermented Foods: Yogurt, kimchi, sauerkraut, kefir, and kombucha.
• Prebiotics: Inulin, FOS, GOS, polyphenols from pomegranate.
• Berberine: Benefits for metabolic health and gut microbiome improvement.

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Ready to dive in? Listen here.

SUBTITLES:

Well, hello and welcome back to the Empower Nutrition Podcast. I’m Erin Skinner, registered dietician. I’m excited about this topic. I’m gonna give you a little tough love and don’t get offended. This might not apply to you, but it sure applies to a lot of really smart, amazing clients that we have. And it’s, it’s not your fault if this applies to you. It’s again, ex extremely common challenge, or I guess lack of GA an information gap that we see in practice. And so I thought it was a really important thing to kind of give a comprehensive overview of this topic in this episode. And if you want more details on a specific piece of this, let us know. We always love feedback on the podcast and we love topic ideas. So I’m gonna give a pretty high level overview of this. But again, we can go deep in future episodes if you all like.
But here’s the topic. The topic is this way back in the day, so maybe 10 years ago, it used to be that people didn’t really understand much about the microbiome or that it was important for health. And now if you know nine outta 10 people, if I say, you know, have you heard of the microbiome? And do you think it’s important for your health? People will say yes and yes. So all is well, right? Actually not the case. Most people don’t fully appreciate why the microbiome is important for health, first of all. Second of all, all of the things they’re doing that are either harmful to their microbiome or that they’re not doing that are really important for their microbiome or the things that they think help their microbiome aren’t helping it, or the problems that they have specifically, most often metabolic problems that sometimes also challenges around mood and hormones.
They know they have these problems. They know they wanna fix the problems. They know that the microbiome is important, but they haven’t connected the two. That’s maybe the biggest thing is just not realizing that microbiome health does not only it, it’s not just connected to your digestive symptoms. It’s not like, oh, you know, as long as I don’t have too much bloating, or if I have normal bowel movements, I’m good. That’s not the case. The microbiome is intimately connected to the most pressing and common health challenges that we see in our practice. So those things, again would be metabolic health challenges. So dysregulation of appetite and satiety and hunger, high BMI or being overweight, insulin resistance, pre-diabetes, diabetes, high cholesterol, hypertension, all the, the, I’m going at the aspects of metabolic syndrome here, but super frequent challenges that we have our patients want help with.
But realizing how much the microbiome impacts that is often a gap. So, but that is a well documented thing that when the microbiome is impaired, what that causes the, the sys the, I know we talked about in podcasts before, but to summarize the, the process that occurs is that the impaired microbiome leads to impaired gut integrity, or leaky gut is the not scientific name for that, which causes translocation or crossing of pro-inflammatory pieces of dead bacteria from the gut or peptides like little pieces of your food will cross over through the gut lining into the bloodstream. And that’s basically like a chronic infection that never goes away in the sense that it causes systemic full body inflammation that in turn, we now know, you probably do realize that inflammation is the underlying driver of metabolic problems that I just listed. Not to mention also of heart disease, cancer, dementia, which are the leading causes of death in the Western world.
So it’s not extreme to say that the microbiome is, IM impaired. Microbiomes are is one of the main drivers of morbidity and mortality in the western world. So, which means like disease and death. And people, I think when you, when they agree that the microbiome is important, they still haven’t made that leap to understanding that fact of like, it actually is tied to the common health challenges that we have and that actually are the top, again, root causes of death in the western world. So we, we CI mean, I don’t mean dramatic like, oh my gosh, if you have bad microbiome, you’re gonna die. Well, we’re all gonna die. But I think you get my point that it’s not just a digestive thing, it’s an overall health thing that is very prevalent and, and with a large impact, the microbiome is also, again, impact, very impactful again, related to that inflammation, further disregulates and impacts neurotransmitter production and metabolism so that it has impacts on anxiety and depression and attention for without a doubt, we’ve seen that in the research.
And so yeah, we, we should care about microbiome. Everybody agrees about that. But no, really we’re like, we really should. And it’s common that I see people confused on what actually is. Let’s say somebody gets really motivated by what it just says. Says, okay, great, I wanna really optimize my microbiome. If I said, okay, well what things do you think would do that? The most common answers I would probably get would be probiotics and maybe fiber. Now let’s go through those very quickly ’cause I wanna get into things that are actually more helpful. Bottom line, up front, those are not the most helpful things actually for, so let’s start with
Probiotics. Probiotics. What that means is that is you’re taking actual live bacteria in a supplement form that is meant to kind of come in and augment the microbiome. Well, you’ve got like two pounds of bacteria in your microbiome. So taking a little capsule of bacteria does have a short term effect, like while you take it, but it’s a transient thing. It’s not really changing your microbiome, it’s, it’s just passing through almost like a one day prosthetic that when you stop taking the probiotic with, with exception of some specialized types that are not the types that people normally get, you don’t see a, a long-term impact of taking probiotics typically. Now, I’m not saying there’s never any purpose. We use tons of probiotics in clinical practice. So I don’t, I’m not saying that. But what I’m saying is if you wanna truly change your microbiome and optimize it, then taking a probiotic is not again, the most evidence way based way of doing that.
’cause it tends to actually not change your microbiome. It’s more like it comes in and gives you this like sort of transient benefit from the bacteria you took. But it doesn’t change your own bacteria environment in the gut. So that’s not the best way. Another thing that understandably people think should work is, is fiber. And again, don’t misunderstand me. It is critical to get enough fiber and the typical, on average, Americans only eat about half of the minimum. So women should be getting 25 grams a day minimum. And on average they get 13 men should be getting 38 grams. And on average they get about half of that. So that’s a big problem for a lot of reasons. But we’ll talk about a study later in this episode where this has been researched. We have seen that unfortunately low, that low fiber diet that what western people eat in the western world, that is the original, one of the main original causes of the impaired microbiome that leads to all those diseases we talked about.
So I inadequate fiber is the original problem. However, un unfortunately it can’t be fixed by eating high fiber. So it’s not that just reversing the original problem will get you out of it. It’s, it’s just not been shown by the research to be that that’s the case. And one obvious reason for that is we know that when you don’t have enough fiber and enough fiber diversity, meaning different types of plant fibers, you actually lose diversity in the gut. Meaning you don’t have as many types of bacteria. And that’s actually a major impact on the outcomes that we talked about. So it’s not just that you need a certain amount of bacteria and it doesn’t matter what type, you need to have a lot of different types. So when you don’t need enough, have a good fiber situation, you lose actual species of bacteria. Kind of like if you imagine a rainforest and then some entire species go extinct, you can’t then change something about the rainforest and all of a sudden those species come back into existence.
It’s like, look, if the panther goes extinct, it’s extinct. You can’t do anything to get the panther back. Think of it like that with the microbiome. Chronic low fiber diet combined with other factors is leading to lower diversity in the microbiome, meaning loss of entire species. If you just suddenly eat more fiber, that doesn’t make these species of bacteria magically return. So hopefully that follows for you. But yes, it’s important to get into fiber, but you can’t just count on some fiber to restore your microbiome unfortunately. And that’s been researched and shown actually by the top microbiome research lab in in the world really. And we’ll talk about a paper they did here in a few minutes.
On that note, let’s go to it. So what things actually truly do improve the microbiome? So there’s a, actually a married couple, Dr. Sonenberg has been and wife that work at Stanford and they’re some of the world top microbiome researchers. So they’re one of their labs at Stanford published a paper in 2021 where, and we’ll link to this in the show notes, but basically it’s fascinating because they, they thought that they would do this study where they got a bunch of adults and got them to eat a bunch of fiber with massive increase in their fiber and that they would see an improvement of the microbiome. Thankfully, one of their, I believe it was a postdoc in their lab, asked to add this sort of second arm to the study, which was an arm that instead of increasing fiber, they increased fermented foods. So they go ahead and do the study. They had, let’s see, let me find the number, 39 participants in the study splitting these two groups. So the improvement of fiber group improvement of fermented foods group. And basically what they expected, of course, was to see that the fiber group had a big improvement of their microbiome and they sure did increase their fiber. They went from about 21 grams a day average to 45 grams a day on average. And plot twist, the results showed no significant improvement in, in the microbiome
And no resulting. They also in the study looked at the thing we talked about where there’s the systemic inflammation caused by impaired microbiome. The inflammatory markers were not improved in this group that basically doubled their fiber. Now let’s talk about the other arm that increased their intake of fermented foods. They went from an average of 0.4 servings per day to 6.3 servings per day, which sounds crazy, but a serving of fermented food can be a very small amount, like a, a couple tablespoons of like kimchi on a plate, for example, a small amount of kombucha, a small amount of yogurt. So you could have a bowl of yogurt and that would be multiple servings. But they again, they went from basically half a serving to six servings a day, which is a 12 x increase. And in contrast to the high fiber group, they saw a significant improvement of their diversity of the microbiome.
So that’s like the microbiome miracle that we all hope for, where it’s like you actually do have restored species living in the rainforest. Like how cool is that? And what it basically is, it’s like, this is not a perfect analogy, but imagine with the rainforest, you had some other backup rainforest somewhere else in the continent and you went and got some of the panthers, brought them back to the rainforest that had lost the panthers and put them in there. Now you’ve got the panthers back. That’s what the fermented foods are doing. And you would think that the probiotics would do that ’cause it is the actual panthers in the sense that it’s, it’s bacteria. But what we know about the microbiome is that it’s more complex than that. It’s if you’ve lost diversity, it’s it’s related to now you have an environment that’s not amenable to diversity anymore.
So you lose the mucus lining that the bacteria needs to live in. You lose the, the gut integrity that keeps the gut the mucus layer healthy so that it can exist for the bacteria to live in. You’ve lost these short chain fatty acids that maintain all of that. So there’s, there’s a whole environment that needs to exist in order to get this diversity back. So maybe in our analogy, the the the fermented food, maybe maybe imagine the rainforest lost its panthers because the rainforest was burned or like cut down and now there’s, if you put a panther in this environment, it, he won’t survive there because it’s not a healthy rainforest anymore. That’s kind of the equivalent to taking a probiotic. It’s like sure, you’re, you’re putting panthers in there, but the environment isn’t healthy for panthers anymore. So the the bacteria don’t live. Whereas like with the fermented foods, what happens, that’s like rainforest restoration.
You make the rainforest robust, healthy, vital. Now it’s a happy and healthy environment for the panther to live in. And, and then you have this beautiful increase in diversity of your ecosystem. So, and again, this isn’t just a, like an imagined concept. This is a published study that is very well done in bio, highly regarded lab. And again, we’ll link to it in the show notes and you can take a look at it. But what’s cool is they, in the fermented foods group that we’re talking about, they have that significant improvement of their diversity, which is awesome, but we don’t, again, why do we care about diversity? It’s because it’s linked to this inflammation that’s linked to all the common health problems that, that we have. The metabolic problems, the hormone problems, the moon problems. So they did in this study measure inflammatory markers and they found that 19 out of 93 inflammatory markers improved.
And some of them are the top known problems in the health of western people. So IL six and IL 10 both decrease, which shows a really important lowering of systemic inflammation. That’s what you want from even thinking about your microbiome is you want this inflammation situation to be improved because of all of the, it’s everything that’s linked to, again, we talked about a bunch of ’em, but it’s also linked to autoimmune conditions. Arthritis, it’s also linked to to like, as we said, mental health hormone metabolic imbalances. So super, super like relevant to almost every health challenge that we see in clinic. So fermented foods are the way to go that I’ve already listed off a few of them, but it’s important to kind of build up a little menagerie of these so that you have the ability to kind of add it in multiple times across your day.
So fermented dairy, like yogurt and kefi, if you can have that, great, not everybody can, but there’s also water key fear. If you don’t, if you don’t tolerate dairy, then there’s the world of kombucha, which I like my clients, to make them make it if they can. It’s really simple once you get started that way you avoid a lot of added sugars. But if, if not it’s not realistic, then just buy kombucha. You don’t need to drink a whole bottle every day, just an ounce or two then. So that way you know, it lowers the cost by dividing, maybe spread out, have one or two bottles spread across your week. And then the third category is fermented vegetables. So things like kimchi sauerkraut, fermented carrots, fermented pickles. It’s just really important to make sure it is a fermented food and not just a brid pickle. If it’s just simply been where like the vegetable is pickled or ferment or b brid in salt water, that’s not it. It needs to be that it was fermented. Okay, so fermented foods are key.
And then the other main, main, main evidence-based thing that we know improves the microbiome is prebiotics. So I already said probiotics don’t do it. That was the live bacteria. Now I’m talking about prebiotics, which basically is defined as some specific compound that is, that specifically feeds and, and targets and improves the amount of healthy gut bacteria. So I think of this as like a fertilizer for healthy gut bacteria. It comes in and like nourishes the healthy gut bacteria in a targeted way and encourages their health and their growth. So it’s like food for these bacteria. A traditional prebiotic is a, a specific tested short chain carbohydrate. So the commonly tested ones are inulin, zos, phos, and goss. Those are acronyms for glyco like glyco compounds. So oligosaccharides basically. And they’re again, little short chain carbohydrates. You can buy prebiotic supplements. Some people are at a place with their gut that they’re so damaged that they can’t even tolerate a prebiotic.
So it’s a little bit of a catch 22 of like, you can’t tolerate the thing that you need because of overgrowth of bacteria. So free sibo for example, if that’s the case that you don’t tolerate one of those traditional prebiotics, then we know that specific polyphenols also have prebiotic property. So those would be the specific chemicals in plants that give them their color so that the polyphenol plant compounds from, for example, pomegranate is known to improve an a keystone healthy species called akkermansia that is lacking in many people and very important. So definitely you can go to polyphenol prebiotics. That’s something we do a lot in cases where the traditional prebiotic isn’t tolerated. So, and again, there’s, there’s a lot, a lot of research on prebiotics and it’s not just been shown to improve digestive conditions. Again, it’s been shown to improve metabolic conditions such as PCOS, the things we keep talking about.
So it’s like a little targeted way of nourishing or fertilizing these healthy gut bacteria and actually actually increasing their number. We know that prebiotics does that. And the final thing I’ll say very quickly, ’cause I’ve done a whole podcast episode on this not too long ago, is berberine, berberine we know is kind of like this holy grail thing where it will, it has both antimicrobial and prebiotic properties to it in the sense that it lowers unhealthy gut bacteria and improves the numbers of healthy gut bacteria and has been shown to improve metabolic health. So we use it a lot in people who have challenges with their weight. Honestly, it’s been, it’s not, there’s, there’s multi mechanisms whereby bur brain works. But in addition to improving this endotoxemia or systematic inflammation that comes from an impaired gut microbiome, it also stimulates the hormone GLP one, which you probably know is the hormone stimulated by the G class of GLP one meds.
So like ozempic wegovy meds like that. So not on the same order of magnitude at all, but berberine can be great if, if the elements of of metabolic syndrome exist or again, it’s been researched in PCOS as well. Okay, so again, the top three things for improving your microbiome are the fermented foods, the prebiotics and berberine. And then let’s go in quickly to the other side of the coin to close this out because a lot of times we get pretty smart and advanced clients so they even maybe, let’s say you already know all the things I already said and you’re already doing a lot of this, I will still often see that client be completely unaware of some of the things that have been shown to harm the microbiome. So you want to, I mean this just kinda almost goes without saying, but if you care, if you wanna improve the healthier microbiome, you wanna do the things that help it, but also stop doing the things that hurt it, right?
So we’re gonna talk, I’m gonna go into the four things that we know are sort of the culprits of impairing the microbiome. And again, I see a lot of health, health conscious people and just not aware of some of this. And there’s a study, I’m gonna frame this around a study that came out. What was this? I’m gonna look down. It was very recently, yeah, it was last month. It was June of 2024 that this study came out. But I presented on it in the spring ’cause it was ePublishing, I had a print. But basically it’s a great little review article. Again, we’ll link it in the show notes where they talk about, yeah, you know, the gut microbiome is critical and related to so many common conditions. There are many food additives in our food supply that harm gut health and there is research showing this.
So they have a great image in this paper that you can look at that summarizes it. But basically there’s four different categories of food additives that we know harm the microbiome. So we need to be more cognizant of it. The first one, and the one that I I think people are missing the most is emulsifiers. And the reason why emulsifiers are a problem is because the microbiome lives in the mucus layer like we were saying before, which is a, like you can imagine, it’s like a little layer of mucus that lines the gut and it’s, it’s the, it’s like the little jello that the, that the bacteria live in and they need that mucus layer in order to survive and stay inside of you.
Emulsifiers basically dissolve that mucus layer, which has been shown to have, of course, huge impacts on the microbiome and on health. And you might not be sit buying something that says emulsifier. I’m sure you’re not, I’ve never seen that. But if you are drinking almond milk or coconut milk or hazelnut milk or any kind of oat milk, any fake milk, it’s gonna almost always have an emulsifier in it. So that’s a common commonplace where I see that non-dairy, coffee creamers, even dairy coffee creamers, there’s emulsifiers and like lots of yogurts, lots of other types of specialty like beverages and foods. So really start to take a look at ingredient labels and start looking for emulsifiers because they’re gonna break down that gut lining and make it so that your microbiome is homeless. And so they have, it’s, it’s gonna, it is not gonna thrive. So definitely that’s probably the top thing I see of just not keeping an eye on modifiers.
Number two, artificial sweeteners. Tons of controversy on this. There’s a number of ways that artificial sweeteners have been shown to impact health. One of them is that they damage gut microbiome diversity, which impairs the production of the short chain fatty acids that nourish the gut lining and keep everything healthy around the inflammation, like we said. So we know that artificial sweeteners increase pro-inflammatory cytokines like nf kappa beta, TNF alpha for example, or some of the main pro-inflammatory pathways that we’ve seen increase with artificial sweeteners. So there’s also been shown that, like we know that when, this is not the microbiome, but we know that when the, when artificial sweeteners are consumed, there is a release of insulin that that perpetuates insulin resistance and health problems. So there’s, there’s significant impact of artificial sweeteners. It’s we’re, we’re not in the glory days of the 1980s and nineties anymore where these sweeteners just got a free ride and we could put sweet and low in everything or crystal light.
They are harmful. So try to minimize artificial sweeteners in your diet. The third category, again, people do not have this on their radar. For most adults it’s not as big of a factor, but if you start paying atten, if you have children and you start paying attention to this, you’ll be freaked out. It’s, and it’s food coloring. We know that food coloring is metabolized by the gut microbiome and then the metabolites that they produce in response have been measured. And those metabolites are pro-inflammatory contributing. Again, to kind of think of it as like this bucket of adding into this systemic inflammation that’s like a chronic infection that causes all the health problems to keep talking about. So food coloring is an issue. It, you see it in so many children foods, I mean it is just wild when you start to like look for it.
And then of course adults get exposed to food coloring. I don’t mean that we don’t, but eating a minimally processed diet will of course help with this. And that’s true of all four of these. So eating whole foods, home cooked foods is gonna cut down on emulsifiers, artificial sweeteners, food colors. And the fourth one, which is generally categorized as nanoparticles, but which sounds like what is that? But some of the biggest ones are silicon dioxide that you’ll see on tons of food labels. Titanium dioxide, which is a lot of toothpaste and a lot of processed foods. It’s a whitening thing. So if you’ll see it in processed foods where they want to have a wider color. So start taking a look for titanium dioxide, silicon dioxide and aluminum silicate is the other one. We know that these nanoparticles impact gut microbiome diversity. They reduce commensal bacteria that are the healthy gut bacteria that modulate inflammation.
They increase inflammatory cytokines and reactive oxygen species in response. So nanoparticles do impact the gut and they do impact health. So they unfortunately are not, you know, you can’t, I’m not a conspiracy theorist at all, but in this specific situation with processed foods, you can’t trust that everything in the food supply has been fully vetted as harmless with respect to your health that that cannot be further from the truth. If it’s something that killed you dead tomorrow, of course the FDA would not allow it to be in foods or even if it could, we could clearly see that it killed you dead within a few years of eating it. Sure they would figure that out. But this is a more insidious long game with the gut that is relatively new in the world of research. However, at this point, well researched. So the food supply hasn’t caught up to this and I’m not sure if it will because there’s a lot of conflict of interest with respect to the billions of dollars involved in processed food.
Not to mention the way that our society runs, it’s kind of dependent on processed foods. So that’s kind of a separate topic. But suffice it to say that just because things are in your food does not mean that they’re harmless, is what I’m tending to say. So emulsifiers, artificial sweeteners, food colors, and these nanoparticles are what to watch out for. If you do all this, you are gonna have a massive improvement in your gut health and in your overall wellness. Without a doubt. If, if it sounds overwhelming, just pick one thing you can do for now. So like last week I had a client where it’s like, yeah, I, I drink, I eat yogurt, I eat cheese, we have milk in our home and I put emulsified almond creamer in my coffee. What if we just put some of the milk in the coffee? Oh yeah, no problem, I can do that.
Done one small step towards the microbiome, that’s better. So just think of one or two things you can do for now. Get that habit routine and then think about the next thing you can do after that. So it doesn’t have to be overwhelming before you know it. You can have a routine habit around getting your fermented foods, getting your prebiotics, replacing processed foods in your diet that contain these harmful items and your microbiome will respond. So I hope this helps. I hope it was enlightening for you. And again, let let us know if there’s anything on this topic or any other topic that you’d like to hear about and we’ll add it to the queue. Have a good rest of your day.

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