[00:01:16] About this Podcast
[00:02:32] Podcast Sponsors
[00:05:48] Note from James
[00:06:47] Introduction to Viome results and recommendations
[00:11:43] Ben’s Gastrointestinal Summary
[00:14:11] Overall Microbial Richness
[00:18:28] Food and Supplement Recommendation
[00:22:42] Metabolic Fitness Score
[00:25:11] Inflammatory Activity
[00:36:35] Proinflammatory microbial activity, and active pro-inflammatory pathways that indicate potential GI inflammation
[00:46:34] Podcast Sponsors
[00:49:40] Butyrate Production Pathways and Active Butyrate Producers
[00:55:34] SCFA Production Pathways and Active SCFA Producing Microbes
[00:58:35] Recommendations for My Diet
[01:03:16] Digestive Efficiency
[01:10:54] Protein Fermenters and Active Protein Fermentation Pathways
[01:17:32] Recommendations Related to Protein Fermentation
[01:19:45] Hydrogen sulfide production pathways and hydrogen sulfide producing microbes
[01:28:09] Few Specialty Organisms
[01:30:37] Vitamins produced by the gut microbes and detox of the microbiome
[01:37:35] Overall Recommendation
[01:40:50] End of Evaluation
Ally: There’s another main reason that may be highlighting walnuts is because of the beneficial fatty acids, like it has ALA. This is just one or two nuggets of information that actually went into the reasoning in our recommendation engines logic. So, you want to be preventative. You want to take action before it becomes bad and needs improvement, especially if it’s an area called pro-inflammatory, meaning —
Ben: I have a master’s degree in physiology, biomechanics, and human nutrition. I’ve spent the past two decades competing in some of the most masochistic events on the planet from SEALFit Kokoro, Spartan Agoge, and the world’s toughest mudder, the 13 Ironman triathlons, brutal bow hunts, adventure races, spearfishing, plant foraging, free diving, bodybuilding and beyond. I combine this intense time in the trenches with a blend of ancestral wisdom and modern science, search the globe for the world’s top experts in performance, fat loss, recovery, hormones, brain, beauty, and brawn to deliver you this podcast. Everything you need to know to live an adventurous, joyful, and fulfilling life. My name is Ben Greenfield. Enjoy the ride.
Hey, so today is kind of a unique episode. You may have heard before about the company Viome, which does a complete analysis of your gut microbiome, and then gives you personalized food recommendations and other lifestyle, and health recommendations based on the results. Well, it’s been quite some time since I have released an update on what they’ve been up to, and some of the latest science on their analysis. So, in today’s episode, you will have the pleasure of listening to a solosode not with me, but rather with one of the chief scientists at Viome, who is going to walk you through all of the latest and greatest tools that they have now to analyze your gut in even greater detail, and they’ll be using yours truly as a case study for that walkthrough. If you would like the video version of this or any of the handy dandy PDFs or downloads that go along with it, you can simply go to BenGreenfieldFitness.com/viomeupdate. That’s BenGreenfieldFitness.com/V-I-O-M-E-update.
This show, like all of the Ben Greenfield Fitness Podcast, is brought to you by Kion, my playground for all things health and wellness. This is where you’ll find extremely unique formulations that I create that blend ancestral wisdom with modern science. And one of the very popular bundles that we have over there is the Recovery Bundle, which is hot on my mind right now because I’m using it like it’s crack cocaine. I just did a doubleheader obstacle course race yesterday. My entire body feels like I got hit by a semi-truck.
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Finally, this podcast is brought to you by Four Sigmatic shroomies. This is my favorite way to get super dense mushroom elixirs down my hatch in a very tasty way. I have all of my favorite mushrooms listed if you go to foursigmatic.com/bengreenfield. I’m going to give you a discount code in just a second. That’s F-O-U-Rsigmatic.com/bengreenfield. You can see all the ones that I use on a regular basis, but in a few future podcasts that you’ll be listening to in the next few weeks, you’re going to hear all sorts of different mushrooms talked about by my guests. Many of them bring up lion’s mane, chaga, reishi, and even lesser-known mushrooms like agaricus is one, tremella is another, maitake for blood sugar management.
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James: Hey, everybody. My name is James and I am Ben Greenfield’s podcast audio editing guy. And Ben was unavailable to record this, but he wanted me to let you know that the podcast today is very video intensive, meaning that you’re going to get the best experience actually watching the video, which is embedded on the shownotes at BenGreenfieldFitness.com/viomeupdate. If you’re set up to listen, you can certainly go ahead. You might have a better experience listening to the hundreds of episodes of the Ben Greenfield Fitness Podcast that have been published over the years. A great way to keep up with those episodes is on the Ben Greenfield Fitness app, and you can just find that on the Android or Apple Store to search for Ben Greenfield Fitness. It’ll come right up. You can listen to your heart’s content. So, whichever episode you listen to, enjoy it.
Ally: Welcome to your Viome results and recommendations. My name is Ally Perlina and I’m the Chief Translational Science Officer here at Viome. And I would like to introduce you to your scores and your microbiome results that are used to give you all of these different food recommendations, and also supplements. Right now in the app, what we show you is actually a very unique perspective that we derived from our metatranscriptomics technology that allows us to see what is actively happening. It’s a very unique perspective where actually, your microbes are telling us what is going on. The activity is what is measured when DNA is transcribed into RNA. RNA is exactly what we measure with metatranscriptomics technology. And the reason why that’s important is because only living active organisms can make RNA from DNA.
So, because what we sequence, the data that we get from your stool sample is all metatranscriptomics. Everything that we see is what is actively going on, and that is the most exciting part. But the next thing that we do is we actually assess specific functional activities. So, you will see in your results that there are things like overall scores, like inflammatory activity or digestive efficiency, and you will also see very specific molecular biological themes like butyrate production or putrescine production, and you may be wondering what is that.
Those are all different nuggets of information that tell us this is what your microbes are doing. And we’re the only ones that are able to deliver you information like this in something like a gut microbiome or any microbiome direct-to-consumer test. What we do with this information is we look at your specific pattern of activities that are associated with certain wellness areas. So, for instance, inflammatory activity. It can be, even it is in the same score of the same level for different people, but each one has a personal story with personal functional blocks that are active or inactive for you versus someone else.
So, we take your unique pattern of these pathway functions and activities and we’ll look at it integratively in order to drive your food recommendations. Same goes for metabolic fitness and digestive efficiency. We’ll also look at your overall microbiome richness and we’ll look at specific precise signaling and metabolic pathways that are taking place to see if some foods need to be minimized or even avoided for you, whereas for someone else, it will be in a superfood area. And you will see that in your recommendations with actual reasons pointing you to the score. So, it could be very clear which foods specifically address this score, and it will call out those scores where you need improvement.
So, when you have this entire profile of your functional activities and you know what is actively going on, only then you can really be empowered to take this biologically informed action on your body. And follow the plan, see if you improve these scores, and I hope you enjoy your wellness journey with Viome.
Hi, Ben. My name is Ally Perlina. I’m a Chief Translational Science Officer for Viome. I’m grateful to be here and thank you for being open to sharing your results of Viome test with your audience. So, let’s get into it.
In summary, I just want to get right to it. I want to tell you what are the areas that you absolutely need to focus on, and then we will actually peel it back, and I will explain little by little how all of these different insights even come together to affect the recommendations that you see in your app.
We’ve done this analysis, and actually, dug behind the scenes and looked at the raw data and analyzed beyond what the app is showing. And the reason we did that is because we want to share the concepts and the thinking that when into the type of scores that you see in your results and how this drives the recommendations. All these bullet points are actually based on expert analysis. And that’s one of the main things that my team does. We take all kinds of different data and we derive insights and connect them to recommendations, and that’s the translational part I guess of translational science.
What you really need to address based on what the microbes are telling us are some of the specific themes within the digestive area. What I mean by that is that there are many things that can affect your digestive system. Digestive system basically covers everything, starting when the food enters your mouth and all the way through. So, digestive system has many different aspects that can make it not function very well. So, if everybody said, “I need some digestive help,” it probably wouldn’t be the same for everybody because everybody needs some specific piece or several parts to be addressed.
So, we will cover those parts, those themes that need to be addressed based on your GI test. And I always say this, like, this is what the microbes are telling me because this is a very unique perspective from your gut microbiome that we sequence and we’ll look at all of the activities, and they’re actively telling me stuff even right now. So, I wanted to say that the digestive themes that we will address will probably be the most important ones. And then it would be also very good for you to take a look at your sources of probiotics and fermented foods. And I know that you already take some good probiotics, and it shows in your test. We will get to that. But still, it’s very important to support richness and diversity of your microbiome because the more of that you have, the more resilient your microbiome will be for you, the better it is for the host. So, that’s the second major point.
And you do have a few viruses. And so, even by probably reading the names, it could be inferred of what kind of foods you may see affected by them. Prunus necrotic ringspot virus is the reason that you have plum on your avoid list, and Pepper mild mottle virus is the reason you have pepper on your avoid list. There are associations in the literature between these viruses and inflammatory response. And for that reason, we recommend that people avoid these foods. You don’t have to avoid them indefinitely. It could be three to four weeks. So, what we usually see is that after retest, these viral activities clear completely after our customers avoid virus affected foods.
Now, let’s look at your actual app screens that showed us the breakdown of your results. This one is microbial richness. Microbial richness score is something–we’ve offered it for a very long time. It’s like the summary, how many microbes do you have active? So, who showed up and was active. And that’s really important. It’s not the same as composition because compositionally, many things can be there, and they may not even be alive anymore. But because we measure RNA, we sequence RNA, that’s why our technology is called metatranscriptomics. And only live organisms can transcribe RNA from DNA. Then just the mere fact that we see it means it’s active. Remember that we see it, therefore, it’s active.
Here, it says you have 134 active microbial species. That means that you literally have 134 species level organisms that are actively transcribing RNA from DNA. So, they’re alive. They live there. Some of them are very good, some of them are kind of so-so, and some are what we call them opportunists. They wait for the right opportunity to do something that is not very good, and they will naughty, and they can cause some chaos. But what you do about that is first, you take care of your microbial richness, and then we will address all these other functions that will assure that all of these opportunists and other themes are in check.
So, when you have 134, that puts you on the lower side of medium or average zone. So, you see in the app, it will show a face like this. It neither smiles nor frowns. With your microbial richness, it’s on the lower side of average, and that’s why you have this purple face that says average. Average just means that this is on average. This is the range where we see results fall. And just like microbial organisms themselves, when you see these average range results, it’s not necessarily by itself good or bad. And I want to go back to that point about microbial organisms. The good ones, the opportunists, if you just focus on just one organism and you have to go and Google and ask, “Is it good? Is it bad?” you’re ultimately trying to make a final statement that supposedly will mean something for your entire health just based on that one guy.
But what we do is we focus on active functional themes. So, it’s the overall microbial or microbiome-wide activity, and the functional profile of these activities that tell us what’s going on. So, we’ll get to that in a lot more details. Right now, I wanted to say that falling on this lower side of average means that yes, your microbial richness can use a boost, but it’s nothing too alarming. And if you want to know more about the distributions, we always provide our reference ranges.
So, for example, here, when we really think that you need improvement, it’s when we see it. Usually, I would say less than 100, but actually, our range here goes up to 108 microbial species present, and average is all the way between 109 and 217. But I’d say if you’re closer to 200, you’re doing really, really good. And the excellence range, I mean we call it good, but in this case, I think it’s a very excellent score to have, 218 and above. And if you see, it actually says that it represents 95th percentile and higher of the population. So, 95th to 100th percentile of the entire Viome population. So, of course, it’s quite remarkable if you get there, but if you’re anywhere closer to 200, then that’s really great.
So, what can we do for your microbial richness? Here’s an example. This is taken straight from your recommendation screen. You can see sauerkraut. You will also see other fermented foods. And the reason why they’re there actually could be many reasons. But one of the reasons is that it will help enrich and diversify your microbiome, and you see some of that is highlighted. But actually, I want to make an introductory point about all of the recommendation texts that you see.
So, you see these paragraphs, right, that says, “Sauerkraut is a superfood for your microbiome,” and gives you explanation. This is just one or two nuggets of information that actually went into the reasoning in our recommendation engines logic. So, when you see this, just know we could only highlight so much, but the complexity of the logic is such that we take so many different factors. It would probably be too lengthy to actually spell it all out and outline it. But we highlight one or two nuggets of information, sometimes three. It depends on their importance. And you can see that here, diverse microbiome importance is emphasized, but there could be many other reasons why sauerkraut is on your superfood list.
In general, when you see recommendations, so here, there is another main reason that may be highlighting walnuts. It’s because of the beneficial fatty acids, like it has ALA. It has other benefits of course. And there’s also olive oil. There are multiple things that are highlighted telling you why the foods are there. But also, these foods happen to improve your microbial richness and diversity. So, if we know that that’s the case, then we try to highlight that as much as possible for you, and you could see that in the text, and that’s with the red highlights.
So, back to your microbial richness. Something that you can also notice is that in your supplement section under your recommendations, it will say, “My recommendations.” So, Ben Greenfield’s recommendations say, “Supplements,” and there are probiotics. Actually, there is more than one type of probiotic you could take, but it lists a specific lactobacillus. There are different kinds of lactobacilli that may be beneficial for you. And I will talk about another one a little bit later. But probiotics is a way to introduce more organisms into your system. So, probiotics come in, and hopefully, if they stay, they will enrich your microbial ecosystem. So, your richness score will probably go up. So, when you retest, we could check it out.
And polyphenols, polyphenols, it looks like a separate category. In a way, it is. It depends how you think about it. Polyphenols are more of a chemical umbrella term for the types of compounds with these aromatic rings. So, a polyphenol that we may all have heard about is resveratrol, or maybe somebody who heard of curcumin, or subclass of polyphenols called flavonoids. Polyphenols, even though it’s in its own class, actually, they can really feed the microbes and promote the type of environment that will help them thrive. In a way, it’s also something that can help your microbial richness and diversity. And I will talk more about why we specifically said that cranberry-containing polyphenol supplements could be good for you specifically. So, all of this is very much, very highly personalized.
Now, the digestive support is blank here, but we will get to it. This screen is where we just want to address your entire ecosystem and what it’s made up of. Next, score, and this is also score that we’ve offered for quite some time, it’s called metabolic fitness score. Your metabolic fitness score is a microbiome score. Still, these are all microbiome scores. Everything that goes into these scores is from the NGS data. It’s something that came directly from sequencing, directly from your sample. But then again, you have to remember that this is what came from the stool sample.
So, we’re not measuring how athletic you are and how much you’re running, or how much intensity training you’re getting, or what’s the percentage of your body fat or lean muscle. What we’re measuring in terms of metabolic fitness, it’s a microbiome’s perspective on those things that are important for the host metabolic fitness. And that includes, as you can see in the text, that includes glycemic control, so things that help us control blood sugar response when we eat different foods. You actually have some really good results in that category. So, some of the foods that are glycemic for a lot of people, for you, are predicted to be just fine. So, your metabolic fitness is great. It’s really good. Moreover, it actually improved.
What the microbes are telling us are those things that are associated with glycemic response or with weight gain control, insulin sensitivity, and lean phenotype. That is very much in line for you. It’s also good to see that you’ve improved since last year. Not that it was bad. Last year, it was average, in the average range. But you could see, it refers to the previous result here. It says September 2018. That’s from your previous kit. And the current one says it’s in the good range, and that’s because your metabolic fitness score is high. It means there’s high level of those really beneficial activities, the pathways, and we’ll talk more about that, and also the microbes that are just associated with more fit, more metabolically fit individuals. That’s really great and that represents–the good score represents 18% of Viome population. So, only 18% of our reference population score as good as you did. So, good job on that one.
Moving on to our next score. It’s also something that our customers are very familiar with. It’s called inflammatory activity. Inflammatory activity score, I mean, it’s really the cornerstone of this whole thing we’re doing here, right? So, if we talk about microbiome or even Google it right now, you’ll see, it’s about controlling, or mitigating, or causing, or something to do with inflammation and how inflammation starts in the gut. I don’t need to talk about why that’s important, but inflammatory activity score that we have here, it’s actually a microbiome score again. So, all of these are microbiome scores, and it’s a huge compilation of sub-scores that go into this score.
We’ve been showing this for quite some time, as well as the metabolic fitness microbiome score, but we never actually showcased all of the different components that have to get scored individually before they come together with different weights, and different criteria, and different decision trees and the logic to make up your inflammatory activity score. We described some of that in your guide to results, but we haven’t shown that in the app. But then we introduced more of these scores that reveal some of these functional patterns behind the scenes.
For example, your inflammatory activity is okay, it’s average, but these are the sub-scores, I should say, or the different components of the score that make up the overall inflammatory activity of your gut microbiome. So, why it’s important is because if you have too much inflammatory activity, then you may see some things either disrupting the lining and leaking out or causing immune response, or some things that may just make it unfavorable for the beneficial organisms to thrive. And you don’t want that, so it could be about the bad guys or the opportunists suddenly taken over. It could be something that tells you that there’s a hostile environment in your gut, which makes it more favorable for the opportunists to come out and thrive, and not so much for your probiotics that you’re taking and getting through your diet.
Inflammatory activity has all of these scores, and you should see them in the app. One of them is LPS biosynthesis pathways, and that is a known inflammatory immune system trigger. LPS is this polysaccharide. It’s called lipopolysaccharides. It has like a lipid part and the sugar parts, and they come together and make this big molecule. There are different kinds, and LPS is something that microbes have kind of like on their outer coat. And a lot of times, the pro-inflammatory LPS is something that the bad guys have. So, the opportunists who you don’t want to basically have them get out of control, those are the guys that are known to have the most pro-inflammatory LPS molecules.
And so, they’re making these molecules because that’s just part of–that’s what they wear. That’s what they do. They can leak out, especially if you have a leaky gut, they can leak out through the intestinal lining. And if they do, these molecules can cause immune response, and we really don’t want that. So, you have that at an average zone, which is okay, but I want to highlight why we even give you such score. That’s a very important part of inflammatory activity. So, all the scores here are just some of the pro-inflammatory activities that we take into account. It’s actually a balance between pro-inflammatory and anti-inflammatory activities.
And overall, I’d like to just emphasize that it’s about keeping that balance, but it’s not just about the balance of who is there. It’s about the balance of what are the activities, what’s going on. So, if what they’re doing, there is something that could be, “I could do without it,” but there is a lot of good things that they’re doing. It’s that balance of activities and functions that is important, and we really believe that and we see it with our customers and our data.
So, these are more of the pro-inflammatory ones, and these are not all of the scores that go into the pro-inflammatory section of this overall score. But LPS is one of them and a very important one. Then there is a couple of gas production scores. We’ll go back to those when we talk about your digestive efficiency. Methane gas production. Actually, you’ve tested with us so many times and I always looked at your data, and you always had high methane gas production, and I just remember that. It’s almost like–you should probably know this. In our translational science team, you are the methanogenesis guy.
So, we analyze a lot of data and we look at different people, and sometimes we do these really deep dives. And we have our flagella guy. I won’t say who it is, but has the highest, most, the brightest flagella. We’ll talk about that score, too. And you are our methane gas production guy. You have the highest methanogenesis, and we don’t know why, but consistently time after time, it’s all lit up. The entire pathway that leads to–well, it’s not just one, multiple pathways that lead to methane production are completely active, overly active, more so than what we see in our usual customer database.
It’s not a terrible thing to have, but too much gas production can lead to some of the disturbances in your GI tract, and it can also be irritating to the gut lining. It can even end up being pro-inflammatory to your gut lining. And that is why this is part of the pro-inflammatory activity. So, too much methanogenesis, which is the same as methane gas production, or too much sulfide gas production, it’s something that could disrupt ultimately the gut lining. But we know that when we see more of that activity than what we usually see, then we may want to take some action with that, and you will see that reflected in your recommendations.
Besides sulfide gas, there’s also ammonia gas, but you scored quite fine in that so we didn’t highlight that here. But sulfide gas production is something we’ll talk about more because it’s not only part of inflammatory activity score, it’s also part of the protein fermentation, which is part of the digestive efficiency score, and it’s also part of the gas production. So, it’s something that in different compilations and with different impact with different weights, it contributes to multiple overall areas. So, when you see something like this, this slide, it’s not the ultimate mapping of all of the different scores and sub-scores and how they come together, it’s just a small slice of those things that I think are important to highlight in your case.
So, you might think, “Well, if this is average, right, why is it highlighted in my case?” Because we took a deeper dive and a look behind the scenes, we looked at all of the different ways that your pro-inflammatory activities are manifesting. And just based on this more of an expert view with everything that we can see right now, it’s like on the higher side of average. So, because a lot of these things, even when they say average, the expert opinion is that it would be kind of almost borderline high, which would be when it needs improvement, we would say we believe in making illness optional.
So, you want to be preventative. You want to take action before it becomes bad and needs improvement, especially if it’s in an area called pro-inflammatory, meaning, promoting inflammation. This is why when we looked at it, you’ll see some of the pathways. I will show them to you. You will see biofilm and chemotaxis and flagella. It’s not too bad, but just something to keep in mind. You will see that in the slides that follow.
Now if we step back and look at this, there’s one major thing that I did not cover, right? These are some themes that are part of pro-inflammatory category of the inflammatory activity score. But they all have all of these ones at least on the screenshots from your results. They have this word pathways at the end, and I have not explained it yet. So, we will actually see some images of your pathways, but what I want to say in general is that we are measuring activities or activity levels of biological pathways. And these biological pathways are kind of like the sequence of events that end up resulting in something that manifests physiologically, biologically, as a final function.
For example, gas production, or there could be something like mucus degradation. So, something with a real functional outcome. Function as in like activity. You think of it as what is functionally going on, right? So, we use gene expression data to light up all of these different sequences of events, like this step goes to this step, and with this, it produces butyrate, or this with this with this makes flagella come together, and activates it, right?
All of these things are pathways. And to put it in a nutshell, pathways are the one way, and maybe the only way available right now to understand what the microbes are doing. Understanding pathway activities is the same as understanding what your microbiome is doing, what is actually going on. Without seeing these activity levels, it would be very hard to take any kind of action because if you don’t know what is actively going on, then how would you take action with your personal diet and supplement plans if you’re not even sure if you’re being a good host, if you’re stimulating the right beneficial activities and functions, and if you are keeping those opportunistic ones or inflammatory ones in check?
So, pathways, in a nutshell, is basically a perspective that we offer into what the microbes are doing, what is actively going on. And I think we’ll move on to actually see some of those now. We have this flagellar structure, and we measure, with all of the different gene expression data that we have from our metatranscriptomics sequencing from your sample, we measure the overall activity that leads to this biosynthesis and assembly, and even transport of this flagellar structure. Imagine it’s like an army and somebody says, a specific general says, “Okay, we have to start making some of this Hook protein or some of the filament proteins, like we got the Hooks, we don’t have enough of the filaments, or we don’t have enough of the ring that will hold it in a specific place, or the motor switch.”
So, there’s a signal that’s sent. Then all of these different genes start firing up, and these genes encode proteins that are structural proteins. It’s not about this enzymatic pathway, it’s not about metabolic pathway like digesting something, converting something into something. No, this is actually all of the signals and all of the actual particles that are needed to make a flagellar structure. And flagellar structure is that tail that helps them swim, and they have many, many tails. You probably have seen a lot of cartoons of microbes. If you’ve seen a cartoon of E. coli, it has like a lot of these different spaghetti looking things usually, depending on if you get it in a form of a toy or if there’s a better cartoon out there.
Those are flagella. Flagella structures, when they need to be made, there’s all this signaling, and we measure the gene expression. And so, what you see here is your actual data, and your data shows–think of it as like the color warmth scale. When it’s blue like deep blue, it means it’s active but it’s underexpressed. And when it’s orange or if you ever see red like here, it means it’s really overexpressed, so highly expressed, more expressed. These genes, these particular genes are more expressed than what we usually see. And yellow is slightly overexpressed.
Here, you see that there are quite a number of those flagellar assembly genes that are overexpressed, but not too highly overexpressed. And some of them are there, but underexpressed. So, it’s definitely not enough to make you the flagella guy that you don’t want to be in the sense because flagella is usually a sign of something pro-inflammatory happening, either pro-inflammatory or reaction to some threat in the environment, because if your microbes have to move more than they usually do in people’s microbiomes, everybody’s microbes move. But if your microbes have to move more than usual, then there’s either some threat or they are the threat, okay? So, they could be the opportunistic guys and they want to move and take over and fight their turf wars, or they’re the good guys that some of the good ones have flagella and they’re swimming away or swimming towards some alternative sources of food or alternative places to stay, actually.
So, in either case, flagellar assembly pathway activity is not a thing that you want to have really high, okay? In this case, it’s good that you’re not our flagellar guy, but you are our methanogenesis guy. So, this is the methanogenesis pathway, part of the pathway of you, Ben Greenfield, methane production right here. It’s circled right here. Actually, there are multiple sources that can yield methane, and you have a lot of these overexpressed genes. So, the genes that are expressed, they encode enzymes, and some of these enzymes are needed for this final conversion of, let’s say methyl coenzyme M molecule to methane, okay?
And so, that is a very directional and committed and critical step in this pathway. And also, the step that is right next to it that is also very important in this coenzyme shuttling that happens is also very lit up. So, you could see, yeah, okay, some genes are underexpressed because they’re blue, but there are so many that are there. A lot of people don’t even have a single one. So, there are so many that are there, and some of them are yellow, and some are orange, means that they’re either slightly or more than two-fold overexpressed. And the red means that they’re very, very over–unusually overexpressed.
And so, what I want to say is in some of the literature, it points to pro-inflammatory potential and things that could be disruptive to the gut lining. Also, methane and other gas production by your microbiota can cause some of the motility issues, which means how the food moves along. So, it could exacerbate things like constipation and other issues that you would actually literally feel, and I guess sometimes that you confirm that that may be true for you, for your case, when we spoke.
In general, okay, so methanogenesis has a bad rep and it’s known to be not a good thing to have. But at the same time, we do see methanogenesis in people who are more athletic. We haven’t figured out exactly if this is always a true pattern. What is the cause? What is the effect? But maybe for you and your microbiome and for–especially with your metabolic fitness that you have going on for you, this may be okay. It may be not so bad. Still, something to keep an eye on because gas production, if excessive, can cause some trouble. This is your methanogenesis pathway.
And something that I will point out here, it’s called trimethylamine metabolism. You see that? This is just a little section of a pathway. It’s not the actual final curated pathways that we use for scoring. But because it has this part, I think it’s important to mention. So, trimethylamine, also known as TMA, is yet another score that we have. And for you, that score is average. So, it’s there, trimethylamine production pathways, but it’s kind of average. And trimethylamine production is associated with not so beneficial effects because it can be converted to TMAO in the liver and lead to more of the fatty liver infiltration and some of the cardiovascular effects.
But in your case, you have trimethylamine used. At least some of it is used up to make methane, you see? So, TMA, trimethylamine metabolism, is carried out by your microbes. So, your microbes are making TMA, but they’re also–or the other guys are taking the TMA and converting it to methane. That’s another point why your methanogenesis may not necessarily be like this alarming theme, but it’s an interesting one, right? It’s good to have this perspective, and this kind of thinking is exactly what goes into our scoring.
So, when I was hovering over these different genes and I was saying that they code for enzymes, we actually go through all the literature and we see the functional significance of every single gene, every single enzyme, what it means for the host, and what actually the gut microbes do and how that applies to the lower GI, lower gastrointestinal tract microbiota. And based on all of that curation and the topology, the proximity of how they’re arranged in the biochemical or molecular pathways, we assign specific weights and specific decision trees that take into account all that gene expression and give you a score.
That is the type of thinking that goes behind automation of the scores that everybody sees. So, that’s end-to-end automated, and our customers are all able to see something that would otherwise take maybe months and months for humans to go through. But now that we’ve automated it, we kind of front-loaded all of these insights and all of that literature curation so that anyone can have their overall pathway activity levels assessed for all of these different pathways.
So, besides methanogenesis here, you have some of these chemotaxis and biofilm and quorum sensing themes that show that maybe there’s some communication between the microbes that say, “Hey, there may be something alarming going on.” Maybe for some microbes, it’s alarming. It doesn’t mean that across the board, there’s something to really worry about because, let’s go back for one second, this score that talks about biofilm, chemotaxis, and virulence pathways, this score is average for you.
So, it’s not something to worry about, but it’s just a combination of all of these things in our sort of a deep dive expert view, puts you in a slightly higher side of this average range for inflammatory activity. And that’s why we want to do something about your inflammatory activity even though that’s not the main area because we’re going to get to the digestive area, which is definitely the top focus for actionability for you. But you’ll see that they’re actually interconnected as well.
Ben: Hey, I want to interrupt today’s show to tell you about saunas. Now, I haven’t seen a whole lot of research that saunas can directly help with your gut health, the topic of today’s show, but they certainly can enhance the elimination of toxins because your skin is your body’s largest detoxification organ. And infrared light actually penetrates quite deeply into tissue. If you’ve never been in an infrared sauna and have only been in a dry sauna or a steam sauna, then you have no clue how heavily you sweat, how deep and cleansing the sweat can be when you are in an infrared.
You also get of course all the heat shock proteins, all the anti-aging benefits, the immune support, the stress reduction. And especially if you do it at night, which I do, followed by a little bit of a hot-cold contrast shower or a quick cold soak, your deep sleep levels explode through the roof. Clearlight, who makes the infrared sauna that I use, has cracked the code on creating extremely low EMF and ELF infrared saunas. So, you are not, as you would be doing in most other saunas on the market, microwaving yourself in the sauna, which kind of defeats the purpose of living a long time.
They also have a lifetime warranty. I own their Sanctuary, which is this enormous sauna. I can do yoga, kettlebell swings in. I can drag a stationary bike in there if I want to do heat acclamation training, you name it. You get 500 bucks off of any sauna, however, if you just go to healwithheat.com for your Clearlight sauna, and you use code BENGREENFIELD. That gets you $500 off, automatically includes the lifetime warranty, and they throw in a free gift with your purchase. So, you go to healwithheat.com and use code BENGREENFIELD.
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Ally: Here, I’m showing your score for butyrate production pathways. The way it goes together is that it’s actually anti-inflammatory. So, butyrate production activity is a well-known microbial theme that is something that provides anti-inflammatory effects. So, in a way, it either compensates for the inflammatory activity that is already there, or it protects your gut lining, your colon epithelial cells, from the disturbance that they may get from all of these chemotaxis and virulence factors being fired at each other by your microbes. So, the gut lining stays unharmed.
Butyrate is really good for nourishing your gut lining and your intestinal barrier, your colonocytes, the cells in your epithelial layer. Really love butyrate. They use it for energy, and it gets easily absorbed. And also, butyrate is good for various functions like your metabolic fitness. One of the reasons why it’s so high and it’s so good is because you have high production of butyrate because butyrate regulates your satiety. So, that’s the metabolic fitness connection to your weight gain and weight control. And also, butyrate production is good for insulin sensitivity. So, that’s the connection between metabolic fitness score and your glycemic response and sugar response control.
So, butyrate production is overall very beneficial, and these are just some of the wellness areas that I mentioned that it’s good for, but it’s across the board, a very beneficial nutrient that your microbiome can produce for you, and you just need to know how to keep it up, and I think you do know. You’re doing something, right? And to incentivize your microbes to keep doing this and do it even more. So, this goes with the inflammatory theme because we actually reconcile all of the pro and anti-inflammatory pathway activities and the microbes themselves to come up with this final microbiome score called inflammatory activity.
So, butyrate production, you’re doing good. You see the green smiley face. These are some of the–actually, if you search, Google it, butyrate pathways literally, you will see something–maybe even this image will come up. You just Google image search and you will see that there’s so much work that’s been done, and it’s amazing what the microbes can do. Some of this well-known kind of chain of carbohydrate metabolism events like pyruvate metabolism, Acetyl-CoA, is something that a lot of us learn in school without any specialization. I mean, I’m talking just like in high school. Kids learn about that.
But what’s amazing is that the microbes, they drive these pathways up and down in ways that we didn’t even learn in school, and they make some products and byproducts that we didn’t learn about because they’re quite esoteric. We’re just still discovering this. It’s a new science. But if you do Google some of this and you want to know or you want to look up this paper, you will see that there are so many different pathways that have already been elucidated to short-chain fatty acid production.
So, butyrate is this short-chain fatty acid. It’s a type of fat molecule that is not too long. So, it’s a short-chain fatty acid. And short-chain fatty acid is associated with mostly beneficial functions for us, the hosts. And you could see how these microbes are driving it from lactate. They can go back and forth from different sources that contribute to pyruvate metabolism. Acetyl-CoA is a molecule that can come from so many different other sources. So, even proteins can be substrates for ultimate butyrate production by some of the microbes.
Now, the beneficial microbes, they usually preferentially make butyrate from carbs, the kinds of carbs that we call either starches or fibers, and people have different names. It’s usually the kind of carbs that are not easily observed right away into our circulatory system. So, we’re not talking about eating some sugar because your butyrate producers won’t even get the message that there is going to be something for them to even do because we will immediately absorb it, and we might have that glucose spike, which may not be so good for you.
So, I’m not talking about the carbs that are syrup and honey and things that are easily absorbed, but more of these polymers. So, more complex carbohydrates that you can find in a lot of the, let’s say leafy greens, a lot of the vegetables. You see a lot of them in your superfood list. And the beneficial butyrate producers are microbes that prefer that. And one of these types of carbs is known as resistant starches or resistant fibers. The reason they’re called resistant is because they are resistant to our digestion. So, they don’t get digested by the host. But guess what, they make it all the way down so that finally, the microbes can get the message there’s something for us to eat and something for us to do. And butyrate producers, that’s what they do really well. They produce butyrate. So, one of the ways is to keep doing what you’re doing with all of the leafy greens, the vegetables that you’re eating because that really seems to be keeping them happy and keeping your butyrate production up.
In your data, we see that there’s a short-chain fatty acid production beyond butyrate. It’s not just butyrate. There’s also other ones. And so, you could see here’s your acetate, propionate. It’s all very active so that’s pretty good. It means you’re getting a lot of that kind of complex carb input in your diet. And based on what you shared with us about your diet three days prior to the test, it really seems to match, and you seem to have a very good sensible and healthy diet. Partly because of that, maybe partly because of the choice of your foods and probiotics, you have an active probiotic in your sample.
So, when we see a well-known beneficial probiotic, we call it out. And in your list of microbes, you will see a little pee next to it. And so, it says, ” Lactobacillus reuteri.” It’s a probiotic. The reason why I started even talking about it right now is because it’s a star butyrate producer. It’s a really well-known producer of butyrate that is actually available in some of the Kefir type of drinks and probiotic supplements as well. So, it’s always good to have a variety of different probiotics that you’re taking or switching between. But when you have L. reuteri as one of them, that’s usually a good idea when you want to keep up your butyrate production pathways signaling and going and making butyrate by your gut microbiome.
So, here’s your butyrate. It’s also called butanoate. And you see in your very immediate conversion steps that lead to butyrate, you have all of these active genes, the genes that are expressed that code for these enzymatic reactions. They are either at average levels or even overexpressed, and sometimes more than one that is needed for that conversion to finally make butyrate. And this is, again, just a partial cartoon. It’s not everything that we take into account for the score, but this is the part that really lit up for you.
So, I wanted to include that in your slide so you can see that there are different routes to butyrate production. That’s why in our scores, you always see something that’s called pathways. You might be thinking, “Why is it plural? It’s just butyrate, so why is it plural?” It’s because there are so many different routes, there are so many roads that lead to butyrate. So, it’s the overall assessment of pathway activity levels of all of the different roads. So, it’s all of the different butyrate production pathways that lead to butyrate. That’s what this is about, and you’re doing really well in that. So, that could help with preventing your inflammatory activities to go any further and to stay at least that average, or even become better.
So, when it comes to your recommendations, there are several things that are highlighted here, but there are many, many more that you’ll find on your superfood and enjoy food list that deal with inflammatory activity. So, you see like bone broth, for instance. That is related to your inflammatory activity in the sense that it helps keep your gut lining intact and have your mucus layer happy there and everything nice and patched up and thick so that it doesn’t become a leaky gut.
And then there is jicama that feeds the butyrate producers, by the way, and can keep your L. reuteri still active and happy there, and maybe some more that you’re taking with your yogurt and things like that. And you can see that there’s anti-inflammatory polyphenols, like turmeric. So, turmeric is a source of anti-inflammatory polyphenols, that’s a source of curcumin. And then you can see also oregano. Oregano is something that has antimicrobial activity. So, for all these opportunists, oregano will help keep them in check.
So, the reason why I actually don’t have a title for this slide is because this deals with inflammatory activity. But it’s not like this is the set of recommendations that just goes to everybody that has average or higher than average levels of inflammatory activity. This is very personalized to your specific patterns of inflammatory activity. So, it’s like this is still the Ben Greenfield slide. It’s not the overall Viome inflammatory activity slide. I was struggling how to name it so I decided to just make these squares bigger so you can read what it says. So, strengthening the mucosal barrier, that’s the bone broth and jicama.
And so, this is keeping your opportunists in check, keeping your pro-inflammatory activity still well-balanced, balanced out by the anti-inflammatory activities, and having all of these good guys or the beneficial microbes, having them happy and thriving, and feeding them what they need to give you the most benefit. That’s the type of recommendation that we make. It’s always based on your specific pattern of inflammatory activities. So, we could all have the same average inflammatory activity altogether. But the ways for me, for instance, to keep it average or even good and prevent it from going bad, can be completely different than for you. So, it’s always a specific activity pattern that gives us this insight into what are the functional interventions that are available here. And that is what you see reflected in your Ben Greenfield recommendations. That’s what these are. That’s why I didn’t name this slide.
And another thing that helps with pro-inflammatory activities, and first of all, balances out your microbiome, second of all actually helps to protect your gut lining as well, are the different fighter metabolizers, which include polyphenol metabolizers. Polyphenols, like we saw before in previous slides, those are types of supplements. But you don’t have to necessarily take supplements to get your polyphenols. A lot of these red berries and dark red or dark-colored berries have a ton of polyphenols that have this anti-inflammatory antioxidant content. And in your pathways, we actually see there are many pathways that show that you’re getting your polyphenols. So, that’s great.
But we actually see this riboflavin and production and consumption of molecules that are also used for energy. This may or may not be related again to your athletic Ben Greenfield Fitness profile. So, I wanted to highlight this specific pathway because this may have to do with the types of polyphenols called flavonoids. That’s where you get this riboflavin shuttling. And when it’s more active than usual, and you can see to some degree it is, then who knows, maybe this is actually you exerting a specific type of pressure on your microbiome to provide energy for you. Could be. It’s a hypothesis, but it may be something to do with that. It’s a good thing.
And now, we’re on to digestive efficiency. Digestive efficiency is a microbiome score, and it’s not about necessarily your microbes digesting. It has to do with that. The way to think of digestive efficiency is to imagine microbiome’s reflection on the host digestion. So, if you can think of all of these different digestive processes, and then imagine how we can read the imprint of that in the active themes of your microbiome, then that is what goes into compilation of this digestive efficiency score. It’s a big score. Over a year in the making, so many different perspectives and avenues, pathways, microbes, different functional groups had to be addressed and really well curated with all of the literature to date and the data set that we have at hand, which is a very unique metatranscriptomics data set to come up with a score.
So, digestive efficiency for you is in the average range. Manual expert curation and analysis actually says that it’s on the lower side, and the lower side means it’s less optimal. So, you want digestive efficiency to be good, meaning that as far as the microbes tell me or tell us, your digestive system is very efficient. If it’s on the lower side, then it’s suboptimal and you may see something that says that you need improvement. You don’t see that right now. It’s still in the average range, but it’s enough for us to dig deeper and to take action on it. And I will explain actually more about why even having average score. Overall, we still need to take action. Some of it is preventative and some of it could be to ameliorate some of the symptoms that you have already experienced that you shared with me.
So, digestive efficiency in the average range, actually, for you is comprised of all of these different scores that do need improvement. For someone else, these scores, maybe three of them would not need improvement, but two of them would need improvement. And even with the same overall digestive efficiency score, someone else may have different recommendations, okay? Of course it’s good to have your digestive efficiency score on the good side, but if you think of it, it measures everything from the gas production that we touched on a little bit already, from that to the movement of the food, how you’re doing with specific macronutrient groups like proteins versus fats. There is a reflection that we can see in the activities of the microbiome that tell us how well your digestive system is working with respect to those very specific molecular functions. So, this is what I want to dig into right now.
What you have is, first, it’s a score called protein fermentation that needs improvement. That, in itself, actually has multiple, multiple components that go into that to assess the overall microbial protein fermentation. But first, you may ask, what is protein fermentation? So, again, it’s a microbiome score. It’s purely from the sequencing data. And it’s telling us how your microbes are processing protein. So, protein fermentation is, in a way, a fancy word for microbial metabolism of proteins. So, if your metabolism of proteins in the microbiome is higher than what we usually see, then it means your microbes are working over time to digest your protein.
So, why are they digesting your protein and working so hard? And what we see, what we’ve learned is that this means that you are not digesting it well enough. Maybe you’re digesting it partly, but a lot of undigested protein makes its way to the lower colon where we get your sample and we see that your microbes are actually finishing that work. What that tells us is that maybe there are some enzymes that you need more of. Maybe it’s about the hydrochloric acid, the stomach acid for efficient digestion of proteins. Or one way or another, there’s something to do with your protein digestion, which is why we see that your protein fermentation score needs improvement, meaning, you have too much protein fermentation done by your microbes instead of you.
So, that’s one of the areas. The other area is gas production. In that area, we have more than just the scores that we went over, the sulfide and methanogenesis, methane, and sulfide gases. There is an ammonia gas. There are the microbes that are specifically known to produce gases. And altogether, this is our overall gas production score for you. And the fact that it says it needs improvement, I think that that very well goes with what you shared with me and with recommendations that you receive. And that’s of course part of your digestive efficiency because gas production can definitely impact some of your digestive processes.
Now, these three scores are actually specific pathway scores, and that’s why you see these are all of the different pathways that lead to methane. We went over some of those. So, that’s your methane gas production. Then you have your sulfide gas production. We’ll look at that in more detail, pathways. And then you also have putrescine production pathways. Putrescine, just like it sounds, like something putrefying, it’s a byproduct of protein fermentation that is not very good for you, and may be harmful if too much of it is produced.
So, if protein fermentation is something that leads your microbes to making too much of these kinds of byproducts, then you may want to do something about that. Again, your ammonia overall wasn’t too high, so that’s why it’s not listed here. For somebody else, it may not be about methanogenesis at all because that’s actually on the rare side, but they might have a lot of ammonia gas production. We see that quite often. You don’t have that in the high range, which is why you need improvement in these specific areas for your digestive efficiency.
So, again, just like inflammatory activity, there’s always a specific pattern that everybody has. Everybody’s functions need to be addressed in a very personalized way. It’s like your own stacking of different functional blocks, and you have this one that’s too much, this one not enough. Everybody has a unique one. So, your unique combination says that these are the five important scores that you need to address. These are the five areas, the five major digestion-related functions that you need to address in order to improve your digestive efficiency, overall microbiome score. Here, we have some scores that are good. We already talked about butyrate, the beneficial short-chain fatty acid. We also talked about–so stress pathways, that’s a fun one.
Now, back to digestive efficiency. We talked about protein fermentation and gas production. Those are scores that are compiled of multiple components themselves. So, you have protein fermentation, and that is where that byproduct that we don’t like called putrescine. That is where it actually belongs. So, putrescine production pathways is one of the components that ways in to protein fermentation microbiome score. We also know some protein fermenters, and it’s not just putrescine, there are other scores. Even to some degree, a smaller degree, your methane gas production and sulfide gas production can also feed into protein fermentation, because one of the sources for methane and sulfide gas production could be from amino acids, the components of protein. But it’s not the only source, which is why these components are important to look at by themselves, not just as part of the compilation score. And gas production, because this is quite obvious, you see methane gas, sulfide gas are the two gases that tilted your gas production overall score to the suboptimal side that says you need improvement in that.
So, when we look at the actual data, here is your putrescine production, because you may still be wondering. What about that putrid thing? So, it’s a byproduct of protein fermentation that usually has the kind of protein source that is rich with arginine, and your microbes are metabolizing arginine, and it often goes through ornithine to putrescine, or it can go through agmatine, which by itself is not so bad at all. It’s one of the pretty good products of protein fermentation. But the fact that you have so many routes lit up that lead to putrescine, your overall putrescine production pathways, again, it’s multiple pathways that lead to putrescine. They are so active. There are so many of these genes that are overexpressed, that this is what made that score, becomes suboptimal and say it needs improvement.
And you see also another thing called cadaverine, which sounds no less morbid than putrescine. Everybody’s thinking of putrefying cadavers. But yeah, that’s kind of what it’s about, like some product of decomposition of something. That actually does go hand-in-hand conceptually. Cadaverine is also another very favorable byproduct of protein fermentation, and that is something that’s usually made from lysine. It’s a type of amino acid. So, arginine, lysine, those are amino acids that can come from your food, and when your microbes are digesting them, having those microbes really be focused on making putrescine and cadaverine is not a very favorable profile.
Some microbes can make overall protein fermentation products that are not so bad, and that would be a good outcome, like some of the indoles or indole acetate that’s produced from tryptophan. You have a little bit of that. That’s not so bad, but if you have a lot of putrescine and cadaverine, then it means that protein fermentation is an area that needs to be addressed for the sake of your overall digestive efficiency.
Here, we also see this is called urea cycle. It’s a very canonical pathway, pretty much the same way that we learned it in school, different iteration. Except here, it’s your data. It’s Ben Greenfield’s data that shows that these things are overexpressed, and this is where it’s showing this is coming from. Aspartate can fit into this particular loop. There’s your ornithine that can come from arginine, and actually more upstream. There’s some glutamate, which in general is pretty good, and some of it is also converted into urea at the end of it all as the final product of urea cycle.
So, you have some activity there. It’s not overly excessive, but it also goes with the theme of protein fermentation. We don’t have a urea cycle score that we show to the users, but we do measure it because it depends. When we say it depends, it means that by itself, it’s not enough to showcase it as a score. But as part of a specific theme, it goes in the backend, it goes into this generation of the overall score, because in the context of protein fermentation, this urea cycle, it depends. And in this case, it goes very well with the protein fermentation theme. But for something else, it may be neither good, nor bad. So, this is why there are a lot of scores, there are actually about 200 scores right now that we’ve generated. There are so many scores, but we only show those that are most telling and most actionable and hold a lot of weight in and of themselves.
So, this is the urea cycle and this is your ammonia production. And in this particular excerpt, you can see it looks like there’s a lot of it from nitrile, and here’s your glutamate and glutamine. But actually, it’s not excessive overall. We actually compare hundreds of reactions and expression of the genes that code for the enzymes for these metabolic reactions that lead to ammonia production. So, we cannot show these hundreds of reactions, but just to let you know that your ammonia production overall for the entire microbiome is not excessive, it’s within the average range. Still, something to keep an eye on, and that’s part of the protein fermentation theme.
In this case, we don’t necessarily have to go and focus on just addressing ammonia or like urea cycle, like I said, because it depends, or just cadaverine, or just putrescine. In this case, to address it all, we just need to address protein fermentation, and that’s going to help your digestive system. So, how we address it? Here, we have recommendations related to protein fermentation. This is definitely not all of them. You will see a lot more references to digestive health and digestive function specifically in your summaries of the reasons why we recommend some of these superfoods for you.
But here are the superfoods that talk about enhancing your digestion, specifically dealing with protein fermentation and how this is going to help improve your protein fermentation score. And you might think, “What are these sprouts have to do with it?” Actually, one of the reasons is that you can take your protein in a way that is more bioavailable elementally. So, instead of very dense protein sources, you can sprout some of the nuts and seeds and legumes, or at least soak them. Not all of them can be easily sprouted.
And you can enjoy those sprouts that give you those amino acids that you need for your performance, for your energy, for a lot of things, and for your digestive system lining as well. And you can get them through sprouts. So, you can buy sprouts of course and you can sprout things yourself, and that can create this more elemental amino acid availability from something that was a densely packed protein that is much harder to digest that can make it down your GI tract undigested and result in microbial protein fermentation, which we want to kind of minimize now, right? That’s why you see these sprouts recommended for you.
In general, for your overall digestive processes, grapefruit and other bitter foods that you’ll see, there’s like dandelion greens, they have these properties that overall will promote your digestion, not just for protein side of things, but overall, your digestion. That’s why grapefruit, I highlighted it in this orange color, it’s not specific to just protein fermentation function, but this is an example to where it can help your overall digestion, whereas the other ones are more of an example for where we’re trying to say something to you, do this for the sake of your protein fermentation function. So, we take actionability from the overall scores, depending on what they tell us, plus the very specific molecular themes, the pathways themselves, the molecules that come up, or these functions like protein fermentation.
So, I said we’d go back to hydrogen sulfide gas production. This is your score and you have hydrogen sulfide gas production pathways very active, highly active more than what we usually see. And because it’s such high levels of these pathway activities, we say that you need improvement in terms of your sulfide production. Here’s some of the background on hydrogen sulfide production. It’s something that is a known function that your microbes do. You do have these microbes that perform this function, and it’s something that’s well-known in the literature. You can have sulfide produced from your amino acids, which is why it’s part of the protein fermentation theme. But you can also have it coming from other sources, and we’ll touch on that in just a little bit.
So, what’s wrong with sulfide, right? So, just to reiterate again, and besides the discomfort of gas itself, it’s also something that could be disruptive to the gut lining. If we see that it’s something that is more active that the sulfide production activities are more than what we usually see, then it needs addressing. So, dietary protein contributes to sulfide production among other things, which is why it’s part of protein fermentation theme. But it’s not only part of protein fermentation theme. Like we showed before, it is also part of your pro-inflammatory theme because of the disruption to the gut lining. And you do have the organisms that go with that. You have other pro-inflammatory organisms and you have these sulfide producing organisms that are opportunistic. They’re not pathogens or anything but it’s something that is an active theme that may be easily addressed.
Another source of hydrogen sulfide production is sulfate that comes directly from some of the sulfate sources. Sulfate, it’s not the same as the protease fermentation, the amino acid sources. So, you may be ingesting actually something that has sulfate or sulfite. Here, you see this particular picture is showing your data in the context of sulfate and then sulfite that can be converted to sulfide. So, that’s where you get the sulfide gas. And you could see a lot of these oranges and reds. So, all these genes that are behind those boxes, these enzymatic reactions are overexpressed, and they may be coming from some of the foods that you are taking that you’ve shared with us in your food diary. And thank you again for doing that.
And you have these very active organisms, like 20 of them that are known as sulfide producing ones. So, they’re sulfide producers, and among them, we have those that are called desulfovibrio, different species of desulfovibrio. And so, you may want to pay attention to both the protein sources. So, it’s a protein fermentation that we already addressed, plus the sources of sulfite and sulfate, which could be different sources that also exacerbate your microbial sulfide production.
There are also other sources that are known for microbial sulfide production to be enhanced. And some of them are actually in those foods that we refer to as the superfoods. We as in not Viome, but they’re generally thought of as such health foods. They are the superfoods if you look them up right now, and they’re from this cruciferous vegetables family. And so, a lot of these vegetables, they have these compounds in the class called glucosinolates. Actually, it’s a class of classes of compounds. They are the types of compounds that are organosulfur compounds. So, glucosinolates, in general, they’re pretty good for you. They can help you detox, and your microbes can also, by the way, help you detox and they do.
But glucosinolates, as good as they are, may not be as good for you if your microbiome is showing too much of that sulfide gas production because it will use those metabolic intermediates that come from glucosinolates from your food to produce sulfide gas. And what we see in you, Ben, is that there are also some themes that go with these high fermenting microbes. High fermenting means kind of both things. High as in like very fast, and also high as in like higher in GI. So, when you have that, if you have them high fermenting, then you don’t want to stimulate gas production because in the colon, it’s one thing, but if it does happen anywhere higher up in the GI, it could be pretty uncomfortable pain and bloating, something that may go with kind of like a small intestinal bacterial overgrowth type of profile. And we want to prevent that from happening or exacerbating because some of these symptoms are in line with what you shared with me when we talked.
So, as much as it’s a health food, glucosinolates and other organosulfur compound-rich foods are on either minimize or avoid even list of foods for you from Viome. And it doesn’t mean that you have to avoid them indefinitely, but we do see quite remarkable results from people who have these types of discomforts and have already tried eliminating gluten and lectins and dairy. And they think, “What else can I take out?” I only have health foods left in my diet. Well, what happens is that they have nothing but broccoli and Brussels sprouts left in their diet, and they’re overdoing it. And if they have that specific profile with high sulfide production, and especially with high fermenters types of microbes, then they suffer even more. So, too much of a good thing for them is actually not good at all.
So, what we’ve seen is that just getting rid of–for some time, getting rid of all of these cruciferous vegetables and other sources of high organosulfur compounds in foods made a huge difference for them. It actually makes a big difference, and it’s something that they never thought of because it just seems like these are just the health foods. I eat nothing but health foods. For this reason, our recommendations say to avoid broccoli and Brussels sprouts. If you do want to, there’s actually more. There’s cabbage and there’s a few more there. You will see it on your recommendations list.
But if you do want to enjoy some of it sometimes, moderation is key, first of all. Second of all, we always say listen to your body. Don’t take it as like the final mandate and you cannot step anywhere left or right outside of it. If your body is absolutely happy and perfectly great with a specific food, then you are your own best judge or consult with your healthcare practitioner to see what’s appropriate. But we recommend that broccoli, Brussels sprouts, cabbage, you’ll see a few others, are to be avoided. Or if you want to enjoy them at least from time to time, it’s best to at least steam or sauté those types of vegetables because it neutralizes some of the effect. It actually will take the glucosinolates and convert them in a way. Neutralize them. Make that class of compounds into different compounds.
But it will not completely get rid of the sulfur that is still in the food. It’s not going to suddenly just completely negate all of the organosulfur that is in there, that in one way or another, depending on what kind of microbiome pattern you have, can be used by your microbes to actively produce sulfide gas. Again, only from time to time, and if you think it’s appropriate, and steaming would be good. That’s one of the recommendations, tips that we offer in our app.
And you have a few specialty organisms. So, oxalate metabolizers, you have them present. That’s really good. And oxalate is something that can contribute to kidney stones. So, when you have your microbes helping you metabolize oxalate, it’s a really good thing, which is why you’re able to see things like spinach and almonds in your enjoy list. So, these are your oxalate metabolizing pathways. And you have the organisms themselves like oxalobacter. It goes with the name. It’s known to metabolize oxalates for you. So, that’s really good.
You also have soy metabolizers. You have the kinds of soy metabolizers that metabolize some components of soy compounds like daidzin and other isoflavonoids into things like equal. And one of the things that you have is actually called adlercreutzia equolifaciens. It’s even in the name. So, it’s a good thing. It gives you benefit from eating foods like soy foods and miso. You’ll see miso in your enjoy list.
And by the way, as fermented foods, they go back to where we started, your richness. So, it can help you improve your microbial richness score. That’s another example to where one food can be on enjoy or superfood, but there are actually many, many reasons why it’s there where it is, and it’s good for you. You also have really good signatures of fiber degradation. So, if you have a lot of this insoluble fiber, you probably get a lot of your prebiotic content from your foods and supplements. We see that and microbes are telling us that you have all of these complex carbohydrates coming through. So, you’re doing well with that, and these are some of the active microbes listed here.
You also have the type of active carbohydrate metabolism that points to pectin that you’re probably getting from the fruit that you eat. So, this higher up set of molecules that these polymers right here, that’s actually a signature of microbial metabolism of pectin. And you have the genes that go with that very much highly overexpressed. In general, that’s a very, very good thing. And some of the organisms that go with that and are active are listed here. And your microbes are also producing some good vitamins for you, just some of them to list. So, there’s thiamine, there’s biotin, and menaquinone that’s part of the vitamin K. Another name for vitamin K2, I believe.
And you also have your microbiome doing detox for you. So, you’re taking something with selenate, or you may be eating Brazil nuts or other sources of selenium. And you could see there’s very highly active cell innate metabolism. And also, selenoprotein incorporation is something that is known to be a beneficial theme. That’s part of a good signature that goes with a detox pattern. And you also have glutathione metabolism and production and utilization. So, glutathione is going everywhere and being made everywhere. And I think it’s not surprising because as you shared with us, you take some glutathione, and so your microbes can use glutathione, but they can also make glutathione from some of the components you have; glutamine and glutamate.
And then what this is showing us is that glutathione is actually being used to carry out the detoxification for you. So, your microbes are quite busy doing the detox. Glutathione is one of these very beneficial sulfur compounds, by the way. So, some of that is very good for you, and moderation and balances is what it’s all about. Some of the other beneficial nutrients or products that are made by your microbiome, I just wanted to highlight a few. So, branched-chain amino acids are good for your metabolic balance because they can be beneficial for sugar metabolism.
And also, indole acetate, it’s something that is known to be anti-inflammatory and good for your gut lining and intestinal barrier support, but it is also something that is significant in terms of regulating blood sugar. Actually, together, these different features came out as significant in our glycemic response prediction model that we’ve developed with our data science group as a result of a really big study where hundreds of individuals had continuous glucose monitoring in response to different foods. And we also had their microbiome data.
Now, we can see how these different pieces and patterns and the oral functions in the microbiome can help us and serve to predict which foods will have high sugar spike to and which not so much. So, you don’t need to worry about it. For instance, for you, you can enjoy banana. You know, not so many people can enjoy banana by prediction of the model, and that’s because it does have a lot of sugar. We have, I mean, quite a few people that cannot–that are predicted to have a high glycemic response to banana. But you can enjoy banana. And so, that goes really well with your high, good metabolic fitness profile. So, your microbiome may have something to do with that, and that means you’re being the good host to your microbiome.
Just an overview of the overall active themes and what we’ve covered in terms of actionability. So, we have the digestive theme, which overall isn’t so bad, but the components of it like protein fermentation and gas production can be addressed with many of these recommendations. Some of the pro-inflammatory pathways may need to be addressed even though you do have some of these anti-inflammatory ones active as well. So, we talked about your butyrate. You’ve always had actually really good butyrate producing capacity, and your butyrate producers like Roseburia, and Dorea, and other ones. They’ve always been pretty active, and you always have a lot of clostridia that are known to produce butyrate.
And so, you have very active butyrate production pathways, which is really good, and you can still give them more inulin, and altogether, balance out your microbiome with the point of controlling these pro-inflammatory pathways and pro-inflammatory activities from organisms that you have that are part of like the gammaproteobacteria class that some are opportunists that you want to keep at bay. Right now, they’re not causing too much trouble or anything, but you want to keep it that way. So, that’s why we want to address the pro-inflammatory pathways.
From the start, we talked about your richness. So, it’s good to improve the richness and diversity of your microbiome. Specifically, about gases, we talked about hydrogen sulfide and why some of these cruciferous vegetables are on avoid, why some of the foods are on your a superfood list for the overall digestive efficiency, some of the bitter foods, and for your protein fermentation, how to handle your dense protein. By the way, another thing you can do is think about when you eat your protein because a lot of people, especially Paleo diet lovers, they like to have a big steak late at night, or maybe it’s not too late, but still, it could be a lot for our bodies to handle. So, then microbes do their protein fermentation thing, and we want to minimize that.
So, it’s how you process your protein, whether animal or not, and how you consume it, and how you even chew it to digest it right. That’s another big part of it. We talked about your active polyphenols and flavonoid pathways, and we provided some various new options, maybe different options for you with explanations why things like cranberry could be especially good for you. And you see turmeric on your superfood list. You have your microbes making some good vitamins and doing some of the detox or just overall known as antioxidant type of functions for you. So, we have that covered. That’s really good, and keep that up.
This is just an interesting bit that came up that I wanted to check with you. So, maybe you can comment or email me about the circadian rhythm. So, we have the circadian rhythm pattern, which we have not yet closed the loop on conclusively, but we’re tracking that. And so, when we have this circadian rhythm pattern, sometimes it’s in people that have either more anxiety or issues with sleep like insomnia. So, if that is true, right now, we don’t have statistical evidence to show that with any kind of validation. But if that’s true, I’d be just curious to know.
Then foods that you see on your recommendation lists that are there for other reasons may also help with things like insomnia. So, oats, walnuts, and salmon may actually help improve insomnia-like symptoms. And you have good fiber metabolism pathways like I just mentioned. You can keep improving or having more variety with your sources of, let’s say inulin to boost and support your butyrate and short-chain fatty acid production, and also just a variety of fibers. So, you have a lot of pectin, but it could be good to diversify with other things that you’ll see in your superfood list, like some of the leafy greens, which you already do a lot of, but it’s just good to keep the diversity going there.
And what you also see in your recommendations is the supplement section. I touched on that earlier when we talked about richness, but I want to say that for digestive support, which is your number one area that we need to address. There are a few things that you can do if you feel like just different ways of preparation and processing of proteins is not enough, then that is when you may have seen in your recommendations. As needed, you would take a motility agent, something like a Berri gas, there are others, and a digestive enzyme complex. You can get some of this digestive enzyme capacity from the foods that we recommend, and you will see that there and the explanations are available for you.
But as needed, if you need it and if it makes sense to you and your healthcare practitioner, then see if some of these digestive enzyme complexes could help you and be good for you because it will minimize some of that harmful byproduct production from your microbiome. Polyphenols, we covered that with cranberry and the gordonibacter and some other specialty organisms that you have that help you get extra benefit from things like urolithins that your gordonibacter will produce for you. And in general, PolyResveratrol or other polyphenols may be good for you.
And for probiotics, we talked about a different lactobacillus. But here, I just wanted to highlight with respect to your digestive health that this specific lactobacillus may help counter the effects of those bacteria that are known to produce a lot of gas, especially like methane. So, if you do have those issues, which seems like you do from time to time based on what you shared with me, maybe choosing a probiotic that has this specific lactobacillus species may be beneficial for you. And as you know, it’s always good to mix it up and keep the variety going in your overall food and supplement recommendations to have your microbiome more resilient and provide better health for the host, who’s you, Ben Greenfield.
So, thank you so much. Thank you for having me review your results and sharing it all with everybody, and I wish the best of luck and health all the way to you and all of the listeners.
Ben: Well, thanks for listening to today’s show. You can grab all the shownotes, the resources, pretty much everything that I mentioned over at BenGreenfieldFitness.com, along with plenty of other goodies from me, including the highly helpful “Ben Recommends” page, which is a list of pretty much everything that I’ve ever recommended for hormone, sleep, digestion, fat loss, performance, and plenty more. Please, also, know that all the links, all the promo codes, that I mentioned during this and every episode, helped to make this podcast happen and to generate income that enables me to keep bringing you this content every single week. When you listen in, be sure to use the links in the shownotes, use the promo codes that I generate, because that helps to float this thing and keep it coming to you each and every week.
This audio/video overview by Dr. Ally Perlina of Viome goes in depth on my latest gut microbiome testing results from Viome. In this episode, you’ll learn how to customize your diet and lifestyle based on the genetics of your gut.
Dr. Perlina is the chief translational science officer at Viome. She leads the Viome team on the development of actionable pathway analytics, functional microbiome profiling, and integration of Viome test results into food and supplement recommendation logic.
Ally came to Viome from working with Dr. Craig Venter at Human Longevity, Inc. She brings over 17 years of industry experience, which include Thomson Reuters, Quest Diagnostics, and several startup organizations where she led R&D groups, scientific product development efforts, and translated knowledge and insights from clinical data analyses into actionable results. She’s a world-class expert in pathway analysis and translational systems biology, which are critical in addressing the complexities of health and disease from different data types in a meaningful holistic way. This cross-functional perspective and passion for making scientifically powered precision medicine insights actionable and scalable has been Ally’s driving force ever since she was investigating gene expression correlates of brain tumors and patient drug response at UCLA while getting her doctorate training in human genetics.
Ally’s ability to “translate” the signals from genomics, transcriptomics, metabolomics, etc., into something valuable for human health today allows her to lead a diverse team of scientific, clinical, and nutritional experts that, together with data science, make truly personalized Viome recommendations with molecular-level precision
To learn more about Viome and what it is, you can click here or check out these previous resources I’ve created on this cutting-edge way to test all the bacteria in your gut, along with the postbiotics they produce:
- Article: What Is Viome? How Gut Metatranscriptome & Microbiome Analysis Can Change Your Health
- Podcast: Age Reversing Via The Gut, The Ultimate Anti-Anxiety Pill, Customized Probiotics & More With Billionaire Entrepreneur & Viome Founder Naveen Jain
- Podcast: Poop, Bacteria & You: The Latest Cutting-Edge Science Of The Human Microbiome (& How To Affordably Test Your Own Gut)
- Podcast: The Ultimate Guide To Self-Quantification – How To Test, Track & Interpret Blood, Saliva, Urine, Hair & Poop
This review is a sneak peek into Viome’s next App release, including the new microbiome scores! The content of this video involves a personalized review for Ben Greenfield on June 20, 2019, based on an expert deep-dive into his microbiome data. What Viome productizes in this next release are the most robust features available based on actionability, literature coverage, and individual data patterns. These results and recommendations are unique to Ben and will differ from your own results and recommendations that Viome assesses from your unique microbiome. Viome does not offer personalized data review as a service at this time.
During today’s episode, you’ll discover:
– My gastrointestinal summary…7:23
- Most important themes to address are several specific functions dealing with digestive efficiency
- Active microbes: There are 134 active microbial species detected in the sample, which means that “richness” is within the average range but may need improvement.
- No active eukaryotes were detected
- There are 2 active plant viruses:
- Prunus necrotic ringspot
- Pepper mild mottle
– Overall microbial richness…9:50
- My score is 134 out of 400; average score (5-95 percentile)
- The microbial could use a boost, but nothing too alarming
- Recommended foods:
- Recommended supplements:
– Metabolic fitness score…18:35
- My score is good, in the 18th percentile of the Viome population (improved from Sep. 2018)
– Inflammatory activity…21:10
- My overall score is AVERAGE
- LPS biosynthesis pathways: average
- Methane gas production pathways: needs improvement
- Sulfide gas production pathways: needs improvement
- Flagella assembly pathways: average
- Biofilm, chemotaxis, virulence pathways: average
- Balance is the goal, not optimal scores in every area
- Although the score is “average” it’s on the higher end of the spectrum
– Proinflammatory microbial activity, and active pro-inflammatory pathways that indicate potential GI inflammation…32:40
– Butyrate production pathways and active butyrate producers…45:45
- Overall score is GOOD
- Butyrateis good for metabolic fitness
- Regulates satiety, good for insulin sensitivity
- Goes hand in hand with inflammation scores
- Butyrate is a Short Chain Fatty Acid (SCFA); associated with beneficial functions for the host
- Resistant starches and fibers: resist the digestive system of the host
– SCFA production pathways and active SCFA producing microbes…51:40
- In addition to butyrate: acetate, acetyl phosphate
- Active probiotic in my sample
- Many different pathways that lead to butyrate production
– Recommendations for my diet…55:23
- Bone broth(mammal)
- Phytometabolizing microbes and active pathways:
– Digestive efficiency…59:20
- My overall score is AVERAGE
- Protein fermentation: needs improvement
- Gas production: needs improvement
- Methane gas production pathways: needs improvement
- Sulfide gas production pathways: needs improvement
- Putrescine production pathways: needs improvement
- Butyrate production pathways: good
- Salt stress pathways: good
- Protein fermenters and active protein fermentation pathways
- Recommendations related to protein fermentation:
– Hydrogen sulfide production pathways and hydrogen sulfide producing microbes…1:15:50
- Exacerbated by certain foods
- Disruptive to the gut lining
- Proinflammatory if produced in excess
- Sulfate (or sulfite) is deleterious
- Recommendations specific to microbial gas production, particularly hydrogen sulfide:
– Vitamins produced by the gut microbes and detox of the microbiome…
– And much more…
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