Tools to Assess and Modify the Microbiota - Dr. Jason Hawrelak

Thanks for hanging with us to the end of the day. And I was told during the lunch break that my talk may be a bit depressing. Sorry. Hopefully the second episode will be give you a bit more tools about being proactive to change things to make your ecosystem a bit healthier. That's gonna be the focus and I should point out too because I realized I could have come across as being quite anti antibiotic and anti proton pump inhibitors and I'm not, I'm just anti inappropriate use of antibiotics and proton pumps. And some of the patients you were presenting, they needed proton pump inhibitors. But there are many patients with reflux that were able to get by with other things. Lifestyle, dietary changes to do the work, supplement with some herbs and dietary supplements and often with antibiotics. We know that 80% of at least study done in Australia last year that 80% of viral infections were treated with antibiotics just last year. It's like inappropriate. So we'll move on to talking about the microbiome and specifically around how dysbiosis is diagnosed. We talked a bit about dysbiosis and the importance of the microbiome earlier today. We can diagnose it based on a patient's medical history and dietary history. So if they present to be going, okay, I've just had recent antibiotic use or had a few courses of antibiotics, recent chemotherapy, radiotherapy, which are things I didn't discuss earlier on, but we know they actually cause a dysbotic gut as well. Born by a C section, they're formula fed. Yeah, you could make the assumptions that there's going to be an imbalanced ecosystem there, long term ppr, NSAID use, if they suffer from any of those diseases I listed before, which could be things like Parkinson's disease, Alzheimer's disease, I'm thinking dysbiosis might be part of that picture. High stress levels, we know and I didn't touch on this before due to lack of time, but stress induces changes to the gut ecosystem and not beneficial changes. Dietary risk factors, we went through most of those. So if someone's eating that sort of diet again, I'm flagged that dysbiosis is going to be part of that picture. But I often and almost always do specialized stool testing for my patients these days. One because we get to see the specifics of that imbalance, because I know that antibiotics in general might impact the gut ecosystem in a way that the research tells me about, but that doesn't mean that's how it's impacted this individual who's in front of me, because each person's ecosystem is unique. How they respond to interventions, dietary exposures, etcetera, Is also unique. And when we have that actual picture of the ecosystem, we can individualize treatment rather than going, okay, well, in general, this disease state is associated with this. Let's give a treatment based on that disease. I'd rather base it on the patient in front of me. So I think this is where specialized stool assessment. And as someone who's been a clinician for 20 years and has a chance to see and been around with the technology that's evolved, we're far more luckier now. Just like genetic testing has evolved so much in that time. In terms of what we have access to, microbiome assessment has gone from the dark days of culturing, where they tell you about three or four species out of the 160 that are in your gut and try to base dysbiosis diagnosis on that. So you're getting a very much more clearer picture of what's going on. So in general, the tools or the tools that you've got access to assess you or your family members, microbiome fall into two broad categories. Culturing what we call molecular techniques. Now, how many of you have had yourselves or family members, microbiome, or stool assessed in any sort of more functional way? Quite a few of you. And how many know whether you're using culturing or molecular techniques? Okay, a smaller percentage. Hopefully, that will change after today. So culture is the traditional approach, essentially evolved in the early 20th century. And most of the microbes that most of us in this room would be familiar with are because we could see them back at that time point. So things like E. Coli, streptococci, Sappho cocci are things that we used to. We've been able to grow in test tubes from the early 1900. Then in 1969, there's a huge leap in technology where they developed anaerobic cultivation chambers and allowed us to actually see a whole range of microbes we did not know existed before, because before we were growing it, we exposed it to air. And as it turns out, almost all the micro. The vast majority of microbes in your gut hate oxygen, die when exposed to oxygen. So in 1969, they changed that, and they're like, oh, my God, there's so many more species there than what we knew before. And what they tend to do is they take an isolate sample of your poo, they grow it, and they wipe it in some petri dishes. And they have different petri dishes. Some will have Tomato sauce in it, some will actually have bile in it or a range of other things. Look to see what grows, how quickly what grows, what color it is, what it smells like. And from that they can work out what species it is. But as you could imagine, it's a very time consuming process. And there's also issues with ideal growth media to try to represent how much is actually there. Because sometimes they'll have almost like a fertilizer for that species that's accidentally just by chance happens to be there. So you can get a biased result. Some labs will talk about this thing called multitof mass spec, which actually takes away a lot of that morphological issues. In terms of working out whether species are present, they can identify quite well and accurately down to the species level, but they still have to culture first. And this is a huge issue as we'll get to momentarily now, there are some pauses with culture that for known organisms. So those that we know exist and those that we know how to grow, culturing is very sensitive at picking them up. That's a good thing. But when you get outside of research settings or hospital settings, in terms of the tests that we often have access to to assess the microbiome, we're often doing a sample, put into a little bag on our front door, gets picked up by the delivery person who probably doesn't know they're picking up a fecal specimen, goes into a truck, into a plane, goes into another truck, gets to the lab. It can be exposed to a myriad of range of temperatures, variations of environment. And we're hoping with culturing that the bugs do not change at all, that they stay the same population identically on their way to the lab. And we know that that's not really true. Certainly research I did as part of my honours and my PhD proved to be pretty conclusively that this is not what occurred. And particularly if you have people who live in a warmer climate. I had a patient stool sample from Darwin, which is up the top end of Australia, where it's in the tropics. And by the time I got to the lab in Melbourne, which is the saloon tip, it had like no live bacteria left. Yet they followed all the instructions proper properly. So that's one of the problems with culture is that what we have access to. Whereas if you did a poo in the lab and they cultured it right away, that gets around that. But the biggest issue with culturing is that it can't actually grow most of what's in your gut, which we now know. And this used to be called the great plate count anomaly. And this has actually led to that adoption of molecular techniques in the early 21st century. So it was likely. I was lucky to be around at that time of evolution. But there's still practitioners who are still attached to the old tech, but we shouldn't be as clinicians or as patients. Lovely quote from some microbiologist. Blot in Clavel. And there's a bug named after blot called Blotia cultivar. Fecal bacteria represent only a tiny fraction of the bacteria actually present in the gut. Proportion of undescribed species vary between 30 and 90%. So for some people, 90% of the species that were present we did not know existed up until 2007. That's hugely different. 240 new species were described by 2014. So this is why people talking about microbiome is because we changed technology, and changing technology allowed us to see what's actually there and allowed us to see patterns. The tools we're using before were too crude to see. Now, with molecular approaches, there's two broad techniques that are used that we, again, we have access to as clinicians or as patients. One is called 16S RRNA sequencing. DNA from that fecal sample is isolated and sequenced with a focus on a single gene, 16S RRNA, and each bacterial genus has essentially a different barcode. And from that they can take out that fecal specimen, work out how much, whether that barcode is present or not, and then how much is there. So that barcode, if it's present at 15% of that whole picture, we know that makes up 50% of that ecosystem. So it's actually quite a clever way of doing it. And we compare that to that sort of library and we can see what's there. And it's very good at getting us down to the genus level data. Maybe not so good for species level data, depending on the species of bug. The downside is only detects bacteria and archaea, which the most common one I got is a guy called Methenobribrobacter snithii, which actually is an important player in gut health, but it does not detect fungi, protozoa or viruses. So that's a bit of a downside. You're focusing on this bit of that ecosystem, ignoring the fact that in our gut we actually do have a range of fungi, a range of protozoa, a range of viruses, as well as bacteria, all composing that microbiome. So labs that offers 16s are ones like American Gut Project, My Micro Zoo, which is in Europe Thrive Ola well and eubiome and eubiome I've highlighted because it's. It doesn't exist now as in a few months it ceased practice. It was a sad day for me and many other clinicians. It was a very cost effective way of looking at someone's gut. But many of you might actually still have ubiome results that are useful and arguably a newer approach and a better approach is called shotgun metagenomics. And it fragments all the DNA from the sample into small pieces rather than just that one 16s RNA gene. And with that we can get a much bigger and more accurate map of the microbiome. And this detects genes from bacteria, fungi, protozoa and viruses potentially as well, determines the relative abundance whether they are 20% or 5% or 0.01% and can even go down to the species and strain level, which is great and much more accurate than 16s. What it can do too is tell us what genetic pathways. So there are microbes in our gut that we don't know what they do. We haven't been named yet. They can find them with 16 SNavy and go okay, well that's there. You know, I might put initial SS2 1. We don't know what it does yet, but with this technique they can actually look at the pathways and go ah, this is what this microbe is capable of doing. Or more broadly this is what pathways are available in your gut independent of whether we can name the species or not. Labs that offer that are fewer biome in the US and then Microbot is an Australian lab that just started selling their labs I think into the US and possibly into Canada. I'll have to follow that up. But I must say biomolks using good technology doesn't necessarily provide useful reports to me anyway. So molecular approach is the good gives us a more accurate, complete picture of the gut ecosystem. You know, it includes species that have just been discovered and those that can't be cultivated. Stool samples are not so environmentally impacted. So if it sits on your doorstep for a few days, it's actually not that bad because the idea with the DNA ones is that they kill everything at that moment of evacuation from one's bowel and then that that keeps it a perfect sample until it gets to the lab. Whereas the cultivable ones you have to have the microbes alive so you can grow them in the lab. And any changes in their populations means what will tell you what it's can determine how accurate that is or not. And because we've adopted these things, we can now see the impact of medications and changes in diet that we could not see. Call writing a review article 2004 looking at the impact of diet on the microbiota and based on culturing, there's almost no changes in people's ecosystem depending on what they ate, which is ludicrous now and at the time it didn't make any sense. But that's what the data said. Again, because we're using such crude tools, we couldn't actually see what was going on. And that was mentioned before with the antibiotics that we saw only worked for a week or two weeks, things were different. Now we know it's a much longer period of time. The poor thing. The downsides of molecular approaches is that it's not necessarily as good at picking up very low levels of certain species. So bugs that are there at less than 10 to the five microbes per gram can go missing. And for us, different labs are using slightly different tweaks on that technique, which means that we can't necessarily easily compare between labs, which is a downside. So if we have a few eubiome results, we can't necessarily compare that with the to the Olawell later on or to the thrive later on with great accuracy, which is a downside. So summing up some important, what I call keystone species can only be identified and quantified using molecular tests. So we should not be using culturing to assess what's in the large bowel. Things like Faecalobacterium, Roseburia, Akkermansia, Eubacterium, other butyrate producers we can only see on molecular tests. We can't see them by culture tests. Bugs that obviously as pathobionts like Bilophylla wadsworthiad, the Sulfava Vibrio. Again we can only see with molecular tests. Methenobrobacter is the archaea I mentioned before. That actually has a huge role to play in how quick or how slow gut transit time is. We can only see with molecular tests diversity, which is a key player in gut health, and we'll look at this momentarily, can only be assessed when you can look at the whole ecosystem. You can't assess diversity if you're only looking at a handful of species, which is what culturing does. Another point I want to make is that dysbiosis is typically about an imbalance rather than a specific infection. And I think people, that old model of medicine where we're looking at specific pathogens causing specific disease states has sort of flowed through. And sometimes we're looking through that stool test, looking for that one pathogen. And that's not really what dysbiosis is about. It's more about imbalanced ecosystem, too much or too little, sometimes the absence thereof of species that should be present. So this is a bit of a table showing again comparing the molecular approaches to culturing. Won't go through it in great detail, but you can see that there's a lot of differences between ticks on this side versus crosses on this side. Where there are certain species I would see are as important to actually assess someone's gut health. I want to see whether they are not reported. They're in. And again, coltrine shows up very poorly for that. And page two also shows up pretty poorly too. The only thing I think that has going for it when it comes to gut assessment is really antimicrobial sensitivity for potential pathogens, where we can grow it, dose it with antibiotics or herbal antibiotics or whatever and see whether it's susceptible to it or not. That's a plus, but there's a lot of negatives to it. There are some labs that again you have access to, they're sort of more functional labs that present results as like a plus system. It'll come up as a 3 plus or a 2 plus or a 4 plus. That sounds great because of its simplicity. It's not. This is the same stool sample sent, the same person sent to two different labs. One was a culture based result and they come up with those four plus four plus. So you'd expect from that, wouldn't you, that a four plus Bacteroides means that there's the same amount of Bacteroides as there is Enterococcus as there is Enterobacter. If they're all four pluses, you'd expect that they'd be the same proportion in the gut. I would assume that. But how much was actually there? You can see that Bacteroides is a dominant player in the gut. It is around usually 20% is pretty typical and relatively healthy level. But look at enterococci, 0.01% that showed up as 4%. And then klebsiel and pneumoniae, which at 4% problematic showed up as a 3 plus on my other system. So do not trust those types of stool test results. Hence the stop, stop using them. So the GI10 microbiota is a bit like your fingerprint and that is completely unique to you. No one else will have the same ecosystem as you do. Your siblings will be similar, but not the same, genetically identical Twins born at that same sort of time will have very similar ecosystems until food gets introduced, they start taking different medications, different environmental exposures, then they'll start diverting at that point, diverging at that point. Each of us harbors about 160 different species. But 30 to 40 even 10% or 10 different species make up genera, make up the bulk of what's there in most people. And I should say that the ideal microbiota is not known. And there's lots of going, oh, we don't know what the ideal microbiota is and I don't necessarily disagree with that. But as someone who's been looking at this area for 20 years, I do think there are certain characteristics that make up what I'd say is a healthy, healthier ecosystem. So what are those? Well, we want an evenness or good spread of genera. Two, we want a good richness of that ecosystem. So we want a wide range of genera present, we want a wide range of species within genera. Now in terms of evenness, the best way of explaining this is let's say you go to the forest over the Vancouver island or something and you're looking at an acre of, of rainforest and let's assume that there's 100 different species present. That's a really rich species rich environment. But if 90% of those are one tree type, it's going to look like a plantation. It's not going to be an actual diverse ecosystem. So when we talk about diversity, we're taking into account the evenness or spread. We'd rather have it being like a 10%, 9%, 8%, 7%, 7.4%, a wide spread, a good evenness of that ecosystem, as well as a wide number of species actually being present. For me, I'm also looking at healthy levels of what we see as beneficial bacteria, low levels of pathobiomes and pathogens. So we want lots of the good, not so much of the bad or the ugly. So diversity really is the spice of life. And we know this is one thing that I'd say microbiome researchers are most in agreement about in terms of a healthy ecosystem is diversity. Lack of diversity is associated with increased risk of allergies and asthma in kids, obesity, insulin resistance, dyslipidemia, autoimmunity and in general body wide inflammation. So not a good thing. And molecular techniques labs that we have access to will generally tell you give you a bit of diversity score. And you can, even if you working with a experienced practitioner can work that out from looking at the evenness and how many species are actually present? So if you've got low diversity, and sadly many of us in this room would, how do we improve that? And I think there's one point I wanted to make here is about recoverable species versus extinct species. Because there are certain species that are there, we wouldn't react. But the test is not sensitive to pick them up. So they're what I would call below detectable level. And this is the assumption I often make when I'm working with patients is if bifidobacteria doesn't show up on the test, I assume it's just below detectable level at that time point until I try and fail to actually bring it back up to nurture that species specifically. And in which case I'll make the assumptions that actually extinct. So we can't bring back extinct species, but we can bring back those that are there in small amounts to the point where they can be noticed by the machinery. And at that point they're actually at a sufficient concentration, they're actually able to be involved with the gut ecosystem more broadly and the health giving effects, if that makes sense. So how do we do this? Take prebiotic supplements daily and we'll get into these later on. What I mean here. Eat a wide diversity of multicolored whole plant foods and fibers each week. This is key. Research tells us that the wider variety of plant foods we eat, the more diverse the ecosystem in our gut is. Why is that? Because we often think of fiber as this one generic substance. It's not. Fibers come in all different shapes, all different sizes, and we eat a wide diversity of those. We feed a wide diversity of microbes. So eating 100 grams of fiber from broccoli will have a different effect than eating 100 grams of fiber from 50 different foods. So for me and the target that I have with my patients, and it's not a magical research number, but it's an achievable number that makes a difference clinically is getting my patients have 40 plus different Whole Foods per week, not per day, per week. And to put this in perspective, brown rice, black rice and red rice are three. Granny Smith apple, Red Delicious apple are two. That makes it easier because the different polyphenols, different color compounds actually feed different bacteria. So it's achievable for most people get out into the earth. We know that people who are doing lots of organic gardening, who grow up on a farm tend to have more diverse ecosystems exercising moderately. So if we exercise too much, it's actually not so good for our Diversity exercise. Too little is not good for our diversity. We have to be moderate. Now. Probiotic supplements and fermented foods, while widely discussed in the blogosphere, will have only a temporary impact on diversity and we're going to highlight this in much greater depth later on. But they're temporary visitors, so whilst you eat them you'll have another eight, maybe 10 species. If you're eating homemade kefir or kombucha, they'll show up whilst eating it, maybe for a week afterwards, then they'll be gone. Temporary visitors, probiotic supplements, temporary visitors. Vast majority of situations they do not permanently stay. Fecal transplants are probably the only way of reseeding or reinoculating a gut. So when I was in Sri Lanka a few years back when I was first putting together run a workshop on this, I couldn't help but marvel at their diversity. They had 12 different types of banana, 30 different types of mango. You know they eat a wide range of rice and this would be a typical meal which would be red rice and like seven different curries for lunch, seven different curries for dinner. So a wide variety of foodstuffs and they're certainly not vegetarian but you can see that the meat portion makes up a small bit of their plate. So it's predominantly plant based, probably whole foods, lots of legumes, lots of onions and garlic. It's actually a very good microbiome friendly environment. As I said, lots of onions and garlic. So I'll do a very brief introduction to some of the key players and it would take many hours to go into great depth but I just want to get you the names more familiar to you and I think it's useful putting into the good, the bad and the ugly. The and I would play the music but I think it's all playing in your minds right now so I won't bother. So the good are what I tell my patients as gut guardians because they can relate to that, some of which you'll be familiar with like Bifidobacteria Lactobacillus. This is probably the two species that most in the room will have heard of, but some of the others less so. Bar today Akkermansia, very important for metabolic health, weight management and gut integrity issues. Slakia. It's not actually slack that one, it's actually a hard working microbe really involved with polyphenol transformation and it's not very well known but it's certainly one that I look at at stool samples and it gives me an idea of how well their ecosystem is going to metabolize the polyphenols in the diet or from medicinal herbs. Range of butyrate producing bacteria from the topmost Faecalibacterium prostniti to rose brea, eubacterium, etc. So all those, the key role that they play, at least that we're aware of, is the production of butyrate. And butyrate is that lovely substance that Dr. Fry was talking about that has the capacity to improve mitochondrial function. But it's the main fuel source for colonocytes as well. The bad for me, it's more about balance. When it comes to the bad guys, bugs like bacteroides, E. Coli, Methenobra bacteriasmithi. It's about balance that actually they play important roles, but too much of them causes problems. When we bring them down to a healthful level, they're actually contributing to the ecosystem and your health. Now, Methenobrevobacter smithii is an interesting microbe because it eats hydrogen gas and it actually eats when it's eating, it eats four big bulky hydrogen gases and shrinks it down to one tiny little methane and actually helps prevent gasolated distension. But we have too much of it. It slows your colon down and we get constipated and we get gas that gets built up because it's no longer moving through. That's where balance is key. The right amount healthful, too much produces unhealthful effects on us. What I would call the ugly would be specific pathogens. C. Diff And I'm not very fond of these hydrogen sulfide gas producers, which, which there certainly is some evidence around disulfibrio being too high in autistic populations. But certainly a lot of population patients I've worked with over the years of irritable bowel syndrome and a condition called visceral hypersensitivity, where their nerves in their gut are hyper responsive and can feel this much gas being produced. And we know hydrogen sulfide gas actually makes those nerves hypersensification. And these patients often have high levels of those species. So what can we do to improve the microbiotic composition? Essentially encourage the growth of those the good guys and discourage the growth of the bad and the ugly. A few things. And we're going to go through these each in turn and we'll start off looking at prebiotics. And I think this is one of the most misunderstood groups of interventions that we actually can access because of a misunderstanding around the diagnosis. The definition of what makes the prebiotic, and I touched on this before, but it's a substrate that is selectively utilized by microbes that confers a health benefit and it's selectivity. Not all fibers are prebiotics. People tend to think that anything that's fermented, any sort of fiber, is a prebiotic. That's wrong. Prebiotics are selectively fermented. And we look at the research and going, okay, I've got a patient who's low in bifidobacteria, low in Akkermansia. I know that there's a prebiotic that feeds those two species up almost exclusively. I can give inulin or fructosaccharides. It will target those two species, their levels will go up. Will lots of other species be impacted by that? No, it's very selective and that's what makes the prebiotic different from a normal dietary fiber. I still love dietary fibers and make sure people eating a wide range of them daily. But when you look at an imbalance and go, okay, they're low in this species, low in that species, I know how to feed those up. And that's where these prebiotics come in handy because you can selectively target those populations and bring their levels up. So to be defined as a prebiotic essentially can't be broken down or absorbed, number one, two, they have to be worked selectively. So it can only be eaten by one or limited number of beneficial species. It can't be eaten by pathogens. It is eaten by pathogen. It's not. A prebiotic by default changes the ecosystem towards a healthier state and that has flow on health benefits for us. So I like this diagram. It's very simplistic, but it does sort of, you know, we ingest the prebiotic, it goes through the stomach, goes through all the small bowel, untouched in general, reaches the colon, and there it's selectively fermented. And we improve the microbiotic composition and in this case sucrose was used as a placebo. And so it's a pretty typical ecosystem that's dominated by Bacteroides. Bifidobacteria make a much smaller proportion. But then on these two prebiotics, you can see that the ecosystem changes, that we have far more bifidobacteria. Present level of things like clostridia generally decreases. So diversity, nothing on anyone, for example. So that's a prebiotic effect. Selectively increase good guys and pathogen levels or path abundant levels tend to decrease. Now, bacteria, unlike us, don't need to have sex to reproduce, which is good or bad, depending on your viewpoint, but it means that we can selectively feed them up and get the population roared up very quickly. So what are prebiotics? So some of these are more accepted on the list, some are more new. So Acacia fiber lactulose, which is often just used as a laxative, sadly, because that's an amazing prebiotic substance. Galactooligosaccharides, fructal oligosaccharides and then partially hydrolyzed guar gum. Now are people here familiar with many or any of those? Some. Great. I put the minimum therapeutic dose there and that's the dose that's been shown to have microbiota enhancing effects in adult humans and the dose in kids, probably from three, four years onwards, is the same, I would say. Now there are some principles about dosing with prebiotics though, and I would suggest if you're not comfortable working with a practitioner who is prebiotic competent, and I wish I could say there's more of those because there's so much confusion between fibers and prebiotics and how to actually utilize prebiotics in practice, a lot more than there should be. But the general rule is go low and go slow. So don't start at that, you know, 5 mils per day of lactulose, if you're particularly sensitive, you can start with a quarter teaspoon for a week, then go up to half a teaspoon for a week, three quarters of a teaspoon for a week and slowly build up over time because your ecosystem adapts. The microbes that eat gas adapt. But if you start off on a 10 gram dose of fruit oligosaccharides, you will bloat, you will distend for the first ten days or so. That doesn't mean it's feeding pathogens. It's not. It's just producing gas as a byproduct of feeding the good guys. And your gut may have trouble dealing with that much gas if it's not used to it. And I'll go through this in great depth, but I just wanted to have it in your notes. But primarily wanted to show you that the different prebiotic types, different dosages that were used and the ecosystem changes, we tend to expect. So the key thing is you see increase in these beneficial bacteria, but we also see looking at 15 grams per day, bifid bacteria went up, but we also had a decrease in Bacteroides and Clostridia infusobacteria, which is a species that seems to be involved with colon cancer. We tend to get a decrease of the bad guys increasing good guys with prebiotics. That's key. One I probably wanted to flag even more so with partially hydrolyzed guar gum, which is specifically good at feeding your butyrate producing bacteria. And there's a study I just came across when I was prepping for this lecture two days ago. Using partially hydrolyzed guar gum in autistic kids who are prone to constipation and giving partially hydrolyzed guar gum, which mirrors my experience, helps with the constipation but also decrease irritability scores as well, which is perhaps not surprising. But most of the other prebiotics work primarily around Bifidobacteria, a little bit around Akkermansia and Faecalobacterium, but this one feeds a whole range of B3 producing bacteria, enhances B production in the colonial Eat more prebiotic rich foods, which are essentially foods that contain fructosaccharides and galactooligosaccharides. Now for our ancestors, we used to eat dandelion roots, dandelion leaves, burdock root, that was a staple part of our diet. We do that now, not so much. So probably things like onions and garlic, maybe chicory root, coffee are probably the things that matter we eat the most. But we traditionally ate a lot more foods high in these fruct oligosaccharides. In terms of galactic oligosaccharides, it's primarily legumes. And in western countries actually do not eat much in the way of legumes. Yet there are small pockets that do, but broadly speaking they do not. Small amounts of beets and fennel ball, but most of it's in legumes. The reason why legumes cause gas is because it's feeding the indigestible sugar called galactooligosaccharide. Feeds beneficial bacteria, but the byproduct of that is gas. You only eat legumes, a big bowl, once a week. Your gut does not adapt. If you eat a small amount every two days, your gut adapts and you can increase the quantity that's there. I know when I went to Sri Lanka, I ate legumes a few times a week. I went to Sri Lanka and we had legumes for breakfast, for lunch and for dinner. My gut had to adapt and after a week it had. But for the first week it was a little bit gassy for the family. Eat more whole plant foods. Try to base our diet on whole food. Minimally processed, prominently plant based, moderate amount of fat. So things like Avocados, olive oil, nuts, seeds as your main food sources of fat, moderate protein. Aiming for a lot of it from plant based protein sources because then you're also getting fibers and polyphenols. Look at something like black beans. Black beans are getting those beautiful black polyphenols, getting resistant starches, you're getting oligosaccharides and a range of soluble insoluble fibers that all feed your good bugs. And you're getting protein. Makes you have a wide variety rich in fiber, rich in color as well. So for me, having whole grains, legumes, fruits, nuts, vegetables, nuts, that's the bulk of the diet. And I know legumes are very out in certain blogosphere circles currently. They are amazingly good for the gut microbiome. And if you have trouble with legumes in terms of causing pain and discomfort, there's a problem with your gut, not the legumes. And if you work on the gut first, we can get you tolerating legumes properly. Normally, again, eat more polyphenol rich foods. Does anybody know what that fruit is up on the top left? Dragon fruit. Yes. Extremely high in polyphenols. That pink and purple. One amazingly good food source for one of your beneficial bugs called Akkermansia. Making sure we eat these brightly colored foods and not looking at that skin that's on almonds, the skin on hazelnuts, that is the prebiotic compound on those foods. So having like blanched almonds will not work. It's actually the skin that works. Having almond butter, the browner the better. You're getting more of the skin compounds. Choosing again, why do we have to use white potatoes? We can have purple potatoes, red potatoes, pink potatoes. Choose colors. Why having to use white rice when you can choose brown and black and pinks and reds, for example, red and black quinoa, purple carrots instead of orange carrots. They're going for that wide variety of foods because that's going to feed the widest variety of microbes. Those different color compounds will feed different beneficial microbes. And resistant starch. So that many of you heard of resistant starch before? Yeah. So it's essentially starch that's resistant to your digestive processes. We don't break it down. Reaches the colon, large intestine where certain species can and they ferment that and create something beautiful like butyrate. In the end, the good sources of resistant starch, again, grains, seeds and legumes, the more finely milled it is, the less resistant starch it is. So you know Our ancestors, using those stone grinders that had pretty chunky milling, you actually got more resistant starch than our super fine milling that we get these days. Cooked oats versus soaked oats. When we cook oats, they sort of explode out their starch, break out their cellulose envelope. You don't get much resistant starch if you soak your oats overnight, even if you warm them to body temperature the next day. Lots of resistant starch. And you notice the difference on your blood sugar regulation. Having porridge versus soaked oats. Soaked oats, you'll have blood, you'll have good blood sugar for many hours, whereas porridge, you'll often have a big of a spike and then you'll go down. Raw potatoes, plantains, green bananas. The key thing here is that cooking those things changes the starch, so it's no longer resistant. So making muffins from green banana flour or potato starch, you won't get the resistant starch. It has to be raw, so you can add it to smoothies, that's fine. You can add it to breakfast cereals, that's fine. But do not cook with it. And last but not least, retrograde starch. So cooked and cooled starchy foods. So baked potatoes, boiled potatoes don't have much steamed or in the middle, but baked potatoes by far have the most heated and cooled. So if you eat them the next day, far more resistant starch there might be slightly less tasty, but far better for your gut. Having cold rice, cold pasta, legumes the next day, fantastic ways of upping your resistant starch intake. And you know what? If you are apparently extinct to the surgenera on a fecal analysis, like Lactobacillus or Bifidobacteria, can you use probiotics or fermented foods to reinoculate or reseed? And I did touch on this before, so sort of giving the answer is no, but we're going to dig into this a little bit more. Probiotics, live microbes that would administer to the host produce health benefits. There's a few aspects to this definition. When you think about it, it's live microbes. So if you have a supplement that has dead bacteria in it, even if it's bacteria, it's no longer a probiotic. If you have a supplement that contains live microbes, in very low doses, it's no longer a probiotic. It actually has to have live microbes. Adequate dose and last but not least, confer a health benefit on the host. And some parts of the world take this definition so seriously, that if you do not have randomized controlled trials showing that your specific probiotic strain in your supplement has health benefits, you cannot use the term probiotic. You term it microbe supplement instead to differentiate it from those that actually have clinical evidence of efficacy. And actually, I'm quite for that sort of regulation myself. So what about probiotics and fermented foods for reseeding and reinoculation? Because again, you look online and people are always talking about you can just damage your gut as much as you want and just pop a probiotic pill. She'll be right. Say an Australian saying or no worries, Nate. But no Inconvenient truth. We look at the last 30, 40 years of probiotic research giving it to humans. Do they permanently stay after you take that supplement? No, they do not. We've had decades of research showing that you can't inoculate, you can't repopulate, you can't reseed the human gut with lactobacilli and bifidobacteria supplied by supplements or fermented foods. I wish you could. I do. I wish it was that easy, that you could damage your butt gut all you want and just pop a pill and fix it. That's not reality. Sorry to break it to you. That's right, any colonization you get is only temporary in research settings. If that microbe, that's that lack of acidilized strain can stick around two weeks, they're content with that. Most pass straight through without sticking around. The best ones will stick around for a week or two. And you see, look at the study right after you put it. Day eight, let's say they've taken it for a week. Day seven and eight, it's here. Then day nine, day 10, day 11, this population goes down and a week after they stop taking it, it is gone. In the ecosystem, that's pretty consistent. There's the odd exception to this, that if you look deeply into literature, out of 100 studies, you might find one bifidobacteria strain that has a capacity to permanently colonize certain proportion of people in certain circumstances. But we can't rely on that. That's pretty unique strain traits. It has that capacity. The other issue here, you know, you have a supplement says it contains multiple strains. They're looking at either just a combination of Lactobacilli and bifidobacteria. That's. It might have eight different types of Lactobacilli, but it's still just lactobacilli. It's 160 different species in there. Let's say you take that coarse antibiotics, that wipes out nine species. Just shoving some lacto sali in there, even if they did stay, isn't going to fix the fact that you lost your subdellal granules and your allostypes and your Oxalobacter, is it? Because they're different, species have different roles. Even if that did happen, how about fermented foods? Because they're certainly more diverse from a culture perspective, but again, they contain quite different bacteria, quite different fungi than we find in the human gut. Usually you might have 80 to 100 different genera in a human gut and maybe one, two or three of those are actually found in a fermented food. Not very much. And again, because a species is good at fermenting cabbage in a jar, does it mean it's going to actually produce lots of health benefits in your gut? Is your gut like that jar? It's quite a different environment. My gut's like, you know, 37 degrees thereabouts. That jar might be 20 degrees, might be 4 degrees. It's quite a different environment. And because something ferments vegetables well doesn't necessarily mean it's going to have any sort of therapeutic effect in our gut. So let's look at an example. Let's look at kefir. This would be a typical kefir, very much dominated by a bug called Acetobacter. Much smaller amounts of Lactobacilli, lactococci, Leuconostoc. These are the fungi that tend to be there. Let's look at the predominant species found in the human gut. Is there overlap? No, there's not overlap. The only thing that's there is Lactobacilli. Only thing, and lactobacilli make up around 0.01% of your gut. Most people's gut ecosystems in this room, it's even that. So even if it could recolonize that bit, it hasn't done very much. You've recolonized 0.01% by having that. Let's look at kombucha. 90% plus of the microbes there are glucon acid factor. Are any of those bugs normally found in the gut besides the lactozilli? No. So you can't like recolonize by drinking kombucha again, I wish you could. I wish it was that simple, but it's not. So my last slide, I know we're probably there time wise, is this reminder that we've got to think of ourselves as custodians of this ecosystem. And I think it cheapens it when we think we can just pop a pillow and fix it up. There are ways. And my first point here is really fecal microbial transplants are a way of reinoculating or reseeding the gut. And I'd actually say that unpasteurized breast milk probably does the same too. There's no research on it yet, but we know there's 100 plus species in breast milk, plus all the special human milk oligosaccharides in there too to help encourage the growth. So I dare say in the future we'll probably consider using breast milk as a source, which probably goes better in chocolate smoothies than pooh. We still have to get our head around both those things. So reminded here it's important to protect the microbiota when we can and restore it. So when we're talking about using prebiotics, talking about using eating prebiotic rich foods, polyphenols, fibers, we're talking about restoring the ecosystem, doing our best to bring it to where from where it is now to as good as it can be without introducing new species in. Because introducing new species in really involves fecal exposure. Most of us are not that super keen on fecal exposure. We've seen a massive loss of microbial diversity in westerns compared to traditional cultures. And we looked at that vanished taxi before. Why is this? Probably three generations of antibiotics, widespread use of NSAIDs and PPIs, standard Western diet, C section bursts, formula feeding and antibacterial everything. It's not a good recipe for a healthy gut ecosystem and diverse gut ecosystem. We tend to select for the ones that can tolerate antibiotics. Well, the ones that can tolerate PPIs, tolerate NSAIDs, tolerate a Western diet, those we select for. And that's what we're passing on to the next generation. And that's the other thing too is what we do to our microbiota can impact our entire lineage because we are passing it on to next generation oxalobacteriformer genes that I talked about in that previous lecture. Key here. So let's say we've got a 20 year old woman being treated for H. Pylori, takes the triple therapy for that and her oxalobacter former genes is gone. And she has kids, her grandkids, great grandkids, will no longer have that species in that ecosystem. All that family line will be at higher risk of kidney stones because of that loss of that species. Unless we can work at a way of introducing that species back in besides poop. Or there was a product research in Canada called Repopulate, very aptly named which they essentially took the poop out and just left the microbes there. So I think the technology is it's theoretically possible. We just have to wait a few years and it might be as simple and actually other research I did in Canada so I think it's been a bit ahead of the game. Here is fecal banking. People going into hospital, they take a sample of Pooh, then they treat you with antibiotics for your infection because it's life saving. Then they give you your poo back and you do not get C. Diff. You get your own ecosystem in the previous state back beautifully. So at some point in the future we're going to be doing fecal sample banking for our kids so we can actually before they have to take that course of antibiotics we actually can preserve that ecosystem that's perfect for them. We choose back in so there's hope for the future. We're just in that transitory time created now. That's it. Thank you.