Professor Paul Cotter on The Science of Fermented Foods

This episode is brought to you by Noishme Organics, your gut health superstore. Now, today, the conversation is going to center around fermented foods and the benefits of fermented foods from a scientific perspective. So guys, if you're interested in making your own fermented foods at home to improve your gut health, do head to www.nourishmeorganics.com and use the code Cotter C O T T e R for 10% off. Hey guys, Crib and Galvanor from the Gut Health Gurus podcast. I've got a background in food science and today I have. I'm so blessed. I've got someone on the podcast that I've been meaning to speak to for some time, one of the world leaders in the space of fermented foods and the actual evidence based information around fermented foods. And a lot of the times people could be a little bit skeptical about the benefits of fermented foods. So what I want to do is get someone who's an expert and who's at the cutting edge of the science to break it down for us on the podcast today. Adjunct Professor Paul Cotter. Welcome to the podcast.

Thank you very much, Cribben. It's a real pleasure to be here. I only hope that I can do justice to that fantastic introduction.

I'm sure you will. I'm a huge fan of your work. I've actually been deeply diving into a paper that you wrote or you co wrote with a couple of your colleagues from quite few a Cork University APC microbiome, the microbiota and health promoting characteristics of the fermented beverage Kefir. So I really wanted to have a deep dive into your work on fermented foods. And so that's the kind of frame for today. But at the start of every podcast I like to get it from the horse's mouth. Who is Paul Cotter?

Oh, okay. So I'm. I'm a microbiologist and that's not just my job. I'm a scientific nerd and I love what I do. I, I gravitated towards microbiology from university and haven't stopped since. I guess we'll be talking a lot about microbiology and fermented foods over the next while, so I won't linger too much on that for now. But I'm a dad. I have three kids ranging from 23 down to 16. I like sport a lot. I help coach my son's Gaelic football team, so our equivalent of Aussie rules. I like to run. I've Done a few marathons, but outside of working outside of those things, I think science is my hobby and my passion. I used to really enjoy going into the lab and having that eureka moment, taking out that agar plate and seeing the next cool result. Unfortunately, as time was moved on, I kind of became more of a manager or ahead of a lab. I don't get that direct kick or that eureka moment any longer. But I live vicariously through my students who do fantastic work on fermented foods. And that's what keeps me passionate and keeps me enthusiastic about what I do.

Wonderful. And I can certainly see from all those interests that you, you mentioned during that beautiful introduction on who you are, on why you potentially chose this field. Because you mentioned microbiome, Sorry, you mentioned microbiology, which lends itself to all the work that you do on the microbiome on fermented foods. You mentioned sports, which you've done a whole lot of work on the impact of sports in the microbiome and also testing poo samples from sports people, which I'm sure we're going to dive into at some point. But what fascinates you about microbiology? Why have you gravitated towards that field?

I think it's something that's become more apparent to the general public in recent years and that is that microbes contribute so much to what we do in everyday life, to our health, to disease, not only in relation to food, but at the moment we're being exposed to infection and discussion in relation to viruses. But there's a lot of things that microbes can do that are head promoting through probiotics and whatnot as well. So I guess I started my microbiology work focusing on a food pathogen, Listeria. So Listeria monocytogenes can cause people to get sick. It's especially a problem for pregnant women and people with weak immune systems. So I spent four years studying how it survives in foods, how to develop countermeasures to stop that. That then evolved into focusing on good bacteria and good bacteria that are in fermented foods and in other sources that produce not antibiotics, but kind of natural sources of antibiotics that are more target specific. They kill the bad guys but don't do so much damage or don't do any damage to your own natural microbiota. So spent quite a lot of time on that and then evolved to looking at broader microbial communities and how they contribute to health as well, how they interact with one another. And so it was a logical process. But I think once I started a course in university that involved being exposed to lots of different aspects of science. Zoology, plant science, biochemistry, microbiology. But as soon as I had my first microbiology lecture, I was won over. I was immediately convinced that that's what I wanted to do for the rest of my life.

I can say hand on heart, you're certainly a kindred spirit because when I think back in my, my food science studies and again, having a broad range of different topics involved in chemistry and biology, but my number one passion was microbiology. It's interesting. I actually started my university journey in computer science and I actually took up electives in microbiology while I was studying computers because I just loved it so much. And then eventually I said, why am I doing this computer stuff? I'm just going to jump to a different degree altogether. And I jumped into food science, which is heavily into the microbiology. So definitely a kindred soul, my friend Paul. How do we start this? How do we start this? I think we've got to deal with the elephant in the room. And we're going through this because you mentioned viruses, right? And so I'm thinking about this massive elephant. We're going through this extraordinary time where the world is in panic and fear with this Corona COVID 19 situation. So what's your thoughts on what's going on, Paul? What's happening in your neck of the woods and what's your thoughts on this issue?

Yeah, so I guess, yeah, things have accelerated in Ireland in recent days. So we're kind of a little bit behind the hot spots in Europe, which are Italy and Spain. But once it became apparent that things were getting serious there, that our government have been, have shown great leadership, I think so they have closed down the schools and the universities quite quickly. I'm based at Telkisk, which is a wing of the Irish Department of Agriculture and Food. So we're still operating but at a very much reduced capacity. And where people can operate from home, they're encouraged to do so. The number of deaths, the number of cases are up to around, I think it's 350, 400 now and two deaths unfortunately so far. But there is very strong messaging in terms of social distancing. People, elderly people encouraged to stay at home as much as possible. I think people have been very good to support one another and there's lots of activity on social media and other resources to show that people are willing to back one another up and to make sure that we get come through this successfully. So it's a tough time. Lots of people are very nervous. I think it's an important time for scientists to be clear in terms of their messaging, because it's clear that through some social outlets that some rumors and false news is circulating. And so it's important that that doesn't enter too strongly into the public consciousness and that scientists enter the fray quite quickly to try to show what the real science out there is. And it's been interesting, in fact, in the UK looking at it from across the Irish Sea, whereby I think their policy attracted quite a lot of concern from scientists initially and the scientific community there, through social media and through other means, through BBC and other outlets, have been able to get their point out there and to convince the British government that maybe their initial approach wasn't the correct. And now I think finally they're starting in the UK to close schools and to really kind of put in place the more extreme measures that are needed in order to prevent spread of the disease.

I'm really sorry to hear about the situation there. And Paul, just for your information, it's a very, very similar situation here in Australia. The borders are closing, a lot of social distancing, very similar. It's an extremely challenging time for all of us. And that's a good segue to explore, explore the microbiology aspects because it's very easy to jump to, you know, that the microbes are bad, they're bad things, you know what I mean? Like, it's part of nature. And I think with this Covid situation, it's the, the immune system that really is killing us. You know, it's the overreaction of the immune system. I mean, there's viruses, there's tens of thousands of viruses in us, around us. They're everywhere. It's just unfortunate that there's this one particular one that's causing these issues. What's your thoughts on that?

Yeah, I guess it's the microbes that, just like in everyday news, it's the bad news that will attract the headlines. And so you don't always hear about the good deed or the. The good work that's going on behind the scenes. And in that regard, there are as many microbes that are doing good things and very many more that are just harmless that are out there, but so they tend to receive less attention. And I think that's probably something that's reflective of just to some extent what's happened in Western society for quite some length of time in that I think fermented foods and other beneficial microbes probably weren't appreciated so much and fell out of favor. They continue to be consumed in certain parts of the world now in the last number of years, because I think of a greater consciousness of gut health and of the microbiome that people are now aware and conscious that they need to be eating the right foods and be exposed to good microbes early in life to prevent the development of allergies and such like. And by doing that, you can give your body a better chance to cope when it is exposed to the bad guys, which undoubtedly everybody will encounter to some extent or another during their life.

Yeah, that's a common thread that you see through the research where there's this almost like this hygiene hypothesis that formed in our approach in society, whether it's through the food industry. The food industry is classic in terms of having to nuke the life out of the food product. Whether it's through a very rigorous canning process where you. You're running F naughts at 6. People probably won't understand that. I think Paul would understand. So it's really high temperature time, 121 degrees, plus nuking it, killing everything, and literally having a very sterile food. It's the same thing we see with pasteurization, where you're literally just trying to kill bacteria. But I think the food industry eventually will. Will transition to a new paradigm where we are actually using microbes to potentially produce things like that. You mentioned, Paul, whether they're antimicrobial compounds or whether you're using it as a crowding strategy. So is that something that's in your sphere as well, in your thinking process?

Yeah, I agree. I suppose from the food industry's perspective, it's safest or they don't have to worry about spoilage or shelf life. If they nuke something, as you say, by killing, canning it, or essentially sterilizing it so that the food has a long shelf life, there's no chance of it getting spoiled or anybody ever getting sick from it. And so that's the safest thing from their perspective. But it's not always the best thing in terms of consuming food. I do think it is important to be able to preserve foods in a way that will keep it safe. So pasteurization is useful and is important because raw milk can make very many people very sick, depending on their, again, their immune status and so on. So we are. We do need to be conscious of how we preserve food. But people for millennia have been preserving food and doing it very well through the act of fermentation. And so it's not coincidence that very many societies around the world have produced fermented Food. And it's not just because in that case that they like the flavor or they were conscious of their gut microbiota. It was just purely because they had a particular product that they had in vast quantities at certain times of the year, but which had a short shelf life, they weren't able to preserve it and to consume it months later. And so by, in several cases, by fluke or by coincidence, they came across a process whereby, for example, milk was fermented to make cheese or some other fermented food product, which meant that it had a much longer shelf life. And so while milk wasn't available, they could still consume the cheese much later. And that same principle is true for fish, fermented fish, fermented grains, and all sorts of other fermented foods as well. And so, in essence, what's happening there is the microbes that are in the food, the good microbes are producing lactic acid or some other sort of metabolite that is lowering the ph or increasing the ph or doing something to it that's making the food inhospitable for the bad guys or for the spoilage microbes, by killing them, the food lasts much longer. And I think in recent years, then we've come to appreciate that not only does it preserve the food, but quite often introduces new flavors. It reduces or removes allergens, it produces metabolites and other things that, when you consume them, have beneficial impacts on the gut and on your gut microbiome and on your immune system and whatnot. But it really is something that we've been doing for thousands of years without necessarily fully appreciating the intricacies of what's underlying all of those processes.

Yeah, that's beautifully articulated, Paul. There's one thing, one point. I want to dig in a little bit deeper because I haven't actually heard anybody talk about that before. How does the fermentation process remove allergens?

Yeah, so in that regard. So the simplest example there is for people who are lactose intolerant. So if you're consuming milk, there's lactose in there. And so you really. You can't consume lactose. You'll have side effects and muscle and stomach cramping and so on and so forth. But if you have the right microbes, in a fermentation process, in a yogurt or a cheese manufacturer, if those microbes very efficiently convert lactose to lactate, then individuals can consume the product because the lactose is no longer present. And so that's the simplest example. And yogurt has a health claim in relation to that particular activity. But there are other things as well in that there are other allergens present in dairy products or in quite a few different plant based products. The raw materials can have materials in them that some people's bodies don't, don't cope well with consuming. But by virtue of the microbes growing in them, they can break down those products and produce either beneficial or at least neutral byproducts that allows us to consume those foods effectively.

Then I'm thinking of some, a study I saw recently around, around sourdough and gluten about potentially how going through that latte fermentation process, maybe the gluten is a little bit easier for the body to digest. Something along those lines.

Other examples, very good example as well.

Yeah, Other examples of the. Perhaps not in a context of allergens, but maybe for anti nutrient compounds, things like phytic acid or, or things of that nature could lend itself to being fermented and reducing the impact in the gut.

Yep, perfect examples. And I guess there are probably other things that people aren't even aware of that they might have potential too, but that are being removed from fermented food. So those are the classic examples, but I don't doubt that there are others out there as well.

Yeah. So what's exactly for people that might be totally new to fermentation, what is going on in the fermentation process?

Okay, so it might be simplest to pick one particular example because there's lots of different twists and variations on a theme. But so one of the fermented foods that we study most frequently here is kefir milk. Kefir. And so kefir is contained, kefir is made from kefir grains. And kefir grains are communities of different microbes that are grouped together in kind of a polysaccharide matrix. So it looks a little bit like a small cauliflower of this size, but it's not plant based. It's used for dairy fermentations. And so within the kefir you have the bacteria and yeast all kind of clumped together, living happily with the, in combination with one another. And for the fermentation process, what you do is you take your milk. So whatever source of milk you like, cow's milk, goat milk, whatever, you add the kefir grain to it. And some of the microbes that are present there, like the milk environment, so they leave the kefir grain and they begin growing in the milk. They grow in conjunction with one another. And they encourage one another's growth and they have all sorts of different synergistic activities between one another. So the primary activity involves the growth of lactic acid bacteria. So things like particularly Lactococcus. So Lactococcus takes the lactose in the milk, the sugar source, and converts that to lactic acid. And there you have your first advantage immediately, as I described previously, whereby the production of lactic acid, it drops the ph, makes the milk slightly more acidic, not more, not so acidic that it's harmful to us, but acidic enough that it stops the spoilage microbes and the disease causing microbes from growing. Lactic acid is particularly good in this regard. And after it grows, the lower ph facilitates the growth of other microbes. So things like Lactobacillus and different types of Lactobacillus like Plantarum or Kypha nilfaciens or Lactobacillus kyphrai. And those are notable because their Lactobacilli are kind of first cousins of other Lactobacilli that you find very frequently in probiotic products. So lots of different strains of Lactobacillus have been associated with health attributes. So these microbes contribute to flavor, but also, when we consume them, contribute to health. And then they also produce other metabolites like kefran, which is a polysaccharide, which is thought to be a prebiotic. And a prebiotic is distinct from a probiotic in that a prebiotic, when you consume it, is used as a nutrient source for the good microbes in your gut as well. Then you have lots of other microbes like Leucanostic, which contributes to flavor. You have yeasts, which can contribute to the kind of distinctive gassy, kind of bubbly nature of some types of kefir. Less is known about how they contribute to health, but I don't doubt that they're important. And so all of those different microbes exist and there's kind of a wave of growth whereby certain microbes dominate after the first few hours, and then others begin to grow and take off. And that's the reason why some people like to to consume their kefir after a relatively short fermentation process, and others longer, because as it goes on longer, the flavor becomes more intense and more considerable. So it depends on your palate. And at the end of that process, you remove the kefir grain again, you sieve it off or just decant it. You put the kefir grain back into fresh milk to begin the process all over again, and you consume the milk and you gain the associated benefit. And I suppose we can get into it in more detail as we go on, but that process reflects maybe the kefir grain that I have in my kitchen at home, but it might vary subtly from the one that you have in your house or that somebody has in San Francisco or London and so on and so forth. So we're doing a lot of things like serving different kefirs and also different other types of fermented foods around the world to see how they differ. And we know, for example, from that there are certain kefirs where you have a community that is good for, say, removing cholesterol, but that might be only 2 out of every 15 kefirs. And so I wouldn't necessarily know if I have the right kefir at home unless I do a study on it. And so what we're trying to do is to identify which communities and which kefir grains are the ones that are best for particular scenarios, and then to make sure that those get to the people that need them most. And then similarly, there might be another kefir grain or another kimchi or another water kefir or kombucha that's better for, say, dealing with anxiety or IBS or some other sort of symptoms that you need addressed. And so by studying the foods in greater depth and really drilling down into the mechanics and the microorganisms and the metabolites that contribute to health, you can make sure that you're harnessing those optimally going forward.

So talking about all those different health attributes that you, you mentioned, are there particular strains that pop out straight away when it comes to, say, for instance, for example, anxiety and depression?

Yeah. So in that regard, that's really very new research that we've been undertaking, and we've been doing it with John Cryon, one of my colleagues in APC Microbiome Ireland. So he. John has an international reputation in the microbiome gut brain axis work. So he's in the past focused a lot on individual probiotic strains. And so what we're trying to do now is to look at the more complex communities in fermented foods, whereby my view, there are some very good probiotics out there, but you have more potential and more metabolic activities when you have consortium groups of microbes. So instead of one, if you have five or nine or ten different microbes together, then what they can potentially do is create much. And so in that regard, we know that some of the Lactobacilli and some of the other microbes are very good at in terms of their things like tryptophan metabolism and producing compound that are quite like serotonin, which is a brain signaling compound. But what not everybody appreciates is that there are a lot of neuroreceptors in the gut. And so you can impact on your brain health or your mental well being through what you eat and through the microbes in your gut as well. And so that's really something that John and his colleague Ten Dinan have been pushing for very many years and educating people about. And I think it's really entered into the public consciousness now. And I think now is the perfect time to apply it to fermented foods. And we've done a couple of initial studies, but we're really hoping to ramp that up in the years to come.

Great. I did get a chance to meet Ted a couple of years ago. He's such a lovely man. I actually met him in Paris during one of the conferences that the Gut Brain Access conference. And actually I had him on the podcast. So if people want to actually want to go back and listen to the whole gut brain connection story from one of the world leaders in that space, the guy that actually coined the term psychobiotic, go back and listen to Ted. He's an amazing character, amazing guy.

I'd highly recommend that. He's a great guy, a great speaker and again, very passionate about his research.

Totally, totally. So I have to ask this question as well. So you mentioned the almost the succession of different bacteria in the dairy medium with all these different microbes. Lactobacillus, lactococcus, some yeast. What's going on when you put those milk kefir grains in a coconut medium.

Yeah. So I know that there's a product that's sold in Canada that essentially is doing that. So that's an interesting question in that we've just put out a paper there now where in the last number of days we've sent it for peer review, but we've made it available to the community at large as a pre peer review document so that people can read about it. What we've done in that regard is we've studied 58 different fermented foods from around the world. As many weird and wonderful fermented foods as we could get our hands on. And some people might have predicted that we would see the results we did, but I still find them very intriguing. So maybe take a step back and do a bit of explaining here so we can do an analysis of the microbiome through DNA based approaches and kind of quite complex computer based analysis afterwards. And basically what we're doing is crunching lots of DNA sequence data and tons of data around the microbiome and condensing that down into a single dot on a graph. And what we can do is plot the microbiomes of lots of different fermented foods and see how similar or dissimilar they are. And so we found that all of the kind of dairy based fermented foods, the kind of cheeses and the nonus and the kefirs all are somewhat similar because all of the dots kind of go to the similar location on the graph. And we found all of the kind of sugar based fermented foods are somewhat dissimilar from the dairy foods, but quite somewhat similar to one another. So you're talking about water kefir and kombucha and things like that. And then we had the brine based foods or the salt fermented foods, which would be kimchi and sauerkraut and they were kind of in another cluster. And then we had a few kind of hybrids or Frankenstein type foods which were, didn't really fall into any one cluster. And so the coconut kefir fell in there. And so it had some of the attributes of a sugar based fermented food, but a little bit to do with the dairy food as well. And there was kind of a dot out there in its own away from all of the others. And so I guess what you're, you're really doing there is you're putting the kefir grain into a different environment. And so the microbes that might like growing in the dairy environment aren't coping or don't like that environment so much. But maybe other microbes that are in the kefir grain are now saying, this is super. We like this kefir environment, we like the sugars and the different nutrients that are based here and we're going to grow in this environment. And so those are the microbes that dominate there. And so when you're, when you're consuming coconut kefir, you're going to get slightly different microbes, but again, a lot of them are still going to be Lactobacillus and others that have at least some suggestion of being health promoting. And so the question then becomes, what are the specific strains doing? And you have to kind of get into deeper human studies to really figure out the specifics. But the type of microbes that are growing are nonetheless suggestive of being able to contribute in some way to good health.

So how do you guys. So I'm assuming you're doing some, is it pico a or some sort of analysis to that effect.

When you. How do you mean in terms of the microbiome analysis?

With the clustering.

With the clustering? Yeah, so, yeah, so yeah, PCOA are different types of beta diversity analysis. So basically microbiologists in recent years know that we're starting to study microbiome environments. We've robbed a lot of terms from ecologists. So when an ecologist is, say, the analogy that I typically use is that of say a rainforest and a desert. So if you're studying the alpha diversity of a food or of a gut environment or something like that, the alpha diversity is where you're comparing, just getting a number relating to how diverse the microbial population of that environment is. So if you think of the Amazon rainforest, you have a high diversity and if you have the Sahara Desert, you have low diversity. And so that's a number put on each environment. Beta diversity is where you're directly comparing the two. And on that sort of plot, the Amazon rainforest and the Sahara Desert will be on either end of the plast, completely away from each other because there's very little in common, but that the various other different rainforests will all be together in one cluster and all the different deserts will be in another. And so that, yeah, it's a clustering based system. And that analogy also serves well to highlight why good microbial diversity or high microbial diversity, especially in the gut, is good. Because typically low diversity scenarios have been associated with quite a number of different diseases, whether it be obesity or different allergies, different inflammatory bowel diseases, and so on and so forth. So things that can increase our microbial diversity, such as fermented foods or prebiotics or other interventions, are regarded as being desirable.

Sure, I should let you know, I'm just getting this warning sign coming up on my screen, so if we do cut off, I'll send you a new link straight away so we can get back into it. For some reason it's playing up. So my apologies. That's fascinating. I agree with you, Paul. Diversity is so, so important because the microbiome field is relatively young and scientists like yourself and others are still trying to work things out. But it's interesting that it's almost common sense that an ecosystem like a rainforest or a desert, if there is more diversity, it is more likely that that ecosystem is going to be more resilient. And the way I think about it is that if there is some form of, I don't know you're going through a period of, of famine or some sort of crisis. If certain microbes are lacking in the gut because you're missing some prebiotics, you're missing vegetables, or your diet's off, or something's off, you're more likely to get some of these other characters stepping in and filling the void. But if you've got a very small team to play with, there's only so many players that can step up if you need them. So is that similar to what you're talking about, Paul?

Yeah, that's a perfect example. And I quite typically relate back to C. Diff infection as being maybe the best example of that whole scenario. So C. Diff is quite typically a hospital acquired infection, but it can occur in other places as well. And C. Diff is actually found in very many people's guts. It's a spore former, so very resilient microorganism. But normally the microbes that we have in our gut keep it in check and so they produce different metabolites that stop it from growing. But when we're exposed to antibiotics or some other sort of stress, but most typically antibiotics that are used to treat another infection but also bring about a collateral damage, so inadvertently also do damage to our gut microbes and wipe them out or do significant damage to them, then the removal of those good microbes allow the C. Diff to grow, they spiral it and produce toxins, and those toxins give you the severe diarrhea that's associated with.

Yeah, so apologies for the disconnection, listeners. So, Paul, I think you were at the point where we just were talking about diversity in the gut and we were also just giving the analogy of the C. Diff scenario.

Yeah, I think that nicely highlights the importance of having high microbial diversity and high risk resilience among your gut microbes. C. Diff is a spore forming microorganism, which means it's quite resilient. It can remain dormant for quite some time before reviving itself and beginning to grow and do dangerous things. And so it can be present in the gut in a harmless form, but then after somebody's been exposed to antibiotics, especially broad spectrum antibiotics, and those are used in instances where a medicine knows that there's an infection, but doesn't know what type of infection it is. So it's easier to give kind of a weapon of mass destruction to try wipe out everything. But of course that causes collateral damage to the gut microbiota as well. And as a consequence the normal commensal good microbes that are in your ghost that can keep the C. Diff at bay are now damaged or wiped out and that that allows the C. Diff to grow and produces toxins. And it's those toxins that give that result in the distinctive symptoms. So the diarrhea, C Diff associated diarrhea or CDAD that can be life threatening for some individuals. And so there's an appreciation now that it's as a consequence of trying to preserve that microbial diversity. You're using narrow spectrum antimicrobials, are trying to bring back in a diverse microbiota that that's the ideal way of curing that illness and controlling that microorganism. But I think there's lots of other instances where low diversity in the gut has been associated with an undesirable outcome or different symptoms.

Yeah, and I think it's a good segue to talk about. How do we. So you mentioned fermented foods and fermented foods from what you were saying earlier, have this broad array of different microbes. So potentially could we use fermented foods? Admittedly we should say we need to understand these things a lot more from a scientific perspective to fully appreciate the benefits that they are exerting on the body. But fermented foods have been with us for thousands of years. They're already parts of many cultures. They're starting to come back into vogue in the west for sure. So could this be a strategy to introduce diversity in the gut people? I mean if you look at the microbiome researchers, most of them will call out plant food diversity, which I 100% agree on. So not not to take anything away from that, but what's your thoughts on using fermented foods is also a strategy to introduce some diversity in the gut?

I think it's a great strategy and it's not always so your consume. If you consume lots of different types of fermented foods, there's more chance of getting the ones that you require in your system. And sometimes it's not even the microbes themselves from the food that establish or colonize us are the ones that contribute to your gut health or that increase diversity. But it's as a consequence of them growing and producing something else like the lactic acid which can then be used by other desirable microbes in the gut kind of next generation health promoting microbes that aren't found in foods like EU bacteria and roseburia and Rheumatococcus and Akkermansia and some of those things like the nutrients and the end products of fermentation and it encourages them to grow as well. So yes, prebiotics and plant based fibers are good for your gut microbiota. But I think fermented foods even early in life can be desirable because again, especially for infants after they're born, there's an issue again in western society where because not every kid is born vaginally, sometimes they're born through C section and then subsequently they're not given breast milk, but they're given formula, their formula fed. And so they're not exposed to as very many different microbes. And just because we're more hygienic, there's more consciousness around our environment and the bad microbes in our environment. Lots of young kids aren't exposed to so many different microbes any longer early in life. And it's thought that phenomena like that contribute to allergy later in life because our immune system has difficulty differentiating between the good and bad guys because it has never been exposed to the good guys early in life. And so I think there's things that can be done among the young, but also as we get older and by virtue of eating different types of foods, and especially fermented foods, that there's lots of merits to be gained, which if you're going to hone in on one particular fermented food, then you're taking a risk that you might just not have the right microbes in that food for your particular scenario. And therefore by consuming lots of different types, you're giving yourself the best chance of there being something in there that will be particularly beneficial for the thing that your body might be susceptible to at that particular time or later in life?

Absolutely well said. So the variety is absolutely critical. What's your thoughts on what the research is suggesting? I know it's really in its infancy, but is there any particular fermented foods that are more, more well studied than others that are perhaps a bit more evidence based to suggest that there are particular health benefits?

So in that regard, I guess I would lean towards milk kefir just because it's the one that our lab has focused on as our kind of model fermented food most extensively. So there's quite a bit known about that there. Cheese is the best studied fermented food, but then it's studied more so from a technological point of view and with respect to its flavor and other different attributes. But nonetheless there are microbes in there that I think there's merit in consuming them. There's an increasing amount of research relating to other foods then, like kimchi, sauerkraut, water, kefir. Kombucha and kombucha in particular is getting very popular now. Both the kind of homemade variety that's made from Scoby's, but a lot of large companies are beginning to produce it. And even some of the companies that are better known for making beer and fermented alcohol products are now looking at kombucha as a means of kind of tapping into the health promoting market as well. So there's a huge revolution. The science is playing catch up in some extent. To some extent, because the suggestion or the public wisdom or the message that's getting out there would suggest that all fermented foods are good. And yes, I do believe that people should consume as very many different fermented foods as possible. But the specific health attributes associated with each different fermented food isn't always very well understood. And then as I mentioned earlier, even within our own example of milk kefir, there is such big variety from different locations. We've done studies in the past where we've gotten milk kefir grains from 25 different locations around the world. We've returned to that sort of approach now, and I've engaged in a Facebook approach to try to get even more kefirs from different communities and different locations so that we can study them, see how they differ. Which versions are the ones that are good, as I say, for cholesterol, which might be the ones that are good for anxiety, which are the ones that are good for ibs. But I think that even that you will have some general attributes that will be shared among all kefirs in that they'll remove or reduce the amount of lactose in the food. But the specific tweaks and the specific health benefits will vary from one to the other, just because there's different microbes in there. And when I go back to the probiotic fields, that's something that I really try to instill when I'm talking to people from the general public, that they think that if they take a probiotic, that it's a panacea, that it's solving every issue under the sun. But you really have to view them on a strain by strain basis that the probiotic for which there's a lot of research relating to IBS won't necessarily do anything for you in terms of your travelers associated diarrhea or some other sort of phenomenon. So you need to do your studies, read up the literature and find out which is the one that is beneficial for you as a probiotic. And I think ultimately with regards to fermented foods at the moment, I would say consume as many different fermented foods as possible. But I'd like to think that through the research that we and others are doing that it would be possible quite soon to have a tailor made fermented food in which you have specific strains that you know will be very good for you in terms of specific desirable effects.

That's very well summarized, Paul. One question I have to follow up from that is let's get back to milk kefir. So you mentioned the grains are quite variable. And so what a lot of the big food manufacturers are doing is they're using these almost these isolates or powdered cultures. How do they differ to the milk kefir grain?

Yeah, so that's something a question that I feel a lot of sympathy for the consumer in relation to because it's very difficult to discern between a good kefir and one that's not so good. And like, for example, there are some products out there that are marketed as being kefir, but if you look at the side of the container, it will say that the microbes in there are Streptococcus thermophilus and Lactobacillus bulgaricus. And you know as a food scientist that those are the microbes that are used to make yogurt. So in essence, you're drinking a dilute yogurt that maybe some flavors have been added to, but it's no different from consuming any other yogurt. So there's nothing particularly special about it. You have other situations where people go a little bit beyond that. So they will mark it maybe something like that yogurt, but will throw in some probiotic strains as well. They won't necessarily be kefir associated strains, but they're trying to get something that's a bit more kefir like, or at least when you look at the side of the label, there's lots more names of microbes at the side, so it looks more convincing. The next level beyond that is I think is at least a somewhat better scenario whereby you can purchase strains that did originally come from kefir. And so you can make a product that you start with milk and so you add in some Lactobacillus kefir, Nafasians and some genuine kefir yeasts into it. And so it will have some of the different attributes that you associated with kefir. The strains themselves won't necessarily have been studied in great depth to know what their health attributes are. But that's probably true for most kefir grains anyway. So that's probably not a bad product to consume. And then you have other kefirs that are made that can still be made on a large scale, but through kefir grains. And that's true what's known as the Russian method. And even some large multinationals use this approach whereby they ferment milk with kefir grains. The microbes enter into the milk and grow there, and then they take some of that milk and they use it to inoculate a fresh batch of milk, which allows them to produce the milk on a much larger scale. And so in that regard, it is very much like a genuine kefir product, but is scalable. It is challenging for large scale production because what you make on one day is harder to control and will be maybe slightly different the next day. So quality control is an issue. But that's also true for people making kefir grains at home. And then you have the actual kefir grains at home type scenario, the artisanal producer that's using the grain immediately themselves. So there's those different alternatives. I guess where we're kind of going is that we like the artisanal approach or the Russian approach where you're using the kefir grains, but as I mentioned, that's quite difficult to reproduce in that. We've actually done a study, it's not published yet, but we've taken one kefir grain and we've put it into fresh milk day after day after day over very many weeks and studied how the microbiota changes in that milk. And it does differ quite significantly because you have more microbes coming in from the milk and different microbes start to take off and others don't do so well. And so you're kind of changing the composition over time. And that's fine because most of the microbes are still good. But if you're making a product and you need to have a particular flavor and you need to be sure of the shelf life and whatnot, then those inconsistencies are problematic. So what we're moving towards is a scenario whereby we can look at the best kefir grains that are out there, study the strains in greater depth by actually doing genome sequencing and figuring out what it is that they do in terms of different cell line analysis and different types of studies, and different agar plate assays and so on. Pick those which grow together and have health benefiting. Properties and also have a nice flavor and then put them all back together so you have a situation that's a little bit like the other scenario where you pick individual strains and put it into milk and ferment it. But no, you're not just picking strains in a willy nilly fashion, in a random fashion, just so that you have lots of names at the side of a bottle, but actually you're getting the best microbes, the best health attributes, but making a product that you can make sure if you make it today, it'll be the same next week and it'll be same next year and you don't have any spoilage or other issues. And that's, I guess, important if you want scalability. Because I'd like, if I have a fantastic kefir grain at home that has lots of good properties and I'd like as many people around the world to consume it, there's only so far I can go with that kefir grain. You can't make tons of it. And so in order to make sure that as many people can benefit from that as possible, then you need to take this alternative approach where you pick best strains and add them back into milk in a more controlled fashion.

That's amazing, Paul. I could not have articulated that any better than you did because this is a huge bugbear for me. In terms of the standard of identity of a kefir product, there is no standard of identity. So again, as you mentioned, the regulators are still catching up in terms of the, the standards, the food standards code here in Australia, I think in the uk, you guys are certainly in your neck of the woods. In Ireland as well, your food legislation is a little bit more flexible when it comes to alcohol production. So I think your tolerance. I know, for instance, I know in England it's about 1%. I'm not too sure about Ireland. In Australia it's 0.5%. So literally it is very difficult for commercial manufacturers to make a true kefir because if you've got yeast in the product, then there's a high likelihood of the product being too high in alcohol, especially when you think of the product moving through the supply chain. So it's going to be extremely difficult in Australia to get a 100% true kefir, even if you're using the Russian bulk substrate method, it is almost impossible. So I feel for the consumer, I really do, and it's extremely annoying to me and it's misleading to the consumer. What a lot of these companies are doing on writing on that kefir trend, especially when you see this wonderful paper written by yourselves and your colleagues on all the particular health benefits and then the consumer thinking they're going to get that with some of these products, which are nothing more than diluted yogurt with sugar and bits of fruit.

Yeah, it's a big bugbear of mine. And in fact, it's something that me and some of the other people who are doing research in the field have gotten together recently to prepare a consensus document for at least trying to convince the scientific community, but to try to influence industry as well. And that was brought together under the auspices of isap, the International Society of Probiotics and Prebiotics, the International Scientific association of Probiotics and Prebiotics. Excuse me. And so what we've done there is to. We're in the process of completing an article whereby we come up with some definitions as to what really is a fermented food and what isn't. And so I think something that might be sold or marketed as a kombucha, which is really just a tea to which sugar has been added and then pasteurized, and there's no living microbes in there, but maybe some flavors added to make it seem like it's pasteurized, should not be defined as a fermented food. So we've tried to lay out some different criteria as to what should be acceptable and what isn't in a manner that we're hoping will influence different legislators around the world world to take a firmer stance as to what is permitted and what isn't. When you put kefir or kombucha or water kefir on the side of the label.

Absolutely. And I felt it from the start of the conversation. We're definitely kindred spirits, Paul. We're definitely trying to wave that flag as much as you can. I think you're in a much better position to influence the regulators in Europe than I am. But I'll do whatever I can to support your mission, because it's certainly my mission as well.

That's super. And I think initiatives through your podcast and bringing all of this information out to the public at large is fantastic because we as scientists try our best. And so we have different innovations or different approaches towards education and public engagement, but our reach is only so far. But by your podcast and other interventions and other discussions with the community, then that's a fantastic way of getting the science out there. So it's no point at gathering dust or being present in a very difficult to access, peer reviewed journal somewhere. We need to be able to translate that information and to explain it in a manner that everybody can understand.

Absolutely, Paul. And I'm very cognizant that I'm taking so much of your time. Just very quickly, I just want to fly through a couple of these benefits from that paper on the particular benefits of milk kefir, because to me, that's my savior with my particular journey and struggles with anxiety and depression and milk air fear was one of the products that really helped me a lot in terms of improving mood. So I can certainly speak anecdotally on the product actually helping me. But in your paper, you guys talk about cholesterol metabolism. Then there's something along the lines of blood. Is it blood pressure?

I think blood pressure, yeah.

Angiotensin converting enzyme, antimicrobial activity, tumor suppression, increased speed of wound healing, modulation of the immune system, including the elevation of allergies and asthma. Are you very quickly able to speak to the actual, the evidence, the fact based evidence behind why you guys made that statement?

Yeah, so I guess what we were doing in that case, so we prepared a review whereby we collated all of the information from all of the different labs that do research in this area. So all of that work wasn't carried out by us, but what we did was we looked to see what was out there already. And so much like you have different qualities of kefir products, you have different qualities of scientific journals as well. And so there are some science studies out there that might suggest that kefir or a kefir byproduct or a kefir strain is good at tumor suppression. But sometimes those studies are using cell lines. And so a cell line is just where you take a cancer cell and you grow it in the lab, not in a human body, see what happens. And a kefir strain might control that cell line, but then if you added water, you probably kill that cell line as well. And so in that case, you're kind of overreaching and it's not really very rigorous scientific evidence. Others there are human studies. And so there is genuine evidence relating to a particular key for strain or particular kefir product. And I think the ACE inhibition, the hypertension side of things, there's a lot of evidence, there's a lot of evidence associated with cholesterol. Whether the particular kefir that you're buying in your local shop or that you're making at home has those particular attributes. It's very difficult for the customer to know without in depth analysis of it. But at least if you're consuming some kefir, there's a better chance of you having consuming a food that has those attributes than if you don't consume kefir at all. The wound healing, there's a little bit of evidence, but not, not so strong. I think there's probably a strong likelihood that for some people there will be benefits from an IBS perspective. I think the anxiety side of things is probably still anecdotal, but based on our understanding of the metabolism and the microbes that are there, I'm not really hugely surprised. And based on our studies with John that I've mentioned earlier, I think we will have some stronger evidence to support that quite soon. So some things that there's good evidence, others that is not so good, but it's really, it's not that there might never be evidence out there that it's really crazy to suggest that there are other benefits as well. But it's just that there haven't been enough scientific studies, especially not enough human clinical interventions to the sort of rigor that would be necessary in order for me to put my hand on my heart and say that undoubtedly you're having this specific attribute. And so that's why we and others are trying to push the boundaries so that we can actually get the science to underpin some of the suggested health benefits and to take them beyond the kind of the quick and not so scientific scientific studies, but actually do them in greater depth so that we can really be sure about what we're seeing.

That's wonderful. So my takeaway from that, Paul, is watch the science space as you and your colleagues and your team do further research and as you publish your papers. I'll be watching with bated breath on what your findings are. But I'm quietly optimistic about the positive impacts that you'll find with Kefia. Now very quickly, let's just give people a little teaser about your work that you've done in the past on the spot sports, the sports aspect of the microbiome, because I'm sure a lot of athletes would be particularly interested. There's a company here in Australia called Microbar who do whole genome sequencing and they're doing a whole lot of work with the rugby teams at the moment because imagine if there is ways to enhance the microbiome and get a benefit from a sporting perspective that that's of huge interest to a lot of sporting clubs around the world. So what's your take on that?

Okay, so real whistle stop tour of our studies in that regard. So we started off doing the first study of its type with the Irish rugby team. It was about two world Cups ago. So back when Paul o' Connell and Brian o' Driscoll and so on were involved, it wasn't too difficult to convince PhD students to get involved there because they got to meet their idols until such time as they received the fecal samples from their idols and then it probably wasn't so pleasant. And they studied those fecal samples in great depth and we saw that they were really amazing. They had really high diversity in their gut microbiota and we refer to microbiota, to diversity in the microbiota previously. So they had really good diversity and that seemed to correlate with diet and exercise and diets particularly in protein in that regard seemed to correlate with high diversity and exercise. So we've done lots since. We've done some studies with pouch potatoes. So people by their own admission, who don't exercise a lot and put them through different exercise regimes and put them on whey protein for a period of time to see if the microbiota diversity changes. It does slightly after eight weeks, not dramatically, which suggests that there's no quick fix, that it's over a longer period that you need to change your lifestyle in order to have these benefits. We've done some studies that are published relating to the Irish athletes that went to Rio. The logic being to see their different microbial communities in different types of athletes. And that did seem to be borne out. It wasn't sport by sport, but it did break down in terms of the type of sport. So whether it's an endurance sport or one that requires a lot of resistance training and so on. So there was a division there, done some studies with cricket, Ireland over the course of a year where they went to lots of different locations in the build up to the World Cup. And so some of those locations were ones where they were going to be exposed to more pathogens. We found that they did have, some of them did have gut symptoms and gut disorders, especially after a trip to India. And it seemed that their microbiota changed quite significantly. And so we're working with them to suggest some different interventions to try to protect them during other trips in the future. And then we've other different ongoing studies with rowing community and other general people in the public. We have a study with different club athletes of different qualities, different VO2 maxes to see how their microbiota changes and differs. So it's really an area of very big interest for us. I think the Big take home. Point is that exercise, but more fitness, extended exercise over a period of time can improve your microbiota and that certain sports nutrients can also have a beneficial impact on your microbiota as well. And that will not only improve your resilience but also your sporting performance, but also potentially provide you with protection if you're traveling around the world and exposed to different pathogens and different viruses.

So I have to ask this question because I'm a huge fitness enthusiast now. What is the. If I was going to pick a.

Sport.

Should it be more high intensity? Should be more of a lower intensity sport that's going to improve my microbiome.

We're still trying to tease that out. And so with the couch potato study, we did study them, we set them up in the university gym and we monitored and we put them through a training plan, but we did allow them to either go down the resistance route or the endurance route. And so they did a little bit of both and some did more than the other. But the number of participants wasn't large enough that fell into each individual category to be able to discern definitively which was the better. And so we're still teasing that out a little bit. So that's ongoing. I have some ideas, but I think it's, it's early days. I'm hoping it'll be more the endurance side. As a runner, I do a little bit of strength core training just, but more for injury prevention. And so I'm hoping that I'm getting more benefits from that. But if necessary I'll change to a more strength based training. If I'm finding that that's, if our results ultimately show that that's where you get the best benefits for your microbiota.

I'm actually the other end of the spectrum. I'm more high intensity kettlebell, you know, heavy weights, short and sharp. 30 minutes in the gym and I'm out. So I'm quietly hoping for the other side of the coin. And you mentioned sports nutrients and I was listening to one of your interviews and you mentioned something about whey protein and ck, but I wasn't sure what CK was. What, what's ck?

That was one of the most interesting outcomes from the athlete, the original rugby study. So we wanted to determine how much exercise they were doing and now they have GPS systems and so on and so forth in their jerseys. But that's not of use if we want to compare them with people in the general public. And that's what we did in that instance. So we compare them with Some amateur athletes, but also people that exercise very much. And so normally when you're doing a study of fitness, you ask questions of people in the general public in terms of how many hours of gardening you do every week or how many flights of stairs do you climb every day. So we weren't going to ask Paul o' Connell and Brian o' Driscoll those sort of questions to assign to the term of their fitness. So we needed to find something that spans both of them. And so in that case, what we did is we looked at creatine kinase and creatine kinase CK is an enzyme that you find in muscle. And when you go through extreme exercise, you have these kind of micro tears in your muscle that give you the kind of muscle pain that you suffer from after you exercise. A lot people think it's lactic acid, but more often than not it's these micro tears in your muscles. And so the enzymes is released into the blood and you can monitor it. And CK is normally used to monitor as a detection of say, a heart attack, because your levels of CK go through the roof if you've had a heart attack recently. So we received the blood samples from our athletes and from our controls and we sent them into our university hospital for analysis. And next time we got a phone call asking us where did these samples come from? These CK levels are through the roof. These people are really ill. We need to get them in and to help them get over their heart attacks very quickly. But ultimately it turned out that those were the athletes who had gone through. They were in pre season training for the World cup and were going through the toughest of training. And so their CK levels were just through the roof. But we use CK as our monitor of levels of exercise. So obviously people in the general public were much lower. Now, a few of our controls had involved in GA teams who had very rigorous training sessions the previous day and one individual had done the marathon recently. So they were a few outliers, but then in general the rugby guys were much higher. And so we were able to correlate the microbiota diversity with CK and show that. And that's where we saw a relationship between extreme exercise and differences in the microbial diversity.

So was it the higher the CK in their blood, the more diverse their microbiome was?

That was kind of the pattern. I'd be careful about over interpreting that because I think going out and really flogging yourself to death and putting yourself through crazy extreme exercise isn't necessarily good for you on a regular basis. But I think it was probably just more a reflection of the combined fitness and exercise that the athletes were doing over an extended period of time, and the reflection of that in the CK values that was impacting or reflecting the microbiota rather than CK per se, or the benefits of one specific, very extreme and exercise workout.

Yeah, I hear. So it was one particular marker, but it seems to be over a period of time. So these athletes have been training over many, many years to potentially achieve those results. So it's not just like Joe Bloggs listening to the podcast where he's going to go and flog himself in the gym and get a better, more diverse gut microbiome.

Yeah, not over the space of a week, but over months. I think you will get a benefit. And then obviously, as we talked about, protein, but I think diet in general is a factor there. So there was one particular rugby player who I suppose ultimately he got the microbiome he deserved because he, despite how conscious we think that her superstars are, regardless of diet, he, at that time, he wasn't a fan of eating well and so didn't consume very much vegetables and fruit and so on and so forth. And his microbiota was very much there with the couch potatoes than with the other people. I've learned since that he's changed his ways, but it really just shows that there's no. There's no shortcuts. I guess you can do all of the exercise and get the benefits from that, but you still need to be conscious of getting a good diet as well.

Absolutely. And I think that's a beautiful way to wrap up and. And I'm so appreciative we've gone well over time. I do apologize and I appreciate the time that you've taken out of your day. You must be incredibly busy. And so with the huge gratitude. And so at the end of the podcast, I always ask my guests, Paul, if there was one thing that an audience member could do to improve their gut health, what would it be?

Eat more fermented food. Great.

Perfect way to end the podcast. Thank you so much. Paul Cotter. All the way from Ireland, isn't it? Yes, Ireland. Cork University, APC Microbiome.

It's been a real pleasure. Really enjoyed it. The time flew. As a science nerd, it's great to talk science, so it's no inconvenience at all. I really enjoyed it.

Thank you so much, Paul. Enjoy the rest of your day.

Okay, super.

We hope you enjoyed this episode of the Gut Health Gurus podcast with the amazing professor Paul Cotter. We covered so many interesting topics like the benefits of fermented foods and Guys, if you are interested in trying to make your own fermented foods, do head to our sponsor to Nourish me Organics at www.nourishmeorganics.com and use the code COTTER for 10% off. Guys, your support means the world to us. So please share with your friends and family members and do leave us a kind review on Apple Podcasts until next time.