Microbiome Insights is proud to be the sponsor of season 2 of Ruairi Robertson's Biomes Podcast. 

In this episode Ruairi talked to Paul Cotter from Teagasc and the APC Microbiome Center in University College Cork. Here are the key takeaways from the conversation: 

• Paul's journey into microbiome research and how it relates to the rich history of food and dairy research in county Cork. 
• How fermented foods were initially discovered and their prevalence across different cultures. How in Western societies, pasteurization and other processing approaches have had an impact on how many microbes we are exposed to through our diet. 
• Paul discusses his work in characterizing the microbiomes of various types of fermented foods, including artisanal cheeses and kefir grains sourced from enthusiasts from around the world. 
• What happens in the gut once we consume fermented foods? 
• Future avenues for this field of research, including the potential for personalized probiotics for athletes, the elderly or to treat diseases. 
  
  

Links to Apple, Spotify, Podbean 

Full Transcript 

Ruairi Robertson:

Welcome back to Episode Three of Season Two of The Biomes Podcast, a place to get a gut full of microbes from the world's leading microbiome researchers. Now, five to 10 years ago, most of us would never have heard of kombucha, kefir, sauerkraut, kimchi, but these foods seem to have transitioned from boutique health shops to regular supermarket shelves around the world. Now much of this food trend can be attributed to the evolving research into the gut microbiome. However, the research into these foods hasn't quite kept track. One man, who has spent a lot of time researching these foods though, is Professor Paul Cotter of one of the leading microbiome research centers in the world, APC Microbiome Ireland, in University College Cork and Teagasc Moorepark Food Research Center, where I spent a few years doing my own PhD.

Now Professor Cotter and his team have spent the last few years systematically collecting and studying various fermented foods like kefir and kombucha around the world, examining their microbial properties and investigating their potential health benefits. His work is slowly uncovering the scientific evidence behind the real health benefits of fermented foods. We discuss whether the evidence for these foods live up to the hype and whether there should be a recommended daily intake of microbes, and how this field will evolve in the future.

This second series of Biomes is sponsored by Microbiome Insights, who are leading providers of end to end microbiome sequencing and bioinformatics analysis. So whether you're performing basic research in nutrition or developing a new pre or probiotic product, Microbiome Insights has the expertise and the experience to help you achieve your research goals. They are offering free study consultations to all Biomes listeners, so head over to MicrobiomeInsights.com to find out more.

Paul, thanks very much for having a chat with me. It's great to reconnect and see what you've been getting up to in the last few years in your research and as well as summarize what you've done before that.

Paul Cotter:

For sure.

Ruairi Robertson:

Maybe if we can start off, you can give us a little introduction to your background and how you got into the field of the microbiome and the microbes within fermented foods.

Paul Cotter:

Yeah, so I was thinking about this morning, because I knew I was going to be chatting with you, and just even thinking about how that whole area became so much an area of focus in Cork over the years. Cork, for those of you not familiar with Ireland, who'd be listening, it's always been an area where there's been a big focus on dairy and agriculture and food and whatnot. In that regard, I guess, what's notable is that in the past there was ... Since research was carried out in Cork, there was always what was know as a dairy research center at University College Cork, a dairy science, even before there was microbiology or any of the kind of standard names that we're used to hearing about these days.

In parallel then as the other institute that's located nearby at Teagasc, where you obviously studied and where I'm located now, that was originally known as the Moorepark Dairy Production Research Center. There was always an interest at dairy fermentation for that reason, cheese in particular, and there was lots of legends of fermented food research who came through those two institutes over the years. I guess, I'm kind of standing on their shoulders or benefiting from the vast history of research in that particular area.

For me in particular, I came to University College Cork, UCC, to do my BSC in microbiology and then kind of a more molecular slant for my PhD, continued on to get some grants and do some lecturing there until 2009, where there was a big jump for me in that I moved to Teagasc, this other institute that's about a 40 minute drive away, to establish a new research group that was really designed to harness research in the microbiome space, but to really apply it to food and the food chain. So we've really been doing that on a large scale ever since. I've been very lucky to have a fantastic team of students and postdocs that have really facilitated that. It's been an exciting journey and one that's still ongoing, but it's been a pleasure every step of the way.

Ruairi Robertson:

That's great. I think what some people might know is that Moorepark is based on a big agricultural research facility as well. It's great that you are that research link from, as they say, from farm to fork, literally. You're looking at the processes which we'll talk about of how microbes influence our foods from the point that they're produced all the way to when they make it into our bodies and then what they're doing to our bodies as well.

Paul Cotter:

Yeah, as you say, it's probably a unique center in that regard in that you can walk the fields during your lunch break and you can see the grass and there's grass research going on and there is cattle grazing, and even the fact that we have facilities there for food processing and a large pilot scale plant where we make the foods and then people consume them and we can study the microbiomes. So literally the whole way along the chain.

Ruairi Robertson:

Everything, yeah. Great. I remember those, going for walks on my lunch times during my PhD, it was great. You could clear the head out in fields with the cows. So lets have a little start off and look back to history of what you know anyway, from your years of experience of the history and the culture around fermented foods. Fermenting was originally a method of preservation, and it still is around the world. Maybe talk us through your own knowledge of fermented foods and where it started and how it's evolved to where these foods are today.

Paul Cotter:

So there's lots of evidence throughout history from thousands of years back of food being fermented from the Middle East, from China. But ultimately, I think, when you drill down into it, almost every society around the world has some history of fermenting foods. For all of that to have happened in parallel is not a coincidence. As you mentioned, it came over the necessity initially in that obviously there wasn't refrigeration and other approaches to store foods and extend the shelf life. So with foods only having a finite shelf life, there was a need to come up with some alternative to overcome that. By fluke or by a variety of different means, people happened to notice that if you stored food in one particular way it spoiled, but if you stored it in another way something happened to it that resulted in it's changing its structure, appearance, taste and so on, but that it allowed the food to stay stable for a longer period of time and you could consume it not only within a number of days, but sometimes over weeks and months.

In parallel with that, I guess, what I'm talking about there relates to foods fermented dairy and whatnot, but obviously wine and other fermented beverages developed over that whole period to extend the shelf life of grapes. In a way, all of that evolved simply because the quality of water in very many locations wasn't sufficiently good, so fermenting a material to increase its safety and shelf life was necessary as well. So, I usually give the example of whereby some of these things happened by fluke, so whereby some tribe or nomadic people stored some milk and it happened in the absence of a proper storage vessel. They may have stored the milk in a pouch that was made from an animal's stomach or something like that. As a consequence, the microbes there entered into the milk and fermented it and produced something that was very distinctive from the original product.

That's thought to be how maybe kefir grains initially became established, or if you think about cheese and the need to introduce rennet as an enzyme that you would typically find in the calf guts. Rennet again, that's something that is done on an industrial scale now, but originally would have been performed by coincidence by people who wanted to store the products, didn't really realize what they were doing, but by fluke came across a nice product or something that was more stable.

Ruairi Robertson:

I think we see that, that's where it originated from, but as we modernize in our food systems, we tend to lose that. We don't have to rely on fermenting anymore and with that we've lost a lot of these fermented foods. I mean, you can still see them in some diets around the world, especially in Asia, and every country seems to have their own fermented food. I was at a conference in South Africa a couple of years ago and they introduced me to amasi, which I'd never heard of before and it's a fermented milk which is really common in South Africa. What is it about that, is it just a trend of our western diets in general that we're losing them? Or why are we losing that connection with fermented food? It's probably more of a philosophical one than a scientific one, but-

Paul Cotter:

It's a good question. In fact, it's something that we've discussed within our group quite a lot recently and we've written some reviews that are due out soon on the topic. But to my mind, I think the lack of or the decrease in the consumption of fermented foods or the lack of exposure to microbes in our diet in general is more of a Western phenomenon. Those fermented foods continue to be consumed on a large scale in Africa, in the Far East in particular, Eastern Europe even. And maybe what happened in Western society is there was kind of a perception of microbes being bad and which pasteurization and other processing approaches like that, microbes were associated with food spoilage or foods and safety issues.

As a consequence of trying to address those through canning and extreme treatment of food and new UHT and other approaches, which did extend the shelf life and increase their safety, you could say, but as a consequence, the baby was thrown out with the bath water, in that all of the good microbes that are present therein were removed as well. Even in some of the fermented foods that continue to be made, were made on a large scale with only maybe one or two starter or adjunct strains in there. It was a very basic microbial composition that didn't really reflect the original artisanal product and to the same extent.

But in recent years, there's really been a movement back towards natural foods and minimal processing and for fermented foods in particular, doing it in such a way making the foods at home yourself, having the right microbes in there. If they're being mass produced, do it in the way that reflects the artisanal process with more strains in there. I think that feeds into a whole other larger discussion relating to the potential that I think some of the issues that we see in Western society in recent decades relating to inflammatory issues and especially autoimmunity and allergy and such, so on and so forth. I think a lot of that is related to a lack of exposure in our diets and in our lives in general. And the movement towards addressing that and reintroducing beneficial microbes into our lives can help to provide solutions to those issues.

Ruairi Robertson:

Yeah, I think you're right, because you're right especially in Eastern Europe let's say, people will preserve everything. They'll ferment berries and any food they have and create their own little unique cultures out of them, which I don't know, we just don't tend to do in more kind of Westernized countries, whether it's time or effort, or whatever it is. So let's talk about some of the work that you've done on particular foods. I know you've done a bit of work on cheeses. Cheese is almost like wine, I suppose, it has these kind of very unique profiles to it depending on where it's produced and how it's stored and how it's made. You've done research into that, into how the microbes within the production process influence a cheese's flavor, how it ripens over time. Maybe tell us a little bit about your work into cheeses and how the microbes within that process effect it.

Paul Cotter:

So, our first venture into this, I'll come into this from an unusual angle. The first study was one whereby we got involved in studying a cheese microbiome using some of the technologies we use for other fermented foods and for the human gut and whatnot. But the only reason we got involved is the PhD student was looking at a phenomenon known as cheese pinking. This was a defect that you find in cheeses. People had been aware of it for maybe 100 years or more. Or at least, it had been in the scientific literature, probably existed for an awful lot longer. It occurred in certain types of cheese that were I guess continental type cheeses, so that had a high temperature treatment process involved.

This student was coming towards the end of his PhD, had set himself the very tough challenge of trying to determine the basis for this phenomenon, despite lots of people having failed previously. He did all sorts of chemical and biological and microbiological characterizations of the cheese and hadn't really gotten very far with it unfortunately. Just out of a sheer sense of desperation, asked us, one of my PhD students, Lisa Quigley to see if she would help him out. We were intrigued and so we gave it a go and low and behold, from the defect cheeses that had this pinking...Now the pinking is just a discoloration, it had no taste defect, or didn't make people sick.

But we noted a particular type of microorganism thermus thermophilus that you more typically find associated with hot springs and extreme environments. It is a microbe that people can culture, but it is one that people from a cheese industry would never want to try to culture, because it's so...You would imagine unrelated to cheese microbiology. Low and behold we cultured the microbe from the defect cheeses. We grew it up. We put it back into fresh cheese and we created the problem, kind of a la Koch's postulate for cheese, so to speak.

Ruairi Robertson:

For cheese.

Paul Cotter:

And actually proved that that microbe was the problem for that defect. So that really intrigued us and from that we branched into lots of other studies looking at things like the difference between the rind of a cheese versus the inside part of the cheese or whether the time of the day that the cheese was made within the processing plant dictated what microbes you would find in there. That indeed proved to be the case. We also found that lots of the microbes that you find in the cheese are present in the cheese making environment. You may be making a cheddar, but you might find some microbes on that particular batch of cheddar from an emmental or something else that was made a couple of days before, because those starters or those microbes are still in the environment. So even despite best efforts for cleaning, for CIP and cleaning practices, you still find some residual microbes. I don't think that's necessarily a bad thing.

I guess, that really culminated in a study then that we published this year whereby Aaron Walsh and Guerrino Macori with our group. What they did is a survey of 55 different artisanal cheeses that were made from around Ireland, all sorts of different cheeses of long and short ripening time, and mold ripened and non surface ripened cheeses, and really compared and contrasted all of those and went a step further and actually collated all of the various different bits of information that was available about cheese microbiomes around the world in general. And did a very deep survey of what you find. What are the consistencies? What are patterns you see related to which microbes correlate with particular flavors and lots of things like that.

Ruairi Robertson:

Ah, that's amazing. I suppose at an industrial scale, as you talk about these companies or people producing cheese, want to make things very standardized and make sure there's no other organisms there. But really, originally, it's those organisms that are in the environment that give the cheese its flavor in the first place when you're talking small scale cheese batches. It's probably the people who are producing it. I don't know, did you look at that? Was it the people working in it who influenced the cheese profiles as well? But cheeses have their own unique microbial signature, I guess. I mentioned wine, you have these amazing wine tasters who can taste wine and tell you exactly what vineyard it's from. Can you do that with cheese? Can you sequence the microbiome of cheese and tell you exactly what region of the world it's from or what production facility it's from?

Paul Cotter:

Yes, there is this concept of a terroir equivalent for cheeses as well. It relates to provenance and the naming of the cheese. It's used a lot in particular in relation to certain French and Italian cheeses. PDO cheese they're referred to, where they can only mark the cheese as being of a particular name based on where it originates from. In that regard, the microbiome of that cheese is distinctive. Strangely enough, I guess, the more research we do and the better we get a sense as to what those microbes are, then the better I think in theory, somebody could create a counterfeit cheese, because you always know which microbes you need to put back together to create the cheese.

But there are undoubtedly some distinctive features. You have the classical scenario whereby certain blue cheeses are fermented by being put into a cave and so it's the cave microbes and cave molds that contribute to the fermentation process. We're involved in a very intriguing project that's lead by Avelino Ordonez in Leon, who you may recall from his time in Teagasc. What we're doing there, what Avelino is doing, and we're helping him with is to study the microbiome of some of those type of cheeses, looking at the cheese microbiota, but also the cave microbiota and where the overlap exists.

Ruairi Robertson:

No way, that's amazing. So we're eating cave microbes in some of our cheeses?

Paul Cotter:

Yeah.

Ruairi Robertson:

That's great. So you kind of moved on to look at other fermented foods, which are becoming more popular, or have a kind of resurgence these days. It's not only cheese. You began looking at things like kefir and I don't know if you looked at sauerkraut and some of these other ones. But kefir I think is a very interesting one, because kefir grains are very hard to acquire. Traditionally, you just get them off your neighbor and kefir get passed around. Now, you can buy kefir drinks, but they're really just a small combination of well known strains, usually. But you've gone through a process of trying to characterize kefir grains from different regions. Maybe tell us a little bit about that and what you've found.

Paul Cotter:

We've done this on different scales over the years. Initially we had a PhD student Allison Dobson that took one kefir grain and looked at the microbiome of the grain and of the milk. We thought that was fantastic and we were very proud of ourselves. Then a couple of years later another student, Alan Marsh, took that to another level and looked at 25 different grains that he sourced from around the world from different enthusiasts. We thought that was fantastic and couldn't improve on it. But actually what we're doing now is part of another project, is just to take this to a whole other level. We've established a Facebook group and have contacted an even wider group of individuals from right around the globe to look at both the milk kefir and the water kefir microbiomes. So those studies are ongoing.

But it's amazing the number of different enthusiasts that are out there and the different history of those grains and how they were as you say, shared among families and friends. But nowadays, with newer alternatives like Amazon and Ebay and so on, the world is the oyster of the kefir grain and they're circulating around and what's intriguing is, a lot of those grains that we've received look so much different from one another. You have the generic classical conventional scenario where you see lots of lactobacilli in the grain and lactococcus blooming in the beverage. But there's lots of other tweaks where you see the acetobacter and the leuconostoc and different molds and different Saccharomyces and things like that, that can also take a foothold and that can result in quite a different flavor as a consequence of what you do. And then, if you combine that with different milks and different storage temperatures and all sorts of other variables, you can really come up with a vast variety of quite different products.

Ruairi Robertson:

So kefir really isn't kind of one thing. When people talk about, "Oh, I'm drinking kefir or eating kefir," it could be drastically different than what someone else is drinking. It's just kind of a combination of various microbes which could differ depending on where you've got it from, I guess.

Paul Cotter:

Yeah. Just on that point before we move one, and this is where I put on a different hat and have a bit of a rant in that. There are some products that are out there that are marketed as kefir, but to my mind are the equivalent of a dilute yogurt. It's tough for the non-microbiologist reading the side of a label and seeing that their so called kefir has lactobacillus bulgaricus and strep thermophilus in it. As you well know and lots of the listeners will know, those are yogurt microbes. You're drinking dilute yogurt. Some other will try a little bit more and add in a token one or two other kefir microbes, but that might only be added in at the end of the fermentation, so it's not real.

I guess, there's a need to ensure quality if something is made from a kefir grain, then fantastic. Or sometimes large scale production, where the grain is challenging, but in that case, what we are trying to do and others, is to pick out what are the key components of the core microbiome of the grain or of the beverage and try to recreate those in way that you are replicating the key attributes of the foods and the health benefits and the flavor, while not sacrificing in terms of quality.

Ruairi Robertson:

Yeah. I think what's probably happening, what you kind of touched on, is much like what we see in the microbiome of humans. Where we're losing a lot of that diversity. We're all becoming more similar to each other, I guess, as we westernize. That's probably what's happening to kefir grains, I guess, as they're pasturing. We're losing that individuality of kefir and they're all becoming more similar and less diverse, I guess.

Paul Cotter:

Yep. Yeah, it's true of every fermented food. I guess when cheese production really began scaling up, about 100 years ago, in New Zealand initially, and starter cultures began to be used instead of relying on the natural microbes that were present in the milk or the environment, there was the addition of one or two specific strains, which is great in terms of mass production and quality control and so on, but you are losing some attributes, and you're also exposing yourself to other challenges like phage, which if they wipe out one, that one particular starter strain, then your whole cheese manufacturing process is impacted. So every time a fermented food is taken and people try to mass produce it there are problems, but I think the greater appreciation of the importance of the microbes and the diversity of the microbes in there means that there's more of an effort now to have a slightly more complicated cocktail of microbes in your fermented food.

Ruairi Robertson:

So, one kind of genera that seems to be common to a lot of these fermented foods are lactobacilli. I mean, I know there's lots of different species in all these different foods, but especially in these kind of milk fermented foods, there's lactobacilli. What is it evolutionarily about lactobacilli that make them suitable for fermented foods? It's the production probably of lactic acid, because that prevents other end species growing into it to spoil it. Is there certain flavors that differ between different lactobacilli or why is that retained itself in all these fermented foods throughout time?

Paul Cotter:

Yeah, and for the molecular taxonomist, that's become even more challenging recently in that lactobacilli are now being reassigned to a whole range of different genera again. So we're all having to relearn our classical microbiology and get used to using these new names. But coming back to your point, what's been intriguing, I know Olivia McAuliffe our colleague at Teagasc has looked at this, and others, is how lactobacilli have evolved, especially those that are used in dairy. So a lot of the lactobacilli are found in the environment and in particular plant based materials. So you find certain types of lactobacilli such as plantarum and others that are dominant in kimchi and sauerkraut and the more plant based fermentations.

But those which you find in dairies, are obviously very closely related to those, but they've gone to a kind of a reductionist evolution in that they've lost some of the genes that are associated with those other sugar source or carbohydrate sources and have focused more specifically on milk and have acquired plasmids for lactose utilization and so on. There's kind of a convergence of activities or evolution amongst certain lactobacilli, those that you find in dairy. In that regard, they have become more specialized. If you use cheese as an analogy, you find a scenario whereby certain microbes and certain general lactococcus and streptococcus dominate early, so they produce the acids that is the protection piece of the jigsaw. But then because of the byproducts they produce and the dropping down of the pH, that's where the lactobacilli then kick in. They're more tolerant of the low pH and they add an extra of complexity by producing a lot of the flavors and they can do lots of different things with proteins and breaking down into peptides and eventually amino acids. It's the combination of those, that can give a very nice or a very awful flavor depending on which particular lactobacilli you have.

Ruairi Robertson:

Great. So, how much, because that was one of the big questions in the field of fermented foods is whether these microbes, these lactobacilli, these lactococcus, all these different species, these yeasts, whether they colonize the gut or what they're doing in the gut. This is kind of the third step in the process that you're looking at. You've looked at production. You've looked at flavors and everything that's happening in the food and now what's happening in humans when we eat them as well. Firstly, what do we know about the strains or the types of microbes that are in the foods and whether they stick in the gut or whether they pass through. Have you looked into that much?

Paul Cotter:

Yeah, that's kind of a very big interest of ours, in particular now. We're doing a lot of surveying of fermented foods at the moment. We've an ongoing survey of as many different African fermented foods as we can study and a corresponding one based in South America. But, our first dipping of our toe into that was a study that's just been published by John Leech, a PhD student with us, where John took, I think it was 58 different fermented foods from around the world, or different types of fermented foods that were, some were plant based, others we would characterize as dairy, and a third group that were ... It wasn't even so much plant, it was more sugar based fermented foods like kombucha and water kefir, and brine based fermented foods like sauerkraut and kimchi and so on. He studied those and did an in depth microbiome characterization of them.

So we had that data and we were analyzing it. In parallel, we were talking to Danilo Ercolini's group. Danilo is based in Naples and he is part of this large U consortium that we lead known as Master. At one of those meetings, we got to talking about what he was up to and what we were up to. At Danilo's institute, Edoardo Pasolli, who'd previously worked with Nicholas Segata, had moved there and he was doing a survey of the lactic acid bacteria that you find in the guts of humans using existing data bases, and was wondering to what extent those overlapped with the lactic acid bacteria that you find in fermented foods. Which was great, but the challenge was that ironically, there's a lot of information about gut microbiomes. But not so much about food microbiomes, even though those microbes are easier to culture and so on.

We had all of this new data that John had generated, so we shared it with Danilo and Edoardo and got involved in an investigation to see how much of an overlap there is. It was quite intriguing in that there is quite a degree of overlap, for particular species at least, between the foods, the species that you find in fermented foods and in the guts. Other scenarios, there were other scenarios where you'd find quite different lineages of species in one versus the other. But so, that's still be teased apart, because undoubtedly, I think a lot of the microbes that you find in fecal samples from humans that can be traced to that origin. The question then becomes, if feces is an indicator of what's present in the gut, but where are those microbes establishing? Are they more so in the small intestine and to an even greater extent? So that would be intriguing to look at in the future as well.

That's one route we've taken. We've also been involved in some other studies, some with John Cryan in fact, more recently, who together we Ted Dinan, who I know has done one of these podcasts previously, is interested in gut brain. We started to look at the impact of fermented foods on anxiety and depression symptoms and so on and so forth, initially in animal models. What we see there is that we can give the animals a milk kefir and it has an impact to a different extent depending on the milk kefir on some of those behaviors. When we look at their microbiome though, it's not always the fermented foods microbes that are changing.

What seems to happen is that either those microbes or the metabolites they have produced are doing something to either the host or to the other microbes in the gut. And its other microbes that are starting to flourish then. It's kind of an indirect effect. I think there's a lot of teasing out to be done. It probably differs from one fermented food to another, or even a particular version of one fermented food to another. We're really only just starting to dip our toes into the water and get to see what's going on. But I think it's something that the whole field is going to enjoy trying to tease apart in the years to come.

Ruairi Robertson:

That's interesting, because what we know about probiotics, I suppose, in recent years, or single strains, is that they don't tend to change the microbiome composition. They don't tend to stick around really. They only stick around as long as you're taking them, unless there's some evidence in maybe in infants that they might stick around for a bit longer. But, the fermented foods might be a bit more beneficial in that because they're more complex, some of the strains might actually stick around from what you're saying and they might have some more global changes to the microbiomes. So is that to do with the microbes that are within those fermented foods, or could it be to do with some of the other things that are in there? Some of the metabolites they're producing. Could it be to do with, you mentioned phage before? These are bacteria phage, if these viruses affect the bacteria. Or do we know that yet, why they're having those changes on the gut microbiome?

Paul Cotter:

I think it's probably a combination of all of those things. When we did the best publication relating to the vast variety of different types of fermented foods all in one, one of the things that we looked for are, I can't remember the exact acronym we used in the end, but it was something like PHAGCs, putative health-associated gene clusters, which is a bit of a mouthful. But the logic there is that we looked for some of the genes that you would typically find in a beneficial gut microbe, in terms of does it produce a bacteriocin, does it have genes associated with colonization, does it have bile resistance genes? Does it produce GABA, which is a neurotransmitter, as you know, and things like that?

We found that quite a number of the fermented food microbiomes, had microbes with all of those activities. That's not just by coincidence. So you could argue that maybe every food microbiome has those, but we also have lots of information from other fermented food. Sorry, other food microbiomes like milk powders and so on. Those traits were very much reduced in those sort of populations. I think the specific microbes can have a direct impact. You also have a scenario whereby there's a prebiotic effect I imagine in that the exopolysaccharides like, kefiran that's produced when lactobacillus kefiri grow in milk kefir and I think that probably contributes and there's other analogous products present in other fermented foods as well.

Then you have the metabolites that are, if you want to use the more buzz words, the post biotics which are produced within the fermented foods that are having the effect either on the microbes in the gut or on the host, and then you're doing something to the host and the immune system and that's changing and that's impacting on the gut microbiome. There's lots of cross talk and lots of teasing apart to be done to figure it all out. It will probably require using quite simple models and building on those with increasing layers of complexity over time to properly stitch to the part of it, so that will be nice.

Another approach that we've engaged in from the kefir perspective, is to make quite simple communities containing maybe four or five bacteria and two or three yeast. We've done this with Ben Willing in University of Edmonton in Canada. What we did with our simple microbial community is see if we could recreate the effective consequences of consuming a kefir in mice who are fed a high fat diet and became obese. See if that more simple community could recreate that beneficial effect and low and behold it has done. Lots of different angles and tangents and things that will help us tease out that part.

Ruairi Robertson:

I think it shows the complexity of it all in trying to tease out the complexity of a fermented food microbiome, which has all these different species in it and all these metabolites, and how that interacts with an even more complex microbiome inside the gut it's a lifetime of work at least. But I think what's interesting in what you're saying is that maybe there might not necessarily have to be live microbes in those foods to have an effect. This is what's kind of discussed in the probiotic field as well, is that sometimes it's what the microbes produce or these exopolysaccharides for example that you talked about on the outside of the microbe, that's having the effect. That is interesting I suppose for fermented foods because of the need for pasteurization sometimes and things like that. What do you know about that? Do microbes necessarily have to be alive or is there any evidence from kind of some of these pasteurized fermented foods whether they would have effect.

Paul Cotter:

I think much like the probiotic area, it's a case by case scenario. I don't doubt that there're some instances where your consumer is going to get a benefit from consuming a fermented food that has been pasteurized or heat treated. But I think there's a better chance for health benefit if you're consuming the product with the live microbes in there. And that I suppose, if you're consuming the one with the heat inactivated strains, you're relying on that attribute being a particular metabolite or a component of the cell wall or something that's left there. Whereas if you consume a product that contains live microbes, all of those attributes will still be there. But if it's some other activity that's reliant on the microbe being live or producing something in situ the gut, then you also have the opportunity of benefiting from that as well.

As we come back to my initial answer, there's a case by case scenario and you need to look at the specific mechanism of action and microbe and metabolite and so on. For a general consumer, I'd say if you have the option between a pasteurized product and the equivalent product, which hasn't been pasteurized, I'd go with the non-pasteurized version.

Ruairi Robertson:

So what do you think this field will bring in the future, both in terms of research and then applying that to consumers as well? Will we be able to create our own personalized fermented foods with our own combination that's specific for us? That's kind of very popular in the microbiome field these days, about how do we get personalized treatments or how will we bring back that diversity for example in the foods. What do you see happening in the next five to 10 years in the field?

Paul Cotter:

I see lots of different tangents and lots of exciting things happening. So even away from the applied perspective, there's lots of people doing really cool fundamental work. People like Rachel Dutton and Ben Wolfe who are using fermented foods almost as a specific environment where you can test fundamental interactions between bacteria and mold and real systems biology type stuff and really exciting research. From an applied perspective, again, I can see multiple different routes being taken. I see the large multi nationals who make fermented foods becoming more aware for the need for natural foods. And move towards increased complexity within their foods and foods that more closely resemble the artisanal product. The artisanal equivalent, so that's definitely happening.

I would like to think, and it's something that we're really passionate about it in our group, is the whole kind of personalization side of things. So I don't want fermented foods to become medicalized. I want them to be available to consumers in general. But if you think about the step before you get to medicalized foods, whereby you have somebody who's pre-diabetic, they may benefit from consuming particular fermented foods. And if we could identify what those foods are and get the right strains, then you can make a version of kefir or kombucha or kimchi or whatever that's designed specifically for them and has the right microbes for their needs. But you might have somebody else who's susceptible to mild bouts of depression, so they may need a different version of that particular product.

We've had a lot of discussions with even say athlete, and professional athletes, but also people who are just interested in keeping fit and whatnot. So there might be a whole different series of products designed for them. And similarly for the elderly and infants and whatnot. I think all of that is possible. The research is playing catch up and still has a way to go to facilitate that, but I don't see why we can't move in that area in the years to come.

Ruairi Robertson:

So, thanks for listening to The Biomes Podcast, sponsored by Microbiome Insights. My name is Dr. Ruairi Robertson. Tune in next time for some more exciting insights into the latest developments in the human microbiome.