Gut Health Gurus Blog

Professor Paul Cotter on The Science of Fermented Foods

Professor Paul Cotter on The Science of Fermented Foods

I had the pleasure of speaking with Professor Paul Cotter about fermented foods from a scientific perspective. He is one of the leading researchers in the field of Fermented foods. People can often be skeptical about fermented foods but today we will be diving into all of the science behind fermented foods! Read on to learn about the proven benefits of Milk Kefir, if exercise will help you have a more diverse gut microbiome, the fermentation process, and which fermented foods have been well studied!

How Did You Get Into Microbiology?

I am a microbiologist. I love what I do. I am a dad, I like to run, and I like sports. Outside of those things, Science is my hobby and passion. I became more of a manager as opposed to a scientist but I live through my students that study fermented foods and that is what keeps me passionate. 

Something that has become more apparent in recent years is that microbes contribute so much to what we do in everyday life. To our health, disease, food and our immune system. I started my microbiology focusing on the food pathogen Listeria. It can cause people to get sick and it’s a problem for pregnant women and people with weakened immune systems. I spent 4 years studying how it survives in foods and how to develop measures to stop it. That evolved into focusing on good bacteria that are in fermented foods and other sources as well. Natural sources of antibiotics that kill the bad guys but don’t do the damage to your natural microbiome. 

Then I looked at other microbe communities and how they interact with one another. I started the course in University that had me exposed to all different aspects of science:


-Plant Science


And once I had my first microbiology lecture I was won over! 

I can say hand on heart you are a kindred spirit. When I think back to my Food Science studies and having a broad range of topics involved in biology my number 1 passion was Microbiology. I started my University journey in Computer Science. I took up electives in Microbiology while I was studying Computer Science. Then eventually I jumped right to a different degree, Food Science, which is heavily into microbiology. -Kriben Govender

What Are Your Thoughts on the Issue of Covid-19?

In Ireland, people are willing to back each other up and help each other. It is a tough time and I think it is an important time for scientists to be accurate with their messaging. It is clear that through some outlets, rumors and false news are going around. We need to beware of this going into the public consciousness. And that scientists enter quickly and show what the real science is out there.

It's easy to jump to “the microbes are bad.” And with Covid, it’s the immune system that is really killing us! It is the overreaction of the immune system. Viruses are all around us and it's just unfortunate that there is one that is causing these issues primarily amongst the elderly and immunosuppressed. -Kriben Govender

The bad news will attract the headlines so you don’t always hear about the good behind the scenes. Many microbes are doing good things and they tend to receive less attention. That is reflective of what has happened in western society for quite some time. Fermented foods and other beneficial microbes weren’t appreciated so much and fell out of favor. They continue to be consumed in certain parts of the world but now in the last number of years, because of gut health, people are now aware and conscious that they need to be eating the right foods, exposed to good microbes to prevent allergies, and by doing that you can give your body a better chance to cope when it comes up against the bad guys. Which will happen at some point in everyone's life!

The common thread that you see through the research is that there is this hygiene hypothesis that formed in our approach in society. In the food industry, it's classic in terms of nuking the life out of the food product through a rigorous canning process. High temperature and killing everything to have sterile food. It’s the same thing with pasteurization where you try to kill bacteria. -Kriben Govender

From the food industry perspective, they have to worry about spoilage and shelf-life. If they “nuke it” there is minimal chance of it getting spoiled or you getting sick from it. It’s not always the best thing in terms of consuming food. It is important to preserve foods in a way that will keep it safe. Pasteurization is useful because raw milk can make many people sick depending on their immune state. We need to be conscious of how we preserve food but people have been preserving food and doing it very well for a millennium...this is through the art of fermentation.

It is no coincidence that many societies around the world have produced fermented foods. And this is not just because they like the flavor. It’s just because they had a product that they had in vast quantities during certain times of the year which had a short shelf life so they weren’t able to preserve them to consume them months later. So by chance, they came across a fermentation process (like cheese making!)

This meant that it had a much longer shelf life. So if milk wasn’t available they could consume the cheese much later. The same principle applies to:



The microbes that are in the food are producing lactic acid or some other form of metabolite that is lowering the pH or doing something else to it that makes it inhospitable for the bad guys or the spoilage microbes. By killing them, the food lasts much longer. And in recent years we have come to appreciate that not only does it preserve the food but it also:

-Introduces new flavors

-Gets rid of allergens

-Produces metabolites and other things so when you consume them they have a beneficial impact on your gut and your immune system.

Fermenting foods is something that we have been doing for thousands of years without fully appreciating all of the intricacies of what's underlying all of those processes.

milk kefir benefits

How Does The Fermentation Process Remove Allergens?

The best example is for people that are lactose intolerant. If you are consuming milk, there is lactose in there so you will have side effects. If you have the right microbes in a fermentation process, such as yoghurt or cheese, those microbes convert lactose to lactic acid then individuals can consume the product because the lactose is substantially diminished.

There are other allergens that are present in dairy products or in quite a few different plant-based products too. The raw materials can have materials in them that some people can’t digest. But having the microbes in there allows us to be able to consume those foods effectively.

I saw a study around sourdough and gluten. Going through a fermentation process like sourdough may break down a substantial amount of gluten making the bread easier for the body to digest.-Kriben Govender

What Is Going On In The Fermentation Process?

To pick a specific example, we can use Milk Kefir. Kefir is made from Kefir grains, These grains are communities of different microbes that are grouped and look like a small cauliflower. You use it for dairy fermentation. Within the kefir, you have the bacteria and yeast both clumped together and living happily together. For the process you: 

-Take your milk (cow or goat)

-Add the kefir grains to it.

Some of the microbes that are present will like the milk so they leave the kefir grain and they begin growing in the milk. They grow with each other, they encourage each other's growth, they have different synergistic activities between one another. The primary activity involves the growth of lactic acid bacteria. So things like lactococcus, take the lactose in the milk, the sugar source, and convert that to lactic acid. That is where you have your first advantage where the production of lactic acid drops the pH and makes the milk slightly acidic. This stops the growth of spoilage microbes and the disease-causing microbes. 

After that grows, the lower pH facilitates the growth of other microbes like lactobacillus and different types of it like plantarum or kefiranofaciens. Many lactobacillus products have been known to have health benefits. These microbes contribute to flavor but they also contribute to health. They also produce other metabolites like kefiran, which is a polysaccharide (a prebiotic and when you consume a prebiotic it is used as a nutrient source for the good microbes in your gut.) And you have yeast which helps with the gassy bubbly nature but less is known about how they contribute to health.

All of these exist and there is a wave of growth. Some microbes dominate after the next few hours and then some grow and take off. This is why some people like to consume their kefir after a relatively short fermentation process and some longer. As they go on longer the flavor becomes more intense. 

After this process, you remove the kefir grain and put it back into fresh milk to begin the process all over again and then you consume the milk to get the benefits.

That process reflects the kefir grain I have but it may vary from person to person. We have been sampling fermented foods from around the world to see how they differ and we know from this that some Kefir is good at helping cholesterol but they may be only 2 out of every 15 kefirs. You may not know unless you have a study done on it.

We are trying to identify which communities and which kefir grains are the best for certain scenarios and then make sure that they get to the people that need them the most. There might be another fermented food that is better for anxiety, or IBS, or other symptoms that you need to use! So by studying these foods in great depth and knowing the mechanics and microorganisms that contribute to health, you can make sure that you are harnessing those optimally going forward. 

What Are The Strains That Are The Best For Anxiety and Depression?

This is very new research. John Cryan, one of my colleagues, has been testing specific strains to see their benefits. We are trying to look at the more complex communities in fermented foods, you have more benefits when you have groups of microbes instead of one. We know that some of the lactobacilli and some of the other microbes are very good at:

-Tryptophan metabolism

-Producing a compound like serotonin

There are so many neuroreceptors in the gut that will have an impact on your brain health or your mental wellbeing through what you eat and the microbes in your gut as well. That's what John Cryan and Ted Dinan (you can learn more about Ted and his research HERE) have been educating people about for years. Now is the perfect time to apply it to fermented foods.

coconut kefir benefits

What Is Going On When You Put Milk Kefir Grains In Coconut Milk?


We have just put out a paper on how we studied 58 different fermented foods from around the world. 


We can analyze the microbiome through DNA approaches and we are crunching a lot of DNA sequencing data to create a single dot on a graph. We can put the different microbes of different fermented foods and see how similar they are:


-We found that all of the dairy-based fermented foods (certain cheeses, yogurt, milk kefir) are somewhat similar

-All of the sugar-based fermented foods (water kefir, kombucha) are similar to one another but not similar to the dairy foods

-The brine-based foods (sauerkraut and kimchi) were in another cluster. 


We had a few different hybrids as well that didn't fall into any cluster. The coconut Kefir fell into this. Some of the attributes from the sugar based foods, a little bit of the dairy, and it was a dot out there on its own.


As far as using Coconut milk for Kefir, you are putting the Kefir Grains into a different medium. And the microbes that like going in a dairy environment aren't coping and don't like that environment but other microbes in the kefir grain are saying “this is great!” so they grow in that environment. When you are consuming coconut kefir, you will get different microbes. They will still be lactobacillus and others that have some health-promoting benefits.


The analogy I use is a rainforest and a desert. If you are studying the diversity of a food or a gut environment you want to get a number to see how diverse that population is. If you think of the rainforest, you have a high diversity and if you think of the desert you have lower diversity. Then you want to compare the two. That analogy also helps to show how high diversity in the gut is good because typically low diversity scenarios have been associated with quite a bit of different diseases (obesity, allergies, and bowel diseases.) Things that can increase our microbial diversity such as fermented foods or prebiotics are regarded as being desirable. 


Diversity is so important because the microbiome field is relatively young. Interestingly, it is almost common sense that if there is more diversity in an ecosystem, it is more likely that the ecosystem is going to be more resilient. The way I think of it is that, if you are going through a period of crisis, if certain microbes are lacking in the gut because you are missing vegetables or your diet is off, then you are more likely to get these other characters stepping in and filling the void. But if you have a small team to play with then you only have a certain number of players that can step in to help. -Kriben Govender

C. Diff infection is the best example of that exact scenario. C. Diff is usually a hospital-acquired infection but it is found in many people's microbiomes and it is very resilient. Normally the microbes we have in our gut keep them in check. They produce different metabolites to limit their growth. But when we are exposed to antibiotics that are used to treat another infection they also do damage to our gut microbes and wipe them out. The removal of those microbes allows the C. Diff to grow. They produce toxins and they give you diarrhea. Low diversity in the gut affects many different instances. 

Using Fermented Foods as a Strategy to Introduce Some Diversity in the Gut?

 If you consume a lot of different types of fermented foods, you have more of a chance of getting the ones that you require in your systems. Sometimes it's not even the microbes in the food that establish but it’s as a consequence of them growing and producing something else. For Example:

Lactic acid which can be used by other microbes in the gut. This is creating next-generation health-promoting microbes that aren’t found in foods such as: 



And some of those like the nutrients and the end products of fermentation, it encourages them to grow as well. Prebiotics and plant-based fibres are good for your microbiota and fermented foods early in life are beneficial. For infants, after they are born, there is a problem in western societies where not every child is born vaginally, and then they are not given breast milk, so they are not exposed to that many different microbes. A lot of young kids aren’t exposed to many microbes anymore. This can contribute to allergies later in life because their immune system has a problem differentiating between the good and the bad guys because they haven’t been exposed to them early in life.

As we get older and we are eating different types of foods, especially fermented foods, this can help greatly. If you were to focus on just one fermented food then you are taking a risk that you might not have the specific microbes in that food for that scenario and therefore by consuming a bunch of different types you are giving yourself more of a chance for that diversity! And diversity is key.

Any Fermented Foods That Are More Studied Than Others?

Milk Kefir has been the model fermented food that our lab has been studying. There is a bit known about it.

Cheese is the most studied but it is more about the flavor and other attributes. There are helpful microbes in cheese

Kimchi, Sauerkraut, and Kombucha have been studied as well.

There is a huge revolution and science is playing catch up in a sense. The message that is getting out is that fermented foods are good for you, which is true but the specific health attributes from each fermented food is not always well understood. 

We have gotten 25 different Milk Kefir grains from different locations around the world so we can study them to see which are good for certain ailments such as:




Even if you will have some general attributes that will be across all kefirs but the specific health benefits will vary, this is because there are different microbes in there. When I go back to the probiotic field this is what I try to instill into people from the general public. They think if they take a probiotic that it is going to solve every problem under the sun. You have to look at them from a strain by strain basis. You have to do research and see which strains will help with your ailment (and working with a practitioner versed in probiotics helps).

At the moment, I would say to consume as many fermented foods as possible. But the research is coming out and we should have a way to have a tailor-made approach in which you have specific strains which you know will be helpful for you in terms of specific desirable effects!

milk kefir benefits

How do Isolated Grains or Powdered Cultures that the Big Food Manufacturers Are Using Differ from the Milk Kefir Grains?

I feel a lot of sympathy for the consumer on this. It is difficult to discern good kefir vs bad kefir. There are products that are marketed as kefir but if you look at the side of the container it will say that the microbes in there are lactobacillus bulgaricus (ones that are found in yogurt!) So you are drinking watered down yoghurt that may have some flavors and sugar added to so it’s no different than consuming any other commercial yoghurts.

Some companies will market as kefir but they will just throw in other probiotic strains. They won’t be kefir associated strains but they are trying to make something more kefir like. If the consumer looks at the side of the label there will be more strains so it looks more convincing.

The next level is that you can purchase strains that did come from kefir so you can make a product that you start with milk and you add in some lactobacilli and genuine kefir yeast. So it will have some of the different attributes that you associate with kefir. The strains haven't been studied in depth to know the health attributes but that is true for most kefir grains so this will be the best product to consume if you do not make your own. 

Other kefirs can be made on a large scale with true kefir grains; it is known as the Russian Method. They ferment milk with kefir grains, then they take some of that and inoculate another batch of milk which allows them to produce the milk kefir on a much larger scale. That is more like a genuine kefir product. The quality might be different because it is hard to mimic this exact process every day on a larger scale. (The Russian Method is not used in Australia due to alcohol regulations) 

Then you have the home-made artisanal Milk Kefir!

We like the home, artisanal approach, and the Russian approach. Where you use the kefir grains but that is quite difficult to reproduce. We did a study on a kefir grain and put it into fresh milk every day over weeks and studied how it changes in that milk and it does differ. You are changing the composition over time. This is fine but if you are making a product and need to have a particular strain and be sure of the shelf life those inconsistencies are problematic.


We are moving towards looking at the best kefir grains that are out there, studying the strains in greater depth by doing genome sequencing to know what it does. Then pick those which grow together and ones that have health benefits, have great flavor and then put those all back together. We have a situation like before where you pick certain strains and then ferment them. But now you're not just picking strains in a willy nilly fashion just so you have a lot of names on the side of a bottle. You will actually be putting the best microbes in and making a product that you know if you make it today it will be the same next week and next year and you don't have any spoilage. This is helpful if you want scalability.

 I have kefir grains at home and I would like as many people around the world to consume it. There is only so far I can go with the kefir grain. I cannot make tons of it. So in order to make sure as many people can benefit from it as possible then you need to take this alternative approach where you take these strains and then add them back in a more controlled fashion. 

There is no standard of identity with products like kefir and kombucha, the regulators are still catching up. In Australia, the alcohol content has to be under 0.5%. It is very difficult for commercial manufacturers to make true kefir because if you have yeast in the product then there is a high likelihood that there is a greater percentage of alcohol produced. Especially when you think of the product moving through the supply chain. It is going to be very difficult in Australia to get a 100% true kefir on the supermarket shelf even if you are using the Russian method. It is almost impossible. I feel for the consumer because it is misleading to them when these companies put kefir on the label. When we see a wonderful paper written by scientists on the benefits of real kefir made using kefir grains and then the consumer thinking they are going to get the same health benefits from these products. They are nothing more than diluted yoghurt with sugar. -Kriben Govender

We are in the process of determining what we think is a fermented food vs what isn't. I think something that is sold as a kombucha which is really just a tea then pasteurized with some flavors should not be defined as a fermented food. We tried to lay out different criteria to analyze what is acceptable and what is not. In a manner that we are hoping will influence different legislatures around the world to take a firmer stance on what is permitted and what isn't. Being able to label kefir, kombucha, water kefir the side of the label and have it be authentic.

milk kefir

What Are The Benefits of Milk Kefir? 

Milk Kefir is my savior from anxiety and depression. This product helped me a lot in improving my mood. -Kriben Govender

Milk Kefir has been found to help with:

-Cholesterol metabolism

-Blood pressure

-Antimicrobial activity 

-Tumor suppression

-Increase speed of wound healing (may help with IBS)

-Modulation of the immune system  

We collected the information from all of the labs that did the research. We looked to see what was out there already. Much like you have different qualities of kefir products you have different qualities of scientific journals as well. There are scientific studies out there that might suggest that a specific kefir strain is good at tumor suppression. But sometimes those studies are using cell lines, that is when you take a cancer cell and grow it in the lab, not in the human body and see what happens. 

A kefir strain might control that cell line but then if you just added water you would probably kill that cell line as well. In that case, you are just overreaching. BUT there are human studies so there is evidence on certain kefir strains and kefir products. With the hypertension side of things, there is a lot of evidence. There is a lot of evidence associated with cholesterol as well. Whether the particular kefir that you are making at home has those attributes is very difficult for the customer to know without an in-depth analysis. BUT if you are consuming some kefir there is a better chance of consuming a food that has those attributes rather than not consuming it at all. 

The anxiety side of things is currently anecdotal. But I am basing that on the metabolism and the microbes that are there. Based on our studies I think we will have some stronger evidence soon. It's not that there might not ever be evidence out there and these aren’t the only things that fermented foods could be good for. The science just hasn’t explored it yet. There haven't been enough human clinical interventions to the rigor that would be necessary to put my hand on my heart and say you are having this benefit. We want to take these studies into great depth so we can be sure about what we are saying.

Exercise and the Gut Microbiome?

We started the first study of its type with the Irish rugby team two world cups ago. We took fecal samples of this rugby team and studied them in-depth. We saw that they had a lot of diversity in their microbiota. That correlated with diet and exercise. High protein correlated with diversity. 

We have also taken studies from couch potatoes, people who don't exercise, then put them on an exercise routine and gave them whey protein to see if their microbiome diversity changed. It did slightly after 8 weeks but not too much, you need to have these lifestyle changes longer.  

We have done studies on the Irish athletes that went to Rio and on the cricket Ireland team over a year where they went to different locations. Some of the places where they were more exposed to pathogens. Some of them did have gut symptoms and gut disorders after a trip to India and it seemed like their gut microbiota changed. We worked with them to get together interventions to help them on other trips in the future. 

Within all of the studies, the big take home point is that extended exercise can improve your microbiota and that certain sports nutrients can have a beneficial impact on your microbiota and that improves your resilience when you are exposed to pathogens around the world. 

Whey Protein and Creatine Kinase?

We did a study and wanted to determine how much exercise the rugby team was doing and compare them to the general public. Normally when you are doing a study on fitness you ask questions of people in the public... you ask how many hours of gardening do you do a week, or how many stairs do you climb a day but we weren’t going to ask professional athletes this. We looked at creatine kinase (CK) instead. This is an enzyme that's in the muscle when you go through extreme exercise. You have these microtears in your muscle that give you pain that you suffer from that makes you sore. People think it's lactic acid but often it is microtears. The enzymes are released into the blood and you can measure it.

CK is normally used to measure a heart attack since your levels will be through the roof. We received the samples from our control group and our athletes and we sent them out. We got a phone call that asked where these samples came from because the CK levels were through the roof. It turned out that those are the athletes that were in the preseason training for the world cup. 

We use CK as our monitor for exercise. People that don't exercise would have low levels of CK. Some of the control group exercised recently so their levels were higher. We were able to correlate the microbe diversity with CK and that's where we saw our relationship between extreme exercise and differences in the diversity. It was the combined fitness and health that the athletes were doing over a period of time that helped them with diversity. 

 These athletes have been training years and years to get these results. You can’t get these overnight -Kriben Govender

The best thing we can do at this moment is to eat more fermented foods! We know that they have a great benefit, we know that exercise helps, and we know that home-made products are your best bet! Have a go at them and make sure to share your results in our Gut Health Gurus Facebook Group! And use code Cotter for 10% off at Nourishme Organics!

Join our newsletter today

Subscribe To Our Newsletter to Get 10% Off Your First Order!

2 thoughts on “Professor Paul Cotter on The Science of Fermented Foods

  1. avatar Eutiquio S. Salfivar says:

    At the moment many of us are using the water plus kefir grain and raw sugar! What do think we are doing, is it fine? We experienced nice long sleeping time and a favorable bowsel movement! Can you confirm of these effects are the true one? Thank you very much!

  2. avatar Margaret says:

    Very interesting to hear! I am fairly new to finding out about gut microbioms and have started drinking home made milk kefir to hopefully help with a health problem. I have been diagnosed with lymphocytic colitis and I’m on a very bland diet until I can see a dr in Oct to advise what diet I should be following But in the meantime I’m hoping by drinking kefir twice a day will be a great help

Leave a Reply

Your email address will not be published. Required fields are marked *