Microbes might be tiny, but their impact on aquaculture is large. This episode sheds light on how these invisible helpers could improve fish farming, protect wild salmon populations, and feed a growing world. In our debut episode, Professor Tom Gilbert and editor Christina Lehmkuhl Noer sit down with Associate Professor Morten Limborg, a biologist, fish expert, and researcher at the Center for Evolutionary Hologenomics, to discuss how microbes are transforming aquaculture. Together, they dive into the surprising ways salmon and their gut microbiomes could revolutionise sustainable food production.
Your hosts are Professor Tom Gilbert and PhD Christina Lehmkuhl Noer. Sound and recording by Christian Grimes Schmidt from Centre for Online and Blended Learning and editing by Christina Lehmkuhl Noer and Ella Zoe Lattenkamp.
The Center for Evolutionary Hologenomics and this podcast are generously funded by the Danish National Research Foundation.
00:00:00 Morten Tønsberg Limborg
These microbes are actually very important for the host in providing a lot of functions that help increase their health and so on.
00:00:10 Christina Lehmkuhl Noer
Welcome to the very first episode of Microbial Connections, a podcast where we, together with experts, explore the hidden but essential connections that we and all other living beings share with microbes. My name is Christina Noer.
00:00:24 Tom Gilbert
And hi, I'm Tom Gilbert, director of the Center for Evolutionary Holo Genomics here in Copenhagen.
00:00:30 Tom Gilbert
And today, I'm delighted that we are able to talk to our colleague and biologist and fish expert and fisherman himself, Morten Limborg, welcome Morten.
00:00:39 Tom Gilbert
Super happy to have you here to join us today and your furry salmon you've brought with you. Can see it's a much-loved toy.
00:00:46 Morten Tønsberg Limborg
Thank you, Tom and Christina likewise.
00:00:48 Tom Gilbert
So Morten you've done a lot of research. A lot of basic biology research, but in recent years you have turned towards studying.
00:00:57 Tom Gilbert
Culture and how maybe using some of your own insights about host organisms like your salmon and the microbes that live alongside your salmon might actually be useful for helping address some of the the challenges that that face the aquaculture industry. And in doing so, help the world meet its growing need for protein to feed people.
00:01:19 Tom Gilbert
But before we get on that and given you were so kind as to bring your furry salmon with you, what is it that you find so special about the salmon and its associated microbes?
00:01:30 Morten Tønsberg Limborg
So yes, you are absolutely right. I have here with me. This is actually a Sockeye salmon, which is one of the Pacific species that we all know from discovery that migrate out to the big ocean to forage, and then they come back to the very same small Creek where they spawn themselves and then they lay their eggs, after which they just die and contribute nutrients to the ecosystem.
00:01:52 Morten Tønsberg Limborg
It's really, really an iconic and fascinating species that we've all known of since we grow up watching animal stories so it's always attracted me to as a study Organism, but then also not just the biology of salmon itself. It turns out that.
00:02:10 Morten Tønsberg Limborg
They offer some really interesting assets about their associated microbes and how they're helping them and also both linking the the wild from the salmon that we eat, which I assume we will get.
00:02:21 Tom Gilbert
Back to well, well, we will. Yeah. Because I mean it is a super popular fish for fishing, as you say in the.
00:02:26 Tom Gilbert
But it is, you know, increasingly farmed in farms and in this part of the world.
00:02:30 Tom Gilbert
Sandinavia, there are very huge numbers done.
00:02:33 Tom Gilbert
And I guess, you know, the salmon industry is viewed in many different ways as we mentioned already, there are some who view it as the solution to some of or at least one of the solutions to some of the future challenges of feeding the world. But what is?
00:02:46 Tom Gilbert
That people would argue is wrong with farming salmon today. What? Why is it such a political topic?
00:02:52 Morten Tønsberg Limborg
Well, I guess there are two main things.
00:02:55 Morten Tønsberg Limborg
The first is that it's a very new industry compared to traditional agriculture that we know from our fields where we have crops. So we have species like cows or.
00:03:04 Morten Tønsberg Limborg
Peaks. So people are not used to it in the same way.
00:03:09 Morten Tønsberg Limborg
And then for the salmon farms, just like any other production, there is pollution.
00:03:14 Morten Tønsberg Limborg
They they poop in the water and they don't eat all the feet that they're given to that are given to.
00:03:20 Morten Tønsberg Limborg
So nutrients are released into the environment and as most salmon farms are in protected areas, so they're very close to the shore, which also means they're visible and people see them and so on and so on.
00:03:34 Morten Tønsberg Limborg
The other thing is that because there are so dense in their in their Nets.
00:03:40 Morten Tønsberg Limborg
When they get sick or get pathogenic bacteria or parasites infecting them from the from the sea, these these parasites, for instance, can can can grow in huge numbers because the salmon are so dense and sometimes they can transfer these to the to the wild salmon.
00:03:58 Morten Tønsberg Limborg
Which the wild populations, especially of Atlantic salmon along Norway, Iceland and northeast Atlantic, are very.
00:04:05 Morten Tønsberg Limborg
They're not doing very well.
00:04:07 Tom Gilbert
So we have this situation where we could be growing fish like salmon in tanks.
00:04:12 Tom Gilbert
There are clearly these challenges of the salmon just being unhealthy, for example, or releasing nutrients. And I guess as famously the cases of broken Nets and people worrying about the salmon spreading out into the world, but.
00:04:23 Tom Gilbert
But how then do the microbes come in?
00:04:25 Tom Gilbert
We we like our.
00:04:26 Tom Gilbert
We're interested in how the microbes in the guts of organisms and on the organisms shape them and affect them and.
00:04:33 Tom Gilbert
We know how they're relevant for humans, for diet and so on. But why do you think they might offer so much potential in the context of, for example, salmon farming?
00:04:42 Morten Tønsberg Limborg
So it actually started when.
00:04:44 Morten Tønsberg Limborg
Some years ago, when we started talking to our colleagues who are from the fish industry, Norway.
00:04:50 Morten Tønsberg Limborg
And they came to us and they're just they always have a lot of challenges and they would love to work with researchers who are interested in helping them solve the challenges. But actually, the original challenge we discussed with them was the.
00:05:01 Morten Tønsberg Limborg
Fact that when these salmon are three 3 1/2 years old.
00:05:05 Morten Tønsberg Limborg
They're harvested.
00:05:07 Morten Tønsberg Limborg
But when they looked at the size range, they had salmon.
00:05:10 Morten Tønsberg Limborg
Were like 1 kilogram and they had other.
00:05:13 Morten Tønsberg Limborg
There were 10 kilograms and then a lot in the middle and normally in biology we if we have to explain that level of variation in in what we call phenotypes or like in how the Semin.
00:05:25 Morten Tønsberg Limborg
We go to one of two.
00:05:28 Morten Tønsberg Limborg
Either it's the genes or it's environment, but in this very scenario both of these factors were more or less identical for all of these salmon.
00:05:38 Morten Tønsberg Limborg
They came from the same.
00:05:39 Morten Tønsberg Limborg
Stock means they're genetically very, very.
00:05:42 Morten Tønsberg Limborg
Basically, if we have a net with 200,000 salmon.
00:05:45 Morten Tønsberg Limborg
They shared only four different fathers.
00:05:47 Morten Tønsberg Limborg
So not enough genetic variation to explain this big variance in size.
00:05:53 Morten Tønsberg Limborg
And the environment they've been in the same tanks and Nets and got the same feed throughout their life.
00:05:58 Morten Tønsberg Limborg
So we talk to.
00:05:59 Morten Tønsberg Limborg
Maybe it's about time we look at the microbiome. So the second genome of the salmon.
00:06:04 Tom Gilbert
The microbiome is what exactly?
00:06:07 Morten Tønsberg Limborg
When we talk about the microbiome in association of a host Organism and in this case the salmon, we refer to all of the microorganisms, basically bacteria that are living inside the salmon in the gut, for instance. Or it could also live in the skin or.
00:06:22 Morten Tønsberg Limborg
Of the sample.
00:06:23 Morten Tønsberg Limborg
And we then know, as you alluded to before, from the literature on humans and other mammals, that these microbes are actually very important for the host in providing a lot of.
00:06:35 Morten Tønsberg Limborg
Functions that help increase their health and so on.
00:06:39 Tom Gilbert
So the microbes are.
00:06:41 Tom Gilbert
They're doing these important things and you think you can somehow control them or tell them what to do or what? What would be your dream to do with them?
00:06:48 Morten Tønsberg Limborg
Yeah. So in the beginning we thought we were gonna just repeat what had been done in humans and and mammals with these salmon and find some of the important ones and develop some products. It could be probiotics where you actually have a culture of a live.
00:07:01 Morten Tønsberg Limborg
That you put in the feed and then they get healthy like we do when we eat yogurt.
00:07:07 Morten Tønsberg Limborg
But then, to our surprise, in the beginning we actually struggled because you could hardly find any bacteria in the salmon and in the beginning we thought our methods were flawed or they didn't work.
00:07:17 Morten Tønsberg Limborg
We had to do it again and again. But then after repeating it many times, you realise OK, the microbiome in salmon is just very different.
00:07:26 Morten Tønsberg Limborg
Compared to us humans, there are a low biomass and not many cells.
00:07:31 Morten Tønsberg Limborg
And there's also not very many different species. We could only count up to 10 different bacteria in one salmon, for instance.
00:07:39 Tom Gilbert
But so fundamentally, given that the gut microbes are so attuned to the the behaviour and the phenotype of the animal, I'm actually curious like.
00:07:48 Tom Gilbert
If you were to look at the microbes in the wild salmon in the gut and what they were doing and the microbes in the farmed salmon and what they're doing, do you think the microbes would be the same? Or would there even be maybe a difference because the.
00:07:58 Tom Gilbert
Salmon are being sort of selected on for different behaviours.
00:08:01 Morten Tønsberg Limborg
So that's a very good question. And actually I would have thought that it would be different in the wild, both because, yeah, the farm salmon have also been through so-called genetic bottlenecks.
00:08:13 Morten Tønsberg Limborg
They don't have the same genetic variation as a wild, but they also.
00:08:16 Morten Tønsberg Limborg
So in the same environment all the time, so I would expect them to have maybe less diversity than the wild, but actually we just published a study last year where we actually looked in wild salmon that we were caught in the in the in the open sea.
00:08:31 Morten Tønsberg Limborg
And surprisingly, we actually found very, very similar microbiomes to the farmed fish.
00:08:37 Morten Tønsberg Limborg
And we also found the same bacteria that we found in the farm fish and the healthy fish were also dominant in the wild fish.
00:08:44 Morten Tønsberg Limborg
So it was a surprise. That actually was very similar.
00:08:48 Morten Tønsberg Limborg
But it's also interesting at the same time, because it kind of tells us that it's not really the environment that is so dominant in shaping the microbiome in the salmon.
00:08:56 Morten Tønsberg Limborg
And it really, really tells us that there has been a strong level of so-called Co Evolution where they have evolved together with the microbes. And even though we've taken them into captivity 20 generations ago, they still.
00:09:09 Morten Tønsberg Limborg
Same microbes and. And that just reinforces the fact that it's a very, very interesting place to look for, for biological solutions to improve the welfare of these fish.
00:09:20 Tom Gilbert
So we have the salmon that are facing many challenges in the farms, the challenges about their growth rate, about just their health in general, all these, you know, sea lice to tapeworms and so on and and you're interested in how the microbes in their guts can help.
00:09:35 Tom Gilbert
That which I guess at first seems pretty weird because their stomach microbes, right? So.
00:09:40 Tom Gilbert
Why is it you are convinced that the the gut microbes can play such an effect on this range of conditions, and in fact, what range of conditions do you think they could actually help fix?
00:09:51 Morten Tønsberg Limborg
One of the prime assets of assembly. So when we eat salmon as food, one of the main reasons why it's so healthy for us is because of very rich in these omega-3 and Omega 6 fatty acids that are extremely good for our health.
00:10:07 Morten Tønsberg Limborg
And we know from from experimental studies in mice that the microbes helps the mice absorb the fat from the feed. So they get a more efficient.
00:10:20 Morten Tønsberg Limborg
Uptake of the fatty acids and into the muscle of the my.
00:10:24 Morten Tønsberg Limborg
And now we also just talked about before how, but the microbes in fish are very, very different.
00:10:29 Morten Tønsberg Limborg
Not very many. So so is it also the case for fish as you ask?
00:10:33 Morten Tønsberg Limborg
And interestingly, there are some studies in zebra fish, so and they're more similar to salmon obviously where they have two groups of zebrafish and 1 is a normal group with its natural.
00:10:46 Morten Tønsberg Limborg
Living in together with the superficial another group got lot of antibiotics, so they're basically deprived of any microbes and then they get the same feed.
00:10:55 Morten Tønsberg Limborg
And then they can see that the normal profile, they have a much more efficient uptake of these fatty acids and they get a much healthier profile of the of the muscle tissue. And we know that that must be because the microbes are helping them. So that is one reason why we are so interested in understanding the same mechanisms, but in salmon.
00:11:14 Christina Lehmkuhl Noer
So. So does that mean that you can use this new knowledge on the collaboration between the host species and the microbes also in like in practically in all farm animals?
00:11:30 Morten Tønsberg Limborg
Basically yes, because what is the biggest difference between the work we do compared to?
00:11:35 Morten Tønsberg Limborg
There's a lot of other people out there looking at the microbiome in fish or in cowa and pigs.
00:11:41 Morten Tønsberg Limborg
What is different in our program is that we're very interested
00:11:45 Morten Tønsberg Limborg
In the direction or by so, so the biological functions by which the salmon, or any other host, as you say.
00:11:53 Morten Tønsberg Limborg
Is actively controlling the microbes that get to live inside it right?
00:11:59 Morten Tønsberg Limborg
So it's not long ago that the consensus in the field was that all the microbes inside an animal is just whatever's in the environment gets in there, right?
00:12:07 Morten Tønsberg Limborg
We now know that that's not the case.
00:12:09 Morten Tønsberg Limborg
So if we can understand how the salmon in this case has evolved over millions of years with its own gene to shape a home, so to speak, in, in its intestine, or it's in the skin.
00:12:23 Morten Tønsberg Limborg
That is a nice place to be for the bacteria that gives them good functions or keep them healthy. Then we can.
00:12:31 Morten Tønsberg Limborg
Make the treatments much more efficient and for instance, that means we can tailor the feed or the disease treatments to the specific genetic background of salmon in Norway and another treatment to salmon in Chile, for instance, whereas today.
00:12:45 Morten Tønsberg Limborg
It seems like these 1 solution fits all individuals of a given species in the whole world.
00:12:52 Christina Lehmkuhl Noer
OK. That sounds like it can have a huge.
00:12:55 Christina Lehmkuhl Noer
Do you think it can actually make a difference for the salmon industry and the other industries?
00:13:02 Morten Tønsberg Limborg
Yes, I also think we might still be some years away before we can actually go in and use these concrete mechanisms that I was saying we're looking for. But in the case of salmon, we've actually already found some very interesting results where.
00:13:21 Morten Tønsberg Limborg
There is this one specific new bacterium, so a species that was never described before. It belongs to a group that's called Mycoplasma, but it's this one bacterium.
00:13:30 Morten Tønsberg Limborg
And we have 5 different data sets. So these are data from completely different fish in different conditions and we had some that were skewed that didn't get sick in an uncontrolled outbreak.
00:13:44 Morten Tønsberg Limborg
We also had an experiment where we made one group sick and the others well, and then we had one where we had some that were large and some that were small and in every single case the fish that were performing the best.
00:13:55 Morten Tønsberg Limborg
Either they didn't get sick when there was a pathogen, or they grew faster.
00:13:59 Morten Tønsberg Limborg
They had a higher abundance of these new bacteria than we found.
00:14:03 Morten Tønsberg Limborg
So even though we don't understand actually what this bacterium is doing yet, we can use it as a marker.
00:14:10 Morten Tønsberg Limborg
So basically it means we can go and monitor so when they count the lice in the salmon every week anyway, it's easy that for us to now.
00:14:18 Morten Tønsberg Limborg
Develop an essay where we just monitor the abundance of this bacteria and in this way.
00:14:22 Morten Tønsberg Limborg
We can maybe help the industry to take disease outbreaks, maybe two or three weeks before they get visible symptoms. Otherwise and in this way they would be able to treat diseases much earlier and more efficiently.
00:14:35 Morten Tønsberg Limborg
Our research can contribute to solutions in the future as we can simply just make these farm fish healthier so they get less disease outbreaks and that would also help the wildfish a lot because that is one of the main problems is that many of these fish farms are.
00:14:51 Morten Tønsberg Limborg
In the in the so-called migration corridors, where the wild fish come back and the rivers spawn.
00:14:59 Christina Lehmkuhl Noer
So if you manage to actually help the agriculture industry get healthier salmon and stronger larger salmon, do you think that it can be a solution to the food crisis that we are facing?
00:15:16 Morten Tønsberg Limborg
It can be one solution.
00:15:18 Morten Tønsberg Limborg
It can definitely help so. But.
00:15:22 Morten Tønsberg Limborg
I think it's important to make this kind of research in aquaculture, which generally I think receives less focus compared to traditional farmed animals that we have on land.
00:15:34 Morten Tønsberg Limborg
Is that it is has been the fastest growing food industry for many years now, and the reason for that is 2/3 of our planet is ocean and we have only using a tiny fraction of the ocean today.
00:15:49 Morten Tønsberg Limborg
To to farm or to produce food for us humans. And we know we have to make more food in the future for a growing population and a growing demand.
00:15:56 Morten Tønsberg Limborg
So if we can develop these production machines to maybe also go offshore, there's a huge potential to.
00:16:03 Morten Tønsberg Limborg
To move our protein production from the land to the ocean because we know.
00:16:08 Morten Tønsberg Limborg
Oh, how terrestrial agriculture is struggling because I think projections proposed that in 20 years from now we can only farm crops in 80% of the area that we can today because of climate change and many, many areas are going to be.
00:16:23 Morten Tønsberg Limborg
Saline or flooded with seawater. Too often so we need to find new frontiers for our future food production.
00:16:30 Tom Gilbert
So marine is one. I mean Marine bi fish for example, but I guess there are other ones that are very hot right now.
00:16:35 Tom Gilbert
Just curious what do you think? Maybe are the most promising new frontiers for food production and are they also systems?
00:16:45 Tom Gilbert
Maybe this application of understanding the microbes might also help things.
00:16:50 Morten Tønsberg Limborg
No. Yeah, indeed, indeed.
00:16:52 Morten Tønsberg Limborg
So if we the reason we that's a big salmon industry today is because we have a lot of consumers that likes to eat salmon.
00:17:00 Morten Tønsberg Limborg
But if you just use biological reasoning, you could look to some some to a place like insects, for instance, right.
00:17:07 Morten Tønsberg Limborg
Insects. They grow for a very short period of time and they eat pretty much anything.
00:17:12 Morten Tønsberg Limborg
Because because with any other food production now, one of the biggest costs goes to the feet to feed feed the animals.
00:17:18 Morten Tønsberg Limborg
And with insects, we can basically feed them waste products from other production chains.
00:17:24 Morten Tønsberg Limborg
So like you can take a waste product from breweries or other food processing plants, and then instead of throwing it out.
00:17:32 Morten Tønsberg Limborg
We can actually use it to feed insects, and here indeed it would be relevant or it's necessary to do some microbiome research because it wouldn't be.
00:17:43 Morten Tønsberg Limborg
Kind of food or feed that the insects have adapted to in in the wild.
00:17:47 Morten Tønsberg Limborg
Right. So they would have to adapt to to a new kind of feed intake, but.
00:17:52 Morten Tønsberg Limborg
With the right composition of microbes in the insects or pre, it could also be like a pre digestion of these food wastes. Then it's highly likely that we'll see something like the insects taking over.
00:18:07 Morten Tønsberg Limborg
In our protein production. So it's basically starting to have this holistic view on on.
00:18:13 Morten Tønsberg Limborg
There are so many microorganisms that are invisible to our eyes, but that are so fundamentally important for the well-being and survival of all the large species that we're so focused on.
00:18:27 Tom Gilbert
Yeah. So I guess accounting for this very tight connection of the microbes and their host from birth and all things that shape it could be very important.
00:18:33 Christina Lehmkuhl Noer
So we need to protect not only the visible species, but also all the species we camp see with our naked eyes.
00:18:41 Morten Tønsberg Limborg
Indeed.
00:18:42 Christina Lehmkuhl Noer
Thank you so much for joining us, Morten, and sharing your insights on how to make the aquaculture industry more sustainable for the future.