Salmon and fieldmice to shed light on the enigmatic hologenome

If we can discover how an animal’s DNA collaborates with the bacteria in its gut, it will open up a wealth of opportunities, for example for developing new drugs for human use and for more effective breeding of animals, such as chickens and salmon, to make the best possible use of fodder.

The collaboration between the animal’s own DNA and the DNA of the bacteria it has in its digestive system is known as the hologenome. And the study of the hologenome – in human beings, too – is one of the fields of biological research which is now gaining serious momentum.

It is also the reason for a range of grants, totalling around DKK 90 million, which a team of researchers, headed by Professor Tom Gilbert from the Natural History Museum of Denmark (SNM) under the University of Copenhagen, has recently received for studies on the hologenome.

The majority of the DKK 90 million entrusted to Professor Gilbert comes from the EU, which has contributed approximately DKK 75 million. The remainder of the funding is from the Lundbeck Foundation, the Danish Council for Independent Research and Norway’s salmon industry.

Tom Gilbert says that, in the coming years, the money will be used to fund a number of carefully selected hologenome projects, all of which are concerned with investigating aspects of a very specific issue:

“Namely, whether within one species – for example, salmon or chickens, but the same applies to people – we actually need to take into account the significance of variations in DNA from individual to individual when we attempt to influence gut flora to achieve something specific.”

Salmon and unaccustomed bacteria
Tom Gilbert emphasises that this is a fundamental issue for which he gives two examples:

“The first concerns farmed salmon – for example, the salmon farmed in vast enclosures in many locations along the coast of Norway. Each enclosure can accommodate around 200,000 salmon. They’re all given the same food but there are enormous variations in weight gain. Some fish grow to a huge size, up to 10 kilos, while others struggle to reach a couple of kilos.”

From the perspective of the salmon industry, and in the greater context of organics, this is not an ideal situation. It would be best if we could achieve a more standard weight based on optimal food efficiency.

“In this context, it’s been considered whether absorption of nutrients and weight gain in the fish could be increased by influencing their gut flora – for example, by adding the ideal mix of microorganisms to their food. In principle, it’s the same idea as the one behind so-called probiotics for human beings, the aim being to promote health, for instance, by adding lactic acid bacteria to a range of foods. And efforts are currently being made to develop solutions to combat the growing problem of obesity by giving those who are greatly overweight gut bacteria from people of normal weight,” says Tom Gilbert.

“But the problem with this type of manipulation is that science can’t say with any certainty whether the desired result is really within reach if we could ‘only’ identify the ideal cocktail of microorganisms to populate and positively manipulate the intestinal system.”

And bearing this uncertainty in mind, Tom Gilbert explains that we are actually back to the need to examine the hologenome, and he illustrates his point by serving his second example:

“It’s all about people being exposed to new and unaccustomed bacteria, for example from food and drinking water. For instance, it’s a well-known fact that westerners often have serious stomach problems when they travel to India and other countries in the East. But why do two people who’ve eaten exactly the same things and been to exactly the same places often react completely differently? Why does one bounce back to health after a few days when it takes the other weeks to recover?”

Tom Gilbert, whose speciality is studying DNA to elucidate evolutionary processes, believes this is explained by the fact that the differences in the response patterns of the two travellers are largely due to specific factors in their respective DNA which, in turn, cause their guts to handle the same unaccustomed bacteria in very different ways:

“And I also believe that the issue of significant differences in weight gain in farmed salmon of the same species – fish in the same enclosure which are given the same food – can, presumably, largely be understood in the light of genetic variations.”

“So, all in all, it makes good sense to focus on the hologenome in a variety of contexts to gain specific, new knowledge. And that’s what we’re working on now.”

Slaughter time
Chickens and farmed salmon. These are the two foods which Tom Gilbert – together with three colleagues from the University of Copenhagen: Morten Limborg and Antton Alberdi (both assistant professors at SNM) and Professor Karsten Kristiansen (Department of Biology) – will initially subject to hologenome analyses.

The hope is that the new knowledge provided by the studies will make the production of both chickens and salmon less resource-intensive and less harmful to the environment, in turn reducing the need to use antibiotics in the process because the animals themselves will be better at combating infection due to their fine-tuned gut flora.

As far as the salmon are concerned, Tom Gilbert and a few of his colleagues have already been in the field – or on the sea, to be more precise. They visited the Norwegian west coast, out from Bergen, where 450 farmed salmon of all sizes had to give up their lives for the good cause.

The researchers took a battery of samples from these fish, from everything from parasites to gut bacteria. They measured fat percentage, body length and weight, and they took a whole range of measurements related to the DNA of the individual fish.

“We’ll use this wide variety of measurements and analyses to identify how the hologenome works in the fish with the greatest weight gain, and we’ll also study the bacterial composition in the guts of both the salmon that grow quickly and the salmon that grow slowly,” says Tom Gilbert.

Mice in traps
Another hologenome trial which the researchers from the Natural History Museum of Denmark intend to conduct involves fieldmice.

This project will be run by Assistant Professor Antton Alberdi, who has begun setting traps in an area in the north of Spain, in the Basque country among other places. There are populations of four species of fieldmouse here which, for a number of reasons, are particularly suitable for the purpose.

In a very controlled laboratory environment, and in strict compliance with animal welfare principles, Antton Alberdi subjects the mice to a wide range of tests: everything from effects of temperature and changes in diet to fasting, the effects of antibiotics, and finally – before they are put down – a series of faeces transplants.

“For several reasons, fieldmice are ideal when you want to investigate a range of factors that give a more general indication of hologenome processes in mammals,” says Antton Alberdi.

“Firstly, their gut flora is stable because they’re exclusively vegetarian and stick to the foods they can find in the area where they live – and never leave. So, we’re familiar with their environment and we know it’s stable. This means that we can eliminate disruptive environmental impacts. Furthermore, the genetic variation seen in fieldmice is far greater than we see in human beings and many other mammals. Their evolutionary history dates back a very long time.”

Each mouse will be fully DNA sequenced, which has never before been done in a hologenome trial. This will enable Antton Alberdi and his Basque colleagues to measure how each mouse responds genetically to the challenges to which it is exposed.

“My aim is to create a hitherto unknown catalogue of genes that play a key role in the bacterial composition and functioning of the digestive system,” says Antton Alberdi.
Initially, it will be assumed that the results he obtains also apply to human beings because, as mammals, fieldmice and people are genetically closely linked in a number of basic respects.