Behind the paper - Salmon gut microbiota correlates with disease infection status

    27.04.21 06:22 AM By HoloFood-KU

    Guest blog post by MSc graduate Davide Bozzi 

    This week Bozzi and colleagues successfully published their study in the journal Animal Microbiome on finding new ways of monitoring salmon health and disease by way of the gut microbiome. 

    You can access the full paper here DOI:

    In this guest blogpost from lead author and MSc student at the time, Davide Bozzi, we hear more about how this study came about, its highlights and why it is important for the future of sustainable aquaculture. 

    Davide Bozzi sampling
    This is me sampling salmon from the experimental trials in Norway!

    Who am I? 

    My name is Davide, I am from Italy,  and in 2019-2020 was an MSc student visiting the Center for Evolutionary HoloGeonomics and Associate Professor Morten Limborg's group. At the time of my visit Morten offered me a unique chance to learn more about salmon hologenomics and as this was pre-COVID even get a chance to visit one of the experimental trials in Norway. This led to the design, execution and eventual publication of my first ever scientific study. In this blog I will try and give you a better overview of what this project was about and what our main outcomes were! 

    Salmon gut described
    This figure is from the published paper where you can see where salmon gut was sampled and where the gut content we took is located

    What is the study's pitch? 

    Fish microbiome health has become a recent focus for those involved in sustainable aquaculture. Of the many bacterial communities associated with fish, the gut microbiome is known to play an essential role in health and growth, and an imbalanced composition of the natural flora (also known gut dysbiosis) is often associated with a disease. However, in cases of fish disease when only the skin appears affected, rarely if ever does the gut microbiome come into question. This has left a knowledge gap about the possible effects of a skin infection on the gut microbial community. Moreover, treatment of skin disease usually involves bath treatments with a chemical called formalin, but how the gut microbiome is affected by such treatments remained unknown till now.

    During our sampling we were working together with our great colleagues from the Norwegian Institute for Marine Research (IMR).

    How did this study come about?

    Talking closely with Lerøy (our industry partner) during the design of the experimental trials of HoloFood was key for this to materialize. Disease outbreaks are not uncommon in the field of aquaculture and although initially unplanned, during one of our sampling trials, salmon started to show symptoms of a skin infection. We were made aware by our expert colleagues on site that oftentimes during disease outbreaks affecting the fish skin, a formalin treatment was applied.

    Even though the outbreak compromised our chances of carrying out the originally intended study, we immediately saw value in collecting and analyzing these samples. We quickly collected gut samples from seemingly healthy and sick fish and repeated the process after the formalin treatment had occurred. In this way, we wanted to check if the disease, or even the treatment itself, was having any effect on the gut microbiome. We were also curious to investigate if perhaps fish which were healthy had some sort of beneficial gut bacteria that protected them from the infection. This was a truly exploratory study and one where we had our hypothesis but we were not entirely confident that the results would be interesting or relevant for us researchers or for our industry partners.

    Although the sampling days were very busy, in the evenings we had the great chance to enjoy the beautiful surroundings of Norway. Pictured here you can see me learning how to fish after our sampling work was done, and my supervisor Morten guiding me through this as well. Fieldwork was a great start as I knew the next steps were to get back to the labs in Copenhagen!

    What were the next steps?

    The on-site vet helped us to identify the pathogen responsible for these nasty ulcers on the fish: Tenacibaculum dicentrarchi, an emergent pathogen in aquaculture. We then came back to our labs at Copenhagen to do the necessary molecular and bioinformatic work to describe the gut microbiome of these salmon. We did this by using DNA metabarcoding of the salmon gut microbiome, also known as 16s rRNA amplicon sequencing or microbial metabarcoding, a method that allows for the DNA sequencing of a targeted region of a universally conserved small region of DNA known as a gene present in all microbes. This tiny region holds all the information necessary to describe the microbial composition of the fish gut microbiome, allowing us to record the presence or absence of every given bacterium in all our samples and estimate their relative abundance (i.e the percentage of one bacteria relative to the total number of bacteria found in the fish gut). 

    What were the key results? 

    The results were somewhat surprising! First off we observed that the seemingly healthy fish had a different collection of microbes in their gut compared to the diseased fish, even though the pathogen seemed to physically attack only the skin tissue and not their gut. Our results showed that the disease also leads to a total imbalance of the salmon gut microbiome. What was even more surprising was the fact that the sterilization process with formalin, although it helped the fish recovering from the disease, did not avoid the expansion of other opportunistic and potentially pathogenic strains in the gut of the diseased fish and may have contributed to compromising the gut microbiome of the healthy individuals. For example, Mycoplasma, a bacteria that appears to dominate the microbiome of healthy salmon, appears to decrease when the salmon experience infection as well when the salmon are treated with formalin. Interestingly, we found that the abundance of Mycoplasma seems to have a relation to the size and overall health of the fish. This leads us to hypothesize that high levels of this particular bacteria might constitute a biomarker of fish health, leading us to propose its utilization in a new fish health monitoring strategy. 

    Our outfits with necessary motivation!

    What was the most exciting aspect of this study?

    It was great to highlight how the communication between us as academic researchers and our partners from aquaculture (Lerøy and IMR) led to this study being so successful. The unexpected disease outbreak may have forced us to abandon the original study aim but gave us the opportunity to gain precious insights into some yet unappreciated aspects of fish disease and treatment. The strong microbial signal observed in the gut, differentiating healthy from sick fish, and the observed effect of formalin treatment, highlight the importance of considering the disease and its treatment from all angles - a holistic perspective. Our results suggest possible ways to improve treatments and identify a possible new biomarker to monitor salmon health. 

    This explorative study has also highlighted the existence of the Mycoplasma bacteria specifically adapted to the fish gut, pointing to a possible co-evolution of the microorganism with salmon. Our study set the ground for further investigation interested in unveiling the molecular aspect of this symbiosis. 

    From a researcher's point of view, I would be thrilled to discover more about the intimate relationship developed by these two organisms during the course of evolution. For me, being there from the very start of the project, during the sampling, going through the whole process of generating and analyzing the data and then working with a diverse team involving people both from academia and industry was a most unique experience that helped me to grow professionally. 

    It is truly remarkable how much can be accomplished when different expertise, driven by the same passion, comes together! 

    Our after work hobby with my supervisor Morten Limborg and my first ever catch!

    This study is the first of many to come from HoloFood project, seeking to understand the hologenomic framework for sustainable aquaculture practices. 

    You can access the full paper here DOI:

    Stay tuned for more outcomes!