Final Report Summary - FISHPROBIO (Metacommunity dynamics of the fish surface mircobiome in health and disease: pathogens and probiotics)
FishProBio is a Marie-Curie actions international outgoing fellowship (IOF) between the Marine Fisheries Genetics Laboratory, Bangor University, UK, and the Institute de Biologie Integrative et de Systemes, Universite de Laval, Quebec, Canada. The project explored the microbiomes (the commensal bacterial flora) of commercially exploitable teleost species in healthy and diseased states. Improved understanding of the role microbiota play in predicting, defining and possibly preventing disease, will be vital as aquaculture increasingly provides our principal source of seafood. This publishable summary details the progress towards fulfilling the project objectives, the work undertaken over the full 36 months of the project and the potential impact of the results.
The Project Aims as described in Part B, Annex I, covered in the first 12 months of the project, of the Grant Agreement are described as follows.
A) Identify community shifts in the surface mucous microbiome of an economically important teleost species in healthy and diseased states
B) Identify key changes in microbial community structure that precede disease or define resistance to disease
C) Understand the genetic mechanisms that underpin competitive exclusion between an invasive opportunistic pathogen and a proven resident probiotic bacterium
The first phase of the project involved the testing of a proven probiotic in vivo, as an effective preventative and curative measure to treat infection with the fresh water salmonid pathogen Flavobacterium psycrophilum. According to the predicted progress and milestones of the project. Completion of the probiotic in vivo portion of the experiment was expected for completion at the end of month 8. 454 amplicon sequencing was predicted to begin by month 10.
As planned the in vivo challenge was undertaken, slightly modified to involve three different probiotic candidates, as well as untreated controls. The experiment involved over 1500 individual fish. We selected only susceptible Salvelinus fontinalis for the study from as single pedigree. Improving on the described experimental design described in the original proposal, replicates were maintained in isolated aquaria to minimize cross-contamination. In total fifteen aquaria were employed, including five triple replicated treatments: stressed, unstressed, probiotic 1, probiotic 2 and probiotic 3.
Skin mucous samples and environmental samples were collected and stored as detailed in the work plan. However, we encountered major difficulties during the stress phase of our experiment. The aquaculture supplier who provided the Rupert pedigree susceptible S. fontinalis fingerlings, through lack of phenotypic control, supplied a resistant population. Thus, despite repeated temperature and anoxic stressing, we were not able to induce F. psycrophilum infection, identified either by PCR detection, or via observed symptoms and mortality. The experiment was therefore terminated at month six. Subsequently, new fish were ordered from a separate supplier, supposedly from a susceptible Rupert phenotype. We, therefore, restarted the experiment. However, once again, repeated stresses failed to induce infection.
Finally, we halted the in vivo experimental work at the end of month 11.
The Project Aims as described in Part B, Annex I, covered in the first 12 months of the project, of the Grant Agreement are described as follows.
A) Identify community shifts in the surface mucous microbiome of an economically important teleost species in healthy and diseased states
B) Identify key changes in microbial community structure that precede disease or define resistance to disease
C) Understand the genetic mechanisms that underpin competitive exclusion between an invasive opportunistic pathogen and a proven resident probiotic bacterium
The first phase of the project involved the testing of a proven probiotic in vivo, as an effective preventative and curative measure to treat infection with the fresh water salmonid pathogen Flavobacterium psycrophilum. According to the predicted progress and milestones of the project. Completion of the probiotic in vivo portion of the experiment was expected for completion at the end of month 8. 454 amplicon sequencing was predicted to begin by month 10.
As planned the in vivo challenge was undertaken, slightly modified to involve three different probiotic candidates, as well as untreated controls. The experiment involved over 1500 individual fish. We selected only susceptible Salvelinus fontinalis for the study from as single pedigree. Improving on the described experimental design described in the original proposal, replicates were maintained in isolated aquaria to minimize cross-contamination. In total fifteen aquaria were employed, including five triple replicated treatments: stressed, unstressed, probiotic 1, probiotic 2 and probiotic 3.
Skin mucous samples and environmental samples were collected and stored as detailed in the work plan. However, we encountered major difficulties during the stress phase of our experiment. The aquaculture supplier who provided the Rupert pedigree susceptible S. fontinalis fingerlings, through lack of phenotypic control, supplied a resistant population. Thus, despite repeated temperature and anoxic stressing, we were not able to induce F. psycrophilum infection, identified either by PCR detection, or via observed symptoms and mortality. The experiment was therefore terminated at month six. Subsequently, new fish were ordered from a separate supplier, supposedly from a susceptible Rupert phenotype. We, therefore, restarted the experiment. However, once again, repeated stresses failed to induce infection.
Finally, we halted the in vivo experimental work at the end of month 11.
