ARCH-Uk finfish and shellfish microbiome workshop report. Over 70 researchers from a wide variety of specialisms and sectors (human and mammalian health, microbial ecology, bioinformatics, metagenomics, shellfish and finfish aquaculture) came together on 22-23 Nov with industry to discuss understanding on microbiomes and their importance in the future development of aquaculture.
The meeting sought to draw on knowledge in microbiome research gained through studies on human and livestock health in particular, where studies of this nature have been ongoing for many years. In contrast microbiome research in aquaculture is in its relative infancy. The meeting was truly interdisciplinary in both the assembled researchers and outlook. A series of thought provoking presentations was followed by round table discussions to identify where research on microbiomes in aquaculture might be best paced. There was a strong representation of early career researchers who gave an important contribution to these discussions and to the resulting statements and recommendations, which included the following:
- A need to focus on causal relationships between microbiota and disease rather than correlations between the assemblages of microorganisms present and diseases.
- Microbiota in a case that precedes a disease will not necessarily be equally relevant (diagnostic) for another case in another area ( i.e. they are likely to be context specific).
- All symbionts should be considered when assessing a disease outbreak (virus, bacteria, eukaryotes, metazoan parasites) as these interrelationships are likely to be hugely important in the progression of a disease.
- Adoption of model systems to better understand the interrelationship between microbiota and health status is needed for aquaculture species.
- Data bases for species specific metagenomies and reference genomes are urgently needed.
- Taxonomy needs due consideration to help provide better functional information.
- Probiotics need more research to better establish how they work and their efficacy. Such studies should also consider including negative controls (which are lacking in current studies).
- Bioinformatics skills are currently lacking in the aquaculture sector and need to be further supported
It was also highlighted, as in other areas in microbial ecology, that due to the lack of well classified reads and well annotated databases, much of the sequence data derived from studies on microbiota data has to be excluded in the analyses and/or assumptions made and this will lead to less conclusive results.
It was also emphasised that although new technologies are available for high through-put sequencing (Nanopore, MinION, Promethean), there is a clear need for further development and consensus over standard methods for specific tasks to improve comparability.
For more information please contact Prof Sam Martin – sam.martin@abdn.ac.uk