Summer School: “Advances in fish aquaculture and microalgae biotechnology”

El Puerto de Santa María (Spain), 17-21th September 2018.

Microbiome importance in aquaculture


Patricia I.S. Pinto e-mail:

Centro de Ciências do Mar, Universidade do Algarve, 8005-139 Faro, Portugal



The terms microbiota or microbiome refers to the community of microorganisms residing in an “environmental sample” or to the collective genomes of these microbes. The field of Metagenomics studies the collective genetic material recovered from a wide range of environments, including terrestrial or aquatic media or the surface or interior of terrestrial or marine organisms. Metagenomics makes it possible to describe the diversity and/or the function of these communities. This talk will give an overview of the methods for the study of microbial communities, from classical culture methods to the current analysis of whole microbiomes using high-throughput sequencing methods. The importance and current state of the art of microbiome analyses in aquaculture are considered. Although relatively few microbiome studies exist for fish relative to humans and mammals, the available results indicate that the fish gut microbiome is important for immune defence, nutrition and metabolism. Furthermore, the microbiome can be affected by captivity, dietary components or by stress. The impact of different treatments or protocols in intensive aquaculture can be evaluated in terms of maintaining or manipulating the fish microbiota and may be a means to improve animal health and welfare and contribute to sustainable aquaculture. Finally, the talk reviews the current practical and bioinformatics methods used for the main types of metagenomics studies as well as some case studies, with particular focus on applications related to aquaculture fish species.


Acknowledgements: The research leading to these results has received European Funds from H2020 MSCA-RISE project 691102 (Algae4A&B) and funds from the Portuguese Foundation for Science and Technology (FCT) through project CCMAR/Multi/ 04326/2013 and grant SFRH/BPD/84033/2012 to PP.