PROMICROBE - Microbes as positive actors for more sustainable aquaculture


The project starts from the concept that the host microbial community (MC) is influenced by the host itself and by the microbial community of the system in which the host is living. It is anticipated that there is a reciprocal interaction between the different compartments of the system in every stage of the life cycle.

The strength and the nature of those interactions can depend on the life cycle stage. Apart from these horizontal interactions, it is anticipated that microbial communities evolve as the host grows or the system changes. A certain degree of top-down conditioning belongs to the possibilities.

This would mean that the early colonisation of the host by certain micro-organisms, might condition the host response and determine the microbial community composition in later life stages. In addition the environment (e.g. temperature, feed, water quality, sanitation measurements) will determine to a great extent the composition and activity of the microbial communities in the different compartments. The environment can be modulated through the composition of the feed or through compounds that directly influence the activity of micro-organisms. On the other hand nutritional compounds or immunomodulators might have a direct influence on the host, modulating the microbial community of both host and system.

Every life stage carries its associated microbial community (MCe: microbial community of the intestine or attached to outer surface as for instance for eggs). The MCe is to an undefined degree in equilibrium with the MC of the system (MCs). The host can influence the MCe through its antimicrobial activities as determined by its immunological capacities in every life stage (horizontal arrows). Yet the MCe is probably also in equilibrium or influenced by the microbial community of the system (MCs). The composition and activities of microbial communities (MCe or MCs) can be modulated to a certain degree, influencing the host. The host can be influenced either by direct interference with its immune system or through nutrition, modulating indirectly the MC. Thick arrows in this scheme are the subject of research activities in this project.


Aquaculture has developed very rapidly over the last 20 to 30 years. Surfacing problems have been solved mostly on an empirical basis. Considering the fact that aquatic organisms live in a matrix (namely the matrix water) that contains the feed as well as the excretion products, it can be anticipated that the environment must have a very strong influence on the microbial community composition, its activity and hence on the host.

In the past the aquaculture ecosystem (being considerable reduced in terms of complexity compared to natural ecosystems) and especially the microbial component has only to a limited degree been studied in a systematic way. However, such studies have been hampered by the lack of the appropriate tools.

This project suggests bringing together various European research groups that have contributed to some important methodological breakthroughs that can be used in the study of host/microbe interactions and can help to disentangle the complex interplay between the different components of the aquaculture ecosystem as depicted above. These breakthroughs are:

  • The demonstration that the composition of the total MC characterized by culture independent techniques deviated tremendously from the composition based on conventional culture dependent techniques.
  • The demonstration by both culture dependent and independent techniques that the MC composition at least in larvae, differ as much between individuals living in the same tank as the variation recorded between different rearing environments.
  • The possibility to set up a gnotobiotic aquaculture food chain for (marine) larval fish
  • The possibility to start feed (marine) larval fish with compound diets.
  • The possibility to modulate intestinal microbiota with feed components, including probiotics and prebiotics.
  • The demonstration that microbial quorum sensing mechanisms operate in vivo in aquatic organisms determining microbial in vivo activity.
  • The possibility to apply the cDNA-AFLP technique to aquatic organisms, allowing for rapid gene expression analysis even in organisms with a poorly characterised genome.

These methodological breakthroughs supply this project with a head start, as they supply the tools (especially when they are applied in combination as established by this EU project proposal) to disentangle to a great extent the complex interactions as depicted in Fig. 1. The work packages (see also “overall work plan”) are directed to the systematic gathering of novel information in relation to the major elements depicted above. It is anticipated that this novel information will allow developing new concepts that will be translated into new or adapted protocols to rear aquaculture organisms in a biological stable and economical efficient way. Some of the major objectives that will be addressed experimentally are the following:

  • How does the microbial community evolve as the host progresses through its life cycle?
  • How stable is the microbial community in relation to perturbation caused by changes in environmental conditions and how resilient is the microbial community?
  • What is the effect of micro-organisms on the host metabolism, its disease susceptibility and viability?
  • Considering that some environmental factors (e.g. salinity, feed composition) have a major influence on the MC composition, to what degree is it possible to influence or steer the MC composition and activity?
  • To what extend can microbes present in aquaculture rearing systems be (re-) used to retain organic wastes and nutrients, and thus reduce the impact on the environment?

Project Details & Acknowledgements

Project full title

"Microbes as positive actors for more sustainable aquaculture"



Funding Body

  • European Commission - DG RTD
  • Seventh Framework Programme: Cooperation Work Programme
  • Theme 2: Food, Agriculture and Fisheries, and Biotechnology
  • Call Identifier: FP7-KBBE-2008-2B
  • Budget: ca. 3 million €

Contact Person:

Dr. Stamatis VARSAMOS
DG RTD, Unit E4: Agriculture, Forests, Fisheries, Aquaculture
SDME 8/92
Square de Meus, 8
B 1050 Brussels