The overall structure of PROMICROBE is presented below, illustrating that this project will work on different levels, from a focus on the host to a focus on the system.

The work plan is structured in a systematic way aiming in the first place at gathering fundamental information on microbial communities associated with aquaculture species that have different feeding preferences (namely Tilapia being herbivore, seabass and cod being more carnivore, with one of the differences between the later two being the optimal growth temperature) and how these microbial communities can interact beneficially with the host.

The first work package is descriptive in that it will gather information on the evolution of the microbial community (MC) as the host develops from hatchling into juvenile and on the stability of the MC composition after a major disturbance. Hence this WP constitutes a baseline study which is surprisingly lacking in the current available literature.
The major innovation in this workpackage is:

1. the determination of the MC composition at the individual level (as recent findings have indicated that variation in MC composition between individuals in the same tank can be very high) and;
2. the gathering of temporal MC composition data as the host progresses through its life cycle, with culture independent genetic tools (MC genetic fingerprinting).

Acknowledging (see state of the art) that host microbial interactions constitute an important factor in an aquaculture system, the following three WP’s set out to investigate the influence of important factors that are anticipated to have a major impact on the MC composition of the host and the system and its activity and the interplay with the host metabolism. Host microbial interactions are notoriously difficult to disentangle due the continuous interplay between the developing host and its evolving MC. In an attempt to investigate components of that interplay, research will be performed relying partly on recent zootechnical advances that have been made by the partners, namely the ability to start a aquaculture food chain axenically, allowing for more experimental control of MC (at least in the early days after hatching) and the ability to start feed (marine) larvae (at least seabass) with inert component feed, allowing for investigating the dose-response relationship of minor feed component that directly influence the host. More particular, the second work package will investigate how the host is benefiting from the complexity of the colonising microbial community to deal with an invasive pathogen. In that respect MC able to interfere with quorum sensing signalling will receive special attention. The host response to identified beneficial microbial communities will be analysed at the transcriptional level by the most advanced genetic tools available. In addition the contribution of micro-organisms to the digestion of the feed will be investigated.

While WP2 is gathering fundamental information on the host microbial interaction, work package three is taking the project one step further in the direction of developing ways to profit from host microbial interactions by steering the MC composition. The possibility of steering of the MC composition will be investigated by a variety of treatments including, special feed components and the addition of prebiotic and probiotic compound or mixtures.

Finally, acknowledging that the overall environmental conditions have a major impact on the performance of a cultured aquatic organisms, in which micro-organisms both host-bound and system-bound are anticipated to have a major play, work package four will mainly focus on the influence of the system MC on the host, and the possibility to use the system-MC to minimize environmental impacts from aquaculture, while benefiting the cultured organisms.

Work package five is focussed on the scientific management of the project which will pay special attention to the scientific integration and the further development of the conceptual model as depicted in the figure above.

Finally work package six is dedicated to the administrative and financial management of the project.