About the project

This project will develop protocols to advance sustainable aquaculture through a microbiota-centered approach to improving early-life development. By identifying beneficial and detrimental microbial communities that influence organogenesis and investigating how hatchery conditions shape these communities, the project aims to improve understanding of the factors contributing to organ deformities. The findings will inform strategies to support healthy organ development and function, with potential benefits for fish welfare and growth performance in Atlantic salmon.

• Background

  Global demand for animal-derived food is increasing as the global population approaches 10 billion by 2050. Aquaculture is central to meeting this demand, with Atlantic salmon among the most important farmed species due to high efficiency and low environmental footprint. However, early-life performance remains a major bottleneck, with substantial mortality and suboptimal development reducing seawater survival and production efficiency. These losses are linked to impaired organ development, immune dysfunction, and reduced robustness.

  Microbial communities (microbiota) associated with salmon eggs and larvae are increasingly recognized as important but poorly understood drivers of development and health. While parental effects, rearing conditions, and environmental microbiota all influence early development, their relative contributions to host-associated microbial assembly and function remain unclear.

  The questions to be answered in StarterPack are:
  • How do parental transmission, environmental exposure, and hatchery practices (including disinfection) shape egg microbiota and affect embryonic development and survival?
  • How is the mucosal microbiota (skin, gills, gut) established under farming conditions, and what is the balance between environmental input and host selection?
  • Does early microbiota influence organ development and immune maturation, and through which mechanisms?

• Objectives

  The primary objective of StarterPack is to (i) use multi-omic data and novel computational approaches to unveil functional links in the environment-microbiota-host triad that shape beneficial configurations of microbiota associated with eggs and alevins, with (ii) emphasis on identifying microbes, mechanisms
  and strategies that support healthy organ development and immune system maturation for robust Atlantic salmon.

  Subgoals (with corresponding work packages)

  • - Determine core microbial taxa and functions associated with Atlantic salmon eggs, their inheritance from parents or acquisition from water, and their metabolic capabilities that influence embryonic development and pathogen resistance (WP1);
  • - Identify functions and structure of well-performing microbial communities associated with healthy eggs and assess whether current disinfection approaches alter microbiota configurations critical for organogenesis and immune system maturation (WP2-3).
  • - Uncover the composition and functionalities of the microbiota that support the generation of alevins with well-developed gills, skin, and gut, and lay the foundation for a robust immune system later in life (WP2-3).
  • - Establish microbiota-based strategies that optimize early-life microbiota in Atlantic salmon, promoting healthy organ development, robust immunity, and protection against pathogens (WP4-5).

• Publications

• Participants

• External Participants

  Nils Niepagen, AquaGen - Researcher

  Thomas Moen, AquaGen - Research Manager

News

September 2026: we are officially live!