Peer-reviewed articles

 The gut microbiome of farmed Arctic char (Salvelinus alpinus) is shaped by feeding stage and nutrient presence


Sigurlaug Skírnisdóttir

Project Manager

Authors: Stephen Knobloch, Sigurlaug Skirnisdóttir, Marianne Dubois, Lucie Mayolle, Laetitia Kolypczuk, Françoise Leroi, Alexandra Leeper, Delphine Passerini, Viggó Þ Marteinsson

Version: FEMS Microbes

Publication year: 2024


The gut microbiome plays an important role in maintaining the health and productivity of farmed fish. However, the functional role of most gut microorganisms remains unknown. Identifying the stable members of the gut microbiota and understanding their functional roles could help in the selection of positive traits or act as a proxy for fish health in aquaculture. Here, we analyze the gut microbial community of farmed juvenile Arctic char (Salvelinus alpinus) and reconstruct the metabolic potential of its main symbionts. The gut microbiota of Arctic char undergoes a succession in community composition during the first weeks post-hatch, with a decrease in Shannon diversity and the establishment of three dominant bacterial taxa. The genome of the most abundant bacteria, a Mycoplasma sp., shows adaptation to rapid growth in the nutrient-rich gut environment. The second most abundant taxon, a Brevinema sp., has versatile metabolic potential, including genes involved in host mucin degradation and utilization. However, during periods of absent gut content, a Ruminococcaceae bacterium becomes dominant, possibly outgrowing all other bacteria through the production of secondary metabolites involved in quorum sensing and cross-inhibition while benefiting the host through short-chain fatty acid production. Whereas Mycoplasma is often present as a symbiont in farmed salmonids, we show that the Ruminococcaceae species is also detected in wild Arctic char, suggesting a close evolutionary relationship between the host and this symbiotic bacterium.