To ensure sustainable aquaculture, it is essential to understand the path ‘from feed to fish’, whereby the gut microbiome plays an important role in digestion and metabolism, ultimately influencing host health and growth. Previous work has reported the taxonomic composition of the Atlantic salmon (Salmo salar) gut microbiome; however, functional insights are lacking. Here we present the Salmon Microbial Genome Atlas consisting of 211 high-quality bacterial genomes, recovered by cultivation (n = 131) and gut metagenomics (n = 80) from wild and farmed fish both in freshwater and seawater. Bacterial genomes were taxonomically assigned to 14 different orders, including 35 distinctive genera and 29 previously undescribed species. Using metatranscriptomics, we functionally characterized key bacterial populations, across five phyla, in the salmon gut. This included the ability to degrade diet-derived fibres and release vitamins and other exometabolites with known beneficial effects, which was supported by genome-scale metabolic modelling and in vitro cultivation of selected bacterial species coupled with untargeted metabolomic studies. Together, the Salmon Microbial Genome Atlas provides a genomic and functional resource to enable future studies on salmon nutrition and health.

为了确保可持续的水产养殖，必须了解“从饲料到鱼”的路径，其中肠道微生物组在消化和新陈代谢中起着重要作用，最终影响宿主的健康和生长。以前的工作报道了大西洋鲑鱼 （Salmo salar） 肠道微生物组的分类组成;但是，缺乏功能洞察。在这里，我们展示了鲑鱼微生物基因组图谱，该图谱由 211 个高质量的细菌基因组组成，这些基因组通过培养 （n = 131） 和肠道宏基因组学 （n = 80） 从淡水和海水中的野生和养殖鱼类中回收。细菌基因组被分类学分为 14 个不同的目，包括 35 个不同的属和 29 个以前未描述的物种。使用元转录组学，我们对鲑鱼肠道中五个门的关键细菌种群进行了功能表征。这包括降解饮食衍生纤维和释放维生素和其他具有已知有益作用的外代谢物的能力，这得到了基因组规模代谢模型和选定细菌物种的体外培养以及非靶向代谢组学研究的支持。鲑鱼微生物基因组图谱共同提供了基因组和功能资源，使未来对鲑鱼营养和健康的研究成为可能。