Kale Varsha, Baldi Germana, Beracochea Martin, Clausen Cecilie, Escobar-Zepeda Alejandra, Leanti La Rosa Sabina, Lecaudey Laurène A, Li Sen, Mak Sarah S T, Martin Michael D, Martin Bideguren Garazi, Pless Louisa A, Rasmussen Jacob A, Rogers Alexander B, Sveier Harald, León Arturo Vera-Ponce de, Verissimo Ana, Gilbert M Thomas P, Richardson Lorna, Limborg Morten T, Finn Robert D
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK.
Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
Anim Microbiome. 2025 Aug 11;7(1):85. doi: 10.1186/s42523-025-00453-5.
Resolving the microbiome of the Atlantic salmon Salmo salar gut is challenged by a low microbial diversity often dominated by one or two species of bacteria, and high levels of host contamination in sequencing data. Nevertheless, existing metabarcoding and metagenomic studies consistently resolve a putative beneficial Mycoplasma species as the most abundant organism in gut samples. The remaining microbiome is heavily influenced by factors such as developmental stage and water salinity. We profiled the salmon gut microbiome across 540 salmon samples in differing conditions with a view to capture the genomic diversity that can be resolved from the salmon gut. The salmon were exposed to 3 different nutritional additives: seaweed, blue mussel protein and silaged blue mussel protein, including both pre-smolts (30-60 g salmon reared in freshwater) as well as post-smolts (300-600 g salmon reared in saltwater). Using genome-resolved metagenomics, we generated a catalogue of 11 species-level bacterial MAGs from 188 input metagenome assembled genomes, with 5 species not found in other catalogues. This highlights that our understanding of salmon gut microbial diversity is still incomplete. A prevalent bacterial genome annotated as Mycoplasmoidaceae is present in adult fish, and a comparison of functions revealed significant sub-species variation. Juvenile fish have a different microbial diversity, dominated by a species of Pseudomonas aeruginosa. We also present the first viral catalogue for salmon including prophage sequences which can be linked to the bacterial MAGs.
解析大西洋鲑鱼肠道微生物群面临诸多挑战，其微生物多样性较低，通常由一两种细菌主导，且测序数据中宿主污染水平较高。尽管如此，现有的宏条形码和宏基因组学研究一致将一种假定有益的支原体物种解析为肠道样本中最丰富的生物体。其余微生物群受到发育阶段和水盐度等因素的严重影响。我们对540个处于不同条件下的鲑鱼样本的肠道微生物群进行了分析，以获取可从鲑鱼肠道中解析出的基因组多样性。这些鲑鱼接触了3种不同的营养添加剂：海藻、蓝贻贝蛋白和青贮蓝贻贝蛋白，包括洄游前幼鱼（在淡水中饲养的30 - 60克鲑鱼）以及洄游后幼鱼（在海水中饲养的300 - 600克鲑鱼）。利用基因组解析宏基因组学，我们从188个输入的宏基因组组装基因组中生成了一个包含11个物种水平细菌宏基因组组装基因组的目录，其中有5个物种在其他目录中未被发现。这突出表明我们对鲑鱼肠道微生物多样性的理解仍然不完整。一种被注释为类支原体科的普遍细菌基因组存在于成年鱼中，功能比较显示出显著的亚种差异。幼鱼具有不同的微生物多样性，以铜绿假单胞菌为主导。我们还展示了首个鲑鱼病毒目录，包括可与细菌宏基因组组装基因组相关联的原噬菌体序列。
