Mathisen Amalie Johanne Horn, Gómez de la Torre Canny Sol, Gundersen Madeleine S, Østensen Mari-Ann, Olsen Yngvar, Vadstein Olav, Bakke Ingrid
Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, 7491 Trondheim, Norway.
Skretting Aquaculture Innovation (AI), 4016 Stavanger, Norway.
FEMS Microbiol Ecol. 2025 Jan 28;101(2). doi: 10.1093/femsec/fiaf007.
In this study, we investigated the influence of host genetics and environmental microbiomes on the early gut microbiome of Atlantic salmon. We aimed at rearing the fish in either r- or K-selected environments, where the r-selected environment would be expected to be dominated by fast-growing opportunistic bacteria and thus represent more detrimental microbial environment than the K-selected water. Eggs from both wild and aquaculture strains of Atlantic salmon were hatched under germ-free conditions. One week after hatching, rearing flasks were inoculated with either r- or K-selected water communities. Three weeks after hatching, no effect of host strain on the gut microbiomes were observed. r-selection was found to take place in the rearing water of all flasks, including in the flasks added K-selected water. Still, the water microbiomes differed significantly between the flasks that had been added r- and K-selected water (Add-r and Add-K flasks, respectively). Lower alpha diversity and higher abundances of Pseudomonas were observed for the Add-K flasks, indicating a potential unfavorable microbial environment. Selection in the host structured the gut microbiomes, but an extensive interindividual variation was explained by stochastic processes in community assembly. The gut microbiomes also differed significantly between the Add-r and Add-K flasks. In Add-K flasks, they had higher similarities to the rearing water microbiomes, and the assembly of gut communities was less influenced by stochastic processes. The fish in Add-K flasks had lower growth rates than in Add-r flasks, probably as a result of negative host-microbe interactions. These findings highlight the importance of, but also the challenges related to, managing the microbial environment when cultivating fish.
在本研究中，我们调查了宿主遗传学和环境微生物群对大西洋鲑早期肠道微生物群的影响。我们旨在将鱼饲养在r-或K-选择环境中，预计r-选择环境将由快速生长的机会主义细菌主导，因此比K-选择的水体代表更有害的微生物环境。大西洋鲑野生和养殖品系的卵在无菌条件下孵化。孵化一周后，在饲养烧瓶中接种r-或K-选择的水体群落。孵化三周后，未观察到宿主品系对肠道微生物群有影响。发现在所有烧瓶的饲养水中都发生了r-选择，包括添加了K-选择水的烧瓶。然而，添加r-和K-选择水的烧瓶（分别为Add-r和Add-K烧瓶）中的水体微生物群存在显著差异。Add-K烧瓶的α多样性较低，假单胞菌丰度较高，表明存在潜在的不利微生物环境。宿主中的选择构建了肠道微生物群，但群落组装中的随机过程解释了个体间的广泛差异。Add-r和Add-K烧瓶之间的肠道微生物群也存在显著差异。在Add-K烧瓶中，它们与饲养水微生物群的相似性更高，肠道群落的组装受随机过程的影响较小。Add-K烧瓶中的鱼生长速度比Add-r烧瓶中的鱼慢，这可能是宿主-微生物负面相互作用的结果。这些发现突出了养殖鱼类时管理微生物环境的重要性，但也凸显了与之相关的挑战。
