Teagasc Food Research Centre, Ashtown, Dublin 15, Ireland.
School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
J Appl Microbiol. 2019 Sep;127(3):648-657. doi: 10.1111/jam.14291. Epub 2019 Jun 28.
Information on the gut microbiota of salmon is essential for optimizing nutrition while maintaining host health and welfare. This study's objectives were to characterize the microbiota in the GI tract of Atlantic salmon (Salmo salar) farmed in waters off the west coast of Ireland and to investigate whether there is a difference in microbiota diversity between the proximal and distal regions of the intestine.
The microbiota from the proximal and distal intestine (PI and DI, respectively) of Atlantic salmon was examined using MiSeq Illumina high-throughput sequencing of the 16S ribosomal RNA gene. The PI region had greater bacterial diversity than the DI region. Six phyla were present in the DI samples, dominated by Tenericutes and Firmicutes. These six phyla were also amongst the 12 phyla detected in the PI samples. The PI microbiota was dominated by Tenericutes, Firmicutes, Bacteroidetes and Proteobacteria. A core microbiota of 20 operational taxonomic units (OTUs) common to both regions was observed.
It was concluded that Tenericutes were the dominant phylum in both PI and DI samples, and the PI region had greater Shannon and Simpson diversity of bacteria. However, further work is required to identify the functionality of the salmon microbiota.
Our study determined the composition and diversity of the intestinal microbiota in adult salmon from a commercial fishery and provides data to improve our understanding of their contributions to the nutrition, health and welfare of Atlantic salmon farmed in Irish waters.
了解鲑鱼肠道微生物群的信息对于优化营养，同时维持宿主健康和福利至关重要。本研究的目的是描述爱尔兰西海岸养殖大西洋鲑（Salmo salar）胃肠道中的微生物群，并研究肠道近端和远端的微生物多样性是否存在差异。
使用 MiSeq Illumina 高通量测序 16S 核糖体 RNA 基因，检测大西洋鲑近端和远端肠道（PI 和 DI）的微生物群。PI 区的细菌多样性大于 DI 区。DI 样品中存在 6 个门，以厚壁菌门和Firmicutes 为主。这 6 个门也是在 PI 样品中检测到的 12 个门之一。PI 微生物群主要由 Tenericutes、Firmicutes、Bacteroidetes 和 Proteobacteria 组成。观察到 20 个存在于两个区域的核心操作分类单位（OTUs）。
本研究认为 Tenericutes 是 PI 和 DI 样品中的优势门，PI 区的细菌 Shannon 和 Simpson 多样性更大。然而，需要进一步的工作来确定鲑鱼微生物群的功能。
本研究确定了商业渔业中成年鲑鱼肠道微生物群的组成和多样性，并提供了数据，以提高我们对其在爱尔兰水域养殖的大西洋鲑的营养、健康和福利贡献的理解。
