Metagenomic analysis of skin-mucus bacterial microbiota from sea caged Atlantic salmon. Mucus microbiota

The dense populations in Atlantic salmon (Salmo salar) aquaculture are beneficial for parasites, pathogenic bacteria and virus, and a rich environmental microbiota. While there are several metagenomic studies of the gut microbiota of the Atlantic salmon, few studies focus on the mucosal layer - an important defence against disease and illness. This study is an initial mapping of the bacterial microbiota of the skin-mucus of healthy Atlantic salmon in sea cages using a metagenomics approach covering seven variable regions of the 16s rRNA genomic region. Metagenomics analysis by Ion Torrent next generation sequencing enable detection of variation on species level, give fever slash calls and miscellaneous reads, and a good species richness. Samples were collected from healthy, sea caged Atlantic salmon to gather a general bacterial population to study the microbiome. Analysis have identified 246 OTUs at family level, as well as 10 unidentified OTUs. Flavobacteriaceae, Moraxellaceae and Colweilliaceae are generally the most abundant OUTs identified across all samples, but species richness varies amongst samples, especially occurrence of less abundant species.

大西洋鲑（Salmo salar）的高密度养殖环境易滋生寄生虫、致病菌与病毒，同时也会富集丰富的环境微生物群。尽管目前已有多项针对大西洋鲑肠道微生物群的宏基因组研究，但聚焦于黏膜层——这一抵御病害的重要防御屏障——的相关研究却寥寥无几。本研究采用宏基因组学方法，针对16S rRNA基因区域的7个可变区，对海笼养殖的健康大西洋鲑皮肤黏液中的细菌微生物群进行了初步图谱绘制。通过Ion Torrent第二代测序（Ion Torrent Next Generation Sequencing）开展的宏基因组分析，可实现物种水平的变异检测，减少假阳性识别，获得有效的杂读段与良好的物种丰富度。研究样本取自海笼养殖的健康大西洋鲑，以获取用于微生物组研究的代表性细菌群落。分析共鉴定出246个科水平的操作分类单元（Operational Taxonomic Unit，OTU），另有10个未分类的OTU。黄杆菌科（Flavobacteriaceae）、莫拉氏菌科（Moraxellaceae）以及科尔韦尔氏菌科（Colweilliaceae）是所有样本中丰度最高的三类OTU，但不同样本间的物种丰富度存在差异，尤其是低丰度物种的出现情况各不相同。