An insight into gill microbiome of Eastern Mediterranean wild fish by applying next generation sequencing

Bacterial diseases of marine fish inflict significant economic damage to fisheries and aquaculture and pose an increasing risk to public health. When addressing fish disease, an accumulating body of research suggests adding another factor to the classic epidemiological triangle of host-environment-pathogen: the microbiome. The gills, being a gateway into the fish body and bearing an important role in fish homeostasis, have been found to be a proxy of the gut microbiota as well as reflecting the microbial communities of surrounding water. In this study, 16S rRNA amplicons of bacterial DNA extracted from the gills of 89 asymptomatic specimens of three wild fish species (Pagrus caeruleostictus, Scomber colias and Saurida lessepsianus) were sequenced using Next Generation Sequencing methodology (NGS). Data analyses revealed the presence of 41 potentially pathogenic species, including several zoonotic agents. Five genera known to include widespread and potentially pathogenic species were chosen for further investigation – Photobacterium, Shewanella, Staphylococcus, Streptococcus and Vibrio. Of these, Photobacterium and Shewanella proved the most prevalent and abundant, making up 30.2% and 11.3% of the Bluespotted seabream (P. caeruleostictus) gill microbiome alone. Photobacterium damselae and Shewanella baltica were most common at the species level. The remaining genera - Vibrio, Staphylococcus and Streptococcus – were less prevalent, and at a species level were comprised of only 1−4% potentially pathogenic representatives. Gill microbiomes exhibited host species specificity, with strong correlations between certain bacterial taxonomic groups. No definite obligatory pathogenic bacteria were found in this study, and it was suggested that pathogenic species are present as either covert pathobionts or as opportunists of the fish found to host them.

海水鱼类细菌性病害对渔业与水产养殖业造成严重经济损失，同时也对公众健康构成日益严峻的威胁。在应对鱼类病害时，日益积累的研究证据表明，需在经典的宿主-环境-病原体流行病学三角模型中纳入另一关键因素：微生物组（microbiome）。
鳃作为鱼类机体的门户，在鱼类稳态（homeostasis）维持中发挥关键作用，研究证实其可作为肠道微生物群的替代监测指标，同时也能反映周边水体的微生物群落结构。
本研究采用下一代测序（Next Generation Sequencing, NGS）技术，对3种野生鱼类——蓝斑鲷（*Pagrus caeruleostictus*）、大西洋鲭（*Scomber colias*）以及龙氏蛇鲻（*Saurida lessepsianus*）共89尾无症状个体的鳃组织细菌DNA的16S rRNA扩增子进行了测序。
数据分析显示，样本中存在41种潜在致病菌，其中包含多种人畜共患病原体。
研究选取5个已知包含广泛分布且具有潜在致病性物种的菌属开展深入分析：发光杆菌属（*Photobacterium*）、希瓦氏菌属（*Shewanella*）、葡萄球菌属（*Staphylococcus*）、链球菌属（*Streptococcus*）以及弧菌属（*Vibrio*）。
其中，发光杆菌属与希瓦氏菌属的检出率和相对丰度最高，仅在蓝斑鲷（*Pagrus caeruleostictus*）的鳃微生物组中，这两个菌属的占比就分别达到30.2%与11.3%。在物种水平上，杀鱼发光杆菌（*Photobacterium damselae*）和波罗的海希瓦氏菌（*Shewanella baltica*）最为常见。
其余三个菌属——弧菌属、葡萄球菌属以及链球菌属的检出率相对较低，在物种水平上，其潜在致病菌仅占总菌群的1%~4%。
鳃微生物组呈现宿主物种特异性，部分细菌分类类群间存在显著相关性。
本研究未检出明确的专性致病菌，研究表明此类致病菌以隐蔽的致病共生体（pathobionts）或宿主鱼类的机会致病菌形式存在。