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.

海洋鱼类细菌性疾病对渔业和水产养殖业造成重大经济损失，并对公共健康构成日益增长的风险。在研究鱼类疾病时，越来越多的研究表明，需在宿主-环境-病原体这一经典流行病学三角（epidemiological triangle）中加入另一因素：微生物组（microbiome）。鳃作为鱼类身体的门户，在维持鱼类稳态（homeostasis）中发挥重要作用，已被证实可作为肠道菌群（gut microbiota）的替代指标，并反映周围水体的微生物群落。本研究采用下一代测序技术（Next Generation Sequencing, NGS），对从三种野生鱼类（蓝点鲷Pagrus caeruleostictus、科氏鲭Scomber colias和莱氏蛇鲻Saurida lessepsianus）的89个无症状个体鳃中提取的细菌DNA进行16S rRNA扩增子（16S rRNA amplicon）测序。数据分析显示存在41种潜在致病菌，其中包括多种人畜共患病原体（zoonotic agent）。研究选取了5个已知包含广泛分布且潜在致病物种的属进一步分析：发光杆菌属（Photobacterium）、希瓦氏菌属（Shewanella）、葡萄球菌属（Staphylococcus）、链球菌属（Streptococcus）及弧菌属（Vibrio）。其中，发光杆菌属和希瓦氏菌属最为普遍且丰富，仅在蓝点鲷（P. caeruleostictus）鳃微生物组中就分别占30.2%和11.3%。物种层面上，美人鱼发光杆菌（Photobacterium damselae）和波罗的海希瓦氏菌（Shewanella baltica）最为常见。其余三个属（弧菌属、葡萄球菌属和链球菌属）分布较少，且在物种层面上潜在致病代表仅占1-4%。鳃微生物组表现出宿主物种特异性，某些细菌分类群之间存在强相关性。本研究未发现明确的专性致病菌（obligatory pathogenic bacteria），推测这些致病物种以隐蔽的致病共生菌（pathobiont）或机会致病菌的形式存在于宿主鱼类中。