Data_Sheet_1_Characterization of External Mucosal Microbiomes of Nile Tilapia and Grey Mullet Co-cultured in Semi-Intensive Pond Systems.pdf

The external mucosal surfaces of the fish harbor complex microbial communities, which may play pivotal roles in the physiological, metabolic, and immunological status of the host. Currently, little is known about the composition and role of these communities, whether they are species and/or tissue specific and whether they reflect their surrounding environment. Co-culture of fish, a common practice in semi-intensive aquaculture, where different fish species cohabit in the same contained environment, is an easily accessible and informative model toward understanding such interactions. This study provides the first in-depth characterization of gill and skin microbiomes in co-cultured Nile tilapia (Oreochromis niloticus) and grey mullet (Mugil capito) in semi-intensive pond systems in Egypt using 16S rRNA gene-based amplicon sequencing. Results showed that the microbiome composition of the external surfaces of both species and pond water was dominated by the following bacterial phyla: Proteobacteria, Fusobacteriota, Firmicutes, Planctomycetota, Verrucomicrobiota, Bacteroidota, and Actinobacteriota. However, water microbial communities had the highest abundance and richness and significantly diverged from the external microbiome of both species; thus, the external autochthonous communities are not a passive reflection of their allochthonous communities. The autochthonous bacterial communities of the skin were distinct from those of the gill in both species, indicating that the external microbiome is likely organ specific. However, gill autochthonous communities were clearly species specific, whereas skin communities showed higher commonalities between both species. Core microbiome analysis identified the presence of shared core taxa between both species and pond water in addition to organ-specific taxa within and between the core community of each species. These core taxa included possibly beneficial genera such as Uncultured Pirellulaceae, Exiguobacterium, and Cetobacterium and opportunistic potential pathogens such as Aeromonas, Plesiomonas, and Vibrio. This study provides the first in-depth mapping of bacterial communities in this semi-intensive system that in turn provides a foundation for further studies toward enhancing the health and welfare of these cultured fish and ensuring sustainability.

鱼类体外黏膜表面定殖着复杂的微生物群落，这些群落可能对宿主的生理、代谢及免疫状态发挥关键调控作用。目前学界对这类群落的组成与功能、其是否具有物种及组织特异性，以及是否能反映周围环境特征的认知仍较为匮乏。鱼类混养是半精养水产养殖中的常见模式，即不同鱼类在同一封闭环境中共存，这是探究此类微生物互作关系的便捷且极具研究价值的模型体系。本研究以埃及半精养池塘系统中混养的尼罗罗非鱼（Oreochromis niloticus）和灰鲻（Mugil capito）为研究对象，采用基于16S rRNA基因的扩增子测序技术，首次对二者的鳃部及皮肤微生物组进行了深度解析。研究结果显示，两种鱼类体外黏膜表面及池塘水体的微生物群落组成均以以下细菌门类为主：变形菌门（Proteobacteria）、梭杆菌门（Fusobacteriota）、厚壁菌门（Firmicutes）、浮霉菌门（Planctomycetota）、疣微菌门（Verrucomicrobiota）、拟杆菌门（Bacteroidota）以及放线菌门（Actinobacteriota）。不过，水体微生物群落的丰度和多样性均最高，且与两种鱼类的体外微生物群落存在显著差异，这表明鱼类体外的土著微生物群落并非外界异源群落的被动反映。两种鱼类皮肤的土著细菌群落均与鳃部的土著群落存在显著差异，这提示体外微生物组可能具有组织特异性。但鳃部土著群落具有显著的物种特异性，而两种鱼类的皮肤微生物群落则表现出更高的相似性。核心微生物组分析显示，除各物种核心群落内部及物种间的组织特异性类群外，两种鱼类与池塘水体间还存在共享的核心类群。这些核心类群包括潜在有益菌属，如未培养皮尔氏菌科（Uncultured Pirellulaceae）、嗜冷杆菌属（Exiguobacterium）和鲸杆菌属（Cetobacterium），以及潜在机会致病菌气单胞菌属（Aeromonas）、邻单胞菌属（Plesiomonas）和弧菌属（Vibrio）。本研究首次对该半精养系统中的细菌群落进行了全面深度的解析，为后续开展提升养殖鱼类健康水平、福利状态及保障养殖可持续性的相关研究奠定了基础。