Supplementary file 1_Microbiome dynamics in tank- and pond-reared Genetically Improved Farmed Tilapia (GIFT).docx

IntroductionTilapia (Oreochromis spp.) are among the most widely cultivated freshwater finfish species worldwide. The industry increasingly relies on tilapia strains selected for improved growth and other traits, particularly the Genetically Improved Farmed Tilapia (GIFT) strain. Despite the industry’s reliance on tilapia, knowledge of microbiome dynamics in reared tilapia remains limited. Understanding normal successional patterns in the microbiome of farmed tilapia is essential for identifying the characteristics that constitute a healthy microbial community.
MethodsIn this study, we assessed the microbiomes of tank and pond-reared GIFT tilapia by analyzing 568 samples, including water, gut, skin, and gill microbiomes of tilapia, from tank systems housing the source GIFT populations in Malaysia. We compared them to those reared in earthen ponds on another farm in Malaysia.
ResultsA total of 2,307 amplicon sequence variants (ASVs) were identified, encompassing a broad taxonomic diversity of 39 phyla, 86 classes, 180 orders, 299 families, 501 genera, and 399 species. Our findings elucidated distinct microbial community structures between rearing environments and across fish tissues, shedding light on intricate host-microbe interactions shaped by environmental conditions and management practices. The gut microbiome of tank-reared tilapia was dominated by Fusobacteriota (71.14%), in contrast to pond-reared fish (22%). At the same time, other taxa, such as Bacteroidota, Firmicutes_A, and Cyanobacteria, also varied markedly between environments and sampling periods. Skin and gill samples exhibited notable variability in the relative abundances of Fusobacteriota and Deinococcota between the two rearing sites. Principal Coordinates Analysis (PCoA) highlighted the distinct clustering of samples by rearing environment, particularly within gut microbiomes. Biomarkers such as Cyanobiaceae (pond water) and Sphingomonadaceae (tank water) underscored the impact of rearing conditions on microbial composition.
DiscussionThese results establish valuable baseline information on the types of bacteria associated with healthy, genetically defined (GIFT) tilapia strains. This foundational information will help identify specific microbial taxa associated with beneficial or detrimental effects on tilapia health and productivity across varying rearing conditions. Such insights can guide the development of practical microbiome monitoring strategies, such as early-warning tools for farm health, and inform targeted interventions to improve aquaculture performance.

引言
罗非鱼（Oreochromis spp.）是全球养殖规模最广的淡水硬骨鱼类之一。当前水产养殖行业愈发依赖经选育获得生长及其他优良性状的罗非鱼品系，尤以遗传改良养殖罗非鱼（Genetically Improved Farmed Tilapia，GIFT）品系为代表。尽管行业对罗非鱼养殖依赖度极高，但人们对养殖罗非鱼的微生物组动态变化仍了解有限。阐明养殖罗非鱼微生物组的正常演替模式，是识别健康微生物群落核心特征的必要前提。
方法
本研究通过分析568份样本，对流水养殖池与土塘养殖的GIFT罗非鱼微生物组展开评估；样本涵盖马来西亚境内原种GIFT种群养殖池系统中的罗非鱼水体、肠道、皮肤及鳃部微生物组，并将其与马来西亚另一养殖场土塘养殖的罗非鱼微生物组进行对比分析。
结果
本研究共鉴定出2307个扩增子序列变异体（amplicon sequence variants，ASVs），涵盖39个门、86个纲、180个目、299个科、501个属以及399个种，分类多样性丰富。研究结果揭示了不同养殖环境与鱼类不同组织间微生物群落结构的显著差异，阐明了环境条件与养殖管理模式塑造的复杂宿主-微生物互作关系。流水养殖池养殖的罗非鱼肠道微生物组以梭杆菌门（Fusobacteriota）为主（占比71.14%），而土塘养殖的罗非鱼该类群占比仅为22%。与此同时，拟杆菌门（Bacteroidota）、厚壁菌门A类（Firmicutes_A）以及蓝细菌门（Cyanobacteria）等其他微生物类群在不同养殖环境与采样周期间也存在显著差异。皮肤与鳃部样本中，梭杆菌门与异常球菌门（Deinococcota）的相对丰度在两个养殖场地间均表现出明显波动。主坐标分析（Principal Coordinates Analysis，PCoA）结果显示，样本可按养殖环境形成清晰聚类，其中肠道微生物组的聚类效果尤为显著。蓝细菌科（Cyanobiaceae，土塘水体样本）与鞘氨醇单胞菌科（Sphingomonadaceae，养殖池水体样本）作为潜在生物标志物，进一步印证了养殖条件对微生物组组成的调控作用。
讨论
本研究结果为健康、遗传背景明确的GIFT罗非鱼品系相关细菌类群提供了极具价值的基准数据。这些基础信息将助力在不同养殖条件下，识别与罗非鱼健康及生产性能存在有益或有害关联的特定微生物类群。相关研究结论可指导实用化微生物组监测策略的开发，例如用于养殖场健康预警的早期监测工具，并为制定靶向干预手段以提升水产养殖生产性能提供理论支撑。