Data_Sheet_3_Diet and Host Genetics Drive the Bacterial and Fungal Intestinal Metatranscriptome of Gilthead Sea Bream.PDF

The gut microbiota is now recognised as a key target for improving aquaculture profit and sustainability, but we still lack insights into the activity of microbes in fish mucosal surfaces. In the present study, a metatranscriptomic approach was used to reveal the expression of gut microbial genes in the farmed gilthead sea bream. Archaeal and viral transcripts were a minority but, interestingly and contrary to rRNA amplicon-based studies, fungal transcripts were as abundant as bacterial ones, and increased in fish fed a plant-enriched diet. This dietary intervention also drove a differential metatranscriptome in fish selected for fast and slow growth. Such differential response reinforced the results of previously inferred metabolic pathways, enlarging, at the same time, the catalogue of microbial functions in the intestine. Accordingly, vitamin and amino acid metabolism, and rhythmic and symbiotic processes were mostly shaped by bacteria, whereas fungi were more specifically configuring the host immune, digestive, or endocrine processes.肠道菌群（gut microbiota）如今已被认定为提升水产养殖效益与可持续性的关键靶点，但目前学界对鱼类黏膜表面微生物的活性仍缺乏深入认知。本研究采用宏转录组学（metatranscriptomic）方法，解析了养殖金头鲷（gilthead sea bream）的肠道微生物基因表达情况。古菌与病毒转录本仅占少数；值得注意的是，与基于rRNA扩增子的研究结论相悖，真菌转录本的丰度与细菌转录本相当，且在投喂植物强化饲料的受试鱼体内含量显著升高。该饮食干预还在针对快速生长与慢速生长筛选出的鱼群中诱导了差异化的宏转录组特征。这种差异化应答不仅验证了此前推测的代谢通路结果，同时还扩充了肠道微生物功能的已知目录。据此可知，维生素与氨基酸代谢、节律调控及共生过程主要由细菌塑造，而真菌则更特异性地参与调控宿主的免疫、消化及内分泌过程。