In many meta-analyses and literature reviews on fish microbiota, the provenance of the animals (farmed vs. wild) is often overlooked. Given the well-established role of diet as a key factor in shaping gut microbiota, this study investigates the impact of dietary nature by comparing the microbiota of gilthead seabream (Sparus aurata) fed a commercial diet versus a wild-type diet, all reared within a recirculating aquaculture system. Over a 60-day period, we tracked changes in gut bacterial diversity, structure, and composition following a shift from a commercial feed to a diet exclusively based on pink shrimp (Parapenaeus longirostris). Gut bacterial communities were assessed using 16S rRNA gene sequencing (Illumina MiSeq platform) with primers targeting the V3-V4 hypervariable regions. Twenty days after the dietary change, microbial diversity (Shannon index) increased in fish fed the shrimp diet compared to those fed the commercial diet, while Dominance index values decreased. Additionally, inter-individual (beta-) diversity based on Bray-Curtis distances also differed between dietary treatments. These results support further that microbiota comparisons between farmed/captive and wild fish are challenging due to the unpredictable feeding regimes and dietary variations in wild fish. However, the diet impact on microbiota diminished over time, with the differences in intra- and inter-individual diversity being reduced after 40 days, which suggests an adaptation of microbial communities to dietary changes. At this point, gut microbial communities also showed a similar taxonomical composition. Moreover, a core microbiota consisting of species belonging to the genera Ralstonia, Paraburkholderia, Fulvimonas, Pseudomonas, and Cutibacterium was maintained in all sampling times under both dietary treatments. Overall, this study serves as a conceptual approach that shows a long-term adaptation of the gut microbiota after a radical dietary change, probably driven by host-inherent factors. Furthermore, these results may be a valuable insight for feed manufacturers aiming to develop sustainable and cost-effective ingredients since they suggest that some alternative feeds and ingredients do not have adverse long-term effects on fish gut microbiota.

中文翻译：

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金头鲷 （Sparus aurata） 肠道微生物群对饮食变化的长期适应


在许多关于鱼类微生物群的荟萃分析和文献综述中，动物的来源（养殖与野生）经常被忽视。鉴于饮食作为塑造肠道微生物群的关键因素的公认作用，本研究通过比较饲喂商业饮食与野生型饮食的金头鲷 （Sparus aurata） 的微生物群来调查饮食性质的影响，所有这些都是在循环水产养殖系统中饲养的。在 60 天的时间里，我们跟踪了从商业饲料转向完全基于粉红虾 （Parapenaeus longirostris） 的饮食后肠道细菌多样性、结构和组成的变化。使用 16S rRNA 基因测序 （Illumina MiSeq 平台） 评估肠道细菌群落，引物靶向 V3-V4 高变区。改变饮食 20 天后，与商业饮食喂养的鱼相比，喂虾饲料的鱼的微生物多样性（香农指数）增加，而优势指数值下降。此外，基于 Bray-Curtis 距离的个体间 （beta-） 多样性在饮食治疗之间也有所不同。这些结果进一步支持，由于野生鱼类不可预测的摄食制度和饮食变化，养殖/圈养鱼和野生鱼之间的微生物群比较具有挑战性。然而，饮食对微生物群的影响随着时间的推移而减弱，40 天后个体内部和个体间多样性的差异减小，这表明微生物群落适应了饮食变化。此时，肠道微生物群落也显示出相似的分类组成。 此外，在两种饮食处理下，由属于 Ralstonia、Paraburkholderia、Fulvimonas、Pseudomonas 和 Cutibacterium 属的物种组成的核心微生物群在所有采样时间内都保持。总体而言，本研究作为一种概念方法，表明在彻底改变饮食后肠道微生物群会进行长期适应，这可能是由宿主固有因素驱动的。此外，这些结果对于旨在开发可持续且具有成本效益的成分的饲料制造商来说可能是一个有价值的见解，因为它们表明一些替代饲料和成分不会对鱼肠道微生物群产生不利的长期影响。