SalmoSim: the development of a three-compartment in vitro simulator of the Atlantic salmon GI tract and associated microbial communities.
SalmoSim: the development of a three-compartment in vitro simulator of the Atlantic salmon GI tract and associated microbial communities.
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DOI：
10.1186/s40168-021-01134-6
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发表时间：
2021-08-31
期刊：
影响因子：
15.5
通讯作者：
Llewellyn M
中科院分区：
文献类型：
--
作者：
Kazlauskaite R;Cheaib B;Heys C;Ijaz UZ;Connelly S;Sloan W;Russel J;Rubio L;Sweetman J;Kitts A;McGinnity P;Lyons P;Llewellyn M
水产养殖部门目前占人类消费鱼类总量的近50%，预计到2030年将提供62%。正在寻求创新战略来改进鱼饲料和饲料添加剂，以提高鱼的生产性能、福利和水产养殖业的环境可持续性。关于硬骨鱼肠道微生物群在鱼类营养中的重要性和功能，人们仍然缺乏认识。体外肠道模型系统可能是研究饲料和添加剂对宿主微生物群落影响的有价值的工具。几种针对单胃脊椎动物的体外肠道模型现已投入使用。在这里，我们报告了大西洋鲑鱼肠道模型SalmoSim的发展，以模拟三个肠道区室（胃，幽门盲肠和中肠）和相关的微生物群落。肠道模型是在一系列连接的生物反应器中建立的，该生物反应器中植入了来自养殖的成年海洋期鲑鱼的生物材料。我们首先旨在获得稳定的微生物组组成，代表来自大西洋鲑鱼的创始微生物群落。然后，在生物重复试验中，比较了体外系统对两种不同饲料配方（鱼粉和无鱼粉）的反应，并进行了40天的平行体内试验。采用基于16S rDNA测序qPCR的元条形码、氨态氮和挥发性脂肪酸的测定来调查微生物群落动态和功能。20天后，SalmoSim菌群与初始接种菌群难以区分（p = 0.230），最丰富的属（如Psycrobacter， Staphylococcus, Pseudomonas）在SalmoSim菌群中增殖（OTUs占与初始菌群共享的所有reads的98%）。真正的鲑鱼和SalmoSim对新饲料的反应相似，大多数类群（96%的鲑鱼，97%的SalmoSim）不受影响，而一小部分类群（例如一小部分Psychrobacter）在两个系统中受到不同的影响。与新型饲料对微生物发酵活性的影响较小一致，SalmoSim饲喂前后挥发性脂肪酸谱无显著差异。通过建立稳定和具有代表性的鲑鱼肠道群落，本研究代表了体外肠道系统作为改善鱼类营养和福利的工具的发展的重要一步。本文中描述的系统开发步骤可以作为开发代表其他鱼类的各种其他系统的指导方针。包括SalmoSim在内的这些系统旨在用作新饲料成分和添加剂的预筛选工具，并用于研究微生物组动力学和组装的抗菌素耐药性和转移以及基本生态过程。视频摘要在线版本包含补充材料，可在10.1186/s40168-021-01134-6获得。
The aquaculture sector now accounts for almost 50% of all fish for human consumption and is anticipated to provide 62% by 2030. Innovative strategies are being sought to improve fish feeds and feed additives to enhance fish performance, welfare, and the environmental sustainability of the aquaculture industry. There is still a lack of knowledge surrounding the importance and functionality of the teleost gut microbiome in fish nutrition. In vitro gut model systems might prove a valuable tool to study the effect of feed, and additives, on the host’s microbial communities. Several in vitro gut models targeted at monogastric vertebrates are now in operation. Here, we report the development of an Atlantic salmon gut model, SalmoSim, to simulate three gut compartments (stomach, pyloric caecum, and midgut) and associated microbial communities. The gut model was established in a series of linked bioreactors seeded with biological material derived from farmed adult marine-phase salmon. We first aimed to achieve a stable microbiome composition representative of founding microbial communities derived from Atlantic salmon. Then, in biological triplicate, the response of the in vitro system to two distinct dietary formulations (fishmeal and fishmeal free) was compared to a parallel in vivo trial over 40 days. Metabarcoding based on 16S rDNA sequencing qPCR, ammoniacal nitrogen, and volatile fatty acid measurements were undertaken to survey the microbial community dynamics and function. SalmoSim microbiomes were indistinguishable (p = 0.230) from their founding inocula at 20 days and the most abundant genera (e.g., Psycrobacter, Staphylococcus, Pseudomonas) proliferated within SalmoSim (OTUs accounting for 98% of all reads shared with founding communities). Real salmon and SalmoSim responded similarly to the introduction of novel feed, with majority of the taxa (96% Salmon, 97% SalmoSim) unaffected, while a subset of taxa (e.g., a small fraction of Psychrobacter) was differentially affected across both systems. Consistent with a low impact of the novel feed on microbial fermentative activity, volatile fatty acid profiles were not significantly different in SalmoSim pre- and post-feed switch. By establishing stable and representative salmon gut communities, this study represents an important step in the development of an in vitro gut system as a tool for the improvement of fish nutrition and welfare. The steps of the system development described in this paper can be used as guidelines to develop various other systems representing other fish species. These systems, including SalmoSim, aim to be utilised as a prescreening tool for new feed ingredients and additives, as well as being used to study antimicrobial resistance and transfer and fundamental ecological processes that underpin microbiome dynamics and assembly. Video abstract The online version contains supplementary material available at 10.1186/s40168-021-01134-6.
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