Environmental and physiological factors shape the gut microbiota of Atlantic salmon parr (Salmo salar L.).
Environmental and physiological factors shape the gut microbiota of Atlantic salmon parr (Salmo salar L.).
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DOI：
10.1016/j.aquaculture.2016.07.017
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发表时间：
2017-01-20
期刊：
影响因子：
--
通讯作者：
Martin SA
中科院分区：
文献类型：
--
作者：
Dehler CE;Secombes CJ;Martin SA
肠道微生物是宿主免疫系统启动、保护和发育的关键角色，也为宿主提供了原本无法获得的营养。由于这一重要性，研究宿主和微生物之间的联系正在开始在养殖鱼类。肠道菌群的建立、维持和随后的变化是决定未来鱼类生理和营养的核心。与哺乳动物不同，鱼类的肠道微生物被认为是在第一次进食时主要从周围的水中获得的，因此它们的微生物组成随着时间的推移是由它们的栖息地形成的。在这里，我们比较了在循环实验室水族箱中饲养的大西洋鲑鱼幼鱼和在商业养鱼场开放的淡水湖泊环境中网箱养殖的年龄匹配的大西洋鲑鱼幼鱼的远端肠道微生物群，以建立淡水阶段肠道中的微生物特征，并调查是否存在一个稳定的细菌亚群，而不管栖息地类型如何。我们对16S rRNA基因的两个可变区域进行了深度测序，每个样本的平均读取深度为180144±12096个原始序列。本研究中使用的所有个体鱼至少有30,000个质量控制读数，对应于每个样本平均342±19个操作分类单位（OTUs），主要映射到厚壁菌门，变形菌门和微内门。结果表明，两组间物种丰富度具有可比性，但两组间肠道菌群组成存在显著差异。此外，鉴定出19个OTUs的核心微生物群，无论处理组如何，所有样品都共有，主要由变形菌门、拟杆菌门和厚壁菌门成员组成。分别测定了各饲养群体的核心微生物群（观景鱼：19 + 4（共23个）OTUs，湖鱼：19 + 13（共32个）OTUs），表明在两种生境中微生物的获得或损失是不同的，但也表明宿主内部存在选择力，为特定的细菌类群提供了生态位。Illumina MiSeq方法在本研究中收集的新信息将有助于理解和定义淡水中健康大西洋鲑鱼的肠道微生物群，并扩展先前使用DGGE， TGGE和T-RFPL的研究。监测这些特征的偏差，特别是无论栖息地类型如何都存在的核心微生物，可能在未来被用作由次优饲料或农场环境中传染病引起的肠道健康问题的早期指标。微生物群对肠道健康、局部免疫功能和营养吸收至关重要。我们使用深度测序方法来显示大西洋鲑鱼的饲养条件差异。这项工作引起了水产营养学家的兴趣。大西洋鲑鱼（Salmo salar）在其远端肠道食糜中蕴藏着大量多样的微生物群。鉴定出所有样品共有的核心微生物群和附属群核心微生物群。两个饲养组表现出不同的肠道菌群特征，具有独特的群体特异性微生物。肠道菌群的维持是一个复杂的过程，受环境因素和宿主生理因素的影响。
Gut microbes are key players in host immune system priming, protection and development, as well as providing nutrients to the host that would be otherwise unavailable. Due to this importance, studies investigating the link between host and microbe are being initiated in farmed fish. The establishment, maintenance and subsequent changes of the intestinal microbiota are central to define fish physiology and nutrition in the future. In fish, unlike mammals, acquiring intestinal microbes is believed to occur around the time of first feeding mainly from the water surrounding them and their microbial composition over time is shaped therefore by their habitat. Here we compare the distal intestine microbiota of Atlantic salmon parr reared in a recirculating laboratory aquarium with that of age matched parr maintained in cage culture in an open freshwater loch environment of a commercial fish farm to establish the microbial profiles in the gut at the freshwater stage and investigate if there is a stable subset of bacteria present regardless of habitat type. We used deep sequencing across two variable regions of the 16S rRNA gene, with a mean read depth of 180,144 ± 12,096 raw sequences per sample. All individual fish used in this study had a minimum of 30,000 quality controlled reads, corresponding to an average of 342 ± 19 Operational Taxonomic Units (OTUs) per sample, which predominantly mapped to the phyla Firmicutes, Proteobacteria, and Tenericutes. The results indicate that species richness is comparable between both treatment groups, however, significant differences were found in the compositions of the gut microbiota between the rearing groups. Furthermore, a core microbiota of 19 OTUs was identified, shared by all samples regardless of treatment group, mainly consisting of members of the phyla Proteobacteria, Bacteroidetes and Firmicutes. Core microbiotas of the individual rearing groups were determined (aquarium fish: 19 + 4 (total 23) OTUs, loch fish: 19 + 13 (total 32) OTUs), indicating that microbe acquisition or loss is occurring differently in the two habitats, but also that selective forces are acting within the host, offering niches to specific bacterial taxa. The new information gathered in this study by the Illumina MiSeq approach will be useful to understand and define the gut microbiota of healthy Atlantic salmon in freshwater and expand on previous studies using DGGE, TGGE and T-RFPL. Monitoring deviations from these profiles, especially the core microbes which are present regardless of habitat type, might be used in the future as early indicator for intestinal health issues caused by sub optimal feed or infectious diseases in the farm setting. The Microbiome is central to gut health, local immune function and nutrient up take. We have used deep sequencing approach to show differences in rearing conditions of Atlantic salmon. This work is of interest to aquaculture nutritionists. Atlantic salmon (Salmo salar) parr harbour a vast diversity of microbiota in their distal intestine digesta. A core microbiota shared by all samples and accessory group core microbiotas were identified. Both rearing groups showed distinct intestinal microbiota profiles, with unique group-specific microbes. Maintenance of intestinal microbiota is a complex process, dictated by both environmental factors and host physiology.
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DOI：
10.1126/science.1195568
发表时间：
2010-12-24
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Lee YK;Mazmanian SK
通讯作者：
Mazmanian SK
影响因子：
14.9
作者：
Klindworth A;Pruesse E;Schweer T;Peplies J;Quast C;Horn M;Glöckner FO
通讯作者：
Glöckner FO
影响因子：
4.5
作者：
Ingerslev, H. -C.;Jorgensen, L. von Gersdorff;Madsen, L.
通讯作者：
Madsen, L.
影响因子：
14.9
作者：
Liu Z;Lozupone C;Hamady M;Bushman FD;Knight R
通讯作者：
Knight R
影响因子：
--
作者：
Austin B
通讯作者：
Austin B