Characterization of mid-intestinal microbiota of farmed Chinook salmon using 16S rRNA gene metabarcoding

被引:18
|
作者
Ciric, Milica [1 ,3 ]
Waite, David [2 ,4 ]
Draper, Jenny [1 ,5 ]
Jones, John Brian [1 ,6 ]
机构
[1] Minist Primary Ind, Invest & Diagnost Ctr, Anim Hlth Lab, 66 Ward St, Upper Hutt, New Zealand
[2] Minist Primary Ind, Invest & Diagnost Ctr, Plant Hlth & Environm Lab, POB 2095, Auckland, New Zealand
[3] Univ Belgrade, Inst Mol Genet & Genet Engn, Vojvode Stepe 444a, Belgrade 11010, Serbia
[4] Univ Queensland, Sch Chem & Mol Biosci, Australian Ctr Ecogen, St Lucia, Qld 4072, Australia
[5] Inst Environm Sci & Res Ltd ESR, Kenepuru Sci Ctr, 34 Kenepuru Dr,Porirua 5022,POB 50348, Porirua 5240, New Zealand
[6] Murdoch Univ, 90 South St, Murdoch, WA 6150, Australia
关键词
farmed salmon; mid-intestinal microbiota; partial 16S rRNA gene sequencing; GUT BACTERIAL COMMUNITIES; ATLANTIC SALMON; RAINBOW-TROUT; MOLECULAR ANALYSIS; SALAR L; FISH; DIVERSITY; WALBAUM; SHAPE;
D O I
10.2298/ABS190402040C
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
With the growing importance of aquaculture worldwide, characterization of the microbiota of high-value aquaculture species and identification of their shifts induced by changes in fish physiology or nutrition is of special interest. Here we report the first 16S rRNA gene metabarcoding survey of the mid-intestinal bacteria of Chinook salmon (Oncorhynchus tshawytscha), an economically important aquacultured species. The microbiota of 30 farmed Chinook salmon from a single cohort was surveyed using metabarcode profiling of the V3-V4 hypervariable region of the bacterial 16S rRNA gene. Seawater, feed and mid-intestinal samples and controls were sequenced in quadruplicate to assess both biological and technical variation in the microbial profiles. Over 1000 operational taxonomic units were identified within the cohort, providing a first glimpse into the mid-intestinal microbiota of farmed Chinook salmon. The taxonomic distribution of the salmon microbiota was reasonably stable, with around two thirds of individuals dominated by members of the family Vibrionaceae. We anticipate that the workflow presented in this paper could be applied in other aquacultured fish species to capture variation or dysbiosis occurring as a result of changes in feed, health or environmental conditions.
引用
收藏
页码:577 / 587
页数:11
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