Characterization of mid-intestinal microbiota of farmed Chinook salmon using 16S rRNA gene metabarcoding
Апстракт
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.
Кључне речи:
partial 16S rRNA gene sequencing / mid-intestinal microbiota / farmed salmonИзвор:
Archives of Biological Sciences, 2019, 71, 4, 577-587Издавач:
- Srpsko biološko društvo, Beograd, i dr.
Финансирање / пројекти:
- New Zealand Ministry for Primary Industries (MPI) operational research program [Int13/1]
DOI: 10.2298/ABS190402040C
ISSN: 0354-4664
WoS: 000505766800001
Scopus: 2-s2.0-85083270846
Институција/група
Institut za molekularnu genetiku i genetičko inženjerstvoTY - JOUR AU - Ćirić, Milica AU - Waite, David AU - Draper, Jenny AU - Jones, John Brian PY - 2019 UR - https://imagine.imgge.bg.ac.rs/handle/123456789/1238 AB - 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. PB - Srpsko biološko društvo, Beograd, i dr. T2 - Archives of Biological Sciences T1 - Characterization of mid-intestinal microbiota of farmed Chinook salmon using 16S rRNA gene metabarcoding EP - 587 IS - 4 SP - 577 VL - 71 DO - 10.2298/ABS190402040C ER -
@article{ author = "Ćirić, Milica and Waite, David and Draper, Jenny and Jones, John Brian", year = "2019", abstract = "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.", publisher = "Srpsko biološko društvo, Beograd, i dr.", journal = "Archives of Biological Sciences", title = "Characterization of mid-intestinal microbiota of farmed Chinook salmon using 16S rRNA gene metabarcoding", pages = "587-577", number = "4", volume = "71", doi = "10.2298/ABS190402040C" }
Ćirić, M., Waite, D., Draper, J.,& Jones, J. B.. (2019). Characterization of mid-intestinal microbiota of farmed Chinook salmon using 16S rRNA gene metabarcoding. in Archives of Biological Sciences Srpsko biološko društvo, Beograd, i dr.., 71(4), 577-587. https://doi.org/10.2298/ABS190402040C
Ćirić M, Waite D, Draper J, Jones JB. Characterization of mid-intestinal microbiota of farmed Chinook salmon using 16S rRNA gene metabarcoding. in Archives of Biological Sciences. 2019;71(4):577-587. doi:10.2298/ABS190402040C .
Ćirić, Milica, Waite, David, Draper, Jenny, Jones, John Brian, "Characterization of mid-intestinal microbiota of farmed Chinook salmon using 16S rRNA gene metabarcoding" in Archives of Biological Sciences, 71, no. 4 (2019):577-587, https://doi.org/10.2298/ABS190402040C . .