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In vitro characteristics of an Atlantic salmon (Salmo salar L.) hind gut microbial community in relation to different dietary treatments


Zarkasi, KZ and Taylor, RS and Glencross, BD and Abell, GCJ and Tamplin, ML and Bowman, JP, In vitro characteristics of an Atlantic salmon (Salmo salar L.) hind gut microbial community in relation to different dietary treatments, Research in Microbiology, 168, (8) pp. 751-759. ISSN 0923-2508 (2017) [Refereed Article]

Copyright Statement

Copyright 2017 Institut Pasteur

DOI: doi:10.1016/j.resmic.2017.07.003


In this study, microbial community dynamics were assessed within a simple in vitro model system in order to understand those changes influenced by diet. The abundance and diversity of bacteria were monitored within different treatment slurries inoculated with salmon faecal samples in order to mimic the effects of dietary variables. A total of five complete diets and two ingredients (plant meal) were tested. The total viable counts (TVCs) and sequencing data revealed that there was very clear separation between the complete diets and the plant meal treatments, suggesting a dynamic response by the allochthonous bacteria to the treatments. Automated ribosomal intergenic spacer analysis (ARISA) results showed that different diet formulations produced different patterns of fragments, with no separation between the complete diets. However, plant-based protein ingredients were clearly separated from the other treatments. 16S rRNA Illumina-based sequencing analysis showed that members of the genera Aliivibrio, Vibrio and Photobacterium became predominant for all complete diets treatments. The plant-based protein ingredient treatments only sustained weak growth of the genus Sphingomonas. In vitro based testing of diets could be a useful strategy to determine the potential impact of either complete feeds or ingredients on major fish gastrointestinal tract microbiome members.

Item Details

Item Type:Refereed Article
Keywords:gut microbiome, salmon feeds, in-vitro model, 16S rRNA gene, dietary treaments, intestinal bacteria, Atlantic salmon
Research Division:Biological Sciences
Research Group:Microbiology
Research Field:Microbial ecology
Objective Division:Animal Production and Animal Primary Products
Objective Group:Fisheries - aquaculture
Objective Field:Aquaculture fin fish (excl. tuna)
UTAS Author:Zarkasi, KZ (Mr Kamarul Zarkasi)
UTAS Author:Tamplin, ML (Professor Mark Tamplin)
UTAS Author:Bowman, JP (Associate Professor John Bowman)
ID Code:121542
Year Published:2017
Web of Science® Times Cited:17
Deposited By:Agriculture and Food Systems
Deposited On:2017-10-02
Last Modified:2018-06-05

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