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

• Published in: Research in Microbiology
• Main Authors: Zarkasi, Kamarul Zaman, Taylor, Richard S, Glencross, Brett, Abell, Guy C J, Tamplin, Mark L, Bowman, John P
• Other Authors: University of Science, Malaysia (USM), Commonwealth Scientific and Industrial Research Organisation (CSIRO), Institute of Aquaculture, University of Tasmania, orcid:0000-0003-1167-8530
• Format: Article in Journal/Newspaper
• Language: English
• Published: Elsevier 2017
• Subjects: Intestinal bacteria; In vitro model system; 16S rRNA gene; Dietary treatments; Atlantic salmon; Salmo salar
• Online Access: http://hdl.handle.net/1893/25845; https://doi.org/10.1016/j.resmic.2017.07.003; http://dspace.stir.ac.uk/bitstream/1893/25845/1/Zarkasi_et_a_2017-GOA_version.pdf

In this study, microbial community dynamics were assessed within a simple invitro 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,Vibrioand Photobacteriumbecame predominant for all complete diets treatments. The plant-based protein ingredient treatments only sustained weak growth of the genusSphingomonas. Invitro 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.