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Atlantic Salmon (Salmo salar L.) Gastrointestinal Microbial Community Dynamics in Relation to Digesta Properties and Diet

  • Microbiology of Aquatic Systems
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Abstract

To better understand salmon GI tract microbial community dynamics in relation to diet, a feeding trial was performed utilising diets with different proportions of fish meal, protein, lipid and energy levels. Salmon gut dysfunction has been associated with the occurrence of casts, or an empty hind gut. A categorical scoring system describing expressed digesta consistency was evaluated in relation to GI tract community structure. Faster growing fish generally had lower faecal scores while the diet cohorts showed minor differences in faecal score though the overall lowest scores were observed with a low protein, low energy diet. The GI tract bacterial communities were highly dynamic over time with the low protein, low energy diet associated with the most divergent community structure. This included transiently increased abundance of anaerobic (Bacteroidia and Clostridia) during January and February, and facultatively anaerobic (lactic acid bacteria) taxa from February onwards. The digesta had enriched populations of these groups in relation to faecal cast samples. The majority of samples (60–86 %) across all diet cohorts were eventually dominated by the genus Aliivibrio. The results suggest that an interaction between time of sampling and diet is most strongly related to community structure. Digesta categorization revealed microbes involved with metabolism of diet components change progressively over time and could be a useful system to assess feeding responses.

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Abbreviations

GI:

Gastrointestinal

DE:

Digestible energy

SGS:

Summer Gut Syndrome

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Acknowledgments

Thanks are extended to the Australian Seafood Cooperative Research Centre, Tassal Group and Skretting Australia for in-kind support and research funding (project 2011/701). The authors would also like to thank Dave Cameron for fish husbandry, Ben Maynard for assistance with research field sample preparation, Warren Muller for statistical advice on the cage trial and David Ratkowsky for statistical advice and discussions related to the experiments presented in this manuscript.

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Authors and Affiliations

  1. School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia

    Kamarul Zaman Zarkasi

  2. Tasmanian Institute of Agriculture, Food Safety Centre, University of Tasmania, Hobart, Tasmania, Australia

    Kamarul Zaman Zarkasi, Mark L. Tamplin & John P. Bowman

  3. CSIRO Agriculture, Hobart, Tasmania, Australia

    Richard S. Taylor & Guy C. J. Abell

  4. University of Stirling, Institute of Aquaculture, Stirling, Scotland, UK

    Brett D. Glencross

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  1. Kamarul Zaman Zarkasi
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Correspondence to Kamarul Zaman Zarkasi.

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All animal handling procedures were approved by the Tasmanian Department of Primary Industries, Parks, Water and Environment (DPIPWE) Animal Ethics Committee (Project 30/2009-10) under the guidelines of the Australian Code of Practice.

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Zarkasi, K.Z., Taylor, R.S., Abell, G.C.J. et al. Atlantic Salmon (Salmo salar L.) Gastrointestinal Microbial Community Dynamics in Relation to Digesta Properties and Diet. Microb Ecol 71, 589–603 (2016). https://doi.org/10.1007/s00248-015-0728-y

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