title: Atlantic Salmon (Salmo salar L.) Gastrointestinal Microbial Community Dynamics in Relation to Digesta Properties and Diet.
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.
authors.affiliation: School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia. kamarul.zarkasi@gmail.com.|Tasmanian Institute of Agriculture, Food Safety Centre, University of Tasmania, Hobart, Tasmania, Australia. kamarul.zarkasi@gmail.com.
authors.forename: Kamarul Zaman
authors.initials: KZ
authors.lastname: Zarkasi
authors.affiliation: CSIRO Agriculture, Hobart, Tasmania, Australia.
authors.forename: Richard S
authors.initials: RS
authors.lastname: Taylor
authors.affiliation: CSIRO Agriculture, Hobart, Tasmania, Australia.
authors.forename: Guy C J
authors.initials: GC
authors.lastname: Abell
authors.affiliation: Tasmanian Institute of Agriculture, Food Safety Centre, University of Tasmania, Hobart, Tasmania, Australia.
authors.forename: Mark L
authors.initials: ML
authors.lastname: Tamplin
authors.affiliation: University of Stirling, Institute of Aquaculture, Stirling, Scotland, UK.
authors.forename: Brett D
authors.initials: BD
authors.lastname: Glencross
authors.affiliation: Tasmanian Institute of Agriculture, Food Safety Centre, University of Tasmania, Hobart, Tasmania, Australia.
authors.forename: John P
authors.initials: JP
authors.lastname: Bowman
mesh_terms: D000821:Animal Feed / Q000032:analysis*; D000818:Animals; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D004063:Digestion; D000069196:Gastrointestinal Microbiome; D041981:Gastrointestinal Tract / Q000378:metabolism / Q000382:microbiology*; D020317:Salmo salar / Q000378:metabolism / Q000382:microbiology*
keywords: 16S rRNA gene; Atlantic salmon; Diet formulations; Digesta properties; Intestinal bacteria