The Gut Microbiome of Juvenile Atlantic Salmon Under Different Feeding Regimes.

Supervisors: David Benahim, Alexandra Leeper (Hólar University College, Iceland).
Global increase in population and a need for food security has resulted in the rapid growth of aquaculture, and necessity to optimise aquafeed usage. For optimal nutrition and feeding in farmed fish, it is crucial to understand the gut microbiome community structure. Atlantic salmon (Salmo salar) is one of the most commercially important fish in Europe, but the aquaculture industry requires innovative changes to reduce its environmental impacts. The juvenile developmental stage represents a crucial period in the life cycle of salmon and is suspected to be characterised by a malleable gut microbiota. Characterisation of the gut microbiome in this stage of growth will be beneficial to understanding nutrition and physiology in greater detail. This study focuses on developing a novel protocol for the extraction of metagenomic DNA from juvenile Atlantic salmon and characterising the gut bacterial communities. The study builds upon a previous study called ProffAqua which was conducted on juvenile Atlantic salmon in which a conventional DNA extraction protocol was used. The sequencing data from this initial trial was analysed and results suggest that the Proteobacteria was the dominant phyla in both control and treated samples(with and without SCP). There was also no significant difference in the alpha diversity of the gut microbiome when the dietary protein type was included. Since this analysis was conducted with a non-standardised protocol not all the samples were successfully amplified. Development of a novel protocol followed investigating, seven DNA extraction methods to optimise DNA extraction and amplification of juvenile Atlantic salmon gut microbiota; out of these two protocols provided optimum results: (1) a modified protocol using the QIAamp Power fecal Pro kit (Qiagen); and (2) a modified protocol using the QIAamp power fecal Pro kit with selective enrichment of prokaryotic DNA. The protocol 7 DNA extraction methods was tested on two types of control samples (a fish meal and a plant-meal diet) the from a feeding trial of juvenile Atlantic salmon that was assessing the effects of single cell protein inclusion on salmon growth. Results show that the selected method was adequate for extracting PCR amplifiable metagenomic DNA from juvenile Atlantic salmon gut samples. Analysis performed on the resulting sequence samples suggest that phylum Firmicutes was dominant (80%) in both control diet fed fish. The dominant class associated with these samples was Bacilli and other classes such as Clostridia, Actinobacteria, and Oxyphotobacteria were present in all samples. At genus level Staphylococcus was the dominant genus both control samples and one another genus detected exclusively in the plant meal diet was Leuconostoc. The results of this study suggest that juvenile Atlantic salmon gut microbiome is more influence by microbiota found in feed than in the tank water. Overall, the study results provide standard method for analysis of feed effects on gut microbiota and basic knowledge to understand the effect of single cell protein on juvenile Atlantic salmon gut.