SalmoSim: Exploring the microbial basis of Atlantic Salmon energetics via a synthetic intestinal system.

Stipend: Industry funded PhD (Alltech)
Start Date: As soon as possible after successful interview

The problem: The expansion of the Salmonid aquaculture industry is unsustainable given the current reliance on over-exploited wild fish stocks as the protein and lipid food source, and poor growth efficiency on alternative plant-based feeds. This situation presents many new challenges to both fish and farmer.
One cause of poor growth efficiency is inefficient digestion (which also leads to pollution from fecal waste), linked to the fish’s metabolic rate. Intestinal microbiota are known to play a central role in nutritional energy harvest, including contributions to host carbohydrate and lipid metabolism in vertebrates. Microbial modification of host metabolism and regulation of fat storage, as well as provision of short chain fatty acids from otherwise indigestible polysaccharides, are all thought to drive growth and fat deposition. A greater understanding of these processes could therefore reveal routes to improve growth efficiency of fish fed on plant-based diets, but this requires a novel experimental approach.

Aim: This interdisciplinary PhD project will explore the contribution of the salmon gut microbiome to observed variation in host energetics (absorption, metabolism, growth), by creating an artificial ‘fish gut’ which will act as a test-bed for salmon microbial fermentation of novel feeds as well as the effectiveness of pro, pre and synbiotics.

Methodology: The principal objective will be to establish a synthetic, continuous culture salmon gut microbial system to explore the role of different microbial communities in affecting the host fish’s digestive efficiency. Using our environmental microbiology laboratory, School of Engineering, a replicated series of linked bioreactors can be established simulating salmon gut compartments (stomach, pyloric caecum, mid-intestine, posterior intestinal segment) representing generalized marine and freshwater lifecycle stages. These bioreactors will be seeded with salmon microbiota collected from the laboratory and their ability to maintain natural community species compositions and mirror natural energetic profiles will be monitored. All microbial diversity profiling will be achieved cutting edge metagenomic sequencing approached and bionformatic pipelines.

The learning experience: The University of Glasgow is a Russell Group university (top 24 leading UK universities). The Institute of Biodiversity, Animal Health and Comparative Medicine links research on animal diseases, production and welfare with ecological and evolutionary approaches. The Division of Infrastructure and Environment, School of Engineering has pioneered the study of environmental microbiota and bioengineering. Alltech is a leading agricultural biotechnology company making important inroads into the aquafeeds sector The aim of this project is to provide the scholar with a multidisciplinary training environment (including significant interactions with industrial partners and overseas collaborators) to allow them to develop academically and technically into a competent and independent researcher. The scholar will have recourse to experienced supervision to help them develop skills in: fish husbandry; respirometry and calorimetry; molecular biology; bioinformatics of metagenomics datasets; microbiology (including bioreactor design and management) and more.

Personal Specification: We are looking for an exceptionally motivated and talented student to fill this generously funded position. The student should have a 2.1 undergraduate degree (or equivalent) in a biological or engineering field and a demonstrable interest and aptitude in one or more aspects of this project. A master’s degree is preferable but not essential.