SalmoSim: Exploring the microbial basis of Atlantic Salmon energetics via
a synthetic intestinal system.
Subject areas: Salmonid biology and microbial ecology; Ecoengineering and
synthetic microbial community design.
Supervisors: Dr. Martin Llewellyn, Dr. Umer Ijaz, Prof. Neil Metcalfe, Prof. Bill Sloan
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. In mice, for example,
transplantation of microbial communities from the gut of obese and lean animals into
germ-free individuals can transmit the corresponding trait. 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), partly 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 first objective will be to establish the link between gut microbiota
and metabolism of wild salmon. The natural diversity of gut microbiota from wild fish
of contrasting metabolic rates can be established via sampling in the Burrishoole
catchment, Co Mayo, Ireland (Dr. P. McGinnity, University College Cork). A second
objective will be to establish a link between gut microbiota and salmon metabolism in
the laboratory. . This will be done for both the freshwater and marine stages of the
salmon’s life cycle (freshwater in Glasgow, marine in Averøy, Norway (Dr. H. Tackle,
Marine Harvest)). Metabolic profile can be established via digestive efficiency,
growth and metabolic rate measurements. The final 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 (Haydon, Helm, Cleaveland, Adams).
The Division of Infrastructure and Environment, School of Engineering has pioneered
the study of environmental microbiota and bioengineering (Quince, Pinto). 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. Our intention is to allow the student to shape multiple
aspects of this project themselves. To achieve this, the scholar will have recourse to
experienced supervision to help them develop skills in: field sampling; 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 1st class
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. This studentship is open to candidates of
any nationality – UK, EU or International.
Application details: Prospective applicants should contact lead supervisor Dr.
Martin Llewellyn (martin.llewellyn@glasgow.ac.uk) to discuss their interest in the
position. Applications for this studentship must be made via the University website
no later than 22 January 2016. The studentship will start in September 2016.