CEFAS: Kill or Cure: Probiotic treatments effects and anti-microbial resistance in Indian aquaculture pond systems.
Probiotics are increasingly used in aquaculture to control diseases and improve feed digestion and pond water quality. This is particularly the case for prawn/shrimp operations, where vaccination against bacterial diseases is not a viable option, as they are largely reliant on non-specific immunological defence mechanisms. However, the impact of most probiotic treatments on crop species health status and pathogen infection levels in aquaculture pond systems is unknown. Whether the net result of treatments reduces the susceptibility of crop species to infection and/or disease or whether the treatments are having any positive effect at all is not known. A concern is that some treatments may increase the diversity and frequency of antimicrobial resistance (AMR) genes and activity with accumulated longer-term detrimental effect.
This PhD project will be allied to a large BBSRC-Newton Fund-DFID-funded GRP project applying novel molecular approaches for advancing prediction and mitigation of disease outbreaks in aquaculture for small scale farmers. Part of that project aims to assess the microbiological effects of the most commonly used water- and feed-based probiotic treatments in Indian east and west coast farms respectively, in which the crop species are prawns. The bacterial composition of some of these treatments is uncertain and importantly, constituents of these probiotic products can be both resistant to antimicrobials and carry well-characterised resistance genes. The effect of adding AMR probionts to the wider development of bacterial resistance in aquaculture ponds is not known.
This PhD studentship will apply high throughput sequencing methods to identify the microbial community composition shifts associated with probiotic treatments in prawn culture ponds. (S)he will carry out additional sequencing of the probiotics themselves that are used in Indian aquaculture to determine the species composition and AMR gene content of the products. A subset of the bacterial isolates that the metagenomics analyses suggest are consistently associated with better performing ponds will be targeted for culture onto specialist agars. Isolates will be screened for their safety and efficacy as probionts, initially through in vitro methods. Additional molecular analyses, including targeted whole genome sequencing, will also be carried out to identify genes that confer both adverse (e.g. potential virulence factors and AMR genes) and advantageous phenotypic properties. Depending on progress and obtaining the required permissions, the final year of the project may see field scale tests of candidate probiont mixtures. The impact of this research is likely to be substantial, by identifying the most effective treatments, and those that have a neutral or detrimental effect and therefore should be discontinued or changed, saving money and increasing yield. Equally importantly, the extent and nature of AMR in the treatments themselves, subsequent effects on the pond and shrimp microbiomes will be revealed for the first time.
The student will benefit from in-house training in cutting edge molecular genetics and statistics at Exeter and in disease (histo)pathology, pathogen culture, aquaculture and business operations at Cefas. The student will spend time at both Exeter and Cefas, balanced by the needs of the experimental work and skills training. (S)he will also accompany the PIs to India on visit(s) as part of the GRP project. PhD studentship truly is an exceptional opportunity for researching into an important area of aquaculture biology with the likelihood of high impact outputs. (S)he will join a large research team with exceptional resources and associated support.