PhD Studentship at The University of Nottingham

Outstanding international students are invited to apply for a PhD scholarship in bioinformatics at The University of Nottingham. Applications are welcome before August 31, 2019.

Research Title

Effect of the prebiotic Galacto-oligosaccharide on the young pig.

Physiological, environmental, and social stressors at weaning lead to production/health problems in commercial pigs such as infectious and non-infectious diarrhoea and lack of feed intake. In addition, intestinal microbiota which protects the pre-weaning pig from infection and promotes gut health is perturbed at weaning These stressors combined with microbiota disruption causes cause the "post weaning growth check" with severe economic losses to pig producers, significantly lengthening the time it takes pigs to reach market weight The use of sub-therapeutic levels of antibiotics has been an effective strategy in this context but the practice has resulted in the emergence of antibiotic resistant bacteria that can disseminate the determinants and enter the human food chain. This practice is now banned in Europe and could become the case elsewhere as the dangers of antibiotic resistance arising from agricultural practice are realised internationally. Prebiotics are non-digestible feed ingredients that can be metabolized by specific members of intestinal microbiota to provide health benefits for the host. It has been evident for decades that the optimization of the gut microbiota of pigs by dietary intervention results in better productivity and fewer veterinary interventions. Here we propose to study the effect of the Prebiotic GOS (Galacto-oligosaccharide) available as Dairy Crest product Nutrabiotic GOS which we hypothesize will stabilize/enhance gut microbiota around the time of weaning and promote gut health.

Effect of prebiotic on zootechnical data: The student will assist in the design, execution and analysis of pig performance trials using prebiotics incorporated into creep feed. Initial trials have focussed on probiotic where we have seen an effect on performance (Le Bon et al, Livestock Science, 133, 179-181) but will be extended to prebiotics. These studies will be undertaken in small weaning pen trials through to commercial trials to enable feed conversion ratio (FCR), rate of feed intake and mortality data to be examined under different conditions, for example, the different stocking densities encountered and differing environmental challenges to the pigs and the resident gut microbiota

Metagenomic approaches: Developmental profiles of the intestinal microbiota of pigs on matched diets with and without GOS will be established using V4 variable domains of 16S rRNA bacterial gene sequences collected on the Illumina MiSeq platform. These data will be analysed using a combination of taxonomic and bioinformatic approaches available within the Mothur program suite (Kozich et al.,Appl Environ Microbiol. 79:5112-20) . Here we will analyse the effect of prebiotic on changes in microbiota following weaning. In addition from these data members of the microbial community will be identified that respond to GOS. Using existing databases and those derived from the project class-specific primers will be designed (based on the gene sequence families within the Operational Taxonomic Units), and these used verify the response to GOS in pigs by quantitative-real time PCR

Recovery of commensal bacteria responding to GOS: For those organisms that have database entries that can be cultured we will attempt to recover prebiotic responsive organisms from the pig intestinal milieu using a combination of culture on selective culture media and DNA hybridisation using species specific probes designed as above or from database entries. Candidate commensal bacterial species will enable studies that examine the causal relationships between prebiotic application and gut health. The candidate GOS responsive isolates will be examined for their growth, competitive index against other species and metabolic profiles (for example, the production of volatile fatty acids) in vitro before being prioritised and fed to pigs with and without GOS to determine effects on their zootechnical performance where the animal will be monitored for any common challenges such as zoonotic pathogens Enterotoxigenic Escherichia coli (ETEC) and Salmonella.

Combating neonatal pathogens: Another aspect of the project is to determine if feeding GOS to sows increases the quality of the colostrum and thereby prevents a neonatal pathogen (Rotavirus) transmission. To do this GOS will be fed to sows and the quality of the colostrum will be measured using an ELISA testing for antibodies against rotavirus. In addition we will test transmission of rotavirus to neonatal pigs using Q-PCR.

Applicant will receive a Stipend of 18,009, University fees will also be covered. This position is restricted to UK and EU nationals who meet the residence criteria.


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