Manipulation of quail intestinal microbiome

This study aims to conduct an investigation into the microbial dynamics of avian gut colonisation, using Japanese quail as a model and provides a broad visualisation of bacterial colonisation dynamics within the developing intestinal tract. Japanese quail was selected as a model due to their small size which allows them to fit in mouse isolators even to full sexual maturity which they reach at only 5 weeks post hatch. Bacterial cells in the gut outnumber host cells by a factor of 10 and contribute 100 times more genetic potential when compared to the host genetic contribution. Despite extensive research, the estimated number of culturable bacteria in the human gut represents only approximately 25% of total gut microbiota. This has been determined by the implementation of DNA sequencing methodology that allows us to screen total bacterial community, including the species that are unculturble within laboratory conditions. There are now significant opportunities to manipulate and harness the complex microbiota in the GIT to improve the health and productivity of agricultural animals. Probiotics are defined as viable microorganisms used as a food supplement with proven beneficial effects on the host and many commercial probiotics are available in the agricultural industry, however they have been used in industry with variable to limited success. This thesis outlines the exploration of the microbial communities present in the Japanese quail gastrointestinal tract and the bird’s intestinal physiology. The isolation of quail intestinal probiotic strains and the knowledge of their intestinal role and distribution was then applied to investigate alternative approach in probiotic administration and the role of hygiene in gut microbiota development. ii We first investigated each section of the healthy qual gastrointestinal tract from mouth to cloaca, and provided detailed analysis of the species dynamics and microbiota seeding between the gut sections, as well as their variable contribution to the fecal microbiome. We used histology and electron microscopy to provide the first detailed tour of the quail gut sections focusing on identifying differences between the quail and chicken gut sections and their relevance for health and nutrition. We then isolated the most abundant strain of Lactobacillus from the quail ileum and performed targeted colonisation experiment that showed, for the first time in poultry, that it is possible to achieve near total colonisation with desired strain. The experiment also indicated the consequences of lack of exposure to the host-specific quail microbiome in early days of the gut development.