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High-throughput sequencing of the chicken gut microbiome

Duggett, Nicholas, A (2016)
Ph.D. thesis, University of Birmingham.

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Abstract

The chicken (\(Gallus\) \(gallus\) \(domesticus\)) is the most abundant and widely distributed livestock animal with a global population of over 21 bill ion. A newly hatched broiler chick increases its body weight by 25% overnight and 50-fold over five weeks. The symbiotic, complex and variable community of the microbiome forms an important part of the gastrointestinal tract (gut). It is involved in gut development, biochemistry, immunology, physiology and non-specific resistance to infection. This study investigated the chicken gut microbiota using high-throughput 16S rRNA sequencing and culture-based techniques. There was specific interest in the proventriculus of which there is limited research currently in the literature and the caecum because it contains the highest density of bacterial cells in the gut at 10\(^1\)\(^1\) per gram. The results showed no significant difference in the first stages of the gut which shared a low-diversity microbiota dominated by a few \(Lactobacillus\) species. The microbiota becomes more diverse in the latter pa1ts of the small intestine where \(C/ostridiales\) and \(Enterobacteriaceae\) were present in higher numbers. The caecum was the most diverse organ with the majority of species belonging to Ruminococcaceae, Lachnospiraceae and \(Alistipes\). A number of novel species were isolated from the chicken gut and six of these were whole-genome sequenced.

Type of Work:Ph.D. thesis.
Supervisor(s):Pallen, Mark J. and Penn, Charles
School/Faculty:Colleges (2008 onwards) > College of Life & Environmental Sciences
Department:School of Biosciences
Subjects:QR Microbiology
Institution:University of Birmingham
ID Code:6678
This unpublished thesis/dissertation is copyright of the author and/or third parties. The intellectual property rights of the author or third parties in respect of this work are as defined by The Copyright Designs and Patents Act 1988 or as modified by any successor legislation. Any use made of information contained in this thesis/dissertation must be in accordance with that legislation and must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the permission of the copyright holder.
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