# High-throughput sequencing of the chicken gut microbiome

Duggett, Nicholas, A (2016). High-throughput sequencing of the chicken gut microbiome. University of Birmingham. Ph.D.

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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: Thesis (Doctorates > Ph.D.)
Award Type: Doctorates > Ph.D.
Supervisor(s):
Supervisor(s)EmailORCID
Pallen, Mark J.UNSPECIFIEDUNSPECIFIED
Penn, CharlesUNSPECIFIEDUNSPECIFIED
Licence:
College/Faculty: Colleges (2008 onwards) > College of Life & Environmental Sciences
School or Department: School of Biosciences
Funders: Biotechnology and Biological Sciences Research Council
Subjects: Q Science > QR Microbiology
URI: http://etheses.bham.ac.uk/id/eprint/6678

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