Date of Award


Document Type

Master Thesis

Degree Name

Masters of Science (Research)


Cork Institute of Technology

First Advisor

Dr. Shea Fanning

Second Advisor

Dr Philippe Glaser, Institut Pasteur


In the last few years, genomics has profoundly changed research in the biological sciences and in particular in microbiology. Recent studies have demonstrated that comparative genomics is a powerful approach contributing to a deeper understanding of the evolution of microorganisms. Bacterial collections are important resources of microorganisms, however, the potential that genomics has to offer remains to be realised as it is still virtually absent in any study involving strain collections. This feature thus framed the experimental objectives for this study, whose aim was to define the most comprehensive way to apply genomic based methods (high throughput sequencing and bioinformatics) to a strain collection in order to solve the critical problem of microbial identification and classification.

The study selected the Coryneform group of organisms, as it constituted a heterogeneous bacterial population, posing a unique technical challenge, containing bacteria which are normally difficult to classify using traditional approaches. Initially a preliminary analysis was performed on the Corynehacterium genus. A total of 207 bacteria of this genus (61 type strains [including 4 non validated isolates], 106 Corynebacterium sp., and 41 C. diphtheriae strains), were obtained from the Collection of the Institut Pasteur (CIP).

Strategies used included 16S rRNA sequencing of all isolates together with multilocus sequence typing for strains of the same species.

The type strains were first analysed to construct a broad phylogenetic tree, which also contained the sequences of as yet unidentified Corynebacterium sp. The majority of IX these were identified within the tree, but some did not cluster with any of the type strains, thus corresponding to new species. Genomic results data obtained were also compared with the already available phenotypic results from the curators of the CIP collection. Sequencing of two selected house-keeping genes (recA and gyrB) was successfully performed for strains of the C. diphtheriae species.

In a final complementary section, to demonstrate the use of the phylogenetic data obtained on the genus corynebacterium, the 16S rRNA gene sequencing strategies developed were applied to surface cheese samples in an attempt to identify any coryneform bacteria present. The latter showed the presence of coryneform along with the biodiversity that naturelly occurs on the surface of the selected cheeses.

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Bacteriology Commons