Trong Thuc Nguyen (MSc Thesis 2020)
Development of a multi locus high throughput assay for identification of Vibrio species: an in silico approach.
|Supervisors: Frederico Batista(Centre for Environment Fisheries & Aquaculture Science – Cefas), Jaime Martinez-Urtaza (University of Barcelona)
|Vibrio, a genus of aquatic bacteria, is notable for including many pathogens of marine animalsand humans. The development of fast and precise methods to identify Vibrios at the species levelis required to improve the diagnostic of diseases caused by these bacteria and the research of themicrobiological community. The traditional method to identify Vibrios, based on sequencingfragments of the 16S rRNA gene, has some limitations mainly caused by the high geneticsimilarity between some species of Vibrio and the presence of several copies of this gene in thebacterial genome. The objective of the present study was to assess the suitability of the full-length sequence of 16S rRNA, fur, and GroL genes to identify Vibrios at the species level. Theanalysis of the intragenomic, intraspecies, and interspecies diversity of full-length 16S rRNAgene showed its limitation to differentiate closely related species. Moreover, a high throughputnanopore sequencing assay targeting the 16S rRNA gene was used to analyse Vibrio mockcommunities. The results of this assay confirmed that even when using the complete 16S rRNAgene sequence, this marker is still not able to differentiate closely related Vibrio species. The insilicoresults indicated the ability to use fur and GroLgenes to improve taxonomy assignment ofVibrios at the species level. Additional experiments are needed to confirm the effectiveness ofthese markers using high throughput sequencing methods for the detection and identification of Vibrios.