Nové fylogenetické markery použitelné v taxonomii řádu Lactobacillales, čeledí Bifidobacteriaceae a Propionibacteriaceae

Ing. Chahrazed Mekadim

Doctoral thesis

Abstract:

Classification and genotyping of bacteria have been primarily performed using DNA-DNA hybridization and 16S rRNA gene sequencing techniques until the beginning of the 21st century. However, the application of the DNA-DNA technique revealed many issues. It is cost-intensive, time-consuming and require specialized instruments. There are many shortcomings associated with the usage of 16S rRNA gene comparative analyzes. Phylogenetics, classification and ecological studies based on the 16S rRNA gene can be misleading due to the presence of different copies in genomes. An alternative approach of genome similarity and relatedness has been presented recently. Taxonomists characterized genes that may replace to a certain extent the phylogenomic analyzes and be specific for particular phylogenetic groups of bacterial strains: called housekeeping genes. Many molecular markers have been proposed for different taxonomic bacterial groups. Nevertheless, none of them has been applicable for different genera of the order Lactobacilles, where different species classified into various genera are taxonomically close. Also, alternative phylogenetic markers have been tested just for a low number of different strains of the Bifidobacteriaceae family. No unique identification marker has been suggested to be used for classification and identification of strains within valuable genera of the family Propionibacteriaceae yet.Therefore, the objectives of the presented PhD thesis are: i) to find novel alternative molecular markers for classification, genotyping, identification and phylogenetic analyzes of bacterial order Lactobacillales, Bifidobacteriaceae and Propionibacteriaceae families, ; ii) to test their functionality and specificity with the selected representative strains ; iii) to select the candidate molecular markers that offer a higher level of discrimination among species and lower taxonomic units; and iv) to select appropriate molecular markers simulating, at least to some extent, taxonomy based on complete genomic analysis.

Keywords

molecular/phylogenetic marker, phylogenetic analysis, Lactobacillales, Bifidobacteriaceae, Propionibacteriaceae

Jazyk práce: English

Datum vytvoření / odevzdání či podání práce: 22. 8. 2019

Obhajoba závěrečné práce

• Vedúci: prof. Ing. Eva Vlková, Ph.D.
• Oponent: Jan Kopečný, externi, Ivo Sedláček, Ing., externi, Dagmar Šrůtková, externi

Czech University of Life Sciences Prague

Faculty of Agrobiology, Food and Natural Resources

Doctoral programme / odbor:
Animal Science / General Animal Science