Molecular taxonomy of prokaryotes

Course unit

title

Scientific direction

Scientific code

Faculty

Department (s)

Molecular taxonomy of prokaryotes

Biology

N 010

Life Sciences Center

Institute of Biosciences

Mode of studies

Number of credits

Mode of studies

Number of credits

Lectures

0

Consultations

3

Self-studies

4

Seminars

0

Aims of course

The objective of the course is to introduce PhD students with the principles of molecular taxonomy of prokaryotes, and to train them to apply these principles in their research work creatively.

Main topics

International Code of Nomenclature of Prokaryotes. Microbial culture collections and their role in taxonomy of prokaryotes. Species – the basic category of prokaryotic taxonomy. Modern species concepts for prokaryotes. The rules and standardized formats for the description of novel species of prokaryotes. The principles, rules and challenges of prokaryotic nomenclature. The concept of genomic species and the category Candidatus in taxonomy. Principles, rules and main methods of taxonomy of cultivable prokaryotes. Type strains of prokaryotic species – the base of modern taxonomy. Traditional DNA-DNA hybridization. Modern alternatives to DNA-DNA hybridization: AAI, ANI, digital DDH. The connection between analysis of 16S rRNA gene and DNA-DNA hybridization. MLSA. Genomic taxonomy. Genome analysis specificity at the level of the different taxons. Genome of a species. Significance of genomic analysis in modern taxonomy of prokaryotes. Taxonomy of uncultivated prokaryotes. The tree of life. Unified taxonomic system for cultivable and uncultivated prokaryotes. NGS in taxonomy of prokaryotes. The problem of the variable number of ribosomal operons and their sequence variability in the NGS approach. Analysis of repetitive elements in taxonomy of prokaryotes. Taxonomic methods in epidemiology and medical microbiology: ribotyping, MLST, VNTR. Numerical boundaries of the different methods in taxonomy. Detailed overview of taxonomy of the indicated group of prokaryotes: methods, problems and their solutions.

Main literature

International Journal of Systematic and Evolutionary Microbiology International Journal of Systematic and Evolutionary Microbiology | Microbiology Society (microbiologyresearch.org)

Systematic and Applied Microbiology Systematic and Applied Microbiology | Journal | ScienceDirect.com by Elsevier

List of prokaryotic names with standing in nomenclature LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net)

Assessment strategy

Assessment criteria

Seminar

Duration of seminar – 30-40 min. Minimum 10 publications published during the last five years must be discussed.

Assessment:

1.     LPSN taxonomy is not followed – a negative score.

2.     The problem isn‘t discussed in detail, the newest methods are not reported and discussed, problematic aspects of the topic are avoided – the score is 5-7.

3.     The problem is discussed in detail, the newest methods are reported and discussed, problematic aspects of the topic are discussed in detail – the score is 8-10.

Nomeda Kuisienė

PhD

Prof.

Approved by the Council of Graduate School of Life Sceinces Center No 600000-…-… on the …. of …… 2021

Chairman