E4050 Metagenomics

Faculty of Science
Spring 2025

The course is not taught in Spring 2025

Extent and Intensity
2/0/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: zk (examination).
In-person direct teaching
Teacher(s)
doc. RNDr. Petra Bořilová Linhartová, Ph.D., MBA (lecturer)
Mgr. Petra Vídeňská, Ph.D. (lecturer)
Guaranteed by
doc. RNDr. Petra Bořilová Linhartová, Ph.D., MBA
RECETOX – Faculty of Science
Contact Person: doc. RNDr. Petra Bořilová Linhartová, Ph.D., MBA
Supplier department: RECETOX – Faculty of Science
Prerequisites
! Bi0036 Metagenomics || Bi4090 General microbiology || Bi2060 Basic microbiology || Bi7170 Medical microbiology
The lecture is intended primarily for students interested in microbiology and students interested in ecology of microorganisms.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 20 student(s).
Current registration and enrolment status: enrolled: 0/20, only registered: 0/20, only registered with preference (fields directly associated with the programme): 0/20
fields of study / plans the course is directly associated with
there are 10 fields of study the course is directly associated with, display
Course objectives
Metagenomics deals with the study of genomes of related, but not entirely identical, microbial populations using genetic and molecular techniques.Part of the lecture cycle will also include lectures by invited experts and demonstration of devices used in the study of microbial communities, especially second generation sequencers.
Learning outcomes
- Bacterial genome and life strategy - Overview of the available next-generation sequencing devices - Principles and differences of individual sequencing platforms - Various metagenomic approaches – whole metagenomic sequencing, sequencing of 16S rDNA gene - Appropriate sampling of different types of matrices for metagenomic studies - Theoretical preparation of libraries - Available technologies, control steps - Analysis of data and databases - The real problems of studying microbial communities - Water, soil and human microbiome - Metatranskriptomics, Metabolomics, Metaproteomics
Syllabus
  • 1. History, metagenomics key words and familiarization with sampling methods and bacterial DNA isolation. 2. Second-generation sequencing and other modern molecular-biological techniques used in metagenomics. 3. Introduction to metagenomics of eukaryotic microorganisms. 4. Introduction to viral metagenomics. 5. Microbial composition in different types of environment, such as human digestive tract, water, soil. 8. Practical demonstration of programs for the analysis of metagenomic studies focusing on bacterial communities. 9. Metatranscriptomics 1. History, basic concepts, meaning of microorganisms 2. Bacterial genome and life strategy of bacteria 3. Second- and third-generation sequencing 4. Other methods used in metagenomics 5. Design of metagenomic studies, sampling, DNA isolation 6. Preparation of samples for gene sequencing for 16S rRNA and WMGS 7. Bioinformatic analysis 8. Metatranscriptome, metametabolome, metaproteome 9. Mycobiome and virome 10. Microbial communities
Literature
  • Beneti,C. Metagenomics: methods, application and perspectives,
  • Schwiertz,A. Microbiota of the human body
Teaching methods
Lecture and discussion of the issue.
Assessment methods
Discussion during lectures, presentation preparation, oral exam
Language of instruction
Czech
Further comments (probably available only in Czech)
The course is taught annually.
The course is taught every week.
General note: Předmět se doporučuje zapsat v 2. nebo 4. semestru.
Information on course enrolment limitations: Min. počet zapsaných studentů je 10
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