In this course, we are going to explore the main approaches applied for microbiome studies based on high-
throughput sequencing technologies. The students will get familiarized with methods for assessment of community
composition, genome sequencing, metagenomics and metatranscriptomics. We are going to tackle subjects from
the project planning and experimental design to the most used strategies for data treatment, data analysis,
exploration and the presentation of results.
Last update: RNDr. Michaela Schierová, Ph.D. (01.03.2019)
Kurs představí hlavní metody masivně paralelního sekvenování používané při studiu mikrobiomu. Studenti se seznámí s metodami pro hodnocení zastoupení různých druhů ve společenstvu pomocí sekvencování genomu, metagenomiky a metatranskriptomiky. Důležitou součástí kursu je plánování projektu, navržení experimentu, zpracování dat a prezentace výsledků.
Literature -
Last update: RNDr. Irena Lichá, CSc. (18.03.2019)
Due to the rapid development of microbiome analysis methods and tools, recommended literature also changes rapidly. The students are thus given compulsory reading during the lectures. In this way, the lecturers can better follow the development in the field.
Selection from recommended literature:
Escobar-Zepeda, A., Vera-Ponce de León, A., Sanchez-Flores, A., 2015. The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics. Frontiers in Genetics 6,348.
Marchesi, J.R., Ravel, J., 2015. The vocabulary of microbiome research: a proposal. Microbiome 3, 31.
Nilsson, R.H., Anslan, S., Bahram, M., Wurzbacher, C., Baldrian, P., Tedersoo, L., 2019. Mycobiome diversity: high-throughput sequencing and identification of fungi. Nature Reviews Microbiology 17, 95-109.
Větrovský, T., Baldrian, P., Morais, D., 2018. SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses. Bioinformatics 34, 2292-2294.
Žifčáková, L., Větrovský, T., Lombard, V., Henrissat, B., Howe, A., Baldrian, P., 2017. Feed in summer, rest in winter: microbial carbon utilization in forest topsoil. Microbiome 5, 122.
Last update: RNDr. Irena Lichá, CSc. (18.03.2019)
Due to the rapid development of microbiome analysis methods and tools, recommended literature also changes rapidly. The students are thus given compulsory reading during the lectures. In this way, the lecturers can better follow the development in the field.
Selection from recommended literature:
Escobar-Zepeda, A., Vera-Ponce de León, A., Sanchez-Flores, A., 2015. The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics. Frontiers in Genetics 6,348.
Marchesi, J.R., Ravel, J., 2015. The vocabulary of microbiome research: a proposal. Microbiome 3, 31.
Nilsson, R.H., Anslan, S., Bahram, M., Wurzbacher, C., Baldrian, P., Tedersoo, L., 2019. Mycobiome diversity: high-throughput sequencing and identification of fungi. Nature Reviews Microbiology 17, 95-109.
Větrovský, T., Baldrian, P., Morais, D., 2018. SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses. Bioinformatics 34, 2292-2294.
Žifčáková, L., Větrovský, T., Lombard, V., Henrissat, B., Howe, A., Baldrian, P., 2017. Feed in summer, rest in winter: microbial carbon utilization in forest topsoil. Microbiome 5, 122.
Requirements to the exam -
Last update: RNDr. Michaela Schierová, Ph.D. (23.10.2019)
Students will be evaluated on the basis of a written test.
Last update: RNDr. Irena Lichá, CSc. (08.08.2019)
studenti budou hodnoceni na základě písemného testu.
Syllabus -
Last update: RNDr. Irena Lichá, CSc. (16.05.2017)
1. Metagenome-Wide Association Studies
Course presentation/overview and discussion about the sequencing revolution on microbial studies. Recent achievements and knowledgement increase as a result of the advances in sequencing technology.
2. Sequencing technology fundamentals
Sequencing concepts, Maxam and Gilbert, Sanger, High-throughput technology (short read: 454, illumina and Ion Torrent; long read: Nanopore and PacBio) and practical library preparation.
3. Experimental design
Importance of formulation of hypothesis or a research question, sampling, replication, homogenization, randomization and control.
4. Sequencing data treatment and genome assembly
Quality check, phred score, expected error in high-throughput sequencing, methods for cleaning data and the problems of not working with quality filtered data and genome assembly.
5. Taxonomic profile based on amplicon data: ‘Who is there?’
Amplicon data generation introduction, ribosomal genes, phylogenetic information. Biodiversity indices, microbial ecology concepts and metataxonomic data visualization.
6. Genomics, Metagenomics and Shotgun data handling
Gene prediction, functional annotation, taxonomy assignment, binning strategies, genomes assembled from metagenomes and data visualization.
7. Analysis of RNA and Metatranscriptomics
Concepts, methods, applications, sampling and RNA preservation techniques.
8. Technical demonstration of the most used methods for high-throughput sequencing data manipulation
High-throughput sequencing data treatment (fastqc, trimmomatic and vsearch), genome assembly (spades and velvet), amplicon and metagenomic data handling, taxonomy and functional assignment (the Seed, QIIME, KEGG and BLAST).
Last update: RNDr. Michaela Schierová, Ph.D. (01.03.2019)
1. Metagenome-Wide Association Studies Course presentation/overview and discussion about the sequencing revolution on microbial studies. Recent achievements and knowledgement increase as a result of the advances in sequencing technology.
2. Sequencing technology fundamentals Sequencing concepts, Maxam and Gilbert, Sanger, High-throughput technology (short read: 454, illumina and Ion Torrent; long read: Nanopore and PacBio) and practical library preparation.
3. Experimental design Importance of formulation of hypothesis or a research question, sampling, replication, homogenization, randomization and control.
4. Sequencing data treatment and genome assembly Quality check, phred score, expected error in high-throughput sequencing, methods for cleaning data and the problems of not working with quality filtered data and genome assembly.
5. Taxonomic profile based on amplicon data: ‘Who is there?’ Amplicon data generation introduction, ribosomal genes, phylogenetic information. Biodiversity indices, microbial ecology concepts and metataxonomic data visualization.
6. Genomics, Metagenomics and Shotgun data handling Gene prediction, functional annotation, taxonomy assignment, binning strategies, genomes assembled from metagenomes and data visualization.
7. Analysis of RNA and Metatranscriptomics Concepts, methods, applications, sampling and RNA preservation techniques.
8. Technical demonstration of the most used methods for high-throughput sequencing data manipulation High-throughput sequencing data treatment (fastqc, trimmomatic and vsearch), genome assembly (spades and velvet), amplicon and metagenomic data handling, taxonomy and functional assignment (the Seed, QIIME, KEGG and BLAST).
