Two streams of intensives on metagenomic analysis were held at Skoltech
The Skolkovo Institute of Science and Technology hosted an intensive course on metagenome analysis for high school and undergraduate students organized by the Skoltech Metagenome Analysis Laboratory. This is a continuation of the Bioinformatics Intensive that the lab team organized in the summer.
The first stream of the Metagenome Analysis Intensive took place on September 23-25, and the second stream took place from September 30 to October 2, 2022.
The author and course facilitator is Matvey Kolesnik, a member of the laboratory and the head of citizen science in the Atlas of Microbial Communities of Russia project.
The course was devoted to the analysis of metagenomes, one of the main areas of scientific work in the laboratory. Metagenomes are obtained by sequencing water or soil samples containing many different organisms at the same time. A metagenome is thus a collection of different genomes.
Visual representation of metagenome fragments. Intensive participants worked with such models built on the basis of sequencing data in the Bandage program
The advantage of the metagenomic approach is that it allows us to study microorganisms that cannot be cultured in the laboratory and therefore cannot be sequenced in isolation. It is such poorly studied organisms that may prove to be the source of new antibiotics or genome editing tools used in biotechnology. Therefore, the study of metagenomes is a very promising area.
The course on metagenome analysis consisted of a theoretical and a practical part. The theoretical part included two lectures by Matvei Kolesnik. At the lecture “Modern Sequencing Technologies,” participants learned about such genome reading methods as nanopore sequencing and Illumina sequencing, and learned how and why sequences obtained using these methods are analyzed.
At the lecture “Search for New Natural Antibiotics” Matvey explained how genomic and, in particular, metagenomic data help in the search for unknown antimicrobial compounds.
The practical part was devoted to mastering bioinformatic methods of working with metagenomic data. The data were obtained by sequencing water samples collected by the laboratory staff on the Oxford Nanopore platform.
Oxford Nanopore Mini Sequencer
The participants of the intensivist found out which bacteria got into the samples, which of them are most likely to produce antibiotics, and looked for defense systems in their genomes. The work was supervised by Matthew, with a team of experts - students and staff - in the classroom to help participants solve any analysis problems that arose.
The course was designed to give participants an introduction to metagenomics and teach the basics of bioinformatic methods. During the two days of the workshop, participants performed a small metagenomic study on real data and gained skills for possible future work.