Přehled

Title: New approaches in computational analyses of bacterial communities for biotechnology
Study program: Biomedical Technology and Bioinformatics
Supervisor: Assoc. Prof. Karel Sedlář, PhD

Topic description:

Thanks to their diversity, non-model bacteria represent an inexhaustible resource for microbial biotechnology. While tools, including the computational ones, to study pure bacterial cultures are developed to at least a certain point, their counterparts for analysis of mixed cultures are underdeveloped or completely missing. This prevent us to further study biotechnological capacity of bacterial consortia to produce value added chemicals or their bioremediation potential.

The topic is focused on computational methods for a comprehensive analysis of microbial consortia in order to reveal their functional capacity for industrial biotechnology, bioremediation, and production of value added chemicals, primarily bioplastics. While particular tools for taxonomic profiling based on amplicon sequencing and metagenome analysis based on shotgun sequencing exist, they are oriented
to perform descriptive rather than functional analysis. This provides only limited use for biotechnology research where the emphasis is put on function. This is partly caused also by the lack of tools oriented on processing of bacterial metatranscriptomes. Finally, there is an absolute lack of tools to connect potential functional capacity inferred from a metagenome with running biological processes measured
with metatranscriptomics and metabonomics approaches. The aim of the research is to set up comprehensive computational pipeline to analyse diversity of a selected mixed bacterial culture, to set up a metagenome of this community, and to match its observed behaviour through analyses of other omics data revealing running biological and metabolic processes. The pipeline will include specific steps to process short NGS as well as long TGS reads to cover all currently used sequencing technologies.

The project will be solved mainly at the Department of Biomedical Engineering. However, cooperation with our national (University Hospital Brno, the Faculty of Chemistry BUT, and Czech Collection of Microorganisms) and foreign partners (Ludwig-Maximilians-Universität München in Germany and HESSO Valais-Wallis in Switzerland) is expected. PhD students will complete a six-month internship at attractive partner universities abroad. UBMI provides doctoral students with a stipend and/or a parttime contract beyond the state stipend when joining a grant project or engaging in teaching.

Your task:

  • Analysis of various microbial consortia with bioremediation and biosynthetic potential.
  • Deploy your own computation pipelines.

Requirements:

  • Previous education in bioinformatics.
  • Good communications skills and desire to work on yourself.

We offer:

  • To join young investigator’s team solving cutting-edge project.
  • Possibility to travel to foreign conferences and cooperating institutions.

For more information about this topic please contact Karel Sedlář – sedlar@vut.cz

How to apply:

Please apply and submit your motivation letter and CV via university website from April 1 to April 30, https://www.vut.cz/eprihlaska/cs/zadani/vybrat-obor/fakulta/5

Funding:
Funding is provided as a combination of part-time or full-time research projects and/or regular scholarships.

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