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Course in Working with bacterial communities and population

posted Apr 22, 2016, 8:49 AM by Mirko Rossi   [ updated Sep 22, 2017, 12:37 AM ]
INNUENDO consortium in collaboration with the Doctoral School in Environmental, Food and Biological Sciences (YEB) of the University of Helsinki, have organized a course entitle "Working with bacterial communities and population" in May (16.-20.5.2016)

General introduction

Microbial community structure and diversity, and population structure are fundamental aspects to understand evolution, niche adaptation and demographic history of bacterial species. As NGS sequencing has become cost effective and accessible, microbial community analysis through 16S rRNA gene sequencing has become popular tool. Moreover, sequencing populations of bacteria across the whole genome provides unprecedented resolution to investigate within-host evolution, transmission history, and population structure. During the one week course the students will learn and apply bioinformatic techniques to study microbial communities and performing population genetics. The goal is to become familiar with the analysis tools and to be able to utilize them in own research after the course.

Target group

This course is targeted at PhD and MSc students who are interested in using 16S rRNA gene-based profiling of microbial communities and/or performing bacterial population analysis using whole-genome sequencing.


Part A: Docent Jenni Hultman, University of Helsinki, Finland
Part B: Assistant Professor Mirko Rossi, University of Helsinki, Finland


Part A:
Docent Jenni Hultman, University of Helsinki, Finland
Doctor Kaisa Koskinen, Medical University of Graz, Austria

Part B:
Assistant Professor Mirko Rossi, University of Helsinki, Finland
Doctor João Carriço, University of Lisbon, Portugal
Doctor Sion Byliss, Bath University, UK

Learning outcomes

Part A: working with bacterial communities
Quality control and clean-up of 16S rRNA gene sequence data (Illumina)
Generation of Operational Taxonomic Units (OTUs)
Taxonomic assignment of 16S rRNA gene sequence data
Calculation of diversity measures and statistical comparisons of microbial community structures
Visualization of data

Part B: working with bacterial populations
QA/QC of the raw data, cleaning and assembly
Gene-by-gene annotation
Genealogy reconstruction and population structure analysis
Visualization of data


A complete set of tutorial is available in a dedicated github account