The 16s rRNA gene has become the standard marker for prokaryote phylogenetic analysis, and combined with high-throughput sequencing technologies it is widely used to infer the structure and composition of microbial communities. Due to the continuous improvements in sequencing technologies and bioinformatics tools, there is a wide choice of methods for sequencing and analysing 16S rRNA gene assemblies. This workshop is designed to give students the necessary background and practical experience of the strategies for the analysis of the diversity and structure of prokaryote communities, covering i) experimental design and primer choices; ii) wet-lab and library preparation options; iii) sequence quality control and analysis and iv) statistical analysis of microbial community data. The many sequencing and analysis options will be discussed, whereas a more in-depth tutorial using real sequence data will provide an opportunity for the student to practice 16S rRNA sequence analysis from raw sequence files to ecological interpretation. Course material, such as presentation slides and necessary model data, will be provided to the students.
This workshop is intended for students and researchers interested in microbial ecology but who are not yet very familiar with the techniques involved. Choosing the appropriate primers, library
preparation kits, sequencing methodologies and bioinformatics pipelines can be quite daunting to the uninitiated. This workshop will allow researchers interested more confidence in their
methodology and analyses choices. The target audience include students of animal or plant microbiomes as well as those studying environmental microbial communities. It is assumed that the
workshop attendees are interested in performing 16S rRNA metabarcoding using the Illumina MiSeq platform, although other sequencing technologies will be discussed during the workshop.
Knowledge of Linux and R or familiarity with working in the command line will be helpful, but for those new to the area detailed instructions will allow students to follow the workshop. Students will need to have a computer running either on Linux or a Linux virtual machine running on MacOX/Windows computers. Contact the instructor at firstname.lastname@example.org if in doubt about computational requirements.
The workshop will consist of both lectures and practical classes. Background information will be provided to help workshop attendees choose the appropriate experimental design, primers, sequencing library preparation kits and to contextualise the bioinformatics and statistical analysis methods. Practical tutorials will be conducted on a step-by-step basis to guide the student from when receiving data from a sequence provider to obtaining plots and tables describing microbial community diversity, structure and relationships to environmental variables or host data.
Freie Universität Berlin, Institute of Biology, Königin-Luise-Str. 1-3, 14195 Berlin-Dahlem.
Classes from 09:30 to 17:30
Session 1: the 16S rRNA gene
The use of the 16S rRNA gene as a marker for prokaryote phylogenetics will be discussed to introduce the students to the concept of conserved and hypervariable regions.
Dr Alexandre de Menezes
Dr. Alexandre De Menezes is a microbial ecologist, and his research career has centred on the investigation of the role of microorganisms in providing ecosystem services, especially in the carbon cycle. He has a particular interest in investigating microbial groups or genes that have been overlooked in this academic field, and which might have an unappreciated role in ecosystem function.
COURSE + REFRESHMENTS
In the all-inclusive package the accommodation is included from Sunday (check-in) to Friday (check-out). A breakfast buffet is also provided in the hotel. Lunch and dinner are also provided during the week, starting from the dinner of Sunday and concluding with the lunch of Friday.
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