Microbial Metagenomics Summer Course 2012

Learn state-of-the-art genomic methods to identify relationships between the structure and function of microbial communities

Sunday June 3th - Saturday June 16th, 2012

Michigan State University, East Lansing, Michigan, USA

Applications are now open!

Please apply to attend the course by filling out this application form.

The deadline for full consideration is March 16th 2012

What will students learn?

A major goal of this intensive two-week course is to provide hands-on experience with some of the molecular and computational tools that can be used to study relationships between microbial communities and ecosystem functions. However, our vision for the course is more than simply learning techniques. You will use them to address questions you formulate about denitrifying bacteria and the production of the greenhouse gas nitrous oxide. In this way you will contribute to an ongoing study of the effects of land use on the production of greenhouse gases at the nearby Kellogg Biological Station Long Term Ecological Research Site (http://lter.kbs.msu.edu). You will also develop ideas about the use of these techniques for your own research.

How is the course structured?


Morning lectures will discuss microbial and ecological principles underlying experiments that you will conduct during the afternoons. The laboratory sessions will include purification of DNA from soils and the construction of clone libraries for Sanger sequencing. You will also prepare DNA samples for 454 pyrosequencing. The abundance of genes of interest will be estimated by quantitative PCR. You will analyze your sequence data with a suite of contemporary programs to measure community diversity, and use multivariate statistics to relate the structures of these communities to ecosystem functions. We will provide the computing facilities required for these analyses. At the end of the course you will present your conclusions to the other students and faculty.

Who can attend?

We can accommodate about 20 students. The course is primarily for graduate students, postdocs and faculty. Advanced undergraduates and other researchers will also be considered. We encourage diversity of backgrounds. The primary pre-requisite is a keen interest in adding metagenomic methods to your research.

Where will it be held?


Lectures and laboratory sessions will be held on the main campus of Michigan State University in East Lansing, Michigan, USA.

Single-room accommodation and dining facilities are available on campus (http://liveon.msu.edu/rivertrail/owen).

Parking permits are required if you are bringing a car to campus.

What will it cost?

The course can be taken as a workshop for a fee of $1,400 per student. It can also be taken as a three-credit course (MMG 490 or MMG 890, Section 432) whose tuition cost is determined by student status and residence.
Summer Tuition and Fees Calculator
Expenses relating to travel, accommodation and food are NOT covered. Single-occupancy rooms on campus can be reserved for $35/night at Owen Hall. Parking permits cost $20.

How and when do I apply?

Please complete the the application form and e-mail it, along with your resume, to ude.usm|enegatem#ude.usm|enegatem. Application is open until March 16th, 2012.


Dr. Thomas Schmidt

is a microbial physiologist and ecologist who uses metagenomics to address questions about the structure and function of microbial communities in soil and the human microbiome. He directed the MBL Microbial Diversity Course and has modeled the metagenomics course after this internationally acclaimed course. An overview of the research and people in the Schmidt Lab can be found here: http://microbiomes.msu.edu.

Dr. Clegg Waldron

worked on crop and bacterial genetic engineering, and natural products discovery, in industrial labs for 27 years. Since retiring in 2008 he has been an Adjunct Professor in Microbiology and Molecular Genetics at Michigan State University. He helps teach laboratory research and scientific writing to undergraduates.

Dr. Jay Lennon

studies the ecology and evolution of microbial communities. He is interested in the biotic and abiotic factors that generate and maintain microbial biodiversity and the implications of microbial diversity for ecosystem functioning. He conducts research in terrestrial and aquatic habitats using molecular biology, simulation modeling, laboratory experiments, field surveys, and whole ecosystem manipulations. See: http://microbes.kbs.msu.edu/index.html.

Other instructors

with expertise in microbial ecology and bioinformatics will be recruited from MSU and elsewhere.

2011 attendees


Feedback from 2011

"What you taught in 2 weeks might have taken me 2 years to learn on my own."

“Life changing … I now believe I may be able to graduate in a reasonable time.”

“Fostering an informal, discussion-like atmosphere was great. We all had a lot of perspectives on each portion of the course, and I learned nearly as much from my classmates as the lecturers.”

“The computer exercises were the best part of this course. I came here intimidated by pyro data sets and wanted to stick to gels and qPCR, but I’m leaving with the confidence and tools to manage immense data returns.”

“I feel that my thesis project will be of a higher caliber since I am now familiar with more tools and have a better critical thinking ability.”

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