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Metagenomics (MGRG)

Mission

Many of the Members on the MGRG have been involved in microbiome analysis for over 20 years and have a strong appreciation for the field. They are dedicated and understand the needs of this new and exciting field that continues to grow at an exponential rate.  

If you would like to be part of the MGRG, please contact Scott Tighe at scott.tighe@uvm.edu. Requirements of the research group are 1) Active membership in the ABRF, 2) copy of your CV, and 3) a letter of interest describing your interest, motivation, and how you can contribute.

The ABRF Metagenomics Research Group is composed of Core lab managers, bench scientists, and bioinformaticists. The goals of the MGRG will be to establish and evaluate techniques that core laboratory operators, directors, managers, and users commonly ask. Initial studies include assembling microbial standards and to characterize shortcomings of current metagenomic techniques. this includes optimizing DNA extraction protocols, library synthesis methods for different NGS platforms and developing best approaches for bioinformatics. The development of bacterial cocktails includes working with specific vendors in the field to establish a bacterial counting platform (similar to simple low cost mammalian cell counters) that can be used for low cost, high speed bacterial cell counting as needed for both research and clinical metagenomic quality control requirements. This enumeration device will be validated against standard techniques such as flow cytometry, Microscopic, and LSC techniques. Development of a fixation technique that preserves DNA and RNA without cell leakage is also required. We intend to work very closely with the appropriate vendor of the field to help advance this technology.

Current Membership

Scott Tighe (Chair) - Vermont Cancer Center 
Ebrahim Afshinnekoo - Weill Cornell Medical College 
Nadim Ajami - Baylor University 
Don A. Baldwin - MicroPath ID Diagnostics 
Nathan J. Bivens - University of Missouri 
Russ Carmical - UTMB - Galveston 
Caryn Evilia - Idaho State University
Stefan J. Green - University of Illinois at Chicago - DNAS Facility 
Ian Herriott - University of Alaska Fairbanks 
Jessica Hoffman – Vermont Cancer Center 
Joshua R. Hyman University of Wisconsin - Madison
Sarah Johnson - Georgetown University 
Samantha Joye - University of Georgia 
Jodie Lee (Ad hoc) - Qiagen 
Shawn Levy HudsonAlpha Institute for Biotechnology
Christopher E. Mason - Weill Cornell Medical College 
Ken McGrath - Australian Genome Research Facility 
Natalia G. Reyero Vinas - Mississippi State University 
Rachid Ounit – University of California, Riverside 
Dev Mittar – ATCC Microbiology Systems 
Matthew L. Settles - University of Idaho 
Alexander J. Spicer – Sheffield Hallam University 
Kelley Thomas - Hubbard Center for Genome Studies 
Christian Lytle - (EB Liaison) – Giesel School of Medicine at Dartmouth

 

Electronic Posters

The 2103 NARG study evaluated many DNA extraction techniques against specific bacteria. Results describe the efficiency of each technique.
Presentation from the 2014 ABRF Metagenomics session describing proper use of controls for metagenomics studies
Poster MGRG and XMP - Albany New York
2015 MGRG poster:  Life at the extreme.

Links

Extreme Microbiome Project Website
    - View Document 
The Pathomap project is authored by many of the MGRG members
    - View Document 
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