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Metagenomics and Microbiome Research Group (MMRG)

Mission

Many of the Members on the MMRG 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 MMRG, 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 and Microbiome Research Group is composed of Core lab managers, bench scientists, and bioinformaticists. The goals of the MMRG 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 (Co-Chair) - Vermont Cancer Center
  • Ravi Ranjan (Co-Chair) - University of Massachusetts Amherst
  • 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
  • Christian Lytle – Giesel School of Medicine at Dartmouth
  • Christopher E. Mason - Weill Cornell Medical College
  • Lisa Mattei, The CHOP Microbiome Center
  • Ken McGrath - Australian Genome Research Facility
  • Dev Mittar – ATCC Microbiology Systems
  • Natalia G. Reyero Vinas - Mississippi State University
  • Rachid Ounit – University of California, Riverside
  • Matthew L. Settles - University of Idaho
  • Alexander J. Spicer – Sheffield Hallam University
  • Kelley Thomas - Hubbard Center for Genome Studies
  • Kevin Knudtson (EB Liaison), University of Iowa

Studies - Ongoing 2019 - 2020: Evaluation of rapid DNA library preparation kit for shotgun metagenomics studies.

The study aims to evaluate and benchmark the performance of rapid DNA library kits for shotgun metagenomics. The general criteria for kits to be evaluated in this study will be based on - variable range of input DNA, enzymatic or transposase-based fragmentation method, one bead clean-up. We will also prep libraries using TE or MQ water to establish baseline data for negative controls and the “kitome”. With this study the MGRG aims to provide a platform to compare the kits for - efficiency, reproducibility, total time, quality, sequencing outcomes, using known DNA known standards, which will be beneficial to the research community.

Electronic Posters

2020 ABRF Annual Meeting: Methods to preserve individual bacteria and microbiome samples for nucleic acid analyses without altering cellular structure or integrity.

 2017 ABRF Annual Meeting. McIntyre A. Life at the Extreme: The ABRF Metagenomics Research Group. Implementing New Standards in Metagenomics and the Extreme Microbiome Project.

 2016 ABRF Annual Meeting. Baldwin DA. Life at the Extreme: The ABRF Metagenomics Research Group. Implementing New Standards in Metagenomics and the Extreme Microbiome Project.

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.

Talks:

2020  ABRF Annual Meeting, Tighe S. Close Encounters of the Third Kind Circumventing the Effects of Extraterrestrial DNA.

2019  ABRF Annual Meeting, Tighe S. Characterizing the Whole Cell Microbial Reference Standard using RNA and DNA-Sequencing.

2017  Current Innovations for Metagenomics used in Antarctica.

2017  Straight up, with a Twist: Innovative Enzyme Cocktail to Improve DNA extractions of Metagenomic Samples 

2017  An automated low-volume, high-throughput library prep for studying bacterial genomes. 

2017  Metagenomic Analysis using the MinION Nanopore Sequencer.

2017  Metasub-"Metagenomics Across the World's Cities.

2016  Standardizing Metagenomics: a Novel Class I Microbial Reference Standard and Improved DNA Extraction Using a Multicomponent Enzyme Reagent.

2015  Development of New Standards for Metagenomics and the Extreme Microbiome Project (XMP).

2014  Challenges and Controls in Metagenomics

Links

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

Satellite Workshops

2018  ABRF Annual Meeting (SW8) Microbiome and Metagenomics Benchtop to Bioinformatics; Technical approaches to Sequencing, DNA Extractions, and Data Analysis

Publications: (Selected)

2019  Tighe S. Metagenomics Research Group Study: Characterizing The Whole Cell Microbial Reference Standard Using RNA and DNA-Sequencing. J Biomol Tech. 2019 Dec;30(Suppl):S55. 

2017 Mason CE, Tighe S. Focus on Metagenomics. J Biomol Tech. 2017 Apr;28(1):1. 

2017  Tighe S, et al., Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP). J Biomol Tech. 2017 Apr;28(1):31-39.

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