Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP).
The Extreme Microbiome Project (XMP) is a project launched by the Association of Biomolecular Resource Facilities Metagenomics Research Group (ABRF MGRG) that focuses on whole genome shotgun sequencing of extreme and unique environments using a wide variety of biomolecular techniques. The goals are multifaceted, including development and refinement of new techniques for the following: 1) the detection and characterization of novel microbes, 2) the evaluation of nucleic acid techniques for extremophilic samples, and 3) the identification and implementation of the appropriate bioinformatics pipelines. Here, we highlight the different ongoing projects that we have been working on, as well as details on the various methods we use to characterize the microbiome and metagenome of these complex samples. In particular, we present data of a novel multienzyme extraction protocol that we developed, called Polyzyme or MetaPolyZyme. Presently, the XMP is characterizing sample sites around the world with the intent of discovering new species, genes, and gene clusters. Once a project site is complete, the resulting data will be publically available. Sites include Lake Hillier in Western Australia, the "Door to Hell" crater in Turkmenistan, deep ocean brine lakes of the Gulf of Mexico, deep ocean sediments from Greenland, permafrost tunnels in Alaska, ancient microbial biofilms from Antarctica, Blue Lagoon Iceland, Ethiopian toxic hot springs, and the acidic hypersaline ponds in Western Australia.
Advanced Genomics Lab, University of Vermont Cancer Center, University of Vermont, Burlington, Vermont, USA.
Scott
S
Tighe
Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA; School of Medicine, New York Medical College, Valhalla, New York, USA.
Ebrahim
E
Afshinnekoo
Center for Genomics and Systems Biology, New York University, New York, New York, USA.
Tara M
TM
Rock
Australian Genome Research Facility, Gehrmann Labs, University of Queensland, St Lucia, QLD, Australia.
Ken
K
McGrath
Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA.
Noah
N
Alexander
Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA.
Alexa
A
McIntyre
Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA.
Sofia
S
Ahsanuddin
Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA.
Daniela
D
Bezdan
DNA Services Facility, Research Resources Center, University of Illinois, Chicago, Illinois, USA.
Stefan J
SJ
Green
Marine Sciences, The University of Georgia, Athens, Georgia, USA.
Samantha
S
Joye
Department of Biology, Georgetown University, Washington, DC, USA.
Sarah
S
Stewart Johnson
Signal Biology Inc., Philadelphia, Pennsylvania, USA.
Don A
DA
Baldwin
DNA Core Facility, University of Missouri, Columbia, Missouri, USA.
Nathan
N
Bivens
Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA.
Nadim
N
Ajami
Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA.
Joseph R
JR
Carmical
Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, USA.
Ian Charold
IC
Herriott
Center for Bioinformatics and Computational Biology, University of Maryland Institute for Advanced Computer Studies, College Park, Maryland, USA.
Rita
R
Colwell
Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA.
Mohamed
M
Donia
Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA; Department of Invertebrate Zoology, American Museum of Natural History, New York, New York, USA.
Jonathan
J
Foox
One Codex, San Francisco, California, USA.
Nick
N
Greenfield
Advanced Genomics Lab, University of Vermont Cancer Center, University of Vermont, Burlington, Vermont, USA.
Tim
T
Hunter
Advanced Genomics Lab, University of Vermont Cancer Center, University of Vermont, Burlington, Vermont, USA.
Jessica
J
Hoffman
UW Biotechnology Center, University of Wisconsin - Madison, Madison, Wisconsin, USA.
Joshua
J
Hyman
Genspace NYC, Inc., Brooklyn, New York, USA.
Ellen
E
Jorgensen
Greenland Institute of Natural Resources, Greenland Climate Research Centre, Nuuk, Greenland.
Diana
D
Krawczyk
Molecular Diagnostics, Qiagen, Germantown, Maryland, USA.
Jodie
J
Lee
HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA.
Shawn
S
Levy
Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, US Army Engineer Research & Development Center, Vicksburg, Mississippi, USA.
Natàlia
N
Garcia-Reyero
Genome Center, University of California-Davis, Davis, California, USA.
Matthew
M
Settles
Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, USA.
Kelley
K
Thomas
Department of Planetology and Habitability, Centro de Astrobiología (CSIC-INTA), Carretera de Ajalvir, Torrejon de Ardoz, Madrid, Spain.
Felipe
F
Gómez
Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA.
Lynn
L
Schriml
Department of Energy, Joint Genome Institute, Walnut Creek, California, USA.
Nikos
N
Kyrpides
Department of Biology, Georgetown University, Washington, DC, USA.
Elena
E
Zaikova
Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Jon
J
Penterman
Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA; The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York, USA.
Christopher E
CE
Mason
D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification; D004783:Environmental Microbiology; D000071251:Extreme Environments; D054892:Metagenome; D064307:Microbiota / Q000235:genetics*; D058889:Molecular Typing / Q000592:standards; D012329:RNA, Bacterial / Q000235:genetics / Q000302:isolation & purification; D012015:Reference Standards; D017422:Sequence Analysis, DNA / Q000592:standards
D004269:DNA, Bacterial; D012329:RNA, Bacterial
Polyzyme; extremophile; metagenomics; shotgun sequencing; whole genome