Genomic methods and microbiological technologies for profiling novel and extreme environments for the extreme microbiome project (XMP)

Scott Tighe, Ebrahim Afshinnekoo, Tara M. Rock, Ken McGrath, Noah Alexander, Alexa McIntyre, Sofia Ahsanuddins, Daniela Bezdan, Stefan J. Green, Samantha Joye, Sarah Stewart Johnson, Don A. Baldwin, Nathan Bivens, Nadim Ajami, Joseph R. Carmical, Ian Charold Herriott, Rita Colwell, Mohamed S. Abou Donia, Jonathan Foox, Nick GreenfieldTim Hunter, Jessica Hoffman, Joshua Hyman, Ellen Jorgensen, Diana Krawczyk, Jodie Lee, Shawn Levy, Natàlia Garcia-Reyero, Matthew Settles, Kelley Thomas, Felipe Gómez, Lynn Schriml, Nikos Kyrpides, Elena Zaikova, Jon Penterman, Christopher E. Mason

Research output: Contribution to journalArticle

19 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)31-39
Number of pages9
JournalJournal of Biomolecular Techniques
Volume28
Issue number1
DOIs
StatePublished - Apr 2017

All Science Journal Classification (ASJC) codes

  • Molecular Biology

Keywords

  • Extremophile
  • Metagenomics
  • Polyzyme
  • Shotgun sequencing
  • Whole genome

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    Tighe, S., Afshinnekoo, E., Rock, T. M., McGrath, K., Alexander, N., McIntyre, A., Ahsanuddins, S., Bezdan, D., Green, S. J., Joye, S., Johnson, S. S., Baldwin, D. A., Bivens, N., Ajami, N., Carmical, J. R., Herriott, I. C., Colwell, R., Abou Donia, M. S., Foox, J., ... Mason, C. E. (2017). Genomic methods and microbiological technologies for profiling novel and extreme environments for the extreme microbiome project (XMP). Journal of Biomolecular Techniques, 28(1), 31-39. https://doi.org/10.7171/jbt.17-2801-004