ABOUT XMP

The Extreme Microbiome Project (XMP) is a scientific effort to characterize, discover, and develop new pipelines and protocols for extremophiles and novel organisms. It was initiated as part of the Association of Biomolecular Resource Facilities (ABRF) Metagenomics Research Group (MGRG) in 2014 as a consortium of microbiologists, geneticists, oceanographers, and bioinformaticists.

ASSOCIATED GROUPS

Association of Biomolecular Resource Facilities (ABRF)

The Association of Biomolecular Resource Facilities is an international society dedicated to advancing core and research biotechnology laboratories through research, communication, and education.

Metagenomics Research Group (MGRG)

As the study of microbiomes and metagenomes expands into environmental, industrial, nutritional, and clinical areas, the need to review and establish standard methods is critical. Shortcomings are apparent at most stages of metagenomic research, from the efficiency of nucleic acid extraction to the accuracy of bioinformatic analysis. The ABRF Metagenomic Research Group seeks to evaluate, study, and refine methodologies related to any aspect of metagenomics and microbiome studies, including study designs, controls, detection methods, and bioinformatics pipelines and software.

THE XMP DIFFERENCE

PRESERVATIVES

The XMP and the ABRF MGRG are actively involved in the development of a metagenomic fixative that meets the following criteria:
1) Will inactivate all life and render the sample
2) Will preserve the cellular morphological state without causing nucleic acid leakage
3) Can be used in the field
4) Compatible with most nucleic acid extraction protocols
5) Designed to preserve RNA, DNA, and methylated DNA
6) Will not impede extraction

NUCLEIC ACID EXTRACTION

Most nucleic acid extraction protocols suffer from low efficiency depending on the types of microbial populations, as determined by the 2010 ABRF Nucleic Acids Research Group. One focus of the XMP project will be to investigate and employ high recovery nucleic acid extraction techniques, including a hybrid enzymatic-CTAB-AlO3 bead-based method, as well as traditional kits used in past projects.

SEQUENCING

The XMP differs from other projects by using multiple sequencing approaches including whole genome shotgun sequencing to reduce bias. All Illumina sequencing will be done with 2x250 or greater. Site specific sequencing will also be performed using the PacBio platform and the Oxford Nanopore Technologies Minion with the latest chemistry.