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Metabolomics Information
Names For Life February 2019 Release (See Names for Life for more information)
Welcome to the GEBA-VI initiative. Our goal is to involve the research community in an initiative to sequence 10,000 bacterial type strains. We are looking for researchers with type strain collections who can provide the JGI with materials so that we can release a comprehensive atlas of type strain information back to the research community.

About the GEBA VI Project

The Genomic Encyclopedia of Bacteria and Archaea VI (GEBA VI) project at DOE-JGI seeks to expand our understanding of life by examining functional genomics of type strains of prokaryotic species. The proposed studies will systematically investigate genome function by a combination of genomics to determine gene content, transcriptomics to elucidate gene expression, metabolomics to examine function, and pangenomics to identify the core genome and evolutionary processes.

GEBA VI has the following specific goals:
  1. Complete the genome sequences of all type strains that are not human pathogens. Currently, the genomes of about 6,300 of the 15,200 type strains have been sequenced. In cooperation with the GCM2.0 initiative of Global Catalog of Microorganisms (GCM), we will sequence the remaining type strains. In addition, we will sequence genomes of type strains in the process of being described.
  2. Initiate studies on the functional genomics of the type and reference strains of understudied groups. The goal of these studies is to advance our understanding of gene function for a wide variety of prokaryotes utilizing the tools of pangenomics, transcriptomics and metabolomics. Two types of experimental designs are envisioned. One, comparative studies of groups of related type strains, including surveys of genome sequences, transcriptomes and metabolomes. Two, more in depth studies of single species, including characterization of the pangenome or transcriptomes and metabolomes under different growth conditions. In studies of this type, the genome of the type strain may have been sequenced in previous studies.
To this end, we are soliciting laboratories that might contribute DNA for genome sequencing, RNA for transcriptome sequencing, or cell pellets for analyses of either polar or nonpolar metabolites. For pangenome sequencing, we are requesting genomic DNA from approximately 5-10 reference strains (and the type strain if not already known) of the same species. Like the other GEBA projects, JGI will release the data as it is completed into the public databases, and the sample contributors will be the lead authors on the resulting publications.

Who we are

GEBA VI is an international consortium dedicated to understanding prokaryotic diversity and includes a team of scientists at DOE-JGI, academic and research scientists from all over the world, representatives of many culture collections, and you.

How you can get involved

GEBA VI welcomes submissions of samples from undersampled taxa for genome, pangenome and transcriptome sequencing as well as exometabolomics analyses. See below for details and submission guidelines.

Submission guidelines

GEBA VI provides resources for genome sequencing of the type strains of prokaryotes and functional genomics of the type and reference strains of understudied groups. Its goal is to advance understanding of gene function for a wide variety of prokaryotes utilizing the tools of genomics, pangenomics, transcriptomics and metabolomics.

Sample requirements:
Genome sequencing: Illumina 0.5 μg of DNA
Transcriptome sequencing: 0.3 μg of undegraded RNA
Metabolite: cell pellets, 15 mg wet weight minimum in 2 ml polypropylene eppendorf tubes

Review Process

Proposals will be reviewed by the JGI team and other GEBA VI participants.
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