Organizing, Setting Standards for Metagenome Data
Source: Janet Jansson
Although investigators are learning a great deal about dominant bacteria and archaea in soils based on 16S rRNA gene sequence data, many of the dominant operational taxonomic units (OTUs) that we detect in soil have no close representatives in culture collections. Researchers are addressing these deficiencies through initiatives such as the Genomic Encyclopedia for Bacteria and Archaea (GEBA) project that Jonathan Eisen of the University of California, Davis (UCD) and JGI coordinates. The long-term goal is to fill in the phylogenetic tree of life by sequencing genomes from underrepresented phyla. Another project, “Microbial Earth,” coordinated by Nikos Kyrpides at JGI, calls for sequencing microbial type strains in culture collections.
Meanwhile, the Earth Microbiome Project (EMP), an initiative that aims to sequence what some call the “dark matter” of biology, the full microbial diversity on Earth (www.earthmicrobiome.org/), will begin sequencing 10,000 metagenomes from various collections and habitats, and eventually will cover hundreds of thousands of such samples, pending dedicated support.
The soil microbial ecology research community has established an international consortium, the International TerraGenome Consortium (www.terragenome.org). The consortium recognizes the high complexity of the soil environment and is focused on determining "the soil metagenome." TerraGenome is a clearinghouse for information about funding for soil metagenomics research, for development and provision of bioinformatics tools, for metadata standards, and for workshops and meetings on these topics. For example, TerraGenome set forth criteria for metadata obtained from analyzing soil samples that researchers must meet before their sequence data may be deposited into centrally held databases. This effort to set the minimum information about an environmental marker sequence (MIMARKS) was coordinated through the Genome Standards Consortium (GSC) (http://gensc.org/gc_wiki/index.php/Main_Page).