And democratization of access to sequencing power... Just one example....
(~80) 41 metagenomes “ Global Ocean Survey” Sanger sequencing (Rusch et al, 2007) Metagenomics: Putting data generating capacity into perspective with an example from Bergen (1) 1 metagenome Sargasso Sea Sanger sequencing (Venter et al, 2005) (~120) 4 metagenomes & 4 metatranscriptomes Bergen mesocosm experiment Pyrosequencing (Gilbert et al, 2008) Gilbert JA, Field D, Huang Y, Edwards R, Li W, Gilna P, Joint I. (2008) Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS ONE. Aug 22;3(8):e3042.
The Bergen ocean acidification study produced 19% of the reads produced in the GOS study and 5% of the total basepairs of sequence. Further evidence for the “Unknown Genome” and the Dark Matter of the Tree of Life
To exploit fully the promise of these data we need both scientific innovation and community agreement on how to provide appropriate stewardship of these resources for the benefit of all. Requires the evolution of our scientific, technological and sociological thinking....
Goal: International effort to sequence a reference genome for every cultured Archaeal and Bacterial organism (~9,000 microbes ) The Microbial Earth Project Phase I: Sequence one representative from every characterized microbial type species GEBA HMP
Source: Jack A. Gilbert Argonne National Labs http://earthmicrobiome.org
Field et al unpublished work on a Metadata Coverage Index (MCI) MCI > 50
Darwin Core GSC MIxS Peter Dawyndt Darwin core vs GSC MixS standard
Darwin Core GSC MIxS standard Taxon Identification Occurrence IPR related info Event Location GeologicalContext SamplingProtocol EnvironmentalConditions Darwin core vs GSC MixS standard Peter Dawyndt