Moore Notes 8 11 10

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Group Call

  • No-cost extension
    • Until the end of June 2011
    • Outcomes due then
    • Most labs will be spent down prior to that
    • JG will sub-award some money to James at SFI
  • Future funding from GBMF
    • Kelly has our proposal and is showing it to folks there
    • Keep sending papers, posters, talks, etc
  • ESA Meeting: Josh and Steve
    • Cathy Lozupone: metagenomic unifrac coming soon
    • Donovon Parks: gengis visualization system, gave example of taxonomic diversity of GOS data sets
    • Poster about microbial communities in fish guts
    • Arctic soil study: no significant distance-decay
    • More microbial talks than in past
  • Short updates
    • Steve
      • Resubmitting PLoS Bio paper this week
      • GOS analysis: PD with marker genes - who else is doing things with GOS? Shared paper or separate? Group call Sept 8.
      • Easy way to get a coarse taxonomic identification of shotgun reads for 100 maker genes - bacteria vs. archaea (like Tom's 16S analysis: compare hits to two profile HMMs or BLAST versus two databases - similar for 16S)
    • Tom
      • PHYLOTU paper in review at PLoS Comp Bio
      • Moving on to protein family analyses, functional characterization
      • Taxonomic subtraction from protein family phylogenies
    • Guillaume
      • Finishing up db of 16S sequences (all PCR based): almost 2 million RNA sequences with meta-data, mrx plus silva db
      • ESPRIT will remove redundant sequences easily - make sure have same meta-data before dropping
    • Martin/Alex
      • Has there been much work on comparing micorobial micro-diversity (strains/ecotypes/popgen)?
      • Sulfolobus biogeography work starting in 2002
      • Johnson & Slatkin papers
      • Comparing ecotypes to OTUs - is finer distinction more ecologically meaningful?
      • Why should we use Unifrac or marker gene PD to compare samples if you can have functional divergence without much sequence divergence? See Gerstein lab paper. Important to consider taxonomy and functional diversity. Meta-transcriptomics. Tom & Rebecca thinking about this.
      • Migrating ecotype code from windows to linux
    • Josh
      • Working on shape estimator paper
      • Will be in Oregon next week
      • Tittensor et al paper: global diversity patterns in marine macro-organisms, 6 hypotheses about evolution of diversity, temperature is primary driver (vs. productivity). True for microbes? Depends on how identified - morphospecies vs. molecular data. See JG & Jed Furman paper. Spatial correlation models.