Moore Notes 11 20 13

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Group Call

  • Participants: Katie, Jonathan, Tom, Stephen, Patrick, Dongying, Ladan, Guillaume
  • Patrick: domain specific markers to estimate percentage of eukaryotes in sample
    • Curtis Huttenhower has a database of phylum specific gene families
      • Not sure if they are good for getting relative abundance (i.e., not necessarily even copy number)
    • Dongying is focusing on markers that work for bacteria (not necessarily absent from archaea)
      • For poorly sampled groups, gene presence isn't a particularly good marker for a clade
    • Stephen: what about kmer-based binning?
      • JE: not likely to work
    • Tom: check the microbiome protocols to see if they actually extracted eukaryote DNA
    • Other markers?
      • JE: ncRNAs
      • KP: noncoding DNA
      • Lineage-specific transposable elements
  • Tom/Guillaume: PICRUSTs vs. Shotmap
    • Previous analysis was using loose classification parameters that were optimal for shorter reads (RAPsearch score threshold 31)
    • Repeated analysis using score threshold of 100
      • Still finding many families with shot map that are not detected by PICRUSTs
    • Jack Gilbert's analysis focused on 1050 families predicted by both methods
    • Stephen: from simulations, at optimal threshold for relative abundance analysis, quite a few families are predicted as present that are actually absent
      • But we also see differences in relative abundance and presence for more abundant families (according to shotmap)
    • Tom will follow up with Morgan, then Jack
  • Josh: soil bacteria niche modeling
    • See slides (emailed to group)
    • Tibet
      • Tom: try unifrac distance (vs. Bray-Curtis)
      • JE: put sampling locations on heat maps
      • JE: assumes that the model between env and bacterial distributions haven't changed
        • Organisms probably haven't evolved too much overall
        • But the organism-organism relationships might have changed: should check if relationships affect the niche model
      • Try past environment with current microbe distributions to see if model is different
        • Might be able to also address if past conditions better predict current conditions
    • N America