Moore Notes 9 4 13

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Group Call

  • Participants: Katie, Jonathan, Sarah, Ladan, Josh, Tom, Dongying, Guillaume, Stephen, Patrick
  • PICRUSt:
    • Tom: summary of how it works
    • Performance is good for enteric gut communities
    • Stephen: what about unannotated genes?
      • Tom: they focused on families with KEGG orthology
      • In theory could use any annotation
      • Probably doesn't deal with proportion of unannotated genes per genome
    • Might be of use to us (e.g., if we apply to MICROBIS 16s data and then make functional maps)
      • Cross validate
      • Independently validate with shotgun metagenomes
    • Concerns
      • Accuracy for marine communities (due to differences in phylogenetic space covered in this ecosystem vs. human body)
      • Maybe better to pick functions where we have measurements of metadata to correlate with the results to independently validate with a "phenotype"
      • Might get more use out of a narrower focus
      • If everything looks OK, could move on to total diversity measurements
      • No viral or eukaryotic predictions
      • Stephen: relative abundance not accounting for unannotated protein families could lead to problems where proportion unannotated varies between places
    • Tom will talk Morgan
      • If we move forward, will do several forms of validation before doing large scale analyses of diversity and many families
      • Could check if error (vs. metagenome annotations) correlates with % unannotated, % eukaryotes, %viral, etc.
  • Sequencing
    • Tara: good coverage of the Atlantic
      • Josh can get more details of the sampling locations
      • When would data be available?
    • AMT
      • N-S Atlantic transect
      • Might complement Tara if it is more coastal
  • Patrick: availability of transcriptional data for human microbiome samples?
    • FEBA Project is going on at JGI
      • Probably not many conditions per organism (maybe 4-5 max) for 50 bacteria
      • RNA-seq and transposon mutagenesis
      • Builds on GEBA
      • Cultured organisms, selected based phylogenetic position
  • Stephen: Important to think about definition of differentially abundant
    • Relative abundance is only relative to known things