Moore Notes 9 4 13

Group Call

• Participants: Katie, Jonathan, Sarah, Ladan, Josh, Tom, Dongying, Guillaume, Stephen, Patrick

• PICRUSt: http://picrust.github.io/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