Moore Notes 9 18 12

Group Call - Journal Club

• Attending: Tom, Josh, Dongying, Stephen, Katie

• Inconsistencies in SFams db (Tom)
  • 1st and 2nd rounds of clustering results disagree due to data encoding changes at IMG
  • How to handle future updates?
    • Just IMG or other data resources?
    • How to handle version control when IMG updates their annotations?
    • Hard to identify the problematic sequences
    • Hard to reinitialize the SFams if they become obsolete
  • Dongying and Tom will follow up
  • Keep it simple for future updates

• Journal Club: Deepwater Horizon http://www.nature.com/ismej/journal/v6/n9/full/ismej201259a.html
  • Two plume communities and one distal community at similar depth
  • Comparisons of:
    • Taxonomic composition
    • Pathways in genomes
    • Pathways in transcriptomes
  • Single cells and filtrate (metagenome/metatranscriptome)
  • Timing of samples and progression of response to spikes of new metabolites and electron donors (waves over time as move through compounds from easiest to hardest to metabolize)
    • Bloom of oceanospirillales and metabolism of hydrocarbons
    • Maybe a rare organism is eating a little bit of benzene (could bloom later possibly), or common organism would shift onto it when other metabolites run out
  • Additional reading: http://www.nature.com/ismej/journal/v6/n9/full/ismej2011197a.html
    • DNA/RNA extraction techniques and library prep bias comparisons of metagenomes and metatranscriptomes
  • Our tools might be useful for annotation of single cell genomes and transcriptomes (growing approach)
  • Josh: good to think about limiting nutrients (alkanes in this study)
    • Who will take over the community?
  • More good work on bioremediation from JGI and others.

• Next time: two weeks from now
  • Josh
  • Guillaume, Tom and Dongying will meet at JGI next week for SFams presentation/mtg