Moore Notes 8 3 15

Group Call

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

• Guillaume: Pangea website update
  • Metadata repository linked to data sets
  • No new data sets

• Josh and Kit: spatial autocorrelation of taxa and functions in metagenomes
  • Central park data as a start: all collected at one time, less confounding
  • OTUs with spatial autocorrelation (out of approx 13000)(e.g., OTU 566966)
  • KOs present in each OTU with picrusts: table
  • KOs with spatial autocorrelation (e.g., KO1850 vs. KO1852)
    • KOs present in OTUs with autocorrelation (e.g., KO1061), see also distribution
    • Tom: what about if copy number of KO is what matters for autocorrelation?
    • KOs with different relationships to OTU autocorrelation (summary)
      • Jonathan: simulation to see if picrusts induces any particular biases
  • Any functional trends?
    • Archaea, photosynthesis
  • Next: Same analyses on Tara Oceans
    • Stephen: make sure to follow the email thread, use ShotMAP annotations

• Stephen: Strain level variation (slides)
  • PhyloCNV pipeline to
    • Estimate abundance of species (genome clusters) using phyEco markers
    • Predict presence/absence of genes in strains in a sample
    • Identify SNPs in core genes
  • Uses a custom reference database of genome clusters
    • Provides species designation for unannotated
    • Splits some species groups
    • About 5% errors in taxonomy annotation
  • Writing methods paper with a few applications
  • Applied to human gut worldwide
    • Reference genomes capture a low percentage of diversity, especially in Africa and South America
    • Jacard dissimilarity in strains from two hosts varies across bacterial species, and can be more than 50%
    • Statistical test for clustering (or lack of clustering) of strains (gene content or SNPs) by geographic location of host
      • Tom: See Anthony Amend paper on null distributions (June ISME J)
      • Unifrac for multiple groups: do it for all pairs
      • Katie: accounting for branch lengths
      • Deep branches (major clades) mixed vs. not - how to discover where in the tree the signal is
  • Ideas for applying to Tara Oceans