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Network analysis for recovering   novel phylogenetic diversity          from next-generation       16S rRNA gene libraries...
Rare taxa andphylogenetic noveltyNetwork analysis fortargeted exploration
Carlos Pedrós-Alió (2012)
Why study the rare biosphere?Produce estimates of total number of taxa in samplesAnswer whether “everything is everywhere....
HypothesisRare 16S rRNA genesequences arephylogeneticallynovel and representpersistent low abundancepopulations.
rare?How rare is
96 indexesV3 or V4/V510 million (MiSeq)200 million (HiSeq)Assembly
Rare taxa andphylogenetic noveltyNetwork analysis fortargeted exploration
Bartram et al. 2011
Phylum      Class     OrderBartram et al. 2011
SILVA
SILVA
SILVA
Genbank hitscultured     uncultured                   Lynch et al. 2012
SILVA
SILVA
Nakai et al. 2012Lynch et al. 2012
“…Gloeobacter violaceus,isolated from limestonebiofilms…alsomost environmentalsequences forming the largeGloeobacterales cl...
UL9Lynch et al. 2012
Mouth    2       3                              1 Supragingival plaque L1                   4                             ...
Humanmicrobiome
ConclusionsSSUnique and AutoQIIME effective for exploring noveltaxonomic diversityPhylogenetic analysis enabled by compleme...
Next stepsFUNCTION: targeted genome retrievalDIVERSITY: explore additional environmentsECOLOGY: indicator species analysis
Additional sample datasets        New graduate student (you?)
University of Waterloo  Michael Lynch (PDF) Andrea Bartram (PhD)  Andre Masella (RA)   Michael Hall (RA) Jennifer Stearns ...
Thank you@JoshDNeufeldjneufeld@uwaterloo.ca
Neufeld CSM 2012
Neufeld CSM 2012
Neufeld CSM 2012
Neufeld CSM 2012
Neufeld CSM 2012
Neufeld CSM 2012
Neufeld CSM 2012
Neufeld CSM 2012
Neufeld CSM 2012
Neufeld CSM 2012
Neufeld CSM 2012
Neufeld CSM 2012
Neufeld CSM 2012
Neufeld CSM 2012
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Neufeld CSM 2012

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Canadian Society for Microbiology 2012 meeting, Vancouver, British Columbia, Canada

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Neufeld CSM 2012

  1. 1. Network analysis for recovering novel phylogenetic diversity from next-generation 16S rRNA gene libraries Josh D. Neufeld University of Waterloo
  2. 2. Rare taxa andphylogenetic noveltyNetwork analysis fortargeted exploration
  3. 3. Carlos Pedrós-Alió (2012)
  4. 4. Why study the rare biosphere?Produce estimates of total number of taxa in samplesAnswer whether “everything is everywhere.”Enable testing ecological mechanisms for subsistenceEnable research into genes with novel applications Reveal phylogenetic novelty, undetected due to previous methodological limitations Carlos Pedrós-Alió Josh Neufeld
  5. 5. HypothesisRare 16S rRNA genesequences arephylogeneticallynovel and representpersistent low abundancepopulations.
  6. 6. rare?How rare is
  7. 7. 96 indexesV3 or V4/V510 million (MiSeq)200 million (HiSeq)Assembly
  8. 8. Rare taxa andphylogenetic noveltyNetwork analysis fortargeted exploration
  9. 9. Bartram et al. 2011
  10. 10. Phylum Class OrderBartram et al. 2011
  11. 11. SILVA
  12. 12. SILVA
  13. 13. SILVA
  14. 14. Genbank hitscultured uncultured Lynch et al. 2012
  15. 15. SILVA
  16. 16. SILVA
  17. 17. Nakai et al. 2012Lynch et al. 2012
  18. 18. “…Gloeobacter violaceus,isolated from limestonebiofilms…alsomost environmentalsequences forming the largeGloeobacterales clade havebeen retrieved fromrock-associated biofilms,stromatolites, or thermophilicmicrobial mats”
  19. 19. UL9Lynch et al. 2012
  20. 20. Mouth 2 3 1 Supragingival plaque L1 4 2 Subgingival plaque L 3 Supragingival plaque L 4 Supragingival plaque L 5 Tongue biofilm 5 Stomach 6 6 Gastric antrum 7 Gastric body 7 8 Duodenum 8 9 10 Colon 9 Transverse colon 11 10 Sigmoid colon 11 Rectum 12 Stool 12
  21. 21. Humanmicrobiome
  22. 22. ConclusionsSSUnique and AutoQIIME effective for exploring noveltaxonomic diversityPhylogenetic analysis enabled by complementingnext-gen data with targeted gene/genome retrievalUL5 (BRC1, rare in multiple soils)UL9 (sister to Cyanobacteria and chloroplasts)UL13 (divergent mitochondria of unknown eukaryotes)
  23. 23. Next stepsFUNCTION: targeted genome retrievalDIVERSITY: explore additional environmentsECOLOGY: indicator species analysis
  24. 24. Additional sample datasets New graduate student (you?)
  25. 25. University of Waterloo Michael Lynch (PDF) Andrea Bartram (PhD) Andre Masella (RA) Michael Hall (RA) Jennifer Stearns (PDF) Katja Engel (RA) University of Toronto Dennis Cvitkovitch Ken Croitoru Howie Tenenbaum Michael GoldbergWilfrid Laurier UniversityGabriel Moreno-Hagelsieb
  26. 26. Thank you@JoshDNeufeldjneufeld@uwaterloo.ca

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