Neufeld CSM 2012
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This document discusses using network analysis of 16S rRNA gene sequences to uncover novel phylogenetic diversity from next-generation sequencing libraries. It hypothesizes that rare 16S rRNA gene sequences represent phylogenetically novel and persistent low abundance populations. The document outlines using network analysis to explore rare taxa and phylogenetic novelty in an effective manner. It also discusses using this approach to retrieve targeted genomes to study function, explore additional environments, and analyze indicator species ecology.
Neufeld CSM 2012
- 1. Network analysis for recovering novel phylogenetic diversity from next-generation 16S rRNA gene libraries Josh D. Neufeld University of Waterloo
- 2. Rare taxa and phylogenetic novelty Network analysis for targeted exploration
- 4. Why study the rare biosphere? Produce estimates of total number of taxa in samples Answer whether everything is everywhere. Enable testing ecological mechanisms for subsistence Enable research into genes with novel applications Reveal phylogenetic novelty, undetected due to previous methodological limitations Carlos Pedr坦s-Ali坦 Josh Neufeld
- 5. Hypothesis Rare 16S rRNA gene sequences are phylogenetically novel and represent persistent low abundance populations.
- 9. 96 indexes V3 or V4/V5 10 million (MiSeq) 200 million (HiSeq) Assembly
- 13. Rare taxa and phylogenetic novelty Network analysis for targeted exploration
- 15. Bartram et al. 2011
- 16. Phylum Class Order Bartram et al. 2011
- 19. SILVA
- 20. SILVA
- 21. SILVA
- 24. Genbank hits cultured uncultured Lynch et al. 2012
- 25. SILVA
- 26. SILVA
- 27. Nakai et al. 2012 Lynch et al. 2012
- 28. Gloeobacter violaceus, isolated from limestone bio鍖lmsalso most environmental sequences forming the large Gloeobacterales clade have been retrieved from rock-associated bio鍖lms, stromatolites, or thermophilic microbial mats
- 29. UL9 Lynch et al. 2012
- 32. Mouth 2 3 1 Supragingival plaque L 1 4 2 Subgingival plaque L 3 Supragingival plaque L 4 Supragingival plaque L 5 Tongue bio鍖lm 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
- 33. Human microbiome
- 34. Conclusions SSUnique and AutoQIIME e鍖ective for exploring novel taxonomic diversity Phylogenetic analysis enabled by complementing next-gen data with targeted gene/genome retrieval UL5 (BRC1, rare in multiple soils) UL9 (sister to Cyanobacteria and chloroplasts) UL13 (divergent mitochondria of unknown eukaryotes)
- 35. Next steps FUNCTION: targeted genome retrieval DIVERSITY: explore additional environments ECOLOGY: indicator species analysis
- 36. Additional sample datasets New graduate student (you?)
- 39. 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 Goldberg Wilfrid Laurier University Gabriel Moreno-Hagelsieb