Neufeld ISME14
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This document discusses targeted recovery of novel phylogenetic diversity from next-generation sequence data. It begins by outlining the value of studying rare microbial taxa, including estimating total taxa in samples and identifying genes with novel applications. The hypothesis is then stated that rare 16S rRNA gene sequences are phylogenetically novel and represent persistent low abundance populations. The document goes on to describe using next-generation sequencing data and 16S rRNA gene phylogeny to potentially identify novel clades, and techniques like SSUnique and network analysis to filter large datasets and help reveal phylogenetic novelty from rare taxa.
Neufeld ISME14
- 1. Targeted recovery of novel phylogenetic diversity from next-generation sequence data Josh D. Neufeld UNIVERSITY OF WATERLOO
- 2. 1. Value of studying rare tax 2. Targeted exploration of phylogenetic novelty UNIVERSITY OF WATERLOO
- 4. Why study rare microbial taxa? Estimate the total number of taxa in samples Answer whether “everything is everywhere.” Test ecological mechanisms for subsistence Identify genes with novel applications Reveal phylogenetic novelty, undetected due to previous methodological limitations Carlos Pedrós-Alió (2012) Josh Neufeld
- 5. Hypothesis Rare 16S rRNA gene sequences are phylogenetically novel and represent persistent low abundance populations.
- 6. Next-gen sequence data Potentially novel clades 16S rRNA gene phylogeny
- 9. Michael Lynch Poster 023A Thursday
- 10. 1. Value of studying rare taxa 2. Targeted exploration of phylogenetic novelty
- 11. Alert, Nunavut 82°28' N, 62°30' W Neufeld et al. 2005
- 12. Bartram et al. 2011
- 20. Genbank cultured uncultured Lynch et al. 2012
- 22. Nakai et al. 2012 SILVA Living Tree Project Lynch et al. 2012
- 23. UL9 Lynch et al. 2012
- 25. Rare taxa represent phylogenetic novelty SSUnique and network analysis help filter data Added value for large datasets