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.

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

3. Carlos Pedrós-Alió (2012)

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

13. Phylum
Class
Order

16. SILVA
SSU-Parc 106

17. SILVA
SSU-Parc 106

18. ssu-align
RDP training set

19. PCR
cloning
Sanger

20. Genbank
cultured uncultured
Lynch et al. 2012

21. SILVA
Living Tree Project

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

28. Thank you
@JoshDNeufeld
jneufeld@uwaterloo.ca