1. Analysis of microbial communities with QIIME Justin Kuczynski February 2012

3. Because Microbial communities are important

4. Microbial communities are important

6. photos: stockphoto.it, eurasnet.info, elkhorn.unl.edu

8. One option: 16S / SSU sequence based profiling

9. Focus on the ribosomal SSU / 16S gene

10. Extract DNA and amplify marker gene with barcoded primers Pool amplicons and sequence SSU / 16S experimental workflow

11. Sequences are not directly interpretable line 12,000 of 1.2 M

12. Sequences are not directly interpretable And beware: ▫chimeric PCR products ▫sequencing error ▫uneven sequencing depth ▫short read effects line 12,000 of 1.2 M

13. From sequences to results

14. E. Costello et al., 2009

16. That is QIIME’s purpose

17. Extract DNA and amplify marker gene with barcoded primers Pool amplicons and sequence Assign millions of sequences from thousands of communities to OTUs Visualize and compare community relationships www.qiime.org Assign reads to communities >GCACCTGAGGACAGGCATGAGGAA… >GCACCTGAGGACAGGGGAGGAGGA… >TCACATGAACCTAGGCAGGACGAA… >CTACCGGAGGACAGGCATGAGGAT… >TCACATGAACCTAGGCAGGAGGAA… >GCACCTGAGGACACGCAGGACGAC… >CTACCGGAGGACAGGCAGGAGGAA… >CTACCGGAGGACACACAGGAGGAA… >GAACCTTCACATAGGCAGGAGGAT… >TCACATGAACCTAGGGGCAAGGAA… >GCACCTGAGGACAGGCAGGAGGAA…

18. QIIME analysis in more detail

20. beta_diversity_through_plots.py QIIME analysis in more detail

21. QIIME analysis example beta_diversity_through_plots.py

22. QIIME analysis example

25. Demo of beta diversity analysis results

27. QIIME tech support www.qiime.org Overview Tutorial QIIME forum

28. Running QIIME images: pcdownload.asia, ostatic.com LaptopEC2 Cluster

29. Acknowledgements Antonio González Bharath Prithiviraj Catherine Lozupone Chris Lauber Dan Knights Daniel McDonald Donna Berg-Lyons Doug Wendel Greg Caporaso Jens Reeder Jerry Kennedy Jess Metcalf Jesse Stombaugh Jesse Zaneveld José Clemente Justin Kuczynski Laura Parfrey Meg Pirrung Rob Knight Tony Walters Ulla Westermann Will Van Trueren RESEARCH Crohn’s and Colitis Foundation of America, the Bill and Melinda Gates Foundation, NASA, the HHMI and the NIH FUNDING justinak@gmail.com www.qiime.org