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Analysis of microbial communities with QIIME

Analysis of microbial communities with QIIME. Justin Kuczynski February 2012. Why are we at this workshop anyway?. Why are we at this workshop anyway?. Because Microbial communities are important. Microbial communities are important. Microbial communities are important.

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Analysis of microbial communities with QIIME

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

  2. Why are we at this workshop anyway?

  3. Why are we at this workshop anyway? Because Microbial communities are important

  4. Microbial communities are important

  5. Microbial communities are important

  6. Microbial communities are important photos: stockphoto.it, eurasnet.info, elkhorn.unl.edu

  7. How might we investigate microbial communities?

  8. How might we investigate microbial communities? One option: 16S / SSU sequence based profiling

  9. Focus on the ribosomal SSU / 16S gene

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

  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. From sequences to results E. Costello et al., 2009

  15. How might one move from raw sequences to interpretable results?

  16. How might one move from raw sequences to interpretable results? That is QIIME’s purpose

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

  18. QIIME analysis in more detail

  19. QIIME analysis in more detail

  20. QIIME analysis in more detail beta_diversity_through_plots.py

  21. QIIME analysis example beta_diversity_through_plots.py

  22. QIIME analysis example

  23. QIIME analysis example

  24. QIIME analysis example

  25. Demo of beta diversity analysis results

  26. Demo of beta diversity analysis results

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

  28. Running QIIME Laptop EC2 Cluster images: pcdownload.asia, ostatic.com

  29. 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 Acknowledgements RESEARCH FUNDING Crohn’s and Colitis Foundation of America, the Bill and Melinda Gates Foundation, NASA, the HHMI and the NIH justinak@gmail.com www.qiime.org

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