A talk on the American Gut at OMICRON in Poland.

3. the
RNA
for
taxonomic
ubiquitous
conserved and

4. A microbe dominated world
The universal nature of biochemistry. Pace NR.
Proc Natl Acad Sci U S A. 2001 Jan 30;98(3):805-8.

5. A microbe dominated world
Lozupone and Knight PNAS. 2007 Jul 3;104(27):11436-40

6. A microbe dominated world
Ley et al Nat Rev Microbiol. Oct 2008; 6(10): 776–788

7. How “human” are we, really?
Hamady, 2009, PhD thesis

8. How “human” are we, really?
Hamady, 2009, PhD thesis

9. How “human” are we, really?
Hamady, 2009, PhD thesis

11. Costello et al. Science 326, 1694 (2009)

12. Photo credit: Steve Miller, CIRES

13. https://commons.wikimedia.org/wiki/File:Wallacea.png

14. Fierer et al. PNAS. 2010 Apr 6;107(14):6477-81

15. Fierer et al. PNAS. 2010 Apr 6;107(14):6477-81

18. Yatsunenko et al. Nature. 2012 May 9;486(7402):222-7

19. Yatsunenko et al. Nature. 2012 May 9;486(7402):222-7

20. HMP HMP
Yatsunenko et al. Nature. 2012 May 9;486(7402):222-7

22. Koeing et al. Proc Natl Acad Sci U S A. 2011 Mar 15;108

23. Video fun time!
Full version here: http://www.youtube.com/watch?v=Pb272zsixSQ

25. • HMP: Human Microbiome Project (2012, Nature 486: 202-214)
• GG: Global Gut (2012, Nature 486: 222-228)
• PGP: Personal Genome Project (unpublished)
• AGP: American Gut Project (unpublished)
http://microbio.me/americangut/img/mod1_main.pdf

26. http://microbio.me/americangut/img/mod1_main.pdf

29. ICU Microbiome pilot
• International Nutritional Survey
• 5 sites around the world
• Multiple time points
• Rich patient metadata

30. Autism spectrum cohort of the American Gut
• 269 families to receive samples
• Conjunction with ASD-clinicians
• Donations for ASD-affected and neurotypical siblings
covered by Jack Gilbert

32. *

33. • Analyses are executable, reproducible, and
BSD-licensed

34. An Introduction to Applied
Bioinformatics

35. The American Gut Consortium
The Knight Lab
Prof. Rob Knight
Prof. Greg Caporaso
Prof. Jack Gilbert
Prof. Tim Spector
Dr. Victoria Vazquez
Prof. Paul Wischmeyer
Dr. Antonio Gonzalez
Dr. Gail Ackermann
Yoshiki Vázquez-Baeza
Dr. Jess Metcalf
Dr. Katie Amato
Acknowledgements
daniel.mcdonald@colorado.edu
Twitter: @mcdonadt
Github: @wasade
www: http://wasade.github.io

36. Links and questions
Projects of interest:
• Earth Microbiome Project (http://earthmicrobiome.org)
• American Gut Project (http://americangut.org)
• British Gut Project (http://britishgut.org)
daniel.mcdonald@colorado.edu
Twitter: @mcdonadt
Github: @wasade
www: http://wasade.github.io
Key labs:
• Knight Lab (http://knightlab.colorado.edu)
• Caporaso Lab (http://caporasolab.us)
• Spector Lab (http://www.tim-spector.co.uk/)
Education:
• Coursera’s Gut Check (https://www.coursera.org/course/microbiome)
• Intro. to Appl. Bioinformatics (http://caporasolab.us/An-Introduction-To-Applied-Bioinformatics/)
Useful software projects:
• Quantitative Insights into Microbial Ecology (http://qiime.org)
• Qiita (http://qiita.colorado.edu)*
• biocore (http://github.com/biocore)
• scikit-bio (http://scikit-bio.org)
• EMPeror (http://emperor.colorado.edu)
*Soon to be opened for the general public