Download - American Gut - OMICRON
Daniel McDonaldKnight Lab
The universal nature of biochemistry. Pace NR.Proc Natl Acad Sci U S A. 2001 Jan 30;98(3):805-8.
A microbe dominated world
A microbe dominated world
Lozupone and Knight PNAS. 2007 Jul 3;104(27):11436-40
A microbe dominated world
Ley et al Nat Rev Microbiol. Oct 2008; 6(10): 776–788
Hamady, 2009, PhD thesis
How “human” are we, really?
Hamady, 2009, PhD thesis
How “human” are we, really?
Hamady, 2009, PhD thesis
How “human” are we, really?
Costello et al. Science 326, 1694 (2009)
Photo credit: Steve Miller, CIRES
https://commons.wikimedia.org/wiki/File:Wallacea.png
Fierer et al. PNAS. 2010 Apr 6;107(14):6477-81
Fierer et al. PNAS. 2010 Apr 6;107(14):6477-81
Yatsunenko et al. Nature. 2012 May 9;486(7402):222-7
Yatsunenko et al. Nature. 2012 May 9;486(7402):222-7
HMP HMP
Yatsunenko et al. Nature. 2012 May 9;486(7402):222-7
Koeing et al. Proc Natl Acad Sci U S A. 2011 Mar 15;108
Video fun time!
Full version here: http://www.youtube.com/watch?v=Pb272zsixSQ
http://microbio.me/americangut/img/mod1_main.pdf
• 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Project (2012, Nature 486: 202-214)• GG: Global Gut (2012, Nature 486: 222-228)• PGP: Personal Genome Project (unpublished)• AGP: American Gut Project (unpublished)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
ICU Microbiome pilot• International Nutritional Survey• 5 sites around the world• Multiple time points• Rich patient metadata
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
*
• Analyses are executable, reproducible, and BSD-licensed
An Introduction to AppliedBioinformatics
The American Gut ConsortiumThe Knight LabProf. Rob KnightProf. Greg CaporasoProf. Jack GilbertProf. Tim SpectorDr. Victoria VazquezProf. Paul WischmeyerDr. Antonio GonzalezDr. Gail AckermannYoshiki Vázquez-BaezaDr. Jess MetcalfDr. Katie Amato
[email protected]: @mcdonadtGithub: @wasadewww: http://wasade.github.io
Acknowledgements
Links and questions
[email protected]: @mcdonadtGithub: @wasadewww: http://wasade.github.io
Projects of interest:• Earth Microbiome Project (http://earthmicrobiome.org)• American Gut Project (http://americangut.org)• British Gut Project (http://britishgut.org)
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
