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Project (2012, Nature 486: 202-214)• GG: Global Gut (2012, Nature 486: 222-228)• PGP: Personal Genome Project (unpublished)• AGP: American Gut Project (unpublished)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

daniel.mcdonald@colorado.eduTwitter: @mcdonadtGithub: @wasadewww: http://wasade.github.io

Acknowledgements

Links and questions

daniel.mcdonald@colorado.eduTwitter: @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