The American Gut
Daniel McDonaldNov. 25, 2014
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.
A microbe dominated world
A microbe dominated world
Lozupone and Knight PNAS. 2007 Jul 3;104(27):11436-40
A microbe dominated world
Lozupone and Knight PNAS. 2007 Jul 3;104(27):11436-40Subway image adapted from http://laughingsquid.com/the-gastrointestinal-system-represented-as-a-subway-map/
A microbe dominated world
Ley et al Nat Rev Microbiol. Oct 2008; 6(10): 776–788Subway image adapted from http://laughingsquid.com/the-gastrointestinal-system-represented-as-a-subway-map/
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)
Caporaso et al. Genome Biology. 2011;12(5):R50
Gevers et al. Cell Host and Microbe 2014 Mar 12;15(3)
Koeing et al. Proc Natl Acad Sci U S A. 2011 Mar 15;108
Video fun time!
Infant time series, https://www.youtube.com/watch?v=Pb272zsixSQGut ecosystem restoration https://www.youtube.com/watch?v=-FFDqhM4pks
Huttenhower et al. 2012 Nature Jun 13:486(7402):207-14
Yatsunenko et al. Nature. 2012 May 9;486(7402):222-7
Yatsunenko et al. Nature. 2012 May 9;486(7402):222-7
Human Microbiome Project
Lozupone et al. Genome Research 2013 Oct;23(10):1704-14
Blinding, randomization
Blinding, randomization
Sequence generation
Data processing
Samples:Stool, fresh, N=11
Stool, freeze-dried, N=7
Robogut N=2
Lab 1
Artificial N=2
Centralized DNA extractionN = 41
Raw Sample TransferN = 53
Control
N = 2Control
96 Tube Sample
Set
96 Tube Sample
Set
Lab 2
Lab 3
Lab 15
.
.
.
HMP DACCFTP Site
Site 1
.
.
.
Site 2
Site 3
Site 9
IntegratedData
Analysis
Slide credit: Dr. Amnon Amir
Variability in methods
HandlingDNA extraction kit manufacturer
Chemagen 1MO-BIO 7Omega BioTek 1Promega 1Qiagen 2Zymo Research Corporation 1Not reported 3
Homogenizer used?Yes 11No 3Not reported 1
PCR primer set318F/806R 1EMP V4 515F/806R 11Schloss 2013 2
Sequencing machine modelHiSeq 2500 1MiSeq 13
Paired end sequencing?Yes 13No 1
Sequencing read length150 4175 1210 1250 6300 2
Fraction of PhiX (range 0-0.3) 0.11 ±0.08Fraction quality bases (range 0.57-0.96) 0.86 ±0.12
BioinformaticsPrimary QC software
QIIME 2Trimmomatic 3UPARSE 2Other/custom 2
Primary OTU calling softwareQIIME 4UPARSE 5
Unsupervised OTU clustering step?Yes 8No 2
Taxonomic assignment strategyClassification 3Clustering 5Mapping 2
OTU filtering?Yes 3No 7
Slide credit: Dr. Amnon Amir
EMPeror
Vázquez-Baeza et al. 2013 Gigascience 2(1)
http://biocore.github.io/emperor/
Genome or microbiome?
Yatsunenko et al. Nature. 2012 May 9;486(7402):222-7
…but with sufficient power
Goodrich et al. 2014. Cell 4(6)789-99
…but with sufficient power
Goodrich et al. 2014. Cell 4(6)789-99
Christensenellaceae
• Analyses are executable, reproducible, and BSD-licensed
Demo of IPython Notebook
Where to now?
Muegge et al. 2011. Science 332(6032):970-974
Muegge et al. 2011. Science 332(6032):970-974
Ridaura et al. 2013. Science 341(6150)
Personal Genome Project
Open Humans
(Some of the) American Gut CollaboratorsProf. Rob Knight Co-founder HHMI, CU-Boulder, UCSDDr. Jeff Leach Co-founder Human Food ProjectProf. Cathy Lozupone Creator of UniFrac, focus on ASD Anschutz Medical CenterProf. Marty Blaser ABX impact NYU School of MedicineProf. Maria Gloria Dominguez
Succession in infants NYU School of Medicine
Prof. Patrice Cani Type-2 Diabetes Universite Catholique de Louvain
Prof. George Church Everything Harvard Medical School, MITProf. Pieter Dorrestein Realtime Mass Spec UCSDProf. Jack Gilbert Hospital microbiome, EMP, ASD U-Chicago, ANLProf. Ruth Ley Env. relationship with human
geneticsCornell University
Prof. Owen White Genomics expert U-Maryland School of Medicine; PI of HMP DACC
Prof. Phil Hugenholtz Taxonomy, microbial diversity U-Queensland, Australian Centre for Ecogenomics
Dr. Tim Spector Genetic epidemiology King’s College
The American Gut ConsortiumThe Knight LabProf. Rob KnightProf. Robin DowellProf. Aaron ClausetProf. Paul WischmeyerDr. Antonio GonzalezDr. Gail AckermannYoshiki Vázquez-BaezaJustine DebeliusAdam Robbins-PiankaEmily TerAvestAlina Prassas
AcknowledgementsDr. Embriette HydeJeff DeReusDr. Jenya KopylovaDr. Eva NovákováDr. Luke ThompsonJustine DebeliusJose Navas