ISB nov 2014

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.



Lozupone and Knight PNAS. 2007 Jul 3;104(27):11436-40


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/


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?





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

https://www.youtube.com/watch?v=Pb272zsixSQ

Huttenhower et al. 2012 Nature Jun 13:486(7402):207-14

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?


…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