human microbiome conference vancouver, bc march 10-12, 2011

Human Microbiome ConferenceVancouver, BC

March 10-12, 2011

HMP Microbloghttp://futureofgenomicsblog.org/HMP/

Status of the NIH Human Microbiome Project

George Weinstockfor

The NIH HMP Consortium

You are here

Metagenomics Unfolds

HMP Mission

The goal of the NIH Human Microbiome Project is to characterize the microbes that inhabit the human body and examine whether changes in the microbiome can be related to health and disease.

URL: http://nihroadmap.nih.gov/hmp/http://hmpdacc.org/

Subjects

Samples

Microbial Communities

Catalog of Reference Sequences Metagenomics

16S rRNA (Sanger; 454)SG454

Illumina

Sources of strains

The HMP Model

DB of 16S Sequences

16S rRNA = bar code identifier of species.Take a species census

SG = shotgun sequencing.Sample every gene in the

community

Virome

Transcriptome

Components of the HMP~30 Awards, ~$150M

DiseaseDemonstration

Projects

HealthCenter Grants

15 Projects

U and R series grants

Reference Sequences

Metagenomic Data

Computational

Laboratory

DACC

R & D

ELSI

Repositories

BEI NCBISRA

dbGaP

Healthy Microbiome CharacterizationCenter Grants

Genome Centers

BaylorBroad Inst.

JCVIWash. Univ.

Data Analysis and

Coordination Center

3,000 Bacterial Genomes

Eukaryotic Genomes

300 Subjects18 Body SitesMultiple visits

16S

Shotgun

Transcriptome

Virome

Information Hub

Data Submission

1

2

3

Science (2010) 328:994-999

Status NumberNot started 439

Awaiting DNA 241

In Progress 425

Complete 398

TOTAL 1503

Distribution by Body Site

Reference Strain Sequencing

From Sarah Highlander, Ashlee Earl, Betty Lobos, Heather Huot Creasy

85% High Quality Draft, 15% Improved

Body sites being sampled• Saliva• Tongue dorsum• Hard palate• Buccal mucosa• Keratinized (attached)

gingiva• Palatine tonsils • Throat • Supragingival plaque • Subgingival plaque

• Retroauricular crease, both ears (2)

• Antecubital fossa (inner elbow), both arms (2)

• Anterior right and left nares (pooled)

• Stool• Posterior fornix, vagina• Midpoint, vagina• Vaginal introitus

Oral Skin Nasal Gut Vaginal

Dec-04Jan-05

Feb-05

Mar-05

Apr-05

May-05Jun-05

Jul-05

Aug-05

Sep-05

Oct-05

Nov-05

Dec-05Jan-06

Feb-06

Mar-06

Apr-06

May-06

0

100

200

300

400

500

600

Screened

1st Sampling

2nd Sampling

Third Sampling

(28 of 100)

525

285 of 300

166 of 300

Clinical Sampling Summary

From Joe Petrosino

May 1, 2010• Data Freeze on 16S rRNA sequencing• >5,000 specimens sequenced• Submitted to NCBI• Processing, analysis in progress

From Dirk Gevers, BI

stoo

l

l_cr

ease

r_cr

ease

l_fo

ssa

r_fo

ssa

a_na

res

bucc

ging

hpal

subg

supr

a

saliv

a

thro

at

tong

ue

tons

ils

v_in

t

mid

_v

pfor

n

020406080

100120140160180200220240260280300

Number of Subjects per Body Site for First, Second, Third Samplings

First visit

Second visit

Third visit

Subj

ects

From Owen White, Dirk Gevers, and Ashlee Earl

Body Site

stoo

l

l_cr

ease

r_cr

ease

l_fo

ssa

r_fo

ssa

a_na

res

bucc

ging

hpal

subg

supr

a

saliv

a

thro

at

tong

ue

tons

ils

v_in

t

mid

_v

pfor

n

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

3,000,000

3,500,000

4,000,000

16S rRNA sequencing on 454: Total Reads per Body Site

total_runsSecondThird

Rea

ds

Body Site

From Owen White, Dirk Gevers, and Ashlee Earl

stoo

l

l_cr

ease

r_cr

ease

l_fo

ssa

r_fo

ssa

a_na

res

bucc

ging

hpal

subg

supr

a

saliv

a

thro

at

tong

ue

tons

ils

v_in

t

mid

_v

pfor

n

0

2,000

4,000

6,000

8,000

10,000

12,000

Average Number of ReadsPer Patient per Body Site

AllV1_V3V3_V5

Rea

ds

Body Site

From Owen White, Dirk Gevers, and Ashlee Earl

Shotgun Metagenomic Sequencing

• Mainly Illumina, paired 100 base reads– Some 454 also performed

• Focus on 6 body sites – Nasal, vaginal, gut, oral (3)– Skin and other sites if enough DNA

• 10 Gb per body site• Remove human sequences and duplicate

microbial sequences => unique microbial seq.

Number of shotgun samples per body site#

sam

ples

sequ

ence

d

skinvaginaloral

gut

nose

747 total samples

Gb of shotgun sequence per body site

from Owen White

Gb To

tal S

eque

nce

8049 Gb Total4649 Gb Unique Microbial

www.hmpdacc.org

Elaborate, Complex Set of Data

• See DACC web site for details• 16S data: Sanger, 454 data

– Human filtered without processing– Processed files: trimmed, chimeras removed, etc.

• Shotgun data: Illumina, 454– Human filtered w/wo processing

• dbGaP– Data without human reads removed– Clinical metadata

Informatics and Analysis

HMP Data Analysis Working Group

• 80 members of the DAWG– Mainly from Genome Centers– People outside of the HMP are welcome– Chaired by Jennifer Wortman (U Md)

• Analysis of 16S data– Co-chairs Erica Sodergren (Wash U), Dirk Gevers (Broad Inst)

• Analysis of Shotgun data– Co-chairs Makedonka Mitreva (Wash U), Owen White (U Md)

• Many subgroups focusing on specific tasks– Core microbiome, novel organisms, assembly of metagenomic

data, pathway analysis, …

The International Human Microbiome Consortium (IHMC)

The IHMC works to:• Generate a shared resource of human microbiome data

– Rapid data release– Common informed consent principles– Common IP guidelines

• Coordinate international efforts to reduce redundancy• Provide a venue for international communication of results and strategies

• Microbiome Meeting in Vancouver, March 10-12, 2011

Acknowledgments• NCCAM• NCI• NHGRI• NHLBI• NIA• NIAAA• NIAID• NIAMS• NIBIB• NICHD• NIDA• NIDCR• NIDDK• NIEHS• NIGMS• NIMH• OD• ORWH

• Baylor College of Medicine – Human Genome Sequencing Center

• Broad Institute• J. Craig Venter Institute• Washington Univ. Genome Center• Clinical Sampling Teams at Baylor College

of Med. and Washington Univ.• Univ. Maryland School of Medicine – Data

Analysis and Coordination Center• 15 Demonstration Projects• Technology Development Projects• ELSI Projects• …and many more