Human Microbiome Conference Vancouver, BC March 10-‐12, 2011
HMP Microblog h4p://futureofgenomicsblog.org/HMP/
Status of the NIH Human Microbiome Project George Weinstock for The NIH HMP ConsorKum
Metagenomics Unfolds
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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: h4p://nihroadmap.nih.gov/hmp/ h4p://hmpdacc.org/
Subjects
The HMP Model
16S rRNA = bar code idenKfier of species. Take a species census
Samples
Sources of strains Catalog of Reference Sequences
Microbial CommuniKes
SG = shotgun sequencing. Sample every gene in the community
Metagenomics
Virome Transcriptome DB of 16S Sequences
SG 454 Illumina
16S rRNA (Sanger; 454)
Components of the HMP ~30 Awards, ~$150M
Reference Sequences
15 Projects
Disease
Health
DemonstraKon Projects
Center Grants
Metagenomic Data
ELSI
U and R series grants
R & D
Repositories BEI
NCBI
SRA dbGaP
Laboratory
DACC
ComputaKonal
Healthy Microbiome CharacterizaKon Center Grants
1
3,000 Bacterial Genomes EukaryoKc Genomes
Genome Centers Baylor Broad Inst. JCVI Wash. Univ.
2 300 Subjects 18 Body Sites MulKple visits
Shotgun
Transcriptome
3
Virome Data Analysis and CoordinaKon Center
InformaKon Hub
16S
Data Submission
Reference Strain Sequencing
Science (2010) 328:994-‐999
Status
Number
Not started
439
Awaiting DNA
241
In Progress
425
Complete
398
TOTAL
DistribuKon by Body Site
1503
85% High Quality Drah, 15% Improved From Sarah Highlander, Ashlee Earl, BeHy Lobos, Heather Huot Creasy
Body sites being sampled • • • • • • • • •
• Retroauricular crease, both ears (2) • Antecubital fossa (inner elbow), both arms (2) • Anterior right and leh nares (pooled) • Stool • Posterior fornix, vagina • Midpoint, vagina • Vaginal introitus
Saliva Tongue dorsum Hard palate Buccal mucosa KeraKnized (a4ached) gingiva PalaKne tonsils Throat Supragingival plaque Subgingival plaque Oral
Skin
Nasal
Gut
Vaginal
Clinical Sampling Summary 600
525
Screened
500
1st Sampling
May 1, 2010 • Data Freeze on 16S rRNA sequencing Third Sampling • >5,000 specimens sequenced 285 of 300 • Submi4ed to NCBI • Processing, analysis in progress 2nd Sampling
400
300
200
166 of 300 100
(28 of 100)
From Joe Petrosino
May-‐10
Apr-‐10
Mar-‐10
Feb-‐10
Jan-‐10
Dec-‐09
Nov-‐09
Oct-‐09
Sep-‐09
Aug-‐09
Jul-‐09
Jun-‐09
May-‐09
Apr-‐09
Mar-‐09
Feb-‐09
Jan-‐09
Dec-‐08
0
From Dirk Gevers, BI
300
First visit
Number of Subjects per Body Site for First, Second, Third Samplings
Second visit Third visit
280 260 240
Subjects
220 200 180 160 140 120 100 80 60 40 20
Body Site
From Owen White, Dirk Gevers, and Ashlee Earl
pforn
mid_v
v_int
tonsils
tongue
throat
saliva
supra
subg
hpal
ging
bucc
a_nares
r_fossa
l_fossa
r_crease
l_crease
stool
0
16S rRNA sequencing on 454: Total Reads per Body Site
total_runs Second
4,000,000
Third
3,500,000
Reads
3,000,000 2,500,000 2,000,000 1,500,000 1,000,000 500,000
Body Site
From Owen White, Dirk Gevers, and Ashlee Earl
pforn
mid_v
v_int
tonsils
tongue
throat
saliva
supra
subg
hpal
ging
bucc
a_nares
r_fossa
l_fossa
r_crease
l_crease
stool
0
All
Average Number of Reads Per Patient per Body Site
12,000
V1_V3 V3_V5
10,000
Reads
8,000
6,000
4,000
2,000
Body Site
From Owen White, Dirk Gevers, and Ashlee Earl
pforn
mid_v
v_int
tonsils
tongue
throat
saliva
supra
subg
hpal
ging
bucc
a_nares
r_fossa
l_fossa
r_crease
l_crease
stool
0
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.
# samples sequenced
Number of shotgun samples per body site
gut
nose
747 total samples
oral
vaginal
skin
Gb of shotgun sequence per body site
Gb Total Sequence
8049 Gb Total 4649 Gb Unique Microbial
from Owen White
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
InformaKcs 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 InternaKonal Human Microbiome ConsorKum (IHMC) The IHMC works to: • Generate a shared resource of human microbiome data – Rapid data release – Common informed consent principles – Common IP guidelines • Coordinate internaKonal efforts to reduce redundancy • Provide a venue for internaKonal communicaKon of results and strategies
• Microbiome MeeXng in Vancouver, March 10-‐12, 2011
Acknowledgments • Baylor College of Medicine – Human Genome Sequencing Center • Broad InsKtute • J. Craig Venter InsKtute • Washington Univ. Genome Center • Clinical Sampling Teams at Baylor College of Med. and Washington Univ. • Univ. Maryland School of Medicine – Data Analysis and CoordinaKon Center • 15 DemonstraKon Projects • Technology Development Projects • ELSI Projects • …and many more
• • • • • • • • • • • • • • • • • •
NCCAM NCI NHGRI NHLBI NIA NIAAA NIAID NIAMS NIBIB NICHD NIDA NIDCR NIDDK NIEHS NIGMS NIMH OD ORWH
