human microbiome conference vancouver, bc march 10-12, 2011
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Human Microbiome Conference Vancouver, BC March 10-12, 2011. HMP Microblog http:// futureofgenomicsblog.org /HMP/. Status of the NIH Human Microbiome Project. George Weinstock f or The NIH HMP Consortium. Metagenomics Unfolds. You are here. HMP Mission. - PowerPoint PPT PresentationTRANSCRIPT
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