1. Human Microbiome Conference
Vancouver, BC
March 10-12, 2011
HMP Microblog

2. Status of the NIH Human Microbiome Project
George Weinstock
for
The NIH HMP Consortium

3. Metagenomics Unfolds
You are here

4. 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:

5. Catalog of Reference Sequences
Subjects
The HMP Model
16S rRNA = bar code identifier of species.
Take a species census
Samples
SG = shotgun sequencing.
Sample every gene in the community
Sources of strains
Microbial Communities
Catalog of Reference Sequences
Metagenomics
Virome SG
454
Illumina
16S rRNA (Sanger; 454)
Transcriptome
DB of 16S Sequences 5

6. Components of the HMP ~30 Awards, ~$150M
15 Projects
Reference Sequences
Health
Center Grants
Disease
Demonstration Projects
Metagenomic Data
U and R series grants
ELSI
R & D
Repositories
Laboratory
DACC
Computational
BEI
NCBI
SRA
dbGaP

8. Healthy Microbiome Characterization Center Grants2
16S 1
3,000 Bacterial Genomes
300 Subjects
18 Body Sites
Multiple visits
Genome Centers
Baylor
Broad Inst.
JCVI
Wash. Univ.
Shotgun
Eukaryotic Genomes
Transcriptome 3
Virome
Data Analysis and Coordination Center
Data Submission
Information Hub

9. Reference Strain Sequencing
Science (2010) 328:
Distribution by Body Site
Status
Number
Not started
439
Awaiting DNA
241
In Progress
425
Complete
398
TOTAL
1503
85% High Quality Draft, 15% Improved
From Sarah Highlander, Ashlee Earl, Betty Lobos, Heather Huot Creasy

10. 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

11. Clinical Sampling Summary
May 1, 2010
Data Freeze on 16S rRNA sequencing
>5,000 specimens sequenced
Submitted to NCBI
Processing, analysis in progress
From Joe Petrosino

12. From Dirk Gevers, BI

13. Body Site
From Owen White, Dirk Gevers, and Ashlee Earl

14. Body Site
From Owen White, Dirk Gevers, and Ashlee Earl

15. Body Site
From Owen White, Dirk Gevers, and Ashlee Earl

16. 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.

17. Number of shotgun samples per body site
747 total samples
# samples sequenced
oral
vaginal
skin
nose
gut

18. Gb of shotgun sequence per body site
8049 Gb Total
4649 Gb Unique Microbial
Gb Total Sequence
from Owen White

20. 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

21. Informatics and Analysis

22. 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, …

23. 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

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