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Human Microbiome Conference Vancouver, BC March 10-12, 2011

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.

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Human Microbiome Conference Vancouver, BC March 10-12, 2011

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  1. Human Microbiome Conference Vancouver, BC March 10-12, 2011 HMP Microblog http://futureofgenomicsblog.org/HMP/

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

  5. Sources of strains Catalog of Reference Sequences Metagenomics 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 Microbial Communities Virome SG 454 Illumina 16S rRNA (Sanger; 454) Transcriptome DB of 16S Sequences

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

  7. Healthy Microbiome CharacterizationCenter Grants 2 16S 1 300 Subjects 18 Body Sites Multiple visits 3,000 Bacterial Genomes Genome Centers Baylor Broad Inst. JCVI Wash. Univ. Shotgun Eukaryotic Genomes 3 Transcriptome Virome Data Analysis and Coordination Center Data Submission Information Hub

  8. Reference Strain Sequencing Science (2010) 328:994-999 Distribution by Body Site 85% High Quality Draft, 15% Improved From Sarah Highlander, Ashlee Earl, Betty Lobos, Heather Huot Creasy

  9. 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) • Antecubitalfossa (inner elbow), both arms (2) • Anterior right and left nares (pooled) • Stool • Posterior fornix, vagina • Midpoint, vagina • Vaginal introitus Oral Skin Nasal Gut Vaginal

  10. 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

  11. From Dirk Gevers, BI

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

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

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

  15. 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.

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

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

  18. www.hmpdacc.org

  19. 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

  20. Informatics and Analysis

  21. 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 MakedonkaMitreva (Wash U), Owen White (U Md) • Many subgroups focusing on specific tasks • Core microbiome, novel organisms, assembly of metagenomic data, pathway analysis, …

  22. The IHMC works to: Generate a shared resource of human microbiome data Rapiddata 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 The International Human Microbiome Consortium (IHMC)

  23. Acknowledgments • Baylor College of Medicine – Human Genome SequencingCenter • 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 • TechnologyDevelopment Projects • ELSI Projects • …and many more • NCCAM • NCI • NHGRI • NHLBI • NIA • NIAAA • NIAID • NIAMS • NIBIB • NICHD • NIDA • NIDCR • NIDDK • NIEHS • NIGMS • NIMH • OD • ORWH

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