Human Microbiome Project: A Community Resource Lita M. Proctor, Ph.D. Coordinator, Human Microbiome Project NHGRI/NIH 2016 HIV Microbiome Workshop November 17, 2016 1
Human Microbiome Project: 2007 to 2017 Building a community resource 2
NIH Human Microbiome Project $215M community resource Phase 1: Survey of the Phase 2: Integrative HMP ihmp What are they doing? microbiome Who s there? i. Healthy cohort (case/control): Exemplar human-microbiome conditions: Clinically-examined 300 male/female 18-40 y.o. 5 major body regions (18 body sites) Up to 3 visits in 2 yrs No antibiotics, probiotics, immunomodulators ii. Disease/disorder cohorts: Skin: eczema, psoriasis, acne GI/oral: esophageal adenocarcinoma, necrotizing enterocolitis, pediatric IBS, ulcerative colitis, Crohn s Disease Urogenital: bacterial vaginosis, circumcision, sexual histories i. Pregnancy and Preterm Birth cohort: Vaginal & gut microbiomes and host (mother, infant) ii. IBD Dynamics cohort: GI microbiome and host iii. Type 2 Diabetes Dynamics cohort: GI & nasal microbiomes and host Longitudinal studies Biological properties of host & microbiome over time: Gene expression profiles Protein profiles Metabolite profiles Other host/microbiome phenotype profiles
Data-mining HMP Metagenomic Data to Discover Important Molecules or Pathways Gut microbiota can play direct and indirect roles in drug metabolism Spanogiannopoulos et al. (2016) Known roles of microbial metabolism for many classes of drugs: increase bioavailability decreases bioavailability increases toxicity
Williams et al. (2014) Data-mining HMP Metagenomic Data to Discover Important Molecules or Pathways Forslund et al. (2014) Prevalence of AR genes across gut metagenomes, including HMP Distribution of novel antibiotics in HMP metagenomes, across multiple body regions Oral Gut Vaginal 10% of HMP gut microbiota synthesize neurotransmitter tryptamine Donia et al. (2014)
ihmp: Dynamics of Pregnancy and Preterm Birth (http://vmc.vcu.edu/momspi)
ihmp: Dynamics of IBD Onset (http://ibdmdb.org)
ihmp: Dynamics of Type 2 Diabetes Onset (http://med.stanford.edu/ipop.html)
Public Repositories for Primary ihmp Multi-omic Data* *Blue represents data from the microbiome, red from the host, black represents global data (host +microbiome) 9
HMP Data Coordination Center (www.hmp2dcc.org) All HMP primary data, tools, pipelines, analytical walk-throughs Owen White (PI, UMD School of Medicine)
ihmp DCC Data Import and Export IBD Subjects Samples Omics data OSDF API ihmp DCC OSDF API Subjects Samples Sequences Anadana Biosample/SRA Preterm birth Subjects Samples Omics data OSDF API OSDF API RNA sequences T2D Subjects Samples Omics data OSDF API OSDF OSDF API Mass-Spec, LC data GEO Uniform submissions thanks to common software and metadata standards. Repository submissions performed by data manager at each ihmp site. Data also shared with the ihmp DCC. PRIDE, MW
ihmp Microbiome Multi-omic Framework Framework will link the three ihmp studies and provide userfriendly access to: Study design, number of subjects, timepoints, clinical metadata Primary data and processed data, etc. Data processing pipelines Derived data such as community profiles, gene expression profiles, predicted metabolic pathways, etc. Analytical pipelines for derived data
HMP Data & Tools in NIH Cloud Commons NIH Data Commons: cloud-based resource HMP data & tools as pilot for Commons HMP phase 1 data & tools in the cloud ~2017 HMP phase 2 data & tools in the cloud ~2018-2019- 2020 13
2012-2013: $100-150M/yr and 18 ICOs invested in the human microbiome
Trans-NIH Microbiome Working Group (TMWG) established 2012 Extramural program staff only, membership from 18 ICOs LM Proctor (NHGRI), TMWG chair Mission: Forum for microbiome-related investments at NIH Identify, gaps, needs, challenges and opportunities Share upcoming FOAs, develop joint FOAs; coordinate joint funding of applications Develop microbiome review panel at CSR Organize NIH-wide meetings Serve as central resource for external community TMWG (external page): www.commonfund.nih.gov/hmp/related_activities
NIST*- NIH Workshop: Standards for Microbiome Measurements (http://www.nist.gov/mml/microbiome-standards.cfm) Special issue in prep., BMC Standards in Genomic Sciences The webcast recording posted online http://go.usa.gov/cw8dt. *NIST = Natl. Institute of Standards & Technology
The Human Microbiome: Emerging Themes at the Horizon of the 21 st Century NIH-wide human microbiome workshop, organized by TMWG 40+ speakers, 500 participants; August 16-18, 2017 Open floor discussion each day Workshop closes with joint agency panel: NIH, FDA, CDC, NIST, USDA Workshop goals: Identify knowledge gaps, technical hurdles, new approaches
Questions? lita.proctor@nih.gov 19