human microbiome project: a community...
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Human Microbiome Project: A Community Resource
2016 HIV Microbiome Workshop November 17, 2016
Lita M. Proctor, Ph.D.Coordinator, Human Microbiome Project
NHGRI/NIH
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Human Microbiome Project: 2007 to 2017Building a community resource
Clinically-examined300 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, acneGI/oral: esophageal adenocarcinoma, necrotizing enterocolitis, pediatric IBS, ulcerative colitis, Crohn’s DiseaseUrogenital: bacterial vaginosis, circumcision, sexual histories
NIH Human Microbiome Project $215M community resource
Phase 1: Survey of the microbiome “Who’s there?”
Phase 2: Integrative HMP “iHMP” “What are they doing?”
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
i. Healthy cohort (case/control): Exemplar human-microbiome conditions:
Longitudinal studies Biological properties of host & microbiome
over time:
Gene expression profiles
Protein profilesMetabolite profilesOther host/microbiome phenotype profiles
Spanogiannopoulos et al. (2016)
Known roles of microbial metabolism for many classes of drugs:increase bioavailabilitydecreases bioavailabilityincreases toxicity
Gut microbiota can play direct and indirect roles in drug metabolism
Data-mining HMP Metagenomic Data to Discover Important Molecules or Pathways
Data-mining HMP Metagenomic Data to Discover Important Molecules or Pathways
10% of HMP gut microbiota synthesize neurotransmitter tryptamine
Will
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Prevalence of AR genes across gut metagenomes, including HMP
Fors
lun
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Donia et al. (2014)
Distribution of novel antibiotics in HMP metagenomes, across multiple body regions
OralGut Vaginal
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)
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*Blue represents data from the microbiome, red from the host, black represents global data (host +microbiome)
Public Repositories for Primary iHMP Multi-omic Data*
• All HMP primary data, tools, pipelines, analytical walk-throughs• Owen White (PI, UMD School of Medicine)
HMP Data Coordination Center (www.hmp2dcc.org)
iHMP DCC
OSDF
OSDFAPI
SubjectsSamples
Omics data
T2D
Preterm birth
IBD
OSDFAPI
SubjectsSamples
Omics data
OSDFAPI
SubjectsSamples
Omics data
AnadanaOSDFAPI
SubjectsSamples
Sequences
Biosample/SRA
GEO
PRIDE, MW
OSDFAPI
RNA sequences
OSDFAPI
Mass-Spec, LC data
• 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.
iHMP DCC Data Import and Export
iHMP Microbiome Multi-omic Framework
Framework will link the three iHMP studies and provide user-friendly 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
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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
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
(http://www.nist.gov/mml/microbiome-standards.cfm)
NIST*- NIH Workshop: Standards for Microbiome Measurements
The webcast recording posted online http://go.usa.gov/cw8dT.
Special issue in prep., BMC Standards in Genomic Sciences
*NIST = Natl. Institute of Standards & Technology
“The Human Microbiome: Emerging Themes at the Horizon of the 21st 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
