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Funded Research

Evaluation of Multi-‘omic Data in Understanding the Human Microbiome’s Role in Health and Disease (U54)
RFA-RM-12-021
PI Name Institution Name Title
BUCK, GREGORY ALLEN (contact)
JEFFERSON, KIMBERLY KAY STRAUSS, JEROME F
VIRGINIA COMMONWEALTH UNIVERSITY A Multi-omic Analysis of the Vaginal Microbiome during Pregnancy
SNYDER, MICHAEL P (contact)
WEINSTOCK, GEORGE M
STANFORD UNIVERSITY Longitudinal Multiomics Microbial Profiling in Healthy and Disease Individuals
XAVIER, RAMNIK J (contact)
HUTTENHOWER, CURTIS 
BROAD INSTITUTE, INC. Characterizing the gut microbial ecosystem for diagnosis and therapy in IBD

 

Human Microbiome Demonstration Projects (UH2/UH3)
RFA-RM 08-012
PI Name Institution Name Title
BLASER, MARTIN J NEW YORK UNIVERSITY SCHOOL OF MEDICINE Evaluation of the cutaneous microbiome in psoriasis
BUCK, GREGORY A. (contact)
CORNELISSEN, CYNTHIA NAU
EAVES, LINDON J.
STRAUSS, JEROME FRANK
VIRGINIA COMMONWEALTH UNIVERSITY The Vaginal Microbiome: Disease, Genetics and the Environment
FORTENBERRY, J. DENNIS INDIANA UNIV-PURDUE UNIV AT INDIANAPOLIS Urethral Microbiome of Adolescent Males
FRASER-LIGGETT, CLAIRE M. (contact)
SHULDINER, ALAN R.
UNIVERSITY OF MARYLAND BALTIMORE The Thrifty Microbiome: The Role of the Gut Microbiota in Obesity in the Amish
FRASER-LIGGETT, CLAIRE M. UNIVERSITY OF MARYLAND BALTIMORE Metagenomic Analysis of the Structure and Function of the Human Gut Microbiota in Crohn's Disease
LI, ELLEN WASHINGTON UNIVERSITY Effect of Crohn's Disease Risk Alleles on Enteric Microbiota
LI, HUIYING UNIVERSITY OF CALIFORNIA LOS ANGELES Metagenomic study of the human skin microbiome associated with acne
PEI, ZHIHENG (contact)
NELSON KAREN E
NEW YORK UNIVERSITY SCHOOL OF MEDICINE Foregut microbiome in development of esophageal adenocarcinoma
RAVEL, JACQUES UNIVERSITY OF MARYLAND BALTIMORE The Microbial Ecology of Bacterial Vaginosis: A Fine Scale Resolution Metagenomic
SEGRE, JULIA U.S. NATIONAL HUMAN GENOME RESEARCH INST Atopic Dermatitis and Immunodeficiency
STORCH, GREGORY A. WASHINGTON UNIVERSITY The human virome in children and its relationship to febrile illness
TARR, PHILLIP I. WASHINGTON UNIVERSITY The Neonatal Microbiome and Necrotizing Enterocolitis
VERSALOVIC, JAMES BAYLOR COLLEGE OF MEDICINE Pediatric Abdominal Pain and Inflammation
WU, GARY D (contact)
BUSHMAN, FREDERIC D
LEWIS, JAMES D
UNIVERSITY OF PENNSYLVANIA Diet, Genetic Factors, and Gut Microbiome in Crohns Disease
YOUNG, VINCENT B (contact)
CHANG, EUGENE B
MEYER, FOLKER
SCHMIDT, THOMAS M
SOGIN, MITCHELL L
TIEDJE, JAMES M
UNIVERSITY OF MICHIGAN AT ANN ARBOR Gut Microbiota in Ulcerative Colitis

 

Construction of a Reference Sequence Data Set for the Human Microbiome Project (U54)
BRFA-RM-08-001
PI Name Institution Name Title
BIRREN, BRUCE W MASSACHUSETTS INSTITUTE OF TECHNOLOGY Defining the Human Microbiome
GIBBS, RICHARD (contact)
HIGHLANDER, SARAH KATHERINE
PETROSINO, JOSEPH FRANK
BAYLOR COLLEGE OF MEDICINE A Microbial Genome Reference Platform for Metagenomics
NELSON, KAREN E J. CRAIG VENTER INSTITUTE, INC. Construction of A Reference Sequence Data Set For The Human Microbiome ProjectARRA Logo
WEINSTOCK, GEORGE WASHINGTON UNIVERSITY Sequencing the Human Microbiome

 

Studies of the Ethical, Legal, and Social Implications (ELSI) of Human Microbiome Research (R01)
RFA-RM-08-030
PI Name Institution Name Title
CHO, MILDRED K. (contact)
SANKAR, PAMELA L.
STANFORD UNIVERSITY Toward a Framework for Policy Analysis of Microbiome Research
SPICER, PAUL G UNIVERSITY OF OKLAHOMA NORMAN Indigenous Communities and Human Microbiome Research
HOFFMANN, DIANE E. UNIVERSITY OF MARYLAND BALTIMORE Federal Regulation of Probiotics: An Analysis of Existing Regulatory Framework
MCGUIRE, AMY LYNN BAYLOR COLLEGE OF MEDICINE Ethical, Legal, and Social Dimensions of Human Microbiome Research
RHODES, ROSAMOND MOUNT SINAI SCHOOL OF MEDICINE OF NYU Human Microbiome Research and the Social Fabric

 

Studies of the Ethical, Legal, and Social Implications (ELSI) of Human Microbiome Research (R01)
RFA-RM-08-006
PI Name Institution Name Title
FARRELL, RUTH
SHARP, RICHARD R (contact)
CLEVELAND CLINIC LERNER COL/MED-CWRU Patient perceptions of bioengineered probiotics and clinical metagenomics

 

A Data Analysis & Coordination Center (DACC) for the Human Microbiome Project (U01)
RFA-RM-08-007
PI Name Institution Name Title
WHITE, OWEN R UNIVERSITY OF MARYLAND BALTIMORE A Quality Assurance, Coordination and Analysis Center for HMP

 

Development of New tools for Computational Analysis of Human Microbiome Project Data (R01)
RFA-RM-09-020
PI Name Institution Name Title
FREDRICKS, DAVID NEAL FRED HUTCHINSON CANCER RESEARCH CENTER Novel Computational Tools for Studying the Human Microbiome
HUTTENHOWER, CURTIS HARVARD UNIVERSITY (SCH OF PUBLIC HLTH) Functional Activity and Inter-Organismal Interactions in the Human Microbiome
LI, WEIZHONG UNIVERSITY OF CALIFORNIA SAN DIEGO Novel Methods for Effective Analysis, Assembly and Comparison of HMP Sequences
SCHLOSS, PATRICK DAVID UNIVERSITY OF MICHIGAN AT ANN ARBOR Identifying Population-Level Variation in Cross-Sectional and Longitudinal HMP Studies

 

Development of New Tools for Computational Analysis of Human Microbiome Project Data (R21)
RFA-RM-09-021
PI Name Institution Name Title
PACE, NORMAN R UNIVERSITY OF COLORADO AT BOULDER High Performance Validation and Classification of Metagenomic Ribosomal-RNA Sequences
STORMO, GARY D WASHINGTON UNIVERSITY AT ST. LOUIS Exploiting Microbiome Seqeunces for Improved Models of Protein-DNA Interactions

 

Development of New Technologies Needed for Studying the Human Microbiome (R01)
RFA-RM-09-008
PI Name Institution Name Title
FREDRICKS, DAVID NEAL FREDRICKS, DAVID NEAL Novel cultivation methods for the domestication of vaginal bacteria
ISMAGILOV, RUSTEM F UNIVERSITY OF CHICAGO Confining single cells to enhance and target cultivation of human microbiome
LEWIS, KIM NORTHEASTERN UNIVERSITY Culturing uncultivatable gut microorganisms

 

Development of New Technologies Needed for Studying the Human Microbiome (R21)
RFA-RM-09-009
PI Name Institution Name Title
ALLEN-VERCOE, EMMA UNIVERSITY OF GUELPH FACS-MABE: a method to sort and enrich the as-yet uncultured bacterial species from the human distal gut
DAVIS, RONALD WAYNE STANFORD UNIVERSITY Isolation, selection, and polony amplification of single cells in a gel matrix
LIN, XIAOXIA UNIVERSITY OF MICHIGAN AT ANN ARBOR Metagenomic dissection of the gut microbiota
NELSON, JOHN GENERAL ELECTRIC GLOBAL RESEARCH CTR Tools for human microbiome studies

 

Development of New Technologies Needed for Studying the Human Microbiome (R01)
RFA-RM 08-026
PI Name Institution Name Title
BRADBURY, ANDREW (contact)
HAN, CLIFF
LOS ALAMOS NAT SECTY-LOS ALAMOS NAT LAB Species-by-Species Dissection of Microbiomes using Phage Display and Flow Sorting
PODAR, MIRCEA UT-BATTELLE, LLC-OAK RIDGE NATIONAL LAB Targeted genomic characterization of uncultured bacteria from the human microbiot
SINGH, ANUP K SANDIA CORP-SANDIA NATIONAL LABORATORIES FISH 'N' Chips: A Microfluidic Processor for Isolating and Analyzing Microbes

 

Development of New Technologies Needed for Studying the Human Microbiome (R21)
RFA-RM 08-027
PI Name Institution Name Title
DOKTYCZ, MITCHEL UT-BATTELLE, LLC-OAK RIDGE NATIONAL LAB Functional Sorting of Microbial Cells From Complex Microbiota
WORTHEN G. SCOTT CHILDREN'S HOSPITAL OF PHILADELPHIA Multi-Dimensional Separation of Bacteria

 

Development of New tools for Computational Analysis of Human Microbiome Project Data (R01)
RFA-RM-08-008
PI Name Institution Name Title
HAFT, DANIEL H J. CRAIG VENTER INSTITUTE, INC Algorithmically-Tuned Protein Families, Rule_Base and Characterized Proteins
KNIGHT, ROBIN UNIVERSITY OF COLORADO AT BOULDER New Tools for Understanding the Composition and Dynamics of Microbial Communities
POP, MIHAI UNIVERSITY OF MARYLAND COLLEGE PK CAMPUS Assembly and analysis software for exploring the human microbiome
YE, YUZHEN INDIANA UNIVERSITY BLOOMINGTON Fragment assembly and metabolic/species diversity analysis for Human microbiome

 

Development of New Technologies Needed for Studying the Human Microbiome (R01)
RFA-RM-08-010
PI Name Institution Name Title
LO, YU-HWA
ZHANG, KUN (contact)
UNIVERSITY OF CALIFORNIA SAN DIEGO An Integrated lab-on-chip system for genome sequencing of single microbial cells
MARZIALI, ANDRE BOREAL GENOMICS INC. SCODA DNA extraction to normalize species representation
RELMAN, DAVID A STANFORD UNIVERSITY Optimization of a microfluidic device for single bacterial cell genomics
SCHMIDT, THOMAS MITCHELL (contact)
YOUNG, VINCENT B
MICHIGAN STATE UNIVERSITY Cultivation and Characterization of Microaerobes from the Human Microbiome

 

Development of New Technologies Needed for Studying the Human Microbiome (R21)
RFA-RM-08-011
PI Name Institution Name Title
CHANG, EUGENE B UNIVERSITY OF CHICAGO Technologies for the discovery of novel human colonic mucosal-associated microbes
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