| Arizona State University | Center for Fundamental and Applied Microbiomics |
| Arizona State University | Center for Health through Microbiomes |
| Boston University | Microbiome Initiative |
| California Institute of Technology | Center for Environmental Microbial Interactions |
| Colorado State University | Microbiome (COSMic) Network |
| Dept of Energy National Lab partnership | National Microbiome Data Collaborative |
| Dept of Veterans Affairs | Military and Veterans Microbiome Consortium for Research and Education |
| Duke University | Duke Microbiome Center |
| Georgia Institute for Technology | Center for Microbial Dynamics and Infection |
| Harvard University | Harvard Chan Microbiome in Public Health Center |
| Johns Hopkins University | Microbiome Research Group |
| Lawrence Berkeley Lab | Microbes to Biomes (M2B) |
| Massachusetts Institute of Technology | Center for Microbiome Informatics & Therapeutics |
| Mayo Clinic | Microbiome Program |
| Medical College of Wisconsin | MCW Center for Microbiome Research |
| Medical University of South Carolina | Program for Human Microbiome Research |
| Michigan State University | Center for Microbial Ecology |
| Northern Arizona University | Center for Applied Microbiome Science |
| Ohio State University | Center of Microbiome Science |
| Oklahoma State University | Center for Integrative Microbiome Science |
| Oregon State University | Microbiome Initiative |
| Pacific Northwest National Lab | Microbiomes in Transition Initiative |
| Pennsylvania State University | Penn State Microbiome Center |
| Rutgers University | Rutgers Microbiome Program (RUMP)
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| Rutgers University | Center for Nutrition, Microbiome, and Health |
| University of California, Berkeley | Joint Berkeley Initiative for Microbiome Sciences |
| University of California, Davis | Microbiome Special Research Program |
| University of California, Irvine | Center for Microbiome Science |
| University of California, Los Angeles | UCLA Microbiome Center |
| University of California, Riverside | UCR Microbiome Initiative |
| University of California, San Diego | Center for Microbiome Innovation |
| University of California, San Francisco | Benioff Center for Microbiome Medicine |
| University of Chicago / MBL / Argonne | The Microbiome Center |
| University of Colorado, Anschutz | The Anschutz Center for Microbiome Excellence (ACME) |
| University of Colorado, Anschutz | Center for Mucosal Immunology and Rheumatic Disease Pathogenesis (CMIR) |
| University of Colorado, Boulder | Center for Microbial Exploration |
| University of Connecticut | Center for Microbial Systems, Ecology and Evolution |
| University of Connecticut | MARS: Microbial Analysis, Resources and Services |
| University of Hawai‘i at Mānoa | Center for Microbiome Analysis |
| University of Maryland | Center of Excellence in Microbiome Sciences |
| University of Massachusetts | Center for Microbiome Research |
| University of Michigan | Microbiome Core |
| University of North Carolina | Microbiome Core |
| University of Oklahoma | Institute for Environmental Genomics |
| University of Oregon | Microbiome Initiative |
| University of Pennsylvania & Children’s Hospital | PennCHOP Microbiome Program |
| University of Pittsburgh | Center for Medicine and the Microbiome |
| University of South Florida | Initiative on Microbiomes |
| University of Utah | Microbiota and Gastrointestinal Immunology Consortium (MAGIC) |
| University of Virginia | TransUniversity Microbiome Initiative |
| Vanderbilt University | The Vanderbilt Microbiome Initiative (VMI) |
