The microbiome refers to the collection of microorganisms—such as bacteria, fungi, viruses, and other microbes—and their genetic material that live in and on all living organisms. In humans, these microbial communities inhabit places like the skin, mouth, gut, and respiratory and reproductive tracts.

Far from being harmful, most of these microbes play essential roles in health: they help digest food, support the immune system, protect against pathogens, and influence many aspects of physiology. Microbiomes also exist in soils, oceans, plants, and animals, shaping ecosystems and driving biological processes across the planet.

In short, the microbiome is a dynamic, interconnected world of microbes that affects nearly every aspect of life. Take a look at important manuscripts from the COBRE leadership that focus on microbiomes across systems

Check out these review articles on the Microbiome by the Center’s Leadership:

• https://pmc.ncbi.nlm.nih.gov/articles/PMC11396321/pdf/ijms-25-09715.pdf
• https://pmc.ncbi.nlm.nih.gov/articles/PMC11238057/
• https://pmc.ncbi.nlm.nih.gov/articles/PMC6580755/

• This program is intended to bring individual microbiome scientists (one per year) who propose to stay in residence at the UPR Medical Sciences Campus for one to three weeks. Often, this extended time is useful for a lecture series, a multi-day workshop at the microbiome research core, for the transfer of new methodologies, establishment of collaborations, writing manuscripts, or preparing research proposals. 
• Request for Micorbiome Scientisit in residence must be a 1pg justification with said scientist expertise, objective of the residence and description of activities. Nih-Bio or equivalent for local scientist and invited scientist in residence are requested.
• The Center will provide full reimbursement of travel,lodging, subsistence, and a modest budget for materials and supplies needed for proposed activities. All members of the COBRE community will be welcome to submit candidates for the Scientist-in-Residence program.

• The COBRE Center for Microbiome Sciences (CMS) will offer Feasibility Awards to support investigators seeking to generate preliminary data using the services of the COBRE Microbiome Core Facility. These awards are designed to accelerate new microbiome-focused projects and strengthen future competitive grant applications.

Priority will be given to:

• Physician–scientists within UPR collaborating with basic scientists
• Mid-career and senior investigators exploring new scientific directions
• faculty members of any UPR campus; Other Puerto Rico Institutions will be considered.

Application Requirements

• Applicants must submit a two-page proposal outlining the scientific question, feasibility of the work, and how the requested services will support future funding applications or publication goals. A short timeline for the use of funds is required. Additional details about collaborations and career development are appreciated.
• Use of Funds: Feasibility Award funds may be requested for services provided by the COBRE Microbiome Core Facility, including but not limited to:
• Data acquisition 
• clinical sample processing for gDNA extraction or metabolite extraction
• DNA sequencing – 16S/ITS/18S
• Metagenomic sequencing
• Multi-omics services 
• Data acquisition and bioinformatics analysis
• Other microbiome-related laboratory services
• Data analyses for papers
• Analyses and figures for ongoing studies

Expectations: 

• Applicants should specify collaborating investigators and describe how the partnership will enhance project feasibility, scientific output, or interdisciplinary integration and timeline for achieving project goals should be clearly outlined
• Career Development Impact: Proposals must clearly explain how the planned experiments will advance the applicant’s professional and research trajectory. Examples include:
• Generating preliminary data for new grant proposals; Addressing gaps identified in summary statements for unfunded applications; Completing additional experiments required for manuscript revision
• Strengthening a developing research direction or multidisciplinary collaboration

• Beginning in 2026, the COBRE Center for Microbiome Sciences will launch a competitive Pilot Project Program to support emerging microbiome investigators across the UPR system. Each Pilot Project will be funded for two years at $50,000 per year.
• Request for Proposals (RFP): A Request for Proposals will be released in February 2026 and distributed widely through Research Deans at all UPR campuses, partner organizations, websites, and social media networks. 
• Full applications will follow the NIH R03/R21 format, with a submission deadline of April 10, 2026.
• Eligibility Applicants must meet NIH criteria for: Early-Stage Investigators (ESIs); New Investigators (NIs); Mid-career applicats will be considered for competitive projects with preliminary data
• Additional requirements: Must hold a faculty appointment at a UPR campus; Cannot receive concurrent research support from another IDeA award
•  Must  clearly demonstrate how microbiome research will be integrated into the proposed project

Application Components:

1-Cover Letter demonstrating, research career stage, history of funding and plans for external funding after pilot award

2-Confirmation of NIH and institutional eligibility by the School

3-Explanation of how microbiome research will be incorporated

4-Three potential external reviewers (names , research emphasis and email addresses)

5-NIH R03/R21-formatted proposal and page limits https://grants.nih.gov/grants-process/write-application/how-to-apply-application-guide/page-limits

Research Strategy: 6 pages

Project Summary/Abstract: 30 lines

Project narrative: three sentences

Biographical Sketch: 5 pages

Specific Aims: 1 page

Review Process: Proposals will be evaluated by external reviewers using standard NIH review criteria:

• Significance
• Innovation
• Investigator Preparation
• Approach
• Environment

Check this link for further information on review criteria: https://www.niaid.nih.gov/research/review-criteria

Opportunities at the Puerto Rico Center for Microbiome Sciences (PR-CMS)

The Puerto Rico Center for Microbiome Sciences (PR-CMS) offers diverse opportunities to support innovative, interdisciplinary microbiome research across the University of Puerto Rico and partnering institutions. The Center provides access to pilot project funding and feasibility studies designed to help investigators generate preliminary data, test novel hypotheses, and develop competitive proposals for external funding.

PR-CMS supports projects spanning environmental, clinical, and translational microbiome science, with a strong emphasis on data generation, bioinformatics, and collaborative research. Through its integrated research cores, the Center offers technical expertise, infrastructure, and mentorship to investigators at multiple career stages, including early-career faculty and trainees.

By investing in pilot projects and feasibility studies, PR-CMS aims to accelerate discovery, foster new collaborations, and strengthen microbiome research capacity in Puerto Rico and the Caribbean region.