Opportunity Information: Apply for PA 15 135
Apply for PA 15 135
- The National Institutes of Health in the education food and nutrition health income security and social services sector is offering a public funding opportunity titled "Advancing Mechanistic Probiotic/Prebiotic and Human Microbiome Research (R01)" and is now available to receive applicants.
- Interested and eligible applicants and submit their applications by referencing the CFDA number(s): 93.121 Oral Diseases and Disorders Research 93.213 Research and Training in Complementary and Integrative Health 93.279 Drug Abuse and Addiction Research Programs 93.321 Dietary Supplement Research Program 93.393 Cancer Cause and Prevention Research 93.394 Cancer Detection and Diagnosis Research 93.395 Cancer Treatment Research 93.396 Cancer Biology Research 93.399 Cancer Control 93.846 Arthritis, Musculoskeletal and Skin Diseases Research 93.847 Diabetes, Digestive, and Kidney Diseases Extramural Research 93.859 Biomedical Research and Research Training 93.865 Child Health and Human Development Extramural Research.
- This funding opportunity was created on Mar 9, 2015 and posted on Mar 9, 2015.
- Applicants must submit their applications by May 7, 2018. (Agency may still review applications by suitable applicants for the remaining/unused allocated funding in 2026.)
- Eligible applicants include: State governments County governments City or township governments Nonprofits having a 501(c)(3) status with the IRS, other than institutions of higher education Nonprofits that do not have a 501(c)(3) status with the IRS, other than institutions of higher education Independent school districts Others (see text field entitled Additional Information on Eligibility for clarification) Native American tribal organizations (other than Federally recognized tribal governments) Small businesses Native American tribal governments (Federally recognized) Public and State controlled institutions of higher education Public housing authorities/Indian housing authorities For profit organizations other than small businesses Special district governments Private institutions of higher education.
- Other Eligible Applicants include the following Alaska Native and Native Hawaiian Serving Institutions Asian American Native American Pacific Islander Serving Institutions (AANAPISISs) Eligible Agencies of the Federal Government Faith based or Community based Organizations Hispanic serving Institutions Historically Black Colleges and Universities (HBCUs) Indian/Native American Tribal Governments (Other than Federally Recognized) Non domestic (non U.S.) Entities (Foreign Organizations) Regional Organizations Tribally Controlled Colleges and Universities (TCCUs) U.S. Territory or Possession Non domestic (non U.S.) Entities (Foreign Institutions) are not eligible to apply. Non domestic (non U.S.) components of U.S. Organizations are not eligible to apply. Foreign components, as defined in the NIH Grants Policy Statement, are allowed.
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Opportunity Summary:
The NIH funding opportunity PA 15-135, titled "Advancing Mechanistic Probiotic/Prebiotic and Human Microbiome Research (R01)," was an R01 grant program designed to push probiotic and prebiotic research beyond broad descriptive associations and toward clear, testable mechanisms that explain how specific microbes, substrates, and microbial communities affect human health and disease. The FOA had two central goals. First, it aimed to stimulate basic and mechanistic science that can directly support the development of effective probiotics or combined prebiotic/probiotic approaches (often thought of as synbiotic strategies) that are relevant to human biology. Second, it sought to identify and validate measurable biological outcomes that can be used to judge whether a given prebiotic or probiotic is working, using appropriate experimental test systems and animal models. In practice, that means the FOA was interested not just in whether an intervention changes the microbiome, but in how it works, what host pathways it engages, which microbial genes or metabolites are involved, and what endpoints best reflect meaningful efficacy.
A major emphasis of the announcement was on mechanistic studies using a range of model systems, including in vitro approaches (such as cell culture, microbial community models, gut-on-a-chip systems, fermentation systems, and controlled consortia), in vivo work (especially animal models that allow controlled testing of causality), ex vivo methods (for example, organoids, tissue explants, or immune cell assays using biologically relevant materials), and in silico approaches (computational modeling, systems biology, and bioinformatic integration of multi-omic data). The FOA explicitly encouraged projects that focus on probiotic and prebiotic strain selectivity, interaction, and function. That focus signals a preference for research that can distinguish between strains rather than treating probiotics as interchangeable, can explain how prebiotics selectively enrich or suppress particular taxa or functions, and can map the downstream consequences of these changes, such as altered metabolite production, immune modulation, barrier function changes, or impacts on disease-relevant pathways.
The opportunity also highlighted the importance of defining biological outcomes suitable for evaluating efficacy. In the context of probiotics and prebiotics, this typically means moving toward endpoints that are mechanistically tied to the intervention, reproducible across systems, and interpretable for future translation. Examples of the kinds of outcomes this program tried to promote include functional microbiome readouts (metabolic outputs such as short-chain fatty acids, bile acid transformations, or other microbial metabolites), host responses (immune signaling, inflammatory markers, epithelial integrity, mucosal responses), and integrated multi-omic signatures that connect microbial activity to host physiology. The key idea is that efficacy should be evaluated with outcomes that reflect function and mechanism, not only shifts in community composition.
Another defining feature was its encouragement of inter- and multidisciplinary collaboration. The FOA pointed to a broad set of relevant disciplines, including nutritional science, immunology, microbiomics, genomics and other omic sciences (such as metabolomics, proteomics, transcriptomics), biotechnology, and bioinformatics. This reflects how microbiome intervention research often requires combined expertise: designing and characterizing microbial strains and prebiotic substrates, measuring community and functional changes, interpreting host responses, and integrating complex datasets to infer causal pathways. Projects that bridge these areas would have aligned well with the stated intent of the program.
From an administrative and eligibility standpoint, this was a discretionary NIH grant using the R01 mechanism, with no cost-sharing or matching requirement. The FOA was posted and created on March 9, 2015, and it closed on May 7, 2018, with an archive date of June 7, 2018. A wide range of applicants were eligible, including state, county, and local governments; public and private institutions of higher education; nonprofit organizations (both 501(c)(3) and other nonprofit categories); small businesses; for-profit organizations other than small businesses; independent school districts; special district governments; tribal governments and tribal organizations; public housing authorities/Indian housing authorities; and other organizations as described in the full FOA. The eligibility text also called out multiple institution types such as HBCUs, Hispanic-serving institutions, tribally controlled colleges and universities, and various minority-serving institutions, as well as faith-based and community-based organizations and eligible federal agencies. Foreign institutions themselves were not eligible to apply, and non-U.S. components of U.S. organizations were not eligible; however, foreign components as defined in the NIH Grants Policy Statement were allowed, which typically means a U.S. applicant could include certain foreign collaborations or performance sites if well-justified and compliant with NIH policy.
The FOA was associated with multiple CFDA numbers spanning oral health, complementary and integrative health, substance abuse research, dietary supplement research, cancer research (across prevention through control), arthritis and musculoskeletal research, diabetes/digestive/kidney research, general biomedical research and training, and child health and human development. That breadth signals that the program was meant to support mechanistic prebiotic/probiotic research relevant to many disease areas rather than being limited to a single organ system or condition. Overall, PA 15-135 was structured to build a stronger scientific foundation for microbiome-targeted interventions by demanding more precise understanding of which strains or substrates do what, under what conditions, through which biological mechanisms, and with which measurable outcomes that can support rigorous evaluation and eventual translation.
Frequently Asked Questions (FAQs): NIH PA 15-135 - Advancing Mechanistic Probiotic/Prebiotic and Human Microbiome Research (R01)
1) What is NIH PA 15-135?
PA 15-135 is an NIH funding opportunity announcement (FOA) titled "Advancing Mechanistic Probiotic/Prebiotic and Human Microbiome Research (R01)." It used the NIH R01 grant mechanism to support research that moves beyond descriptive microbiome associations and toward clear, testable mechanisms explaining how probiotics, prebiotics, and microbial communities influence human health and disease.
2) What type of grant mechanism did this FOA use?
This opportunity used the NIH R01 mechanism.
3) What were the main scientific goals of this FOA?
The FOA had two central goals: (1) stimulate basic and mechanistic science that can directly support development of effective probiotics or combined prebiotic/probiotic (synbiotic) strategies relevant to human biology, and (2) identify and validate measurable biological outcomes that can be used to evaluate whether a given probiotic or prebiotic is working, using appropriate experimental systems and animal models.
4) What kind of research focus did NIH emphasize in PA 15-135?
The emphasis was on mechanistic research. The FOA prioritized studies that can explain how an intervention works (for example, which host pathways are engaged, which microbial genes or metabolites are involved, and what endpoints best reflect meaningful efficacy), not just whether the microbiome changes after an intervention.
5) Does the FOA support research on probiotics only, prebiotics only, or both?
It supports mechanistic research on probiotics and prebiotics, including combined approaches often described as synbiotic strategies (prebiotic/probiotic combinations).
6) What does the FOA mean by moving beyond "broad descriptive associations"?
It means the FOA was looking for more than correlations between microbiome composition and health outcomes. Projects were expected to pursue clear, testable mechanisms that explain causality and function, such as identifying specific strains, substrates, microbial genes, or microbial metabolites that drive specific host responses.
7) What kinds of model systems were encouraged for mechanistic studies?
The FOA highlighted mechanistic studies across multiple model system categories, including in vitro, in vivo, ex vivo, and in silico approaches.
8) What are examples of in vitro approaches mentioned in the FOA?
Examples included cell culture, microbial community models, gut-on-a-chip systems, fermentation systems, and controlled microbial consortia.
9) What are examples of in vivo approaches mentioned in the FOA?
The FOA particularly emphasized animal models that allow controlled testing of causality.
10) What are examples of ex vivo approaches mentioned in the FOA?
Examples included organoids, tissue explants, and immune cell assays using biologically relevant materials.
11) What are examples of in silico approaches mentioned in the FOA?
Examples included computational modeling, systems biology, and bioinformatic integration of multi-omic data.
12) Why did the FOA emphasize strain selectivity and strain function for probiotics?
The FOA encouraged work that distinguishes between specific strains rather than treating probiotics as interchangeable. That includes defining how particular strains interact, what functions they perform, and what downstream biological consequences follow.
13) How did the FOA describe the role of prebiotics in mechanistic studies?
The FOA encouraged research that can explain how prebiotics selectively enrich or suppress particular taxa or functions and map the downstream consequences of those selective effects.
14) What downstream consequences or pathways were highlighted as examples of mechanistic outcomes?
Examples included altered metabolite production, immune modulation, changes in barrier function, and impacts on disease-relevant pathways.
15) What does the FOA mean by "measurable biological outcomes" for evaluating efficacy?
It refers to endpoints that can be used to judge whether a probiotic or prebiotic is working in a biologically meaningful way. The FOA emphasized outcomes that are mechanistically tied to the intervention, reproducible across systems, and interpretable for future translation.
16) What kinds of functional microbiome readouts did the FOA highlight?
Examples included metabolic outputs such as short-chain fatty acids, bile acid transformations, and other microbial metabolites.
17) What kinds of host response outcomes did the FOA highlight?
Examples included immune signaling, inflammatory markers, epithelial integrity, and mucosal responses.
18) Did the FOA encourage multi-omic or integrated endpoint strategies?
Yes. It highlighted integrated multi-omic signatures that connect microbial activity to host physiology and emphasized bioinformatic integration of multi-omic data as part of in silico approaches.
19) Was changing microbiome composition alone considered sufficient?
The FOA signaled that composition shifts alone were not the primary goal; it emphasized functional and mechanistic endpoints rather than only community composition changes.
20) Did the FOA encourage interdisciplinary or multidisciplinary teams?
Yes. Inter- and multidisciplinary collaboration was explicitly encouraged.
21) Which disciplines were specifically called out as relevant?
The FOA pointed to nutritional science, immunology, microbiomics, genomics and other omic sciences (including metabolomics, proteomics, transcriptomics), biotechnology, and bioinformatics.
22) Was cost-sharing or matching required?
No. The FOA specified no cost-sharing or matching requirement.
23) When was PA 15-135 posted and created?
It was posted and created on March 9, 2015.
24) When did the FOA close and when was it archived?
The FOA closed on May 7, 2018, and the archive date was June 7, 2018.
25) What types of organizations were eligible to apply?
A wide range of applicants were eligible, including state, county, and local governments; public and private institutions of higher education; nonprofit organizations (501(c)(3) and other nonprofit categories); small businesses; for-profit organizations other than small businesses; independent school districts; special district governments; tribal governments and tribal organizations; public housing authorities/Indian housing authorities; and other organizations as described in the full FOA.
26) Were minority-serving institutions and community-based organizations included in eligibility?
Yes. The eligibility description called out multiple institution types such as HBCUs, Hispanic-serving institutions, tribally controlled colleges and universities, and other minority-serving institutions, as well as faith-based and community-based organizations.
27) Were federal agencies eligible to apply?
Yes. Eligible federal agencies were included in the eligibility description.
28) Are foreign institutions eligible to apply as the applicant organization?
No. Foreign institutions themselves were not eligible to apply.
29) Are non-U.S. components of U.S. organizations eligible?
No. Non-U.S. components of U.S. organizations were not eligible.
30) Are any foreign collaborations allowed under this FOA?
Yes. Foreign components, as defined in the NIH Grants Policy Statement, were allowed. This typically means a U.S. applicant could include certain foreign collaborations or performance sites if well-justified and compliant with NIH policy.
31) What research areas or disease topics could fit this FOA?
The FOA was associated with multiple CFDA numbers spanning oral health, complementary and integrative health, substance abuse research, dietary supplement research, cancer research (from prevention through control), arthritis and musculoskeletal research, diabetes/digestive/kidney research, general biomedical research and training, and child health and human development. This suggests the program was meant to support mechanistic probiotic/prebiotic research relevant to many disease areas rather than a single condition.
32) What is the overall intent of PA 15-135?
Overall, the FOA was structured to strengthen the scientific foundation for microbiome-targeted interventions by requiring more precise understanding of which strains or substrates do what, under what conditions, through which biological mechanisms, and with which measurable outcomes that can support rigorous evaluation and eventual translation.
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