ASM Responds to NIAID Strategic Plan

May 27, 2024

Jeanne Marazzo, M.D., MPH
National Institute of Allergy and Infectious Diseases
5601 Fishers Lane, MSC 9806
Bethesda, Md. 20892-9806

Re: Request for Information (RFI): Inviting Comments and Suggestions on NIAID’s Strategic Plan

Dear Dr. Marrazzo,

On behalf of the more than 36,000 members of the American Society for Microbiology (ASM), thank you for this opportunity to respond to the draft National Institute of Allergy and Infectious Diseases (NIAID) strategic plan.  As one of the largest life science societies, ASM’s mission is to promote and advance the microbial sciences. The National Institute of Allergy and Infectious Diseases supports life-saving research and is an important source of funding for scientific research on bacteria, viruses, fungi and other microbes, areas of research in which many ASM members are engaged. ASM is implementing a new strategic roadmap that intends to empower microbiologists and related stakeholders to guide and shape the future of the microbial sciences. We view ASM's input on the NIAID strategic plan as an additional step to shape the future of the microbial sciences, and we appreciate the opportunity to provide feedback. 

In preparing these comments, ASM convened members with an interest in NIAID priorities to solicit their feedback on the NIAID strategic plan. We also encouraged ASM members to submit their comments as individuals. Several themes emerged throughout the feedback process, which can be separated into 2 overarching categories—first, the integral role of microbiology in advancing NIAID’s mission, and second, the responsibility to leverage microbiology to address key societal issues. 

The Future of NIAID and the Future of Microbiology are Interconnected

ASM recognizes the integral role of microbiology in advancing NIAID’s mission, NIAID’s role in developing the microbiology workforce and the need to ensure adequate infrastructure to achieve scientific progress. While the strategic goals of NIAID will shift over the next 5 years, NIAID will remain the largest federal funder of basic microbiology research. The rapid pace of advancement in the biological sciences will only continue to accelerate with the application of new tools, including artifical intelligence (AI). NIAID’s strategic plan should provide the necessary flexibility to adapt to these changes. 

Support Foundational Research

Foundational research gaps remain in our understanding of host-pathogen interactions and pathogen biology, including how microbes interact. For example, a recent retreat of ASM’s Host-Microbe Biology community identified a need for a more nuanced understanding of interactions between microbes and their hosts, as well as among microbes, beyond the lens of pathogenesis. Besides categorizing the microbiota by metagenomics and their participation in various aspects of the host-microbe interface, the retreat report recommends that the field should strive to understand the functions of these microbes in their native community setting. Our members noted that NIAID could support research into these knowledge gaps and lead coordination of interdisciplinary pathogen research across NIH institutes. ASM members noted that inter- and transdisciplinary research are fundamental to advancing infectious disease research, and existing funding streams frequently do not support this type of research. 

Within the field of microbiology, research is often siloed between pathogenesis and environmental, resulting in neglecting the intricate connection between microbes, host organisms and the biosphere. Collaborations between health- and non-health-focused microbiologists, including One Health work, are often difficult due to funding restrictions on health and non-health research from both NIAID and funders of non-human health research, including the National Science Foundation and the Department of Energy. NIAID and NIH should collaborate with other science funding agencies to find suitable funding mechanisms for research projects that span human, animal and environmental health. This collaboration could be coordinated by an interagency coordinating committee on microbiological research.

To better understand function, host-microbe biology research will need to build stronger inter- to transdisciplinary ties to allow researchers from various fields to integrate large data sets beyond genotypic characterization to embrace a more comprehensive functional classification of the systems biology. To promote this cross disciplinary and discovery-based research, NIAID could support high risk and multi-investigator initiative collaborative projects that focus on big picture questions and solutions, rather than discipline-based research. Increased NIAID support for R35 and DP2 awards could facilitate this kind of research. These could include requiring multiple principal investigators (PIs) on grants from different disciplines. 

As noted above, pathogen research is often funded by multiple institutes and centers within NIH. NIAID should convene institutes and centers within NIH to ensure that the agency is funding virus and pathogen research in a holistic manner. NIAID could also increase collaboration with other institutes and centers in NIH, other agencies and private philanthropy. As an example, NSF and the Paul G. Allen Family Foundation partner to fund research on organismal biology, ecology and evolution to develop and implement action plans and technologies that advance biodiversity conservation.

Finally, our clinical members noted gaps in NIAID’s clinical portfolio that would improve patient care. This includes a need to fund effectiveness studies and validate clinical diagnostic tools. These kinds of studies require many resources and extensive collaboration. Significant NIAID investments in this research would make this work possible. Clinical members also called out a lack of pediatric infectious disease coordination networks for research clinicians. Similar pediatric disease coordination networks for other diseases exist across other NIH institutes.

Scientists Need Support Across Career Stages

ASM appreciates the inclusion of workforce training and diversity, equity, inclusion and accessibility as cross-cutting areas in the strategic plan. Maintaining a pipeline of microbiologists across career stages and helping early career scientists enter the field is essential to the continued viability of the microbial sciences. Early and mid-career microbiologists often face hurdles while renewing NIAID funding, forcing those investigators to leave academia. When these investigators leave academia or science because of funding restrictions, this represents a loss of the investment that NIAID has already made in that investigator earlier in their career and training, as well as a loss of new and innovative researchers in the NIAID ecosystem.

Our members noted that principal investigators often struggle to hire and retain post-doctoral researchers in their laboratories because caps on salary support from NIH often are not competitive with industry salaries for early-career Ph.D.s. The low salary caps are disproportionately likely to drive underrepresented minorities, women, members of the LGBTQIA+ community, international scholars, scholars with disabilities and other members of vulnerable communities. ASM supports NIH implementing the recommendations of the Advisory Committee to the Director Working Group on Re-envisioning NIH Supported Postdoctoral Training. Our members also raised concerns that institutions that receive NIH training grants, such as T32s, F31s and F32s, cannot use federal dollars to supplement awards to make salaries for trainees competitive. ASM supports increased flexibility to allow institutions to use federal funding to supplement salaries.

One notable disparity between NIAID and other NIH institutes is that NIAID only funds 2-year R00 awards, which funds promising early-career scientists as they transition to tenure track faculty positions, while other NIH institutes fund 3-year R00 awards. Because NIAID only funds 2-year R00 awards, NIAID funded researchers are functionally ineligible for diversity supplement awards, which require 2 years of funding and diverse personnel within an existing lab. Increased flexibility in the timing of awarding career training grants would also help researchers as they transition from postdoctoral researcher positions.

ASM recommends partnering with scientific societies to strengthen the pipeline of diverse scientists in the workforce in NIAID-funded fields. For example, in 2023, the National Institute of General Medical Sciences awarded ASM a 5-year cooperative agreement to support early-career scientists from underrepresented groups as they transition successfully from postdoctoral positions to tenure-track faculty positions, known as the Maximizing Opportunities for Scientific and Academic Independent Careers (MOSAIC) program. Through this partnership, ASM has selected a cohort of ASM MOSAIC 2023 scholars consisting of 7 promising early-career scientists from diverse backgrounds. This cohort is receiving additional mentoring and career support through ASM for the next 5 years, such as leadership and lab management training and training about the responsible conduct of research.

Research and Data Infrastructure

NIAID plays an important role in supporting research infrastructure across institutions. Over the next 5 years, NIAID should expand its role in supporting common infrastructure to advance NIAID priority research. Examples of needed research infrastructure include, ordered transposon mutant libraries for bacteria, CRISPR libraries for host cells and collections of isolates of a given species. One existing example of similar NIAID-supported research infrastructure is the BEI Resources Repository.

Support for common infrastructure for storing and sharing data about microbes, infectious diseases and omics and genomics is needed, particularly as AI is generating more biological data and models. Researchers often struggle to identify where and how to store data. For example, microbiologists working with genomic data from human patients struggle to store and securely share this data with other researchers and public health officials.

Current NIAID data infrastructure and strategy is piecemeal. NIAID can address this problem by funding research infrastructure for sharing, storing and analyzing data, as well collaborating with NIH’s Office of Data Science Strategy. In order to produce robust and reproducible studies, researchers need both infrastructure and training to share data with context. Examples of these kinds of data programs outside of NIH-funded research include the Department of Energy’s National Microbiome Data Collaborative, which provides a standardized platform for storing and sharing microbiome data, as well as training for microbiologists on using and analyzing those data. The National Science Foundation’s Biological Sciences Directorate has also recently expanded its synthesis centers, which focus on building capacity to use and analyze biological data. 

There is a critical need for a comprehensive policy on open science and open data. Such a policy should promote transparency, reproducibility and collaboration across the scientific community. In addition to data infrastructure, NIAID must prioritize funding for open access publication avenues for publicly funded research. The dissemination of research findings without paywalls is essential for advancing scientific knowledge and public health. Open access ensures that researchers, policymakers and the public can freely access and build upon the latest discoveries. This is crucial for addressing urgent health threats and fostering innovation. NIAID can support this by allocating funds specifically for covering reasonable publication fees in open-access journals and by encouraging grantees to publish in open-access venues. Explicit support for open access aligns with the broader goals of transparency, equity and the democratization of scientific knowledge.

Research Security

Members expressed concerns regarding the implementation of the recent guidance on pathogens with enhanced pandemic potential (PEPP) and dual use research of concern (DURC) guidelines from the White House Office of Science and Technology Policy (OSTP). NIAID should exercise leadership in implementation of the May 2024 OSTP U.S. Government Policy for the Oversight of Dual Use Research of Concern and Pathogens of Enhanced Pandemic Potential. Specifically, they raised questions regarding the additional burden on researchers and noted that implementation will require support and education from NIAID, which to our knowledge has not been funded. 

Support for biosafety facilities and institutional biosafety committees is also key. A 2023 American Academy of Microbiology roundtable report about gain of function research with infectious agents recommended increased funding for research on biosafety measures, biorisk management training, occupational medicine services, improved facilities and protocols, and personal protective equipment can ensure biorisk management is taken more seriously and effectively across institutions and laboratories, improving the safety of the public and laboratory workers. Improved reporting systems and responses for lab accidents, such as anonymous reporting or constructive (rather than punitive) responses, can allow for more data collection on lab accidents and safety breaches, better informing the risk-benefit analysis when evaluating research with infectious agents. NIAID can play a role in funding these efforts and creating requirements for grantee institutions.

Other important parts of NIAID’s biosafety portfolio are the biosafety level 3 (BSL3) regional biocontainment laboratories and the two national BSL4 facilities. NIAID has invested approximately $1 billion in these facilities and should reinforce this investment by drafting and implementing a national strategy to strengthen and expand the NIAID National Biodefense Laboratory Network. This strategy should address workforce training, the safe and secure maintenance and operations of biosafety facilities and create a NIAID-led national network of BSL3 and BLS4 laboratories. NIAID should offer funding opportunities to facilitate and encourage collaboration within this network.

Improvements to Study Sections

ASM appreciates that NIH is taking steps to reduce reputational bias in grant reviews and shares concerns that the NIH grant review processes lead to unintentional bias toward more senior researchers and research at major research institutions, as well as potential bias against proposals with components outside of the U.S. Clear information is needed about how NIAID is implementing this guidance for both reviewers and grant applicants. We recommend that NIAID can prevent this bias by recruiting researchers from outside of large research institutions to participate in study sections. ASM can help with identifying and recruiting reviewers through calls to our membership lists, events at ASM Microbe and other ASM meetings, webinars and more. NIAID can also lessen this bias by providing training to reviewers about how to recognize and correct bias.

Animal Models

ASM appreciates the inclusion of “support[ing] the development of animal models and non-animal alternate methods for basic and translational research within the NIAID mission space" in priority #1. ASM members noted a dire need for further development of animal models for pathogen research to develop better infection models. Other animal models used in infectious disease research are also cost prohibitive, in addition to raising ethical concerns. NIAID support for partnerships between veterinary schools and infectious disease researchers could lead to better animal models. Alternatives to animal models, such as artificial intelligence, also show promise, but further research is needed to develop and validate these models.

Microbiology Holds the Power to address Key Societal Issues

Increasingly, we live in a world of microbial threats to health and well-being, which are exacerbated by a changing climate and increasing antimicrobial resistance. Infections frequently complicate other types of medical care, including organ transplantation, cancer treatment, cesarean sections and other surgeries, making infectious disease research essential to the very foundation of health care. The specter of the next pandemic also looms large. ASM members continue to rise to these challenges by leveraging NIAID funding to overcome these pressing health concerns.

Pandemic Prevention and Global Health Security

ASM strongly supports innovative research efforts to prepare for and respond to nationally or internationally significant biological incidents affecting public health. A core principle of pandemic prevention and response should include efforts to understand and address underlying health disparities and access to health care. 
While NIAID funds research around the world, most research is focused on outbreaks that could spread to the U.S. However, outbreaks are most likely to emerge in and pose a disproportionate burden on low- and middle-income countries. NIAID could play several roles in easing this burden, including developing cost-effective diagnostics, tailored to the context of countries, as well as better dissemination of knowledge about diagnostics in low- and middle-income countries. To support scientific and public health infrastructure in low- and middle-income countries, NIAID could support programs to train scientists to clean and analyze data and write and publish journal articles.

Infectious disease research often requires international collaboration. For example, it often makes most sense to study parasites or tropical infectious diseases in the countries where they are endemic. However, NIH requirements for international collaborations are often cumbersome and intimidating for international partners in the infectious disease space, who often operate in resource-poor environments in low- and middle-income countries. ASM recognizes the need to balance research security and biosecurity concerns with enabling research to prevent pandemics internationally, and recommends that NIAID investigate the potential negative impacts of increased requirements on international collaborations and develop recommendations for supporting researchers who are carrying out this work.

Opportunities for collaboration with the Centers for Disease Control and Prevention, U.S. Agency for International Development and other federal programs should be explored to support global efforts for disease surveillance, rapid pathogen genomic characterization and data sharing. Public health and scientific infrastructure that was built out during the COVID-19 pandemic is key to preventing future pandemics, and is currently at risk of losing funding as COVID-19 supplemental funding expires. One example of this is the Pathogen Genomics Centers of Excellence (PGCoE), which are part of the Centers for Disease Control and Prevention’s Advanced Molecular Detection program. PGCoEs are collaborations between U.S. public health agencies and academic institutions to better prevent, control and respond to microbial threats of public health importance. The PGCoE network is meant to foster and improve innovation and technical capacity in pathogen genomics, molecular epidemiology and bioinformatics to better prevent, control and respond to microbial threats of public health importance. Given the relatively stable nature of NIH funding, NIH and NIAID could play a role in maintaining this infrastructure.

Microbiome Research and Applications

The NIH has been on the forefront of supporting microbiome research since 2007 with the Common Fund’s Human Microbiome Project, which was formed to develop research resources to study microbial communities and how they impact human health and disease. Thanks to NIH’s cross-cutting work that the Common Fund enabled, we now have a foundational understanding of how microbial communities interact with humans, especially the human gut microbiome, and the world around us. A better understanding of microbiome development, composition and function—in people and beyond—will continue to inform strategies that harness the power of microbes to foster human and planetary health.  

ASM strongly encourages NIAID to increase support for microbiome research. Microbiome treatments are an emerging area for drug development and show promise as alternatives to antimicrobial drugs. While collective genomic and bioinformatic knowledge of the microbiome is expanding, there is a lack of research and fundamental explorations into the physiology and molecular biology and functional studies of microbiome communities. 

Climate Change and Health

Climate change, both in terms of the impacts of climate on microbial communities and the role of microbes in mitigating and adapting to climate change, is area of heightened interest. As climate changes in terrestrial, urban and aquatic environments, the human, animal and plant pathogens living in those environments must adapt, presenting opportunities for pathogens to move about and evolve in unknown ways that may increase virulence and host-range. Shifts in temperature, precipitation, humidity, CO2 concentrations and nutrient availability can increase water and food-borne infections and the risk of zoonotic diseases. 

NIAID can be a leader in health-climate research by funding research to better improve surveillance and understand the impact of climate on pathogens and forward-looking solutions to prevent, mitigate and treat infectious diseases that are more prevalent due to climate change. ASM encourages NIAID to collaborate across NIH on research that addresses the ever-growing human health threats due to climate change, particularly the evolving geography of pathogens including fungal pathogens.

Antimicrobial Resistance

Antimicrobial resistance (AMR) is a daunting public health challenge and considered a global crisis by the World Health Organization, the G20 and the United Nations. Continued investment in research to better understand how microbes become resistant and develop more precise clinical diagnostics, novel therapeutics and vaccines is greatly needed. Robust AMR research funding at NIAID would support the training of new investigators; enhance basic, translational and clinical research on mechanisms of resistance, therapeutics, vaccines and diagnostics; and support the development of a clinical trials network to reduce barriers to research on difficult-to-treat infections.

ASM thanks NIAID for its leadership in infectious disease research and the microbial sciences and for engaging the research community in this strategic plan development process. We look forward to continued partnership with NIAID to build the scientific workforce and infrastructure needed to harness microbiology to solve societal issues, such as preventing pandemics and the spread of antimicrobial resistance over the next 5 years and beyond. If you have any questions, please contact Nicole Zimmerman, Senior Specialist, Federal Affairs at

Warm regards,


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Stacey Schultz Cherry
Chair, ASM Public and Scientific Affairs Committee

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