ASM Responds to Department of Energy's RFI

December 22, 2022

Office of Science
U.S. Department of Energy
Attn: Ms. Natalia Melcer
1000 Independence Ave SW
Washington, D.C. 20585

Re: Department of Energy Request for Information Accelerating Innovations in Emerging Technologies Docket DOE-HQ-2022-0031

Dear Ms. Melcer:

The American Society for Microbiology (ASM) appreciates the opportunity to respond to this request for information on accelerating innovations in emerging technologies. With more than 30,000 members in the U.S and around the globe, ASM’s mission is to promote and advance the microbial sciences. Our members include basic, translational and clinical researchers with expertise in genomic science and related biotechnologies that contribute to clean energy development, basic energy science and leadership in the bio-based economy.

Support and funding from the DOE Office of Science and the National Laboratories have generated some of our most scientifically and economically important innovations and have served as primary drivers of basic research, including critical areas of genome-scale quantitative analysis of microbial research. This has enabled researchers to use microbes to address energy and environmental problems, and to bring those solutions to scale by developing empirical, computational and mechanistic modeling tools. In addition, the complex data systems created and managed by DOE scientists benefit biologic and environmental research across domains, including agriculture and human health. Below we have provided responses to the specific questions set forth in the RFI.

(1) What are the barriers or challenges that need to be addressed to transition basic scientific discoveries to applied technologies?

The Department of Energy plays an instrumental role in funding microbial research that is both fundamental and aimed at translating scientific research into practical solutions. Through DOE investments, scientists have discovered how microbes can serve as industrial catalysts and form the basis of next generation biofuels and chemicals. Despite these advances in basic science, consistent support for interdisciplinary and transdisciplinary science and scaling of new technologies, particularly across domains, remains challenging.

Microbiome research, which has been advanced significantly through DOE-supported entities like the Joint Genome Institute (JGI) and National Microbiome Data Collaborative (NMDC), is inherently transdisciplinary and would benefit greatly from greater coordination across federal agencies that fund this research. Microbiomes have positive influences on human and ecosystem health, and they drive greenhouse gas cycling. Dysfunctional microbiomes are associated with numerous problems, including chronic human diseases; disruption of beneficial ecosystem services; and reductions in agricultural productivity. A multitude of industrial processes, such as biofuel production and many food processing operations, depend on healthy microbial communities.

New technologies in genetics and genomics supported by the DOE Office of Science have led to exciting discoveries about the importance of microbiomes. The next steps, which are to further understand and then manage microbiome systems, require additional knowledge and tools. ASM has been a strong advocate for interagency coordination in this work, and we support DOE’s leadership in this space through NMDC, JGI, and the DOE National Laboratories.

We hope to see continued scaling up of these programs, the strengthening of interagency agreements on microbiome data, and we highly encourage the Office of Science and Technology Policy at the White House to renew the charter for the Microbiome Interagency Working Group to develop a new Interagency Strategic Plan for Microbiome Research. The former Plan, which ended this year, promoted the enhancement of microbiome research and the federal research and development enterprise by embracing diversity, recognizing that inclusion of a broad range of backgrounds and perspectives is critical to achieving robust intellectual dialogue and advancement of emerging technologies.

It is also important to address gaps in relation to the ‘valley of death’ between innovation and basic scientific discoveries at an early stage, making it difficult for researchers to advance and develop their work into applied technologies. Continued advances made by microbial scientists focused on turning renewable resources into fuel and chemicals could propel work by private sector entities to produce products that are not based on fossil fuels, plus those that cannot currently be produced at industrial scale.

The work of DOE’s Office of Science Bioenergy Research Centers (BRC) exemplifies a fully integrated approach to guide and accelerate research and development of advanced biofuels, bioenergy or biobased materials, chemicals and products that are produced from a variety of regionally diverse feedstocks, and to facilitate the translation of research results to industry.

Programs that create opportunities for translation and scaling of this research, including the Small Business Innovation Research (SBIR) and Small Business Technology Transfer (STTR) programs are also critical in the biologic and environmental technology areas. We also encourage increasing the focus on microbe-based innovations under ARPA-E. Sustained funding for these programs across the key technology areas will allow foundational research to continue while providing opportunities to explore commercial applications of new scientific discoveries.

(2) What opportunities are there to build research teams that bridge the discovery to production spectrum, providing an “end to end” approach that fully integrates “science push” and “technology pull” processes to guide research to realize new technologies?

The greatest scientific challenges will not be solved by individual scientists, disciplines or laboratories. Rather, we can start to address them by supporting interdisciplinary collaboration and coordination through research centers or centers of excellence. As noted above, the Bioenergy Research Centers, which are funded through DOE’s Genomic Science Program, were created to break down the barriers to actualizing a domestic bioenergy research industry. BRCs leverage the fundamental research of the genomic sciences to engineer microbes for more effective biofuel production.

Institutes and centers of excellence, which are often based at academic institutions, are adept at bringing together experts across disciplines to target inherently interdisciplinary areas like data science, precision medicine, complex systems and emerging technologies. Researchers at these centers collaborate across disciplines, such as bioinformatics, engineering, computer science, chemistry and molecular biology, and work together to address our most complex societal issues. However, they are frequently hobbled by inconsistent funding from a myriad of sources and would greatly benefit from sustained coordinated funding that supports interdisciplinary collaboration.

(3) What new opportunities could be realized by combining 2 or more of the ten key technologies to accelerate the development of innovative products?

As noted above, microbiome research, which combines several of the key technology areas, is emerging as a key to solving our most pressing societal challenges. Microbiome research is essential for understanding how communities of microbes interact for next generation biofuel development; researchers are also exploring innovations in microbial fuel cells. Other potential applications of microbiome research to product development include prebiotic and probiotic supplements and drugs to support human and animal health, microbial inoculants for agricultural productivity and ensuring a clean and safe water supply. Microbiome research is interdisciplinary and leverages DOE resources to harness the power of their data science, bioinformatic, AI, and genomic science capabilities to support innovation in biopreparedness, biotechnology and other focus areas. As with all emerging technologies, programs and funding streams that allow for failure, as opposed to only rewarding success, are a necessary component of innovation.

(5) To prepare for future industries, what opportunities are there for ensuring a robust workforce related to the ten key technologies? What skills are needed for students preparing for a career, and which of these skills are not commonly available in educational institutions?

One way to prepare for future industries is to invest in education and training programs that focus on these fields. This could include providing funding for degree programs in genomics, data analysis, synthetic biology and biotechnology, as well as supporting ongoing professional development and training opportunities for workers in these fields. Another opportunity is to encourage interdisciplinary collaboration and cross-training between different fields, such as genomics, data analysis, synthetic biology and biotechnology. This can help to build a diverse and well-rounded science workforce that is equipped to tackle complex challenges in these fields. DOE should continue and strengthen efforts to ensure a diverse and inclusive science workforce. ASM strongly encourages DOE and other federal agencies to continue their initiatives to recruit and retain underrepresented groups in these fields, as well as providing support and resources to help them succeed.

(6) What specialized facilities or capabilities are needed to support research activities related to the ten key technology areas? Are there new capabilities needed that could be provided through the scientific user facilities at the DOE National Laboratories, such as the light and neutron sources, particle accelerators, nanoscience centers and high-performance computing facilities?

DOE’s increased capacity for high throughput sequencing and advanced pathogen genomics will improve all aspects of infectious disease outbreak management—from surveillance and detection, to response, containment and recovery. As ASM membership includes many clinical microbiologists and infectious disease physicians, we are grateful to see the opportunity for collaboration through the recent establishment of an interagency Biological Threat Preparedness Research Initiative to address prevention, preparedness, prediction and response efforts to infectious diseases using the Office of Science's analytical resources, user facilities and advanced computational capabilities.

DOE can strengthen the ability to translate scientific discoveries into tools, technologies and therapies that will benefit Americans, our economy and the world at large by scaling up the National Microbiome Data Collaborative (NMDC) within the Joint Genome Institute (JGI), which seeks to unlock the promise of microbiome science with a collaborative and integrative data science ecosystem. The NMDC is striving toward a seamless integration of many data systems, with the goal of Findable, Accessible, Interoperable and Reusable (FAIR) data and strong community engagement. The NMDC is a highly respected resource that engages researchers across four National Laboratories and around the world; it should serve as a model for other research initiatives.

The DOE National Laboratories provide an opportunity to continue research and response efforts to remaining threats posed by COVID-19 and future biological threats. Sustainable support can be achieved specifically through the codification of the National Virtual Biotechnology Laboratory (NVBL) as a joint program between the Office of Science, the National Nuclear Security Administration (NNSA) and the other National Laboratories. We believe continued support for the National Virtual Biotechnology lab would enhance innovation through specialized facilities or capabilities focused on lifesaving research activities needed to protect Americans against COVID-19 future biological threats. Recognizing that some projects are at risk of ending with the expiration of supplemental funding and emergency programs, we encourage DOE to find innovative ways to perpetuate this important work, and ASM is positioned to advocate for its continuation with Congress.

(7) What new mechanisms will help a region, especially those centered on underserved communities, establish a vibrant innovation ecosystem to foster training, recruitment and retention of technical personnel, support spinoffs and growth of existing companies develop entrepreneurs and catalyze future industries in the key technologies?

Across disciplines, demographic representation throughout the ranks of academia and in industry still fails to reflect the diversity of our society, so this continued work is critical. We are hopeful that as the Agency explores the role of diversity, equity and inclusion within the key ten technologies, rapid progress will be made in academic communities and industry. A scientific enterprise that reflects the diversity of our nation will be more innovative and better equipped to address the challenges before us.

Specifically, we support prioritizing funding for students from diverse and historically unrepresented populations in Science, Technology, Engineering and Mathematics (STEM) professions through programs such as the Community College Internship at DOE’s National Laboratories. ASM also encourages the agency to consider that traditionally underserved institutions lack research infrastructure and may not even have sequencing centers and other cutting-edge technologies on which to train students. In the bioinformatics field, researchers have tailored curricula to help strengthen students’ technical skills while incorporating diverse values. One such program has been designed to incorporate indigenous values and approaches while teaching basic command line skills and interpretation of microbiome data. The program features an elder-in-residence to facilitate discussions and provide support. DOE and other federal science agencies should continue to support these approaches and supplement with additional training materials.

We thank the DOE Office of Science for the opportunity to provide feedback on accelerating innovative technologies. If we can be of further assistance, please contact Amalia Corby, ASM Senior Federal Affairs Officer at


H:\allen d segal sig.jpg
Allen D. Segal
ASM Chief Advocacy Officer

Author: ASM Advocacy

ASM Advocacy
ASM Advocacy is making it easy and providing opportunities for members to advocate for evidence-based scientific policy.