Future of biomedical, agricultural, and biological systems research using domesticated animals

Abstract

Increased knowledge of reproduction and health of domesticated animals is integral to sustain and improve global competitiveness of U.S. animal agriculture, understand and resolve complex animal and human diseases, and advance fundamental research in sciences that are critical to understanding mechanisms of action and identifying future targets for interventions. Historically, federal and state budgets have dwindled and funding for the United States Department of Agriculture (USDA) National Institute of Food and Agriculture (NIFA) competitive grants programs remained relatively stagnant from 1985 through 2010. This shortage in critical financial support for basic and applied research, coupled with the underappreciated knowledge of the utility of non-rodent species for biomedical research, hindered funding opportunities for research involving livestock and limited improvements in both animal agriculture and animal and human health. In 2010, the National Institutes of Health and USDA NIFA established an interagency partnership to promote the use of agriculturally important animal species in basic and translational research relevant to both biomedicine and agriculture. This interagency program supported 61 grants totaling over $107 million with 23 awards to new or early-stage investigators. This article will review the success of the 9-year Dual Purpose effort and highlight opportunities for utilizing domesticated agricultural animals in research.

Increased knowledge of reproduction and health of domesticated animals is integral to sustain and improve global competitiveness of U.S. animal agriculture, understand and resolve complex animal and human diseases, and advance fundamental research in sciences that are critical to understanding mechanisms of action and identifying future targets for interventions.

Introduction

Research that involves domesticated animals (cattle, swine, sheep, goats, poultry, horses, and aquatic species) is integral to sustaining and improving global competitiveness of U.S. animal agriculture, understanding and resolving complex animal and human diseases, and advancing fundamental research in sciences that are critical to understanding mechanisms of action and identifying future targets for interventions. Historically, federal and state budgets have dwindled and funding for the United States Department of Agriculture (USDA) National Institute of Food and Agriculture (NIFA) competitive grants programs remained relatively stagnant from 1985 through 2010. This shortage in critical financial support for basic and applied research, coupled with the underappreciated knowledge of the utility of non-rodent species for biomedical research, has hindered funding opportunities for research involving livestock and limited improvements in both animal agriculture and animal and human health. This dilemma served as the rationale for a grassroots effort spanning >15 years to promote the utilization of and enhance funding opportunities for research in animals with dual benefit to agriculture and biomedicine. In 2010, the National Institutes of Health (NIH) and USDA NIFA established an interagency partnership to promote the use of agriculturally important animal species in basic and translational research relevant to both biomedicine and agriculture. The “Dual Purpose with Dual Benefit” program encouraged “One Health” approaches for comparative medicine studies that use farm animal models that mimic human developmental, physiological, and etiological processes to promote human and animal health, to better understand disease origins, interspecies transmission, and mitigation strategies, and to improve the efficiency of assisted reproduction technologies.

To examine program evolution and outcomes, identify new and continued frontiers in biomedical and translational research in animals of dual impact, and define the pillars for the next generation of an interagency partnership and competitive grants program using non-rodent animals, the University of Missouri and Michigan State University organized a strategic stakeholder planning workshop entitled Future of Biomedical, Agricultural and Biological Systems Research using Large Animals. The workshop was held at the Eunice Kennedy Shriver National Institute of Child Health and Human Development on May 28–29, 2019. There were 90 workshop participants including 14 program leaders from USDA-NIFA and USDA Agricultural Research Service (ARS), three program directors from the National Science Foundation (NSF), 14 program directors or branch chiefs from five different NIH institutes (NICHD, NIAID, NHGRI, NIDCR, and ORIP), and one program director from the Foundation for Food and Agriculture Research, as well as key scientists at a variety of career stages from federal agencies, universities, medical schools, and research institutes across the United States that use livestock in their research programs. The goals of this workshop were

Highlight successes of the Dual Purpose with Dual Benefit: Research in Biomedicine and Agriculture Using Agriculturally Important Species (an Interagency Partnership) grant program.

• (1) Identify key scientific challenges to improve human health, animal production, and, thus, quality of life.

• (2) Discern advantages of using farm animal models to study key scientific challenges in biomedicine and agriculture.

• (3) Provide recommendations for new interagency partnerships and grant programs among NIH, NSF, and USDA.

Goal 1. Highlight the success of the Dual Purpose with Dual Benefit: Research in Biomedicine and Agriculture Using Agriculturally Important Animal Species Interagency Partnership (2010–2019)

History

Rationale for the above-described interagency cooperation was developed following two NIH- and USDA-sponsored workshops at Michigan State University (2004) and on the NIH campus (2007) and a series of face-to-face meetings with NIH program managers, NIH Center for Scientific Review administrators, and USDA NIFA administrators. These meetings resulted in a white paper as well as editorials in Science [1] and other scientific journals [2–5], which are chronicled in Advantages of Domestic Species as Dual Purpose Models (http://www.adsbm.msu.edu/). The combined efforts of scientists and university administrators with NIH and USDA Animal Systems program leaders provided the rationale, broad support, and impetus for the interagency partnership that was launched in 2010. This NIH and USDA NIFA interagency partnership was developed to promote the use of agriculturally important species in basic and translational research relevant to both biomedicine and agriculture. The Dual Purpose with Dual Benefit program encouraged “One Health” approaches for comparative medicine studies using farm animal models that mimic human developmental, physiological, and etiological processes to better understand disease origins, interspecies transmission, and mitigation strategies, and to improve the efficiency of assisted reproduction technologies (ART).

As part of the program, NICHD, NIFA, and the National Heart, Lung, and Blood Institute issued a funding opportunity announcement (FOA) in July 2010 [PAR-10-276: Dual Purpose with Dual Benefit: Research in Biomedicine and Agriculture Using Agriculturally Important Domestic Animal Species (R01)]. In April 2013, NICHD and NIFA reissued the FOA (PAR-13-204). Based on the success of the program, NICHD and NIFA issued the FOA for a third time in July 2016 (https://grants.nih.gov/grants/guide/pa-files/PAR-16-366.html). Because interagency competitive grant programs make better use of limited public funds for the public good, congressional support for the nine-year NIH-USDA interagency “Dual Purpose” program was included in the Senate Labor/Health and Human Services appropriations subcommittee report and Senate Agriculture, Rural Development, Food and Drug Administration appropriations subcommittee report for FY2016, FY2019, and FY2020. Supportive language was also included in the FY2018 Farm Bill.

Criteria for research activities supported jointly by NIH and USDA-NIFA in the above FOAs stated research must be consistent with the broader missions of both agencies and advance scientific knowledge to improve human health, animal health, and farm animal production. FOA topic areas that were determined to be of interest included: (1) Reproduction, Stem Cell Biology, and Regenerative Medicine; (2) Metabolism; (3) Developmental Origins of Adult Health and Disease; and (4) Infectious Diseases.

Outcomes

A total of 61 grants were funded by either the NIH (NICHD) or USDA-NIFA through this interagency program. Program applicants represented 42 states, encompassing nearly all Land Grant universities and numerous private–public universities including schools of veterinary and human medicine, private industry, and the USDA-ARS. Applicants also represented a breadth of departments and disciplines including animal science, genetics, nutrition, food science, infectious disease, vaccine development, pathology, and veterinary and human medicine. As depicted in Table 1, NICHD made 33 awards totaling over $57 million with 12 of the 33 awards to early-stage investigators. USDA NIFA-AFRI made 28 awards totaling about $50 million with nine to new investigators and two to early-stage investigators. Funding of new and early career stage investigators within both agencies was a key metric of the program’s success.

Table 1.

Distribution of awards from NIH (NICHD) or USDA (NIFA-AFRI) to investigators during the 9-year Dual Purpose with Dual Benefit: Research in Biomedicine and Agriculture Using Agriculturally Important Domestic Animal Species interagency program

	NICHD	NIFA-AFRI
Award total (millions)	57	50
Number of awards to new or early investigators	12	11
Total number of awards	33	28

At the 2019 workshop, participants highlighted advancements including new breakthroughs to genetically modify pigs more efficiently to study human diseases; study how diseases negatively impact brain development and function; improve therapeutics to reduce the impact of uterine infections on ovarian function; reduce viral infectious diseases, including rotaviruses; develop vaccines against zoonotic diseases, herpes, human parasitic roundworms, salmonella, influenza, and hepatitis C; reduce embryonic mortality; enhance muscle growth in low birth weight offspring; and correct nutritional problems and genetic perturbations during gestation that lead to developmental issues and increased susceptibility for neonatal and adult diseases. This new knowledge, generated from grants awarded by the NIH-USDA interagency cooperative grants program, significantly strengthened One Health efforts among human medicine, veterinary medicine, and animal sciences, including agricultural applications. Importantly, the program greatly increased return on investment for both funding agencies because of the relevance of research funded through this interagency program to both agriculture and human health. The program also remains unique among interagency funding partnerships in that the awarded grants were relevant to the mission of both funding agencies, an important attribute that is not apparent in the numerous other interagency programs among federal funding agencies.

Goal 2. Identify key science challenges and approaches to improve human health, animal production, and thus, quality of life for Americans

The quality of life for human beings is threatened by numerous new and persistent grand challenges: (1) chronic human diseases such as diabetes, respiratory diseases, and cardiovascular diseases, which account for 50–60% of deaths globally [6, 7]; (2) existing, emerging/reemerging, and new infectious and zoonotic diseases, such as malaria, SARS-CoV-2 (COVID-19), tuberculosis, and influenza, that cause or contribute to 15–20% of annual deaths globally [6–8]; (3) infertility, miscarriages, low pregnancy success rates, and high cost of ART [9], which affect 10–30% (depending on the country) of all human couples globally [10, 11] and significantly affect the sustainability of protein production by all farm animals [12]; and (4) the looming necessity to efficiently produce twice as much food to feed the rapidly expanding world population [13, 14] to circumvent death and malnutrition by 2050 [15]. As explained below in Goals 3 and 4, future interagency partnerships targeting research to improve translational relevance emphasizes integrated One Health approaches and is foundational to the resolution of these daunting scientific challenges threatening human health and animal production.

To continue to address and effectively resolve these complex challenges, major federal agencies that fund competitive research grants in agricultural (USDA-NIFA), biomedical (NIH), and biological systems (NSF) must consider greater efforts to partner in supporting scientific research. Recent relevant examples of such partnerships include the Dual Purpose with Dual Benefit: Research in Biomedicine and Agriculture Using Agriculturally Important Domestic Species (NIH and USDA NIFA), and the Ecology and Evolution of Infectious Diseases (joint with NIH, NSF, and the U.K. Biotechnology and Biological Sciences Research Council) programs. Novel cooperative undertakings of this nature are critical for developing a deeper understanding of the biological systems critical to the design of new preventative strategies and therapeutic methods to mitigate chronic and infectious (including zoonotic) diseases, reduce infertility and improve ART outcomes, and enhance global animal food production. Global food production is important as food impacts neonatal, childhood, and adult health and disease outcomes [14]. Consequently, a better understanding of factors influencing health, reproduction, the microbiome, and nutrient utilization in domestic animal species is paramount to enhancing our ability to produce and maintain healthy food animals more efficiently [14], whereas comparative biological systems and biomedical studies are necessary to shed light on similar global health concerns in human medicine (e.g., fertility, obesity, chronic conditions, dysbiotic microbiota, and infectious pandemic zoonotic diseases).

The federal response to the coronavirus pandemic also serves as a real-life model for why interagency cooperation to integrate, focus, and fund scientists engaged in One Health approaches that incorporate agricultural, biomedical, and biological systems research is critical to the resolution of the scientific challenges that impact human health and animal production for several reasons. First, interagency cooperation affords a unique opportunity to foster more cogent areas of cooperative research vital to the health and well-being of human beings and agriculturally important food animal species. Second, funding at the federal level for research is limited but critical to meet these scientific challenges; thus, interagency partnerships make better use of limited resources. Third, interagency funding of collaborative research affords scientists engaged in research in biological systems, biomedicine, and agriculture unique opportunities to work together using the One Health paradigm to resolve key scientific challenges. Fourth, improving the quality of life for human beings depends on federal commitments to major research funding agencies (NIH, NSF, and USDA NIFA) and the agricultural, biomedical, and biological systems scientists they support to resolve these complex scientific challenges. Thus, vigorous interagency cooperative research programs are vital to the rapid resolution of these scientific challenges, promotion of One Health [16], and sustained national security. The next sections of this paper illustrate some of the advantages of using alternative animal models as research models to resolve the key scientific challenges and provide recommendations for future research using domesticated animal models to facilitate interagency grants programs between the NIH, NSF, and USDA.

Goal 3. Discern advantages of using livestock models to study key scientific challenges in biomedicine and agriculture

Since 1901, 18 Nobel Prizes have been awarded to scientists who used cattle, chickens, pigs, horses, and sheep as biomedical models in their research with the most recent Nobel Prize in Physiology or Medicine in 2020 awarded to Charles M. Rice of Rockefeller University for his discovery that the hepatitis C virus alone causes hepatitis. Agriculturally important animal species models not only have underappreciated advantages critical to the resolution of key scientific challenges, but also provide high-quality food for humans and offer enormous economic value to the US economy of >$150 billion annually [17]. Indeed, diverse genetic lines along with specialized facilities and faculty expertise exist at research facilities throughout the United States. Despite significant advantages that the domesticated animal models confer, economically important resources are substantially underutilized for studies to benefit human health, development of new models with more direct application to humans, and for basic studies to better understand biological systems for a variety of reasons [1]. Traditionally, the primary focus of animal and veterinary science disciplines has been on the translational science aspects for improvement of production traits, genetic merit, reproductive and growth performance, health and well-being, and disease diagnosis and prevention in domesticated animal species. Over the past decade, these species have become increasingly important models for human disease and xenotransplantation research, as well as bioreactors to produce therapeutics and sources of tissues for regenerative medicine applications. Indeed in 2021, the U.S. Food and Drug Administration (FDA) approved a first-of-its-kind intentional genomic alteration in a line of swine, referred to as GalSafe pigs [18, 19]. This is the first intentional genomic alteration in an animal that the FDA has approved for both human food consumption and as a source for potential therapeutic uses.

All animal research has entered a new and exciting phase of biomedical research due in part to reduced costs of next-generation sequencing and the availability of genome editing tools such as CRISPR-Cas9 [20, 21], TALENs [22], and Zinc Finger Nucleases [23]. Animal and veterinary scientists are poised to revolutionize the bioengineering of domesticated animals to create models that more accurately recapitulate various human conditions and diseases. In parallel, they will advance mainstream agricultural, biomedical, and biological systems research to resolve key scientific challenges in order to improve human health, animal production, and quality of life for people. In the same way that genetically modified mice revolutionized biomedical research, we are now positioned to use genetic modifications and comparative biology with other species to further refine the gaps left by the almost exclusive focus on the murine model and to provide critical comparative medicine perspectives and preclinical translational animal models for human health [20, 21, 24–30].

An emphasis on using alternative animal species as models for biomedical research has gained momentum in light of findings that mouse models and the resulting phenotypes are in many instances confounded and/or dependent on the genetic background of the employed mouse strains. Moreover, the mouse model has not met expectations due to differences in anatomy or physiology for studies on cystic fibrosis [31, 32], ocular [33], and cardiac diseases [34], gastrointestinal diseases [24], and regenerative medicine [35]. As almost all livestock species are outbred and genetically diverse, resulting phenotypes from these animal models are more representative and applicable to the human disease conditions than are inbred mouse strains. This advantage greatly facilitates the study of genetic factors of diseases and varied host susceptibilities. In contrast to popular belief, this genetic variation does not necessarily increase phenotypic variation [36, 37]. Further, domesticated animal species are often optimal for zoonotic or infectious disease research, particularly wherein the species serve either as reservoir, carrier, or natural host of the disease. Indeed, swine are recognized as an alternative to traditional model species (rodent, zebrafish, and worm models), since they are more similar genetically, anatomically, physiologically, and immunologically to humans [38–41], while maintaining the advantages of being a litter bearing species. This facilitates rapid production of genetically modified animals with a relatively long life span that permits long-term investigations. In addition to serving as models of human chronic disease, large animal species are ideal for studies where their relatively long life span and close similarity in body size and physiology are advantageous [38, 42]. Like humans, pigs are monogastric and preferred models for nutritional studies including nutrient absorption, trafficking, and metabolism [43]. An increased availability of germ-free livestock animals and human microbiota colonized gnotobiotic pigs should expedite the use of these models for human microbiome research [39].

In the area of ART, cattle have played a major role in the development of artificial insemination, gamete cryopreservation, in vitro fertilization, in vitro embryo culture, and embryo transfer procedures for reproductive science research [44, 45] and outcomes have been widely translated to human fertility clinics. Sheep were used to pioneer cloning technologies [46]. Chickens are used as a model for developmental fate mapping [47] and growth physiology [48]. Indeed, the FDA is now recommending the use of both small and large animal species models to generate safety and efficacy data for therapeutic cells in regenerative medicine [49]. The FDA has further stated that for some fields, such as cardiac disease, preclinical data obtained from only the use of small animal models are not sufficient [50]. Unique advantages of alternative animal species as models for biomedical research include integrated approaches and the ability to study long-term effects; the ability to capture detailed phenotypes; large body size allows use of methodological approaches not available for rodents; unique aspects inherent to specific animal species (e.g., intrauterine manipulations of fetal development in sheep, known nutritional requirements of pigs as monogastrics and omnivores like humans); and similar immune, gastrointestinal, and brain structure and function in swine and humans. This facilitates translation of certain surgical procedures and experimental drug and treatment schedules and enables longitudinal sampling or collection of larger samples.

Another important advantage of large animal species is that some species are altricial having a prolonged neonatal period like the human enabling the study of infant and childhood diseases, as well as the neonatal immune system. Also, they are precocious and can be artificially reared from birth on an experimental formula to study questions pertinent to pediatric nutrition (vs. rodents, which require pup-in-a-cup type approaches for artificially rearing). An extended life span also allows longitudinal studies of immune development, studies of persistent disease, and investigation of aging and infection in a natural host model. It is increasingly appreciated that gender differences including sex hormones, age, and genetic factors have significant impacts on the immune system, vaccine efficacy, and disease progression. Large animals are ideal for investigating these factors, given their outbred genetics and many known breed differences, which are already well described and are much more reflective of variation in human populations than are inbred lines. Further, they are advantageous to perform serial sampling to track animals through multiple pregnancies and to conduct long-term analyses of disease progression and the influence of vaccination on prevention of disease and transmission.

Depending on the biological question to be addressed, a suitable or even preferred livestock species is often widely available for investigation. Nevertheless, there has been a lack of incentive for the use of large animal species as a preferred model due to the perceived high costs of maintenance, lack of suitable funding mechanisms, frequent absence of species-specific reagents, and difficulties producing genetically engineered models that lag behind mouse models. With the ease and cost-effectiveness of sequencing and resequencing of animal genomes, the advent of advanced genomic editing tools, species-specific immunoreagents, and the development of stem cell technologies, domesticated animal species biotechnology is truly at the brink of realizing a newer and fuller potential [51]. The availability of these powerful tools provides unique opportunities for reshaping the animal and veterinary science disciplines and realizing the potential of non-rodent models for agricultural, biomedical, and biological systems research. Table 2 summarizes the areas of research using domesticated species recommended for support by interagency partnerships between NIH, USDA, and NSF.

Table 2.

Recommendations for interagency partnerships involving NIH, USDA NIFA, and NSF to support research using domesticated animals

• Infrastructure, tools, and practices to enable efficient and appropriate model species selection.

• Translational programs to support efforts to employ animals as models to improve translation of basic research to biomedical and/or agricultural applications.

• Immunology and infectious disease to better understand immunology and the immunological response to infection to improve the design of therapies and vaccines to combat infection.

• Nutrition and pediatrics to better understand metabolism and improve the design of therapeutic interventions and preventative strategies that improve growth, mitigate stress, and promote the health of domesticated animal species and human beings.

• Reproduction to improve diagnosis and therapeutic interventions to alleviate infertility and enhance outcomes of assisted reproductive techniques.

• Next-generation biomedical and agricultural animal models to develop reagents and resources to generate animal models in livestock species for biomedical and agricultural research.

Goal 4. Recommendations for interagency partnerships using agriculturally important animal species involving the NIH, NSF, and USDA NIFA

Based on the advantages of many non-rodent animal models to resolve key scientific challenges, participants of the May 2019 Stakeholder Workshop recommend future research using domesticated animal models to facilitate interagency partnerships and grants programs between multiple NIH institutes, NSF, and USDA in five research areas: (1) translational biomedicine; (2) immunology and infectious disease; (3) nutrition and pediatrics; (4) reproduction; and (5) creation of novel biomedical and agricultural animal models.

Area 1. Infrastructure, tools, and practices

As noted above, basic information, methods, and practices often drive animal experiments toward rodent models without complete considerations of appropriateness for the application at hand. Federal agency coordination and collaboration may be able to resolve some of these issues. Recommended efforts include

1. Establish organ/disease-specific working groups, consortia, or coordination centers tasked and funded to develop rubrics for model species selection. Knowledge related to species-specific physiology, anatomy, and behavior from across disciplines would inform this group in establishing parameters to consider when selecting a model species for hypothesis and/or therapy testing.

2. Establish species-specific centers to enable and facilitate basic research that would be difficult or unlikely at most research institutions. Examples that may provide guidance include the NIH-funded nonhuman primate centers or the NIH-funded National Swine Resource and Research Center. The new centers should be enabled to provide services and support across federal agency applications for all research needs—biomedical, agricultural, ecological, physiology, behavior, and development.

3. Develop workshops to help train both reviewers and investigators regarding model species inclusiveness and selection. These efforts should provide unbiased perspectives on pros and cons regarding species selection and model type (induced, spontaneous, or genetically engineered).

4. Identify and develop reagents or protocols for unmet needs in non-rodent model species that would otherwise have scientific utility. Standardization and validation should be a part of these efforts.

5. Develop tools that integrate genotype, phenotype, and functional annotation using pan-omic approaches that compare and contrast genomes of human, mouse, and domesticated animal species. Cross-discipline access to these tools will improve genome-wide association studies in humans and domesticated species, will advance our understanding of the genetic basis of complex traits from “big data” studies, and will improve genomic selection practices in agriculture.

6. Develop tools to facilitate appropriate selection of model species through creation of atlases for developmental events (organogenesis) and anatomical annotation (brain function maps) in domesticated species.

7. Encourage and fund efforts to find and describe symptom/phenotype parallels between applications and across species. Examples may include muscle biology parallels between meat production, muscle atrophy, and athletic performance, or metabolism parallels between human metabolic disorders and agricultural feed efficiency.

8. Develop cell lines and culture systems to facilitate model species selection. For example, with an appropriate cross-species set of organoid culture systems or other “organ-on-a-chip” strategies, small molecular drug metabolism may be evaluated in vitro to inform model species selection without having to raise and examine large animal models.

9. Develop and adopt clear and consistent policies on the use and distribution of genetically engineered food animals as research models for biomedical and/or agricultural applications similar to current NIH/OLAW policies for rodents. Unlike genetically engineered/edited rodents, FDA hinders the use and sharing of food animals that have been modified for research purposes. Congruence in regulations between animal models is disparately needed.

These efforts will allow for efficient and appropriate model selection and will provide a greater understanding of opportunities to leverage knowledge across fields and applications. The establishment of species-specific centers will nurture collaboration and enable cross-institution research.

Area 2. Translational programs—Lab to clinic/lab to field

These efforts employ animals as models to improve translation of basic research to biomedical and/or agricultural applications. Recommended efforts include

1. Generate large animal models that produce proteins similar to humans to facilitate direct translation of preclinical research. These new models should target somatic cell genome editing, cellular therapy research, and preclinical testing of therapeutic molecules and procedures. These efforts may require development or expansion of model-building centers.

2. Establish a funding mechanism to rapidly develop patient-specific mutations in appropriate animal models. This infrastructure may expand physical centers that already develop engineered models or may utilize a virtual network of laboratories that harbor the required skills and facilities.

3. Develop species-specific or disease/system-specific centers specifically for preclinical research that are likely to transition to the clinic. These centers would facilitate participation of clinical researchers in animal experiments that approximate clinical observations. Further, these centers should facilitate cross-training between human health clinicians and animal researchers.

4. Develop cell lines and reagents for evaluation of preclinical applications of cell-based therapies to replace injured, lost, and/or dysfunctional tissue.

5. Develop antibodies and methods to detect and to differentiate analytes from humans and livestock species. For example, it is imperative to be able to differentiate various human and swine hormones or cytokines in validation of stem cell therapies or xenotransplantation experiments.

6. Develop large-animal models to study molecular, cytological, epigenomic, genomic, and/or physiological phenomena associated with animal and human reproduction, ART, and reproduction/environment interactions. A better understanding of toxicological impacts on animal fertility may be directly translatable as recommendation for human exposures.

7. Encourage and fund efforts to evaluate health recommendations for the public in animal production settings. Given the very large sample sizes that can be mustered for agricultural species, diet, or behavioral recommendations for the public could be robustly validated for outcomes that have an identified animal counterpart.

Tangible benefits include improved gene-editing techniques to develop new translational animal models with enhanced application to human diseases; better biological understanding of immunology, pathogenesis, and host disease resistance in humans and domesticated animals; and enhanced integration of genotypic and phenotypic information from big data to improve genetic selection of animal models. Benefits also include smooth transitions of preclinical research directly into clinical studies. These efforts will also enable clinical applications of precision medicine.

Area 3. Immunology and infectious disease

This research area uses domesticated animals to better understand immunology and the immunological response to infection to improve the design of therapies and vaccines to combat infection. Recommend areas of study include

1. Develop vaccines and novel adjuvants and investigate host factors influencing vaccine efficacy (i.e., nutrition, age, gender, the microbiome, virome, probiotics, coinfections/covaccinations, and environmental factors).

2. Understand pathogen evolution, including the pathogen–host interface, interspecies transmission, zoonotic diseases, and emerging and reemerging diseases.

3. Conduct comparative biomedical studies, including comparative pathogenesis in the natural versus adoptive host, comparative susceptibility, and persistence mechanisms (highly relevant to zoonotic diseases including COVID-19 and animal reservoirs).

4. Understand antimicrobial resistance.

5. Use immunometabolomics to better understand mechanistical impacts of both subclinical and clinical infection/dysbiosis on metabolism.

6. Understand the microbiome and virome (bacteriome, mycobiome, etc.) and their impact on health, infection, and immunology, including ontogeny and the skewing of neonatal immunity into adulthood.

7. Understand interspecies and pathogen transmission among and within animal populations and develop vaccines or other strategies to block transmission at the animal level before emergence into the human population.

8. Understand immunogenetics that shape genetic determinants of disease susceptibility and resistance as well as responses to therapy and vaccinations.

9. Develop cross-agency RFAs and organize consortia to understand and circumvent the potential roles of animals (agriculture, wild, and pet species) and meat processing in zoonosis and human health. These consortia should be focused on disease prevention and eradication within human endeavors. As an example, all technologies should be evaluated and appropriately applied to human and animal health to prevent viral epidemics (influenza, coronavirus, etc.) and foodborne illnesses.

Tangible benefits are new preventative measures to better control zoonotic diseases. For example, the successful control of rabies and milk-borne Mycobacterium and Brucella provides clear examples of how new vaccine strategies to block disease transmission in zoonotic host animals before emergence into the human population can now be applied to other pathogens such as emerging zoonotic animal coronaviruses, avian and swine influenza, Escherichia coli O157: H7, and Salmonella. Tangible benefits also include improved understanding of antimicrobial resistance leading to development of new, more effective antibiotics, and a better biological understanding of the impact of the microbiome on infection and immunity and the impact of infection on metabolism.

Area 4. Nutrition and pediatrics

This research area will utilize domesticated animals to better understand metabolism and to improve the design of therapeutic interventions and preventative strategies that improve growth, mitigate stress, and promote the health of domesticated animal species and human beings. Recommended areas of study include

1. Understand inter-organ communication and the influences of nutrients on structure and function.

2. Determine the role of nutrition during specific developmental windows of perinatal life on short- and long-term health outcomes.

3. Determine the role of micro/macro nutrients and nutrient signaling for organ development, growth, and function and on the response to stress, microbiota, infection, and immunity.

4. Examine the influence of therapeutic interventions on nutrient requirements, metabolism, and body composition.

5. Determine the optimal microbiome for each stage of development, as well as during and after stress, including environmental effects (e.g., diet, nutrient profiles, antimicrobials, pre- and probiotics) on the development of the microbiome, metagenome structure and function, and host–microbe interactions in health and disease.

6. Determine the role of nutrition, stress, and the microbiota-gut-brain axis on behavior and well-being with specific emphasis on the regulation of feed intake and cognitive behaviors.

7. Understand the role of nutrients in modifying the epigenome of the newborn and subsequent effects on the regulation of growth, tissue composition, and stem cells, especially over multiple pregnancies (life cycle effects).

8. Understand the mechanism of colostrum effects on newborn development, organ size, and later disease risk (e.g., obesity, response to infection).

9. Determine the effects of maternal nutrition on fetal and maternal tissue growth and function especially placental development, placental transport of nutrients, and nutrient signaling as influenced by maternal ingestion of nutrients.

10. Establish the roles of maternal nutrient status that influence the risk for stage-specific congenital structural and functional defects and long-term organ function.

11. Determine the early-life nutrition effects on lean body mass, whole-body energy balance, tissue composition, and disease risk.

12. Understand metabolic regulation and nutrient transport within the gut and how this influences other tissues.

13. Understand the role of nutrition in building healthy populations, balancing nutrient partitioning between central and peripheral tissues, and optimizing development in various environments that might also have concomitant infectious disease challenges.

Tangible benefits to NIFA, NIH, and NSF include the development of a better basic understanding of adipose regulation, causes of obesity and potential therapies in humans, improved meat quality and enhanced performance (e.g., fertility, fecundability, lactation) in farm animals, and elucidation of the basic biological rules of life that apply across diverse species besides humans, mice, and farm animals. Tangible benefits also include improved mechanistic understanding of the role of nutrient intake and stress on microbiome/metagenome structure and function, on the epigenetic regulation of growth and congenital diseases during early childhood and adulthood and the development of new therapies to regulate the effects of the environment on embryo/fetal development and subsequent health of human beings and on economically important traits (e.g., growth, fertility, disease resistance) in farm animals. Benefits also include improved biological understanding of inter-organ communication and influence of nutrients and nutrient signaling including colostrum, on organ structure and function and the mechanisms involved, as well as placental development and transport of nutrients.

Area 5. Reproduction

This research area will use domesticated animals to improve diagnosis and therapeutic interventions to alleviate infertility and enhance outcomes of ART. Recommended areas of study include

1. Understand the mechanisms that regulate the competency of oocytes to develop into viable offspring (egg quality) and to identify reliable markers of high-quality oocytes.

2. Establish the mechanisms and predictive potential of reproductive tract microbiome and metagenome on reproductive function and pregnancy outcome.

3. Develop population-based studies of genetic and phenotypic influences on pregnancy outcomes.

4. Develop new procedures to improve and predict natural and ART outcomes including but not limited to procedures to diagnose, genotype, and manipulate gamete and embryo quality (e.g., CRISPR, pre-implantation genetic diagnosis or PGD).

5. Determine the impact and mechanism (genomic and epigenetic) of maternal stress, nutrition, and environment on gamete quality and offspring fertility.

6. Determine the role of microbiome, virome, and metagenome and relevant mechanisms on embryo survival, placental function, and gamete quality in offspring.

7. Understand the genetics, genomics, and epigenetics of placental development and differentiation to optimize fetal, neonatal, and adult outcomes.

8. In vitro gametogenesis as a means for overcoming fertility issues in human couples and as a means for in vitro breeding of agricultural animals. Research in this field will improve our understanding of gametogenesis.

Tangible impacts are to improve diagnosis and therapeutic interventions to alleviate infertility, enhance ART, such as improved success of in vitro fertilization and embryo transfer, and improved success of natural pregnancies and ART, as well as to advance knowledge of the fundamental rules of life that govern continued proliferation of species through sexual reproduction.

Area 6. Next generation biomedical and agricultural animal models

The intent of this effort is to develop reagents and resources to generate animal models in livestock species for biomedical and agricultural research. Recommended topics for study include

1. Provide a supplement to awarded grants that develop new reagents, resources, and transgenic livestock as part of the overall research plan (in place of “stand-alone” funding for reagent, resource, and transgenic animal development). Supplements could include additional funds to develop critical antibodies, therapeutics, transgenic animals, tissue repositories, gene chips, high throughput genome screening, and complete genome sequencing of all food animal species of economic importance.

2. Make genetically modified large animal models (CRISPR modified, knockouts, knockins, etc.) more accessible, both by access and through enhanced animal facilities, to scientists to expedite and improve the quality of research.

3. Create new funding strategies such as P01 program grants, which are large enough to allow more significant strides in reagent development. The potential also exists for funding agencies to contract with industrial partners (such as the Phased SBIR grants) or use funds to establish a reagent clearinghouse for veterinary species, similar to the NIH BEI Resources or the ATCC.

4. Support single-cell RNA sequencing studies [52] on domestic animal species to provide data to study cell function as well as to identify genes marking specific cell types within complex tissues and organs. Such data could be used to rationally design panels of markers to detect and analyze specific cells and their responses during disease and return to homeostasis [53, 54].

5. Create and support new training programs across disciplines (DVM, MD, and PhD) in the use and handling of large domestic animals to promote broad utility for their use in research.

Reagent availability, including transgenic animals, was identified as the most significant obstacle to fully utilizing large animal models for biomedical and agriculture research. Thus, tangible benefits include improved basic research capacity to enhance experimental designs, interpretation of results, and pace of discovery.

Summary

In summary, a continued partnership between NIH, NIFA, and other relevant federal research and development agencies, such as NSF, DOD, and BARDA, is necessary to develop the next-generation interagency program using agriculturally important animal species. There is a growing consensus among practitioners in the field and key stakeholders that large animals are relevant, if not ideal, dual-purpose models for understanding and addressing complex challenges associated with both agriculture and biomedicine. Importantly, continuation of important cooperative programs that further strengthen ties between human medicine, veterinary medicine, and animal sciences are essential to improving animal and human health, providing enhanced applicability and return on investment in research, and supporting the development of the next generation of scientists.

Funding

This workshop was funded, in part, by the United States Department of Agriculture (USDA) Agriculture Food and Research Initiative (AFRI) National Institute of Food and Agriculture (NIFA).

Conflict of interest

The authors have declared that no conflict of interest exists.