Interagency Strategic Plan for Microbiome Research FY 2018-2022

The Interagency Strategic Plan for Microbiome Research FY 2018-2022 is a national sectoral strategic plan of the United States of America. The goal of this Interagency Strategic Plan for Microbiome Research is to identify and prioritize research needs across Federal agencies to efficiently promote understanding of how microbiomes function and how to manipulate those functions to address societal problems. The aim is to accelerate the development of new products and services that improve human health and nutrition, the health and safety of crop and animal production, ecosystem services, and industrial applications of microbiomes. To that end, the plan focuses on the study of microbiomes across different ecosystems to seek organizing principles that shape all microbiomes, with the ultimate objective of developing predictive capabilities of microbiome function and the effects of disruptions in a wide range of environments. The plan advances efforts across three key Research Objectives, outlined below. These objectives reflect commonalities across agencies and thus represent an opportunity to increase Federal efficiency through leveraging and coordination.
Among others, the Plan also aims to understand the impact of antimicrobial drug use on the emergence of antimicrobial resistance and microbial dynamics in humans, terrestrial and aquatic farm animals, and the environment; understand the mechanisms that drive the spread of antimicrobial resistance in the hospital and between livestock, poultry, aquaculture, and humans in order to develop strategies for reducing this spread; discover new and novel antimicrobial drugs isolated from the human and other microbiomes that can replace those drugs that are no longer effective; develop microbiome-based antimicrobial resistance monitoring; develop novel microbiome-altering therapeutics to block colonization by resistant microbes or treat refractory infections; illuminate the functions the gut microbiome and its metabolites have in modulating nutritional status and human health through their interaction with diet; evaluate the effect of specific foods in the diet on the microbiome and its metabolites, and the impact on obesity, heart disease, and cancer. Identify whether metabolites produced serve as biomarkers for heath and disease; and investigate the effect of fermented foods on the human gut microbiome.
Additionally, the document also provides to advance the knowledge of complex soil microbial communities in agricultural soils in general—and in and around roots of high-yielding, disease and drought resistant crops in particular—to accelerate the development and use of these crops; understand the interactions among soil microbes within the soil ecosystem and how these interactions contribute to healthy, productive, resilient, and sustainable systems; understand the impacts of applied amendments to soils, especially manures, to elucidate practices that can reduce antimicrobial resistant bacteria and genes; explore individual microbes and their interactions in agriculturally important microbiomes in order to enhance food, feed, and fiber production; understand the signaling pathways between plant-associated microbes and between microbes and plants and how these communications contribute to plant yield, nutrient acquisition, and stress tolerance, thereby enhancing overall health and productivity; determine the mechanisms by which the microbiota supports the development and maintenance of the immune system; develop veterinary medical interventions to modulate the microbiomes of animals to enhance disease resistance and prevent or treat infectious diseases; develop countermeasures to reduce/mitigate exposure of non-target free ranging species to antibiotics intended for agriculture; investigate the microbial ecology of animals to decipher the mechanisms that promote antimicrobial resistance; develop alternatives to antimicrobial drugs to reduce the use of medically important antimicrobial drugs; investigate the synergistic use of prebiotics and probiotics to enhance digestibility and thereby animal production; investigate food microbiomes for foodborne pathogen detection and authentication, and to potentially use metagenomics approaches in routine regulatory testing of foods; survey the microbiome of the built environment and the farm environment, which impact the farm to fork continuum; evaluate the safety of veterinary antimicrobial drug residues and pesticides in food and harmonize guidelines used by national and international regulatory agencies to assess the effects of animal drug residues in animal-derived foods as part of the risk assessment for humans consuming food containing antimicrobial drug residues; investigate the effects of contaminants such as arsenic, lead and mercury, and organic substances such as low levels of pesticides or endocrine disrupting compounds in food, water, and incidentally ingested soils or dusts on the gut microbiome and its metabolites, and the subsequent impact on human health; evaluate the effect of pre- and pro-biotics on microbial human pathogens such as Salmonella; and investigate the impact of the plant microbiome on pathogenic bacteria such as Salmonella on food crops such as lettuce and tomato.
Finally, the document also provides for waste conversion and utilization; sustainable bioenergy crop production; production of renewable resources; wildlife health and conservation & natural resource management; and chemical, metal, water, and carbon cycles.