Novel applications of the tomato microbiome: Roles and considerations for agriculture, human health, and society

Societal Impact Statement Plants, like humans, have a microbiome that helps them grow, defend themselves against pathogens, acquire nutrients, and protect themselves against environmental stresses. The microbiome of tomatoes, a staple crop grown worldwide, could be utilized not only to reduce fertilizer and pesticide applications, but also to clean up harmful pollutants, enhance fruit flavor and nutrition, and be used for various aspects of human health. These aspects include drug and vaccine enhancement and development, as well as the incorporation of beneficial microbes into the human gut. In utilizing these microbes, we offer an alternative to time‐consuming and costly breeding programs and provide a sustainable solution to combat major societal issues. Summary Plant microbiomes are poorly explored and understood, and may represent an underutilized reservoir of growth‐promoting microbes that could be employed in agriculture and human health. We focus on the tomato microbiome and its use in agriculture and beyond, emphasizing phytoremediation, culinary and biomedical applications, and influencing the human gut microbiome. Insight is provided on how tomato microbes are already aiding in more effective phytoremediation and enhancing the flavor and nutritional quality of tomatoes, bypassing costly traditional breeding methods. We also cover ways that tomato microbes can be utilized in biomedical applications, including aiding in the development and efficacy of plant‐based vaccines and examples of medicinally beneficial secondary metabolites enhanced by or produced by these microbes. Lastly, we explore ways that these microbes may colonize the human gut microbiome and offer a proposed strategy, incorporating “One Health probiotics” by specifically manipulating and targeting microbes that may play a dual purpose in plant and human health. We examine the various microbes and the mechanisms involved, with an emphasis on endophytes due to the breadth of research on the subject and the potential they possess in terms of application. Our review aims to showcase the capabilities of the tomato microbiome and present areas outside of agriculture with the most to gain from its utilization.