Microbes in soil ecosystems and on human internal and external surfaces are essential for maintenance of function in both agricultural systems and the human body. Although two seemingly disparate systems, an analysis of microbial diversity in soil and human microbiomes (entire microbial communities associated with either soil or humans) is necessary in order to understand the importance of the microbiome, the risks of low microbial diversity, and solutions for restoring these microbiomes and their functions. This thesis addressed the role of microbial communities for human health and wellness, with a focus on the gut microbiome that directly supports vital human functions, as well as the soil microbiome that not only supports human food security but also seeds components of the human gut microbiome. This review identifies parallel microbial services for plants and humans, and reviews the current evidence on the impact of specific aspects (antibiotic and pesticide use, urbanization, diet changes, etc.) of the transition to modern life on reducing microbial biodiversity in both soil ecosystems and the human body. Resulting repercussions for human health, land degradation, and food security are summarized. These insights are used to formulate evidence-based solutions for regenerating microbial diversity and the associated essential functions in both systems.