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During analyzing morbidity data, it is obvious that the ratio of infections has decreased significantly since the beginning of the 20th century, but the proportion of metabolic and inflammatory diseases has increased. This may be related to the degradation of soils. At the same time, mobilization of nutrient elements primarily depends on the activity of soil microbiota, which is subjected to negative anthropogenic impact. Although plant nutritional value has a direct impact on human health; however, modern agricultural practices that aimed at deep cultivation are causing disturbances in the soil microbiota composition. Subsequently, this resulted in maladaptation of the human immune system, as contacts with xenobiotics occur instead of evolutionarily calibrated interactions; potentially endangering the gut microbiota. This review aims to represent recent data on the relationships among human intestinal, soil, and plant microbiota. Nowadays, it is evident that there is a broad range of influences on human health not only from intestinal microbiota but also from its connection with the environmental microbiota (i.e., soil microorganisms in particular). Today, with respect to the background of active use of modern technologies, including genetical ones, we have the opportunity to examine such volumes of data that will allow us to fully analyze microbiological diversity of the different ecological niches in terms of their common features, differences, and mutual influences. Such studies will make it possible to identify potential factors determining the composition of microbiota in different loci, assess their potential impact on human health, and adjust methods to diagnose and restore the optimal composition of human, plant, and soil microbiota.