Adaptive and metabolic convergence in rhizosphere and gut microbiomes

Abstract

Microbial ecosystems such as the plant rhizosphere and the human gut microbiome are crucial for the health and functionality of their hosts. Despite their differences, these ecosystems share core evolutionary principles shaped by agriculture, lifestyle, and nutrient-driven selection, demonstrating resilience to environmental pressures. We introduce the concept of the human gut, particularly the colon, as an "inside-out" version of the rhizosphere, highlighting the functional and ecological parallels between the two. This review explores these analogies, focusing on metabolites and receptors involved in host-microbiome communication. By integrating insights from both ecosystems, we aim to bridge knowledge gaps and promote interdisciplinary approaches, with the potential to address global challenges in human health and agricultural sustainability. Video Abstract.

Keywords: Comparative microbiomes; Host-microbiome interactions; Human health; Microbial metabolites; Microbial resilience; Sustainable agriculture.

Fig. 1

The “inside-out” framework linking rhizosphere and gut microbiomes. The parallels between the rhizosphere and gut microbiomes are represented as dynamic interfaces mediating host-microbe interactions. Root exudates in the rhizosphere recruit and shape microbial communities, analogous to the nutrient-driven colonization of the gut. Both systems emphasize microbial diversity, nutrient exchange, and pathogen suppression, highlighting shared principles relevant to agriculture, human health, and potential interconnections between microbiomes through food consumption or environmental exposure

Fig. 2

Environmental influences and functional parallels in rhizosphere and gut microbiomes. Environmental and anthropogenic factors shape microbial community composition and functionality in both the rhizosphere and human gut microbiomes. In the rhizosphere, factors such as soil texture, pH, nutrient availability, temperature, soil moisture, and agricultural practices like pesticide and fertilizer use play a critical role. Similarly, the gut microbiome is shaped by dietary habits, pH, hydration, lifestyle, antibiotic usage, and exposure to pre- and probiotics. These parallels underscore the shared principles of the role of the environment in shaping microbial communities and interactions

Fig. 3

Comparative immune modulation and defense mechanisms in plants and the human gut. Rhizosphere and gut microbiomes are integral to regulating host immune responses through diverse and interconnected mechanisms. In both systems, PRRs detect microbial signals, activating innate defense pathways. In plants, secondary metabolites such as glucosinolates and benzoxazinoids modulate immunity and pathogen resistance. Similarly, gut microbiota produces metabolites like SCFAs and AHR ligands, which enhance epithelial integrity and regulate inflammation. While the plant immune system relies exclusively on innate mechanisms, the gut incorporates both innate and adaptive responses, including T and B cells for specificity and memory. Shared principles and distinct adaptations underline the ecological and functional parallels between the rhizosphere and gut microbiomes

Fig. 4

Overview of the main pathways of tryptophan transformation in the rhizosphere and human gut. Tryptophan acts as a central molecule for host-microbiome communication in both the rhizosphere and the human gut, driving essential metabolic and signaling pathways. In the rhizosphere, tryptophan-derived indoles such as IAA enhance plant growth, root elongation, and nutrient uptake and also facilitate plant–microbe symbiosis. In the human gut, tryptophan metabolism produces bioactive compounds like indole-3-propionic acid and indole-3-aldehyde, which play roles in immune modulation and oxidative stress reduction. Both plant and human utilize tryptophan for serotonin biosynthesis, where it influences microbial interactions and host physiological functions. Shared and unique metabolic transformations of tryptophan in these systems highlight its pivotal role in maintaining host-microbiome interactions in both environments