Molecular Mechanisms Shaping Host–Microbe and Microbe–Microbe Interactions: From Symbiosis to Pathogenesis

Abstract:

Host–microbe and microbe–microbe interactions are fundamental to life on Earth, governing processes ranging from host health and disease to ecosystem function. Over the past decade, advances in molecular biology, multi-omics, and imaging technologies have unraveled the complex molecular mechanisms underlying these interactions, revealing how microbes communicate, compete, and cooperate with each other and their hosts. This review synthesizes recent progress (2022–2025) in understanding the molecular basis of symbiosis, pathogenicity, immune modulation, microbiome interactions, and microbial communication. We discuss how symbiotic microbes establish beneficial relationships with hosts via molecular signaling, nutrient exchange, and immune modulation, while pathogenic microbes employ virulence factors, immune evasion strategies, and host cell manipulation to cause disease. Additionally, we explore the dynamic interactions within microbial communities, including quorum sensing, metabolic cross-feeding, and competitive exclusion, and their impact on host health and environmental processes. We also highlight emerging technologies enabling the study of these interactions at unprecedented resolution, and address current challenges and future directions in the field. This review underscores the pivotal role of molecular mechanisms in shaping host–microbe and microbe–microbe interactions, and their potential for translating basic research into novel therapeutics, probiotics, and environmental management strategies.