Microbial communities shape life at every stratum of environmental hierarchy, ranging from a wide spectrum of functionalities such as nutrient cycling processes that support ecosystem functioning in soil biome to those of intricate balance between disease causal and responsive immune defenses in animals. This review explores the roles of microbial niches in shaping pathogen persistence, antimicrobial resistance (AMR) dissemination, and host–microbe interactions at the human–animal–environment interface. Emphasis is placed on microbial community assembly, environmental drivers of pathogen survival, zoonotic reservoirs, and the contribution of metagenomics and genome-resolved approaches, including metagenome-assembled genomes (MAGs). We examine how microbial diversity is structured by environmental factors, host behaviors, and microbial interactions, with particular attention to the conditions that allow pathogens and antimicrobial resistance genes to emerge or persist. The review highlights how abiotic and biotic factors regulate microbial succession and disease spread across interconnected ecosystems. Literature used in this review was retrieved through a comprehensive search of peer-reviewed publications using major scientific databases using relevant search terms. Findings from this review demonstrate that microbial niches are not passive habitats but dynamic systems that regulate microbial adaptation, pathogen invasion, and ecosystem resilience. Recent advances in metagenomics, genome-resolved metagenomics, and MAG reconstruction and multi-omics technologies have improved the detection and characterization of unculturable microorganisms, antimicrobial resistance genes, and complex microbial interactions. Nevertheless, important knowledge gaps remain regarding how microbial communities respond to environmental pressures and how these responses influence pathogen persistence and antimicrobial resistance dissemination. Therefore, sustained investment in interdisciplinary One Health and MAG-based research, especially in under-resourced regions, will assist in building a resilient and equitable preparedness against emerging infectious diseases and AMR threats.