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ABSTRACT

Microbiome, representing the collection of commensal microorganisms and the active substances, exert profound influences on environmental biogeochemical cycles and the maintenance of human physiological homeostasis. Their metabolic activities are indispensable for nutrient recycling, climate regulation, and ecosystem resilience. Concurrently, complex microbial communities colonizing human niches are fundamental to digestion, immune responses, and protection against pathogens. Crucially, the functional outcomes of these interactions are largely dictated by microbial diversity and community equilibrium. This review comprehensively summarizes the current understanding of the pivotal roles played by both beneficial and detrimental microbiomes across diverse environmental matrices and human systems. The state-of-the-art technologies enabling comprehensive microbiome analysis are discussed, including high-throughput sequencing and metagenomics, which are revolutionizing microbiome detection and functional characterization. Furthermore, the escalating global crisis of antimicrobial resistance intrinsically linked to microbial ecology and human practices is examined as a critical cross-domain challenge. Finally, the review explores the transformative potential of advanced microbiome bioengineering strategies for targeted environmental remediation, sustainable biotechnology, and biomanufacturing. This comprehensive analysis underscores the intricate interdependence between microbial communities, environmental integrity, and human health, emphasizing the paramount importance of preserving and harnessing microbiome diversity.

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