Role of Environmental Microbiota in Shaping Human Gut Microbiome and Health: A Comprehensive Multi-omics Analysis

Abstract

The human gut microbiome, comprising trillions of microorganisms, plays a crucial role in host metabolism, immune function, and overall health. Environmental microbiota from diverse sources, including diet, soil, air, water, and built environments, significantly influence the composition and functional capacity of the human gut microbiome throughout life. This comprehensive study examines the bidirectional relationship between environmental microbiota and the human gut microbiome, analysing recent research that demonstrates how environmental pollutants, dietary factors, antibiotics, and lifestyle changes reshape microbial communities. Through analysis of metagenomic data, metabolomic profiling, and immune response assessments across 2,500 participants from urban, rural, and industrial environments, we reveal that environmental exposures can select for specific microbial functions, including xenobiotic degradation pathways, while disrupting beneficial microbial networks. Our findings indicate that environmental microbiota not only serve as a reservoir for gut colonisation but also influence host-microbe interactions that determine health outcomes. The integration of multi-omics approaches with germ-free animal model validation provides compelling evidence that environmental microbiota management represents a promising therapeutic target for preventing and treating microbiome-associated diseases. Understanding these complex ecological relationships is essential for developing personalised microbiome-based interventions and public health strategies.