Planetary microbiome structure and generalist-driven gene flow across disparate habitats

Area of Science:

• Microbiology
• Ecology
• Bioinformatics

Background:

• Microbes form ubiquitous microbiomes essential for life and biogeochemical cycles.
• Microbial dispersal connects ecosystems, but comparative studies often focus on single habitats.

Purpose of the Study:

• To analyze the global structure, function, and interactions of microbiomes across diverse habitats.
• To identify key drivers shaping microbiome composition and ecological similarity worldwide.

Main Methods:

• Systematic integration of 85,604 public metagenomes from diverse global habitats.
• Species-based unsupervised clustering and parameter modeling to delineate habitat clusters.
• Inference of genomic and functional traits from 2,065,975 genomes.

Main Results:

• Delineated 40 distinct habitat clusters, revealing ecological similarities and differences.
• Identified key drivers like ocean temperature and host lifestyle influencing microbiome structure.
• Microbiome structure is primarily driven by host-associated or environmental conditions, irrespective of geography.

Conclusions:

• Generalist microbes act as crucial vectors for gene flow across disparate habitats.
• Demonstrated generalist-mediated horizontal gene transfer of antibiotic resistance from human gut to environmental habitats.
• Highlighted human activities as significant drivers of planetary microbiome alteration and dispersal.