Abstract Description

Microbial life underpins Earth's ecosystems, driving vital biogeochemical processes like nutrient cycling and carbon fixation. Despite their microscopic size, microorganisms comprise most of Earth’s biodiversity and biomass, thriving from deep-sea sediments to arid deserts. Early microbiome research relied on amplicon sequencing with limited resolution, but the advent of metagenome-assembled genomes (MAGs) enables near-complete genome reconstruction, improving understanding of microbial identity and function. However, global patterns of microbial prevalence and dominance remain poorly understood. To address this, a large-scale metagenomic study identified globally dominant and prevalent microorganisms and examined their distribution across diverse environmental niches. The SPIRE database, containing over 90,000 publicly available metagenomes from terrestrial, aquatic, host-associated, and built environments, was utilized. Taxonomic classification was performed using Kraken2 and refined with Bracken. Samples with fewer than 2 megabases of bacterial DNA were excluded, yielding 82,936 high-quality metagenomes spanning all continents (including Antarctica and the International Space Station), marine and extreme habitats. More than 65 billion reads were classified into 67 microontologies based on sample origin. Of these, 95.94 % were bacterial species, confirming bacteria’s dominance over Archaea, fungi, and viruses globally. Among bacterial taxa, Escherichia coli emerged as the most prevalent generalist. Using thresholds of >75 % prevalence amongst samples and >50 % occurrence across microontologies, E. coli was found in 90.16 % of qualifying metagenomes and 58 microontologies, more than any other species, across aquatic, terrestrial, host-associated, and built environments worldwide. Yet global prevalence did not always mirror local abundance. For instance, E. coli had relative abundances of 3.62 % in air and 2.22 % in built environments, but Stenotrophomonas maltophilia dominated these niches, with prevalences of 98.33 % and 91.45 %, respectively, highlighting niche-specific ecological dominance. In host-associated niches (humans, animals, plants, insects), E. coli showed high prevalence (91.31 %) and abundance (4.14 %). Human body site analysis further revealed niche specialization. Staphylococcus aureus was prevalent in five of seven sites (84.74 %), while E. coli was more abundant in the intestines, skin, and cerebrospinal fluid. Conversely, Streptococcus pneumoniae was dominant in the nose, throat, bone/synovial tissue, mouth, and oesophagus. These findings show that species like E. coli function as widespread generalists, but their dominance is shaped by local ecological conditions. This study offers a global perspective on microbial prevalence and dominance, supporting Baas Becking’s (1946) classic hypothesis: “Everything is everywhere, but the environment selects.”