Skip to main content
Research article - Peer-reviewed, 2021

Metagenomic assessment of the global diversity and distribution of bacteria and fungi

Bahram, Mohammad; Netherway, Tarquin; Frioux, Clémence; Ferretti, Pamela; Coelho, Luis Pedro; Geisen, Stefan; Bork, Peer; Hildebrand, Falk


Bacteria and fungi are of uttermost importance in determining environmental and host functioning. Despite close interactions between animals, plants, their associated microbiomes, and the environment they inhabit, the distribution and role of bacteria and especially fungi across host and environments as well as the cross‐habitat determinants of their community compositions remain little investigated. Using a uniquely broad global dataset of 13 483 metagenomes, we analysed the microbiome structure and function of 25 host‐associated and environmental habitats, focusing on potential interactions between bacteria and fungi. We found that the metagenomic relative abundance ratio of bacteria‐to‐fungi is a distinctive microbial feature of habitats. Compared with fungi, the cross‐habitat distribution pattern of bacteria was more strongly driven by habitat type. Fungal diversity was depleted in host‐associated communities compared with those in the environment, particularly terrestrial habitats, whereas this diversity pattern was less pronounced for bacteria. The relative gene functional potential of bacteria or fungi reflected their diversity patterns and appeared to depend on a balance between substrate availability and biotic interactions. Alongside helping to identify hotspots and sources of microbial diversity, our study provides support for differences in assembly patterns and processes between bacterial and fungal communities across different habitats.

Published in

Environmental Microbiology
2021, volume: 23, number: 1, pages: 316-326

Authors' information

Swedish University of Agricultural Sciences, Department of Ecology
University of Tartu
Frioux, Clémence
Quadram Institute Bioscience
Ferretti, Pamela
European Molecular Biology Laboratory (EMBL)
Coelho, Luis Pedro
European Molecular Biology Laboratory (EMBL)
Geisen, Stefan
Netherlands Institute of Ecology (NIOO-KNAW)
Bork, Peer
European Molecular Biology Laboratory (EMBL)
Hildebrand, Falk
Earlham Institute
Swedish University of Agricultural Sciences, Department of Ecology

UKÄ Subject classification

Biochemistry and Molecular Biology

Publication Identifiers


URI (permanent link to this page)