Phylogenetic and ecological drivers of the avian lung mycobiome and its potentially pathogenic component

Salazar-Hamm, Paris S.; Gadek, Chauncey R.; Mann, Michael A.; Steinberg, Madeline; Montoya, Kyana N.; Behnia, Mahgol; Gyllenhaal, Ethan F.; Brady, Serina S.; Takano, Oona M.; Williamson, Jessie L.; Witt, Christopher C.; Natvig, Donald O.

doi:10.1038/s42003-025-08041-8

Phylogenetic and ecological drivers of the avian lung mycobiome and its potentially pathogenic component

Journal Article · Sat Apr 19 00:00:00 EDT 2025 · Communications Biology

DOI:https://doi.org/10.1038/s42003-025-08041-8· OSTI ID:2570893

^[1]; ^[2]; Mann, Michael A. ^[1]; Steinberg, Madeline ^[1]; ^[1]; ^[1]; ^[3]; Brady, Serina S. ^[4]; Takano, Oona M. ^[1]; ^[5]; Witt, Christopher C. ^[1]; ^[1]

Univ. of New Mexico, Albuquerque, NM (United States)
Univ. of New Mexico, Albuquerque, NM (United States); Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
Univ. of New Mexico, Albuquerque, NM (United States); Texas Tech Univ., Lubbock, TX (United States)
Univ. of New Mexico, Albuquerque, NM (United States); Carnegie Museum of Natural History, Pittsburgh, PA (United States)
Univ. of New Mexico, Albuquerque, NM (United States); Cornell Univ., Ithaca, NY (United States)

Vertebrate lungs contain diverse microbial communities, but little is known about the drivers of community composition or consequences for health. Microbiome assembly by processes such as dispersal, coevolution, and host-switching can be probed with comparative surveys; however, few studies exist for lung microbiomes, particularly for the fungal component, the mycobiome. Distinguishing among fungal taxa that are generalist or specialist symbionts, potential pathogens, or incidentally inhaled spores is urgent because of potential for emerging diseases. Here, we characterize the avian lung mycobiome and test the relative influences of environment, phylogeny, and functional traits. We used metabarcoding and culturing from 195 lung samples representing 32 bird species across 20 families. We identified 526 fungal taxa as estimated by distinct sequence types (zOTUs) including many opportunistic pathogens. These were predominantly from the phylum Ascomycota (79%) followed by Basidiomycota (16%) and Mucoromycota (5%). Yeast and yeast-like taxa (Malassezia, Filobasidium, Saccharomyces, Meyerozyma, and Aureobasidium) and filamentous fungi (Cladosporium, Alternaria, Neurospora, Fusarium, and Aspergillus) were abundant. Lung mycobiomes were strongly shaped by environmental exposure, and further modulated by host identity, traits, and phylogenetic affinities. Our results implicate migratory bird species as potential vectors for long-distance dispersal of opportunistically pathogenic fungi.

View Accepted Manuscript (DOE)

Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: National Science Foundation (NSF); USDOE National Nuclear Security Administration (NNSA)

Grant/Contract Number:: 89233218CNA000001

OSTI ID:: 2570893

Report Number(s):: LA-UR--25-25181; 10.1038/s42003-025-08041-8; 2399-3642

Journal Information:: Communications Biology, Journal Name: Communications Biology Journal Issue: 1 Vol. 8; ISSN 2399-3642

Publisher:: Springer NatureCopyright Statement

Country of Publication:: United States

Language:: English

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