The avian mycobiome: Phylogenetic trees and alignments for key fungal groups

Vertebrate lungs contain diverse microbial communities, but little is known regarding 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 provide the first characterization of the avian lung mycobiome, and we 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..., The data represent ribosomal internal transcribed spacer (ITS) sequences obtained by a combination of typing fungal isolates and amplicon analysis with Illumina sequencing. Sequences were aligned with MAFFT and subjected to maximum likelihood tree-builidng analyses with IQ-Tree using the best subsititution model as determined by ModelFinder. Alignments and Newick files are presented in NEXUS formats., , # The avian mycobiome: Phylogenetic trees and alignments for key fungal groups

[https://doi.org/10.5061/dryad.hqbzkh1t3](https://doi.org/10.5061/dryad.hqbzkh1t3)

## Description of the data and file structure

***Contacts for datasets***

1. Donald Natvig, Department of Biology, University of New Mexico, Albuquerque 87131, [[e-mail]](mailto:[e-mail])
2. Paris Salazar-Hamm, Department of Biology, University of New Mexico, Albuquerque 87131, [[e-mail]](mailto:[e-mail])

***Related manuscript in press***

Paris S. Salazar-Hamm, Chauncey R. Gadek, Michael A. Mann, Madeline Steinberg, Kyana N. Montoya, Mahgol Behnia, Ethan F. Gyllenhaal, Serina S. Brady, Oona M. Takano, Jessie L. Williamson, Christopher C. Witt, and Donald O. Natvig. 2025. Phylogenetic and ecological drivers of the avian lung mycobiome and its potentially pathogenic component. *Communications Biology* (Nature).

Corresponding authors: Paris Salazar-Hamm, [[e-mail]](mailto:[e-mail]); Cha...,