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%) 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.

Methods
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.