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.