Dancing with the Dust Devil: Examining the Lung Mycobiome of Sonoran Desert Wild Mammals and the Effect of Coccidioides Presence

Microbiome studies report a decrease in diversity associated with active infections. Under the endozoan hypothesis, <i>Coccidioides</i> can inhabit a host without causing disease. In this study, we describe and compare the lung mycobiome of <i>Coccidioides</i>-positive and -negative samples obtained from wildlife. If <i>Coccidioides</i> is not causing infection, we predict there will be no differences in the mycobiome between positive and negative samples. Lung samples were obtained from mammals previously trapped in Tucson, Arizona, USA (<i>n</i> = 26), and Mesa, Arizona, USA (<i>n</i> = 14). Samples were screened for <i>Coccidioides</i> with CocciDx, and mycobiome was characterized through Illumina-based amplicon sequencing of the internal transcribed spacer 2 (ITS2). We compared alpha and beta diversity of the mycobiome to assess the effects of <i>Coccidioides'</i> presence and host taxonomy. A greater number of reads were captured from Tucson samples (114,706.4 ± 57,945.8) than from Mesa (384.9 ± 953.5); however, Mesa (16.8 ± 8.8) and Tucson (12 ± 7.8) had a similar number of fungal genera per sample. CocciDx detected <i>Coccidioides</i> in more samples than the ITS2 amplicon sequencing. All samples from Mesa and five from Tucson tested positive for <i>Coccidioides</i>. Therefore, Mesa samples were excluded from statistical analysis. No difference in alpha and beta diversity was associated with <i>Coccidioides</i> presence, which is consistent with the endozoan hypothesis. Host taxonomy had a significant effect on beta diversity. This effect is likely driven by host behavioral and physiological differences.