Intestinal and tracheal microbiomes inhibit in vitro growth of Coccidioides immitis

Abstract Valley fever is a disease caused by Coccidioides, a fungal pathogen, and is frequently misdiagnosed as community acquired bacterial pneumonia and treated with several rounds of antibiotics prior to accurate diagnosis. Antibiotic treatment changes the microbiome repertoire and host immunity; the impact of these microenvironmental changes on Coccidioides invasiveness is unknown. A soil microbial antagonist related to Bacillus subtilis inhibits in vitro growth of Coccidioides immitis through a clear zone of inhibition between fungi and bacteria. Whether host microbiota also could inhibit Coccidioides is unknown. To assess host microbiota inhibition capabilities against Coccidioides, we performed two types of inhibition assays. A 50/50 inhibition assay was performed in which the host microbiota and Coccidioides were placed in direct competition simultaneously on agar plates. A spike in inhibition assay was also performed in which the host microbiota was allowed to reach ~80% confluency, to mimic an established in vivo microbiome, before spiking in Coccidioides. The area of growth was observed and measured at day 4, 7, and 11. Our in vitro data indicate that specific intestinal and tracheal host microbiome species inhibit Coccidioides growth. To assess if partial in vitro depletion of host microbiota allows greater Coccidioides growth, antibiotic disc diffusion assays were performed. Our data suggests that depleting commensal microbiomes, allows a niche for Coccidioides growth. These in vitro findings could have clinical relevance and shape the way physicians assess prescription of antibiotics and coccidioidomycosis diagnosis. Experiments to identify the inhibitory microbiota and proteomic interactions are ongoing.