Oral Mycobiome Analysis of HIV-Infected Patients: Identification of Pichia as an Antagonist of Opportunistic Fungi

Pranab K Mukherjee,Robert E Brown,Michael M Lederman,Patrick M Gillevet,Mahmoud A Ghannoum,Richard Jurevic,Mauricio Retuerto,Robert A Salata,Jyotsna Chandra,Masoumeh Sikaroodi,Deborah A Hogan

doi:10.1371/journal.ppat.1003996

Abstract

Oral microbiota contribute to health and disease, and their disruption may influence the course of oral diseases. Here, we used pyrosequencing to characterize the oral bacteriome and mycobiome of 12 HIV-infected patients and matched 12 uninfected controls. The number of bacterial and fungal genera in individuals ranged between 8–14 and 1–9, among uninfected and HIV-infected participants, respectively. The core oral bacteriome (COB) comprised 14 genera, of which 13 were common between the two groups. In contrast, the core oral mycobiome (COM) differed between HIV-infected and uninfected individuals, with Candida being the predominant fungus in both groups. Among Candida species, C. albicans was the most common (58% in uninfected and 83% in HIV-infected participants). Furthermore, 15 and 12 bacteria-fungi pairs were correlated significantly within uninfected and HIV-infected groups, respectively. Increase in Candida colonization was associated with a concomitant decrease in the abundance of Pichia, suggesting antagonism. We found that Pichia spent medium (PSM) inhibited growth of Candida, Aspergillus and Fusarium. Moreover, Pichia cells and PSM inhibited Candida biofilms (P = .002 and .02, respectively, compared to untreated controls). The mechanism by which Pichia inhibited Candida involved nutrient limitation, and modulation of growth and virulence factors. Finally, in an experimental murine model of oral candidiasis, we demonstrated that mice treated with PSM exhibited significantly lower infection score (P = .011) and fungal burden (P = .04) compared to untreated mice. Moreover, tongues of PSM-treated mice had few hyphae and intact epithelium, while vehicle- and nystatin-treated mice exhibited extensive fungal invasion of tissue with epithelial disruption. These results showed that PSM was efficacious against oral candidiasis in vitro and in vivo. The inhibitory activity of PSM was associated with secretory protein/s. Our findings provide the first evidence of interaction among members of the oral mycobiota, and identifies a potential novel antifungal.

Highlights

Organisms residing in the oral cavity contribute to health and disease, and influence diseases like oral candidiasis, the most common oral complication of HIV-infection [1,2]
Oral microbiota contribute to health and disease, and their disruption may influence the course of oral diseases like oral candidiasis
We identify the core oral mycobiome (COM) and core oral bacteriome (COB) in HIV-infected and uninfected individuals, and demonstrate that the COM differs between these two groups

Summary

Introduction

Organisms residing in the oral cavity (oral microbiota) contribute to health and disease, and influence diseases like oral candidiasis, the most common oral complication of HIV-infection [1,2]. Pathogenesis of oral candidiasis is linked to variables like changes in the CD4+ cell count and antiretroviral therapy (ART) in HIV-1-infected patients [3]. The introduction of ART has reduced mortality and morbidity as well as the incidence of opportunistic infections among HIV-infected patients, oral candidiasis remains a significant disease, even in the era of ART. In this regard, recent studies indicate that the decline of oral candidiasis among ART-experienced HIV-infected patients is transient in some HIV-infected individuals [4]. Patel et al [6] reported symptomatic oral candidiasis in 27% (59/215) HIV-infected patients. Even in the era of ART, oral candidiasis remains a significant problem

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