Effect of HIV/HAART and Other Clinical Variables on the Oral Mycobiome Using Multivariate Analyses

Abstract

The oral microbiome is considered an important factor in health and disease. We recently reported significant effects of HIV and several other clinical variables on the oral bacterial communities in a large cohort of HIV-positive and -negative individuals. The purpose of the present study was to similarly analyze the oral mycobiome in the same cohort. To identify fungi, the internal transcribed spacer 2 (ITS2) of the fungal rRNA genes was sequenced using oral rinse samples from 149 HIV-positive and 88 HIV-negative subjects that had previously undergone bacterial amplicon sequencing. Quantitative PCR was performed for total fungal content and total bacterial content. Interestingly, samples often showed predominance of a single fungal species with four major clusters predominated by Candida albicans, Candida dubliniensis, Malassezia restricta, or Saccharomyces cerevisiae. Quantitative PCR analysis showed the Candida-dominated sample clusters had significantly higher total fungal abundance than the Malassezia or Saccharomyces species. Of the 25 clinical variables evaluated for potential influences on the oral mycobiome, significant effects were associated with caries status, geographical site of sampling, sex, HIV under highly active antiretroviral therapy (HAART), and missing teeth, in rank order of statistical significance. Investigating specific interactions between fungi and bacteria in the samples often showed Candida species positively correlated with Firmicutes or Actinobacteria and negatively correlated with Fusobacteria, Proteobacteria, and Bacteroidetes. Our data suggest that the oral mycobiome, while diverse, is often dominated by a limited number of species per individual; is affected by several clinical variables, including HIV positivity and HAART; and shows genera-specific associations with bacterial groups. IMPORTANCE The oral microbiome is likely a key element of homeostasis in the oral cavity. With >600 bacterial species and >160 fungal species comprising the oral microbiome, influences on its composition can have an impact on both local and systemic health. We recently reported significant effects of HIV and several other clinical variables on the oral bacterial community in a large cohort of HIV-positive and -negative subjects. We describe here a comprehensive analysis of the oral mycobiome in the same cohort. Similar to the bacterial community, HIV under highly active antiretroviral therapy (HAART) had a significant impact on the mycobiome composition, but with less impact compared to other clinical variables. Additionally, unlike the oral bacterial microbiome, the oral mycobiome is often dominated by a single species with 4 major clusters of fungal communities. Together, these results suggest the oral mycobiome has distinct properties compared with the oral bacterial community, although both are equally impacted by HIV.

Determinants and Interactions of Oral Bacterial and Fungal Microbiota in Healthy Chinese Adults

“…However, it is noteworthy that while we focused mainly on oral-related variables in this study, the list of included variables is not exhaustive and has likely missed variables that might explain the variation of the microbiomes, such as fat-free mass ( 7 ) and flossing habit ( 5 ). In agreement with our findings, a study on the oral mycobiome of a population comprising HIV-positive and HIV-negative individuals based on ITS2 sequencing has identified sex as a significant variable affecting the oral mycobiome, with brushing frequency, mouthwash usage, frequency of alcoholic beverage intake, and frequency of oral sex being some of the insignificant variables ( 31 ). However, in contrast to our findings, the oral mycobiome in that study was also affected by caries status and missing teeth, and not by gingivitis and diet.…”

“…Zakaria et al ( 30 ) studied the salivary mycobiome in a healthy Japanese population of community-dwelling elderly and revealed the dominance of Candida albicans in most samples. Candida is also reported to be the predominant genus in the oral mycobiome of an American population comprising HIV-positive and HIV-negative individuals ( 31 ). The dominance of Candida in the oral mycobiome was also observed in our population, indicating its importance as a major member of the healthy oral mycobiome.…”

Alterations in the oral microbiome in HIV infection: causes, effects and potential interventions

“…However, the most abundant fungi in HIV-uninfected controls were Candida , Pichia , and Fusarium , presenting in 58%, 33%, and 33%, respectively. [ 67 ] Fidel et al [ 68 ] have also demonstrated the relative abundance of oral fungal communities in 149 HIV-positive and 88 HIV-negative subjects. This study suggested that 168 species can be identified in 12 dominant genera by sequencing of the ITS2 region of the rRNA gene repeat.…”

“…Several oral diseases often occur in PLWH, including periodontal diseases, OPC, oral warts, oral hairy leukoplakia, and Kaposi sarcoma (KS), even in those receiving ART. [44] Globally Fidel et al [68] 149 HIV+ subjects 88 HIVÀ subjects…”

HIV-Associated Interactions Between Oral Microbiota and Mucosal Immune Cells: Knowledge Gaps and Future Directions

“…Colonization of C. albicans and C. dubliniensis are the most prominent taxa observed in high abundance in saliva of HIV infected individuals. While incidence of oral candidiasis typically declines after HAART initiation, recent evidence suggests that the impact of HIV/HAART on the mycobiome is modest but not more considerable than other factors such as sex ( 105 ).…”