Topographic Diversity of the Respiratory Tract Mycobiome and Alteration in HIV and Lung Disease

Abstract

Rationale: Microbiome studies typically focus on bacteria, but fungal species are common in many body sites and can have profound effects on the host. Wide gaps exist in the understanding of the fungal microbiome (mycobiome) and its relationship to lung disease.Objectives: To characterize the mycobiome at different respiratory tract levels in persons with and without HIV infection and in HIVinfected individuals with chronic obstructive pulmonary disease (COPD).Methods: Oral washes (OW), induced sputa (IS), and bronchoalveolar lavages (BAL) were collected from 56 participants. We performed 18S and internal transcribed spacer sequencing and used the neutral model to identify fungal species that are likely residents of the lung. We used ubiquity-ubiquity plots, random forest, logistic regression, and metastats to compare fungal communities by HIV status and presence of COPD.

Lung microbiome dynamics in COPD exacerbations

“…Data from these populations could be informative in defining the normal lung microbiota as well as the changes of microbial composition resulting in COPD onset. Second, besides bacteria, the importance of viruses and fungi in COPD is just beginning to be appreciated and studied [36][37][38]. A systems biology view of bacterial, viral and fungal microbiomes integrating additional host response factors such as host transcriptome and metabolome profiles would boost our understanding of the host-microbiota interaction and its implication in disease aetiology.…”

The lung mycobiome in the next-generation sequencing era

“…Fungi have been linked to such chronic lung diseases as asthma and COPD. 8,9 Given the ubiquity of fungi in the environment, the potential respiratory exposure to fungi, and the ability of fungi to trigger inflammation, the mycobiome may play a key role in shaping the respiratory immune response and contribute to lung damage.…”

“…Compared to bacterial diversity in the lungs, average fungal diversity in the same samples is lower, 13 but has a higher coefficient of variation, or ratio of standard deviation to the mean. We see in our own data, a subset of 35 BAL samples from a study of the lung mycobiome in HIV-infected and uninfected individuals for which we have both 16S and ITS sequence data., 9 a coefficient of variation for bacterial diversity, as measured by the Shannon diversity index, of 22.9% and a coefficient of variation for fungal diversity of 73.9%. Because bacterial diversity is relative stable, other factors, including patient health and environmental exposures, appear to have a greater impact on the diversity of the fungi.…”

Airway bacteria and respiratory symptoms are common in ambulatory HIV-positive UK adults

“…The Lung HIV Microbiome Project [17] is currently the largest study of this type and may further our understanding of the interaction between the host and microbiome in HIV-related respiratory health.…”