Magnetic Activated Cell-Sorting Identifies a Unique Lung Microbiome Community Associated with Disease States

Abstract Background: The advent of culture-independent, next-generation DNA sequencing has led to discovery of distinct lung bacterial communities. Studies of lung microbiome taxonomy often reveal only subtle differences between health and disease, but microbial host response may distinguish members of similar communities in different populations. Magnetic-activated cell sorting has been applied to the gut microbiome to identify numbers and types of bacteria eliciting a humoral response. We adapted this technique to examine populations of immunoglobulin-bound bacteria and investigate the lung microbiota in Human Immunodeficiency Virus (HIV) as a representative disease.Methods: 42 people living with HIV and 22 HIV-uninfected individuals underwent bronchoalveolar lavage. We separated immunoglobulin G-bound bacteria using magnetic-activated cell sorting and sequenced the 16S rRNA gene on the Illumina MiSeq platform. We analyzed microbial sequencing data and quantified cytokines and bacterial rRNA copy numbers from bronchoalveolar lavage. Results: Immunoglobulin G-bound bacteria were detectable in the healthy lung microbiota. Comparison of raw bronchoalveolar lavage by HIV status showed no significant taxonomic differences, but the immunoglobulin-bound lung microbiota differed by HIV status with greater abundance of Pseudomonas in people living with HIV. Lung cytokine levels were also higher in people living with HIV, which correlated with increased quantity of immunoglobulin G-bound bacteria. Conclusions: We report a novel application of magnetic-activated cell sorting to identify immunoglobulin G-bound bacteria in the lung. This technique identified distinct bacterial communities which differed in composition from raw bronchoalveolar lavage, revealing differences in health and disease not detected by traditional analyses. Cytokine response was also associated with differential immunoglobulin binding of lung bacteria, suggesting functional importance of these communities.