Human pharyngeal microbiota in age-related macular degeneration

Abstract

Background: While the aetiology of age-related macular degeneration (AMD)-a major blinding disease-remains unknown, the disease is strongly associated with variants in the complement factor H (CFH) gene. CFH variants also confer susceptibility to invasive infection with several bacterial colonizers of the nasopharyngeal mucosa. This shared susceptibility locus implicates complement deregulation as a common disease mechanism, and suggests the possibility that microbial interactions with host complement may trigger AMD. In this study, we address this possibility by testing the hypothesis that AMD is associated with specific microbial colonization of the human nasopharynx.

Results: High-throughput Illumina sequencing of the V3-V6 region of the microbial 16S ribosomal RNA gene was used to comprehensively and accurately describe the human pharyngeal microbiome, at genus level, in 245 AMD patients and 386 controls. Based on mean and differential microbial abundance analyses, we determined an overview of the pharyngeal microbiota, as well as candidate genera (Prevotella and Gemella) suggesting an association towards AMD health and disease conditions.

Conclusions: Utilizing an extensive study population from Singapore, our results provided an accurate description of the pharyngeal microbiota profiles in AMD health and disease conditions. Through identification of candidate genera that are different between conditions, we provide preliminary evidence for the existence of microbial triggers for AMD. Ethical approval for this study was obtained through the Singapore Health Clinical Institutional Review Board, reference numbers R799/63/2010 and 2010/585/A.

Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1. Pharyngeal microbiome profile of the study population, at genus level.

Cumulative relative abundance of each of the 63 bacterial genera in case and control samples. Microbial community members with relative abundance

Fig 2. DESeq2 differential abundance analysis expressed as Log2FC comparison of AMD-positive samples and control samples.

Negative fold change scores (log2) indicate genera with decreased abundance in AMD-positive samples, and positive fold change scores indicate genera with increased abundance in AMD-positive samples. Each point represents a genus. Genera detected to have significant difference in abundance (Adj-p < 0.05) are shown.

Fig 3. Relative abundances of significant genera between 245 case and 386 control samples.

AMD-positive and control samples are denoted by (+) and (-) respectively. Statistical significance is indicated by (*Adj-p < 0.05), (**Adj-p < 0.005) or (***Adj-p < 0.0005). Mean relative abundances, standard deviations and P-values are presented in S4 Table.

Fig 4. Relative abundances of significant genera between 386 controls and 165 individuals with late AMD.

(-) and L-AMD denote controls and late AMD samples respectively. Statistical significance is indicated by (*Adj-p < 0.05), (**Adj-p < 0.005) or (***Adj-p < 0.0005). Mean relative abundances, standard deviations and P-values are presented in S6 Table.

Fig 5. Microbial loads from qPCR.

qPCR-derived copy numbers of each genera were expressed as a percentage of total microbial copy number within each sample. Twenty samples were randomly selected for each disease status. Statistical significance is indicated by (*P