Identification of an intraocular microbiota

Abstract

The current dogma in ophthalmology and vision research presumes the intraocular environment to be sterile. However, recent evidence of intestinal bacterial translocation into the bloodstream and many other internal organs including the eyes, found in healthy and diseased animal models, suggests that the intraocular cavity may also be inhabited by a microbial community. Here, we tested intraocular samples from over 1000 human eyes. Using quantitative PCR, negative staining transmission electron microscopy, direct culture, and high-throughput sequencing technologies, we demonstrated the presence of intraocular bacteria. The possibility that the microbiome from these low-biomass communities could be a contamination from other tissues and reagents was carefully evaluated and excluded. We also provide preliminary evidence that a disease-specific microbial signature characterized the intraocular environment of patients with age-related macular degeneration and glaucoma, suggesting that either spontaneous or pathogenic bacterial translocation may be associated with these common sight-threatening conditions. Furthermore, we revealed the presence of an intraocular microbiome in normal eyes from non-human mammals and demonstrated that this varied across species (rat, rabbit, pig, and macaque) and was established after birth. These findings represent the first-ever evidence of intraocular microbiota in humans.

Microbiota and Ocular Diseases

“…As the first and foremost finding, our group identified the presence of an intraocular microbiota via quantitative PCR, negative staining transmission electron microscopy, direct culture, and high-throughput sequencing technologies. We also analyzed aqueous humor samples collected from four species, i.e., rat, rabbit, pig, and macaque, and confirmed the existence of an intraocular microbiota ( Deng et al., 2021 ). These observations raise an intriguing question of how microbes enter the eye ( Figure 1 ).…”

“…Although a growing amount of evidence suggests that ocular disease progression is associated with altered gut microbial composition, the direct interconnections between gut microbiota and eye function require a solid molecular mechanistic foundation. We have recently identified an intraocular microbiota in normal living animals and in patients with ocular diseases ( Deng et al., 2021 ). These observations raise several interesting questions: How did the microbes enter the eye and affect the ocular diseases?…”

“…However, culture-based techniques can only be used to characterize a small percentage of the actual microbial populations in a sample because they are limited by the phenotypic characteristics of microbes, for example, the ability of microbes in a sample to proliferate in or on a specified growth medium under a specified growth condition (Schabereiter-Gurtner et al, 2001;Hori et al, 2008;Fernańdez-Rubio et al, 2010;Ozkan et al, 2017). Meantime, combining quantitative PCR with negative staining transmission electron microscopy is an effective means of identifying microbial populations (Deng et al, 2021). In fact, cultivated bacteria represent only half of the bacterial phyla thus far Schloss (Schloss and Handelsman, 2004) Given the widespread use of next-generation sequencing technologies, the high-throughput analysis of microbial communities has become a much lower cost and less timeconsuming approach that allows researchers to achieve a more complete understanding of the composition of commensal communities.…”

“…Several platforms, such as MetaLab (Cheng et al, 2017), MetaQuantome (Easterly et al, 2019), Galaxy-P (Jagtap et al, 2015), and MetaProteomeAnalyzer (Muth et al, 2018), are available for processing metaproteomic data. Metaproteomics enables a clear identification of how disease conditions (or their triggers) result in gut microbial dysbiosis and which microbial protein may directly affect the Identifying the intraocular microbiota signature in glaucoma and AMD (Deng et al, 2021) Inconformity of taxonomic abundance and transcriptional activities Veillonella as the predominant genus in patients of chronic dacryocystitis (Eguchi et al, 2017a) Lack of abundance of gene functional annotation database…”

“…These two groups of patients show distinctly abundant microbial species compared with controls. Interestingly, by using metagenomic sequencing, our group provided preliminary evidence that the intraocular microbiota signature might also be disease-specific in ocular diseases such as glaucoma and AMD ( Deng et al., 2021 ). Veillonella have been found as the predominant genus in patients of chronic dacryocystitis through metagenomic sequencing ( Eguchi et al., 2017a ).…”