Overview of Microorganisms: Bacterial Microbiome, Mycobiome, Virome Identified Using Next-Generation Sequencing, and Their Application to Ophthalmic Diseases

Abstract

This review outlines technological advances in pathogen identification and describes the development and evolution of next-generation sequencers that can be applied to the ocular microbiome. Traditional methods such as culture and PCR have limitations in detecting the full spectrum of resident microorganisms, prompting a transition toward metagenomic analysis. As microbiome research expands across body systems, the comprehensive identification of ocular bacteria, fungi, and viruses has become possible. The commensal ocular microbiome may influence disease development through changes in the immune system and ocular environment. Next-generation sequencing enables detailed microbial profiling, aiding in disease diagnosis and treatment selection. Alterations in the microbiome may also induce metabolic changes, offering insights into novel treatment methods. This review outlines the evolution of next-generation sequencing technology, summarizes current knowledge of microorganisms found on the ocular surface and in intraocular fluid, and discusses future challenges and prospects. However, the large volume of microbiome data obtained must be interpreted with caution due to possible analytical biases. Furthermore, determining whether the microbiome is truly pathogenic requires comprehensive interpretation beyond the clinical findings and results of traditional identification methods.

Keywords: PCR; infectious diseases; microbiome; mycobiome; next-generation sequencing; ocular; virome.

Figure 1

Comparison of the commensal bacterial microbiome across four body sites [137]. Samples were collected from the conjunctiva, meibomian gland, periocular area, and hand using a sterile cotton swab. Metagenomic analysis showed the relative proportions of the bacterial flora at each site and compositional differences, shown in the pie chart. The top five microorganisms composing the ocular surface bacterial microbiome at the family level were Propionibacteriaceae, Corynebacteriaceae, Staphylococcaceae, Neisseriae, and Comamonadaceae. Principal component analysis (PCA) was performed to assess microbial similarity among the four sites. The PCA plot shows relatively small distances between the conjunctiva (red) and meibomian gland (blue), and between the periocular skin (purple) and hand (green). In contrast, a large distance was observed between the conjunctiva and hand. The ocular surface has a distinct bacteria flora that is independent of other sites.

Figure 2

Workflow of comprehensive microbiome identification. After taking samples from the ocular surface, aqueous humor, and vitreous body, whole genomes are extracted, and the commensal bacterial flora is identified using a next-generation sequencer [137,144,145,146]. Bacterial flora resides on the ocular surface and plays a role in maintaining homeostasis [137,139,140,141]. The bacterial flora produces short-chain fatty acids such as butyric acid, acetic acid, and propionic acid, and these secondary metabolites also contribute to stabilizing the ocular surface environment [147,148]. The ocular bacterial flora is affected by both internal factors such as cardiovascular disease, immune disease, and intestinal disease, and external factors such as ultraviolet light, topical or oral antibiotics, and contact lens wear [141,142,143]. Disruption of this homeostasis may lead to infectious, allergic, or neoplastic diseases [137,144,145,146]. When investigating the relationship between changes in the microbiome and the onset of disease, multi-omics analysis combining transcriptomics, proteomics, and metabolomics may be useful for identifying biomarkers [118,119,120,149].