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Chowdhary A, Van Gelder RN, Sundararajan M. Methodologic Considerations for Studying the Ocular Surface Microbiome. OPHTHALMOLOGY SCIENCE 2023; 3:100408. [PMID: 38025161 PMCID: PMC10654231 DOI: 10.1016/j.xops.2023.100408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 12/01/2023]
Abstract
The ocular surface microbiome, unlike that of the skin or gut, has not been well characterized. Culture experiments historically suggested a nearly sterile ocular surface, but initial application of molecular methods such as 16S ribosomal RNA and high-throughput sequencing demonstrated a surprisingly rich ocular surface microbiome. However, a major limitation in studying such a low-biomass niche is the potential for artifactual results when amplification-based techniques such as ribosomal polymerase chain reaction and shotgun sequencing are used. It will be essential to establish standards across the field for sample collection, positive and negative controls, and limitation of contamination in both the laboratory setting and computational analysis. New developments in ocular microbiome research, including the generation of reference reagents and fluoroscopic imaging techniques, provide improved means to validate sequencing results and to visualize complex interactions between host cells and bacteria. Through more thorough characterization of the ocular surface microbiome, the connections between a dysregulated surface and ophthalmic disease may be better understood. Financial Disclosures Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.
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Affiliation(s)
- Apoorva Chowdhary
- Department of Ophthalmology, University of Washington, Seattle, Washington
| | - Russell N. Van Gelder
- Department of Ophthalmology, University of Washington, Seattle, Washington
- Roger and Angie Karalis Johnson Retina Center, Seattle, Washington
- Department of Biological Structure, University of Washington, Seattle, Washington
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Miel Sundararajan
- Department of Ophthalmology, University of Washington, Seattle, Washington
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Sajiki AF, Koyanagi Y, Ushida H, Kawano K, Fujita K, Okuda D, Kawabe M, Yamada K, Suzumura A, Kachi S, Kaneko H, Komatsu H, Usui Y, Goto H, Nishiguchi KM. Association Between Torque Teno Virus and Systemic Immunodeficiency in Patients With Uveitis With a Suspected Infectious Etiology. Am J Ophthalmol 2023; 254:80-86. [PMID: 37356647 DOI: 10.1016/j.ajo.2023.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/27/2023] [Accepted: 06/03/2023] [Indexed: 06/27/2023]
Abstract
PURPOSE To determine the correlation between the presence of torque teno virus (TTV) in the aqueous humor of patients with uveitis and clinical information, including immunodeficiency history. DESIGN Multicenter, retrospective, cross-sectional study. METHODS Fifty-eight patients with uveitis with a suspected infectious etiology and 24 controls with cataract or age-related macular degeneration were included. We used quantitative polymerase chain reaction to test all subjects for TTV and multiplex polymerase chain reaction to test uveitis subjects for common ocular pathogens. When possible, both serum and aqueous humor samples were tested. Ocular TTV positivity was compared with age, sex, and a history of systemic immunodeficiency with logistic analysis. RESULTS Ocular TTV positivity was found in 23%, 11%, and 0% of patients with herpetic uveitis, nonherpetic uveitis, and controls, respectively. Among patients with herpes infection, positivity for ocular TTV was found in 43%, 8%, 14%, and 50% of patients with cytomegalovirus retinitis, iridocyclitis, acute retinal necrosis, and Epstein-Barr virus-positive uveitis, respectively. Patients with cytomegalovirus retinitis showed a significantly higher rate of ocular TTV infection than controls (P = .008). Serum analysis revealed TTV positivity in 90% of patients with uveitis and in 100% of controls. Age- and gender-adjusted logistic analysis revealed a correlation between ocular TTV positivity and systemic immunodeficiency (P = .01), but no correlations between ocular TTV and age, gender, or viral pathogenic type. CONCLUSIONS These findings suggest that positivity for ocular TTV was correlated with a clinical history of systemic immunodeficiency.
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Affiliation(s)
- Ai Fujita Sajiki
- From the Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan (A.F.S., Y.K., H.U., K.K., K.F., D.O., M.K., K.Y., A.S., H.K., K.M.N.).
| | - Yoshito Koyanagi
- From the Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan (A.F.S., Y.K., H.U., K.K., K.F., D.O., M.K., K.Y., A.S., H.K., K.M.N.)
| | - Hiroaki Ushida
- From the Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan (A.F.S., Y.K., H.U., K.K., K.F., D.O., M.K., K.Y., A.S., H.K., K.M.N.).
| | - Kenichi Kawano
- From the Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan (A.F.S., Y.K., H.U., K.K., K.F., D.O., M.K., K.Y., A.S., H.K., K.M.N.); Department of Ophthalmology, Yokkaichi Municipal Hospital, Yokkaichi, Japan (K.K.)
| | - Kosuke Fujita
- From the Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan (A.F.S., Y.K., H.U., K.K., K.F., D.O., M.K., K.Y., A.S., H.K., K.M.N.)
| | - Daishi Okuda
- From the Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan (A.F.S., Y.K., H.U., K.K., K.F., D.O., M.K., K.Y., A.S., H.K., K.M.N.)
| | - Mitsuki Kawabe
- From the Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan (A.F.S., Y.K., H.U., K.K., K.F., D.O., M.K., K.Y., A.S., H.K., K.M.N.)
| | - Kazuhisa Yamada
- From the Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan (A.F.S., Y.K., H.U., K.K., K.F., D.O., M.K., K.Y., A.S., H.K., K.M.N.)
| | - Ayana Suzumura
- From the Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan (A.F.S., Y.K., H.U., K.K., K.F., D.O., M.K., K.Y., A.S., H.K., K.M.N.)
| | - Shu Kachi
- Shohzankai Medical Foundation, Miyake Eye Hospital, Nagoya, Japan (S.K.)
| | - Hiroki Kaneko
- From the Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan (A.F.S., Y.K., H.U., K.K., K.F., D.O., M.K., K.Y., A.S., H.K., K.M.N.)
| | - Hiroyuki Komatsu
- Department of Ophthalmology, Tokyo Medical University, Tokyo, Japan (H.K., Y.U., H.G.)
| | - Yoshihiko Usui
- Department of Ophthalmology, Tokyo Medical University, Tokyo, Japan (H.K., Y.U., H.G.)
| | - Hiroshi Goto
- Department of Ophthalmology, Tokyo Medical University, Tokyo, Japan (H.K., Y.U., H.G.)
| | - Koji M Nishiguchi
- From the Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan (A.F.S., Y.K., H.U., K.K., K.F., D.O., M.K., K.Y., A.S., H.K., K.M.N.)
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Peter VG, Morandi SC, Herzog EL, Zinkernagel MS, Zysset-Burri DC. Investigating the Ocular Surface Microbiome: What Can It Tell Us? Clin Ophthalmol 2023; 17:259-271. [PMID: 36698849 PMCID: PMC9870096 DOI: 10.2147/opth.s359304] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 01/10/2023] [Indexed: 01/20/2023] Open
Abstract
While pathogens of the eye have been studied for a very long time, the existence of resident microbes on the surface of healthy eyes has gained interest only recently. It appears that commensal microbes are a normal feature of the healthy eye, whose role and properties are currently the subject of extensive research. This review provides an overview of studies that have used 16s rRNA gene sequencing and whole metagenome shotgun sequencing to characterize microbial communities associated with the healthy ocular surface from kingdom to genus level. Bacteria are the primary colonizers of the healthy ocular surface, with three predominant phyla: Proteobacteria, Actinobacteria, and Firmicutes, regardless of the host, environment, and method used. Refining the microbial classification to the genus level reveals a highly variable distribution from one individual and study to another. Factors accounting for this variability are intriguing - it is currently unknown to what extent this is attributable to the individuals and their environment and how much is artifactual. Clearly, it is technically challenging to accurately describe the microorganisms of the ocular surface because their abundance is relatively low, thus, permitting substantial contaminations. More research is needed, including better experimental standards to prevent biases, and the exploration of the ocular surface microbiome's role in a spectrum of healthy to pathological states. Outcomes from such research include the opportunity for therapeutic interventions targeting the microbiome.
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Affiliation(s)
- Virginie G Peter
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland,Correspondence: Virginie G Peter, Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Freiburgstrasse 15, Bern, 3010, Switzerland, Email
| | - Sophia C Morandi
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland,Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Elio L Herzog
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland,Department for BioMedical Research, University of Bern, Bern, Switzerland,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Martin S Zinkernagel
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland,Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Denise C Zysset-Burri
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland,Department for BioMedical Research, University of Bern, Bern, Switzerland
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