Ocular microbiome changes in dry eye disease and meibomian gland dysfunction

Alterations of ocular surface microbiome in glaucoma and its association with dry eye

Introduction. Alterations in ocular surface microbiota (OSM) have been noted in both dry eye disease (DED) and glaucoma. However, the combined effects of these conditions on OSM have not been explored.Hypothesis. We hypothesized that patients with both glaucoma and dry eye would exhibit distinct changes in OSM composition and diversity compared to those with only glaucoma, only dry eye or healthy individuals.Aim. We employed amplicon sequencing to investigate OSM profiles in patients with glaucoma and/or dry eye disease.Methods. Swab samples from the conjunctiva of both eyes were collected from 28 glaucomatous patients [13 without dry eye syndrome (G-only) and 15 with dry eye syndrome (G-DED)], 13 DED patients without glaucoma (DED-only) and 31 age-matched healthy controls (HCs). After V3-V4 16S rRNA sequencing, MOTHUR tools and R language were used to elucidate and compare OSM composition and diversity between groups.Results. Our data revealed very diverse bacterial communities with 28 phyla and 785 genera. All the groups shared the three most abundant phyla, Actinobacteria (67.47%), Firmicutes (17.14%) and Proteobacteria (13.73%). Corynebacterium (54.75%), Staphylococcus (10.71%), Cutibacterium (8.77%) and Streptococcus (3.20%) were the most abundant genera. Only the G-DED group showed higher alpha diversity than the HC group (P<0.05). However, significant differences in beta diversity were observed between all three patient groups and the HC group. The Differential Expression for Sequencing 2 (DESeq2) analysis unveiled an increased presence of opportunistic bacteria across all pathological groups, with the G-DED group demonstrating the most pronounced alterations.Conclusions. Our findings confirm the predominance of Gram-positive bacteria in normal OSM and the rise of opportunistic Gram-negative bacteria in glaucoma and dry eye disease. This is the first study to characterize OSM in glaucoma patients with DED.

Multi-cohort analysis identifying core ocular surface microbiome and bacterial alterations in eye diseases

PURPOSE

Inconsistency exists among reported studies on the composition of human ocular surface microbiome (OSM). The roles of OSM in ocular diseases remain uncertain. In this study, we aimed to determine the composition of OSM and to evaluate its potential roles and functions from multiple cohorts.

METHODS

Raw 16 s sequencing data were obtainable from publicly available repositories, sourced from 17 published studies. Employing a standardized method, we processed the data and conducted a cross-cohort analysis. Through bioinformatics pipelines QIIME2 and PICRUSt2, we processed a total of 1875 ocular surface samples. Core microbiome analyses, genera comparisons, and MetaCyc pathway analyses were performed within each cohort independently. The results were then combined to identify shared patterns across different datasets.

RESULTS

The core OSM comprised seven genera: Corynebacterium, Staphylococcus, Acinetobacter, Streptococcus, Pseudomonas, Cutibacterium and Bacillus. Corynebacterium and Staphylococcus are the most abundant genera on ocular surface. Most ocular diseases showed OSM alterations and eight genera demonstrated a non-specific, shared response among two or more ocular diseases. Moreover, changes in various metabolic pathways were predicted following OSM alteration, indicating potential roles of OSM in biological processes.

CONCLUSION

We refined the core OSM candidates combining multiple cohorts. The common pattern shared by different cohorts is worth further investigation. Changes in metabolic pathways based on bioinformatic analysis indicated a role of OSM on ocular diseases. Our results help extend the knowledge and encourage further investigations on the associations between OSM and ocular diseases.

Meibum and lid margin microbiome in eyes with chalazion: exploring an infectious aetiology

PURPOSE

The current study evaluated the meibum and lid margin microbiome of eyelids with chalazion and compared it with contralateral uninvolved eyelids and healthy controls.

METHODS

Chalazion contents (group 1) and expressed meibum swabs from the lid margins of seven patients with chalazion (mean age 29±12 years; >6 weeks chalazia duration) and age-matched healthy controls were sequenced using next-generation 16S rDNA V3-V4 variable region sequencing. The meibum from the contralateral eye of patient with chalazion served as sample control (group 2), and healthy individuals served as negative control (group 3). The contents were also plated using conventional culture techniques.

RESULTS

Meibomian glands expressed thick turbid meibum in the area of chalazion in five out of seven eyelids. Contralateral uninvolved eyelids and healthy control glands were expressible with clear meibum. The mean Schirmer I value was 24.6±4.9 mm. Lid margin and meibum microbiome profiling revealed significant differences between the patients (involved or uninvolved sides) and healthy controls. The predominant phyla were Proteobacteria, Bacteroidota and Actinobacteria in all three groups. Acinetobacter, Moraxella and Paracoccus were the predominant genera in groups 1 and 2. Significant differences were noted in the predominant genera between group 3 versus groups 1 and 2. Principal coordinate analysis revealed overlap between groups 1 and 2, whereas group 3 had a distinct cluster. None of the culture media (for aerobic, anaerobic bacteria and fungus) showed any bacterial growth.

CONCLUSION

In patients with unilateral chalazion, involved and uninvolved eyelids share similar lid margin and meibum microbiome but differ from the healthy controls.

Ocular Surface Microbiota and Corneal Transplant Outcome: Is There a Link?

Recent research has highlighted the critical role of microbiota in organ transplant outcomes, particularly in the gut. However, the impact of ocular surface microbiota (OSM) on corneal transplantation remains largely unexplored. This piece examines the potential connection between OSM imbalances and corneal graftoutcomes, suggesting that microbial shifts could influence immune responses and transplant success. The OSM, though characterized by low microbial density, plays a critical role in local immune modulation and ocular surface homeostasis. Dysbiosis in this microbiota may compromise the immune privilege of the cornea, potentially increasing the risk of graft rejection. Looking at gut microbiota studies, where dysbiosis has been linked to graft failure, it is reasonable to hypothesize that similar mechanisms might be at play on the ocular surface. Disruptions in cornea's immune tolerance pathways, such as anterior chamber-associated immune deviation (ACAID), may lead to pro-inflammatory responses that threaten graft survival. In addition, ocular surface diseases such as dry eye disease, microbial keratitis, and allergic conjunctivitis, already associated with OSM dysbiosis, may further exacerbate post-transplant complications. Despite the lack of direct studies linking OSM to corneal transplant outcomes, this opinion piece highlights the necessity for future research. Standardizing microbiota analysis methodologies and exploring therapeutic interventions, such as ocular probiotics, could open new roads for improving corneal transplant success and patient prognosis.

Systems biology of dry eye: Unraveling molecular mechanisms through multi-omics integration

Dry eye disease (DED) is a multifactorial condition with complex and incompletely understood molecular mechanisms. Advances in multi-omics technologies, including genomics, transcriptomics, proteomics, metabolomics, and microbiomics, have provided new insights into the pathophysiology of DED. Genomic analyses have identified key genetic variants linked to immune regulation and lacrimal gland function. Transcriptomic studies reveal upregulated inflammatory pathways in ocular surface tissues, implicating these as core drivers of chronic inflammation. Proteomic research highlights significant alterations in tear protein composition, especially proteins involved in inflammation and tissue repair. Metabolomics studies focus on disrupted lipid metabolism and oxidative stress, which are crucial in maintaining tear film stability. Furthermore, microbiome research has demonstrated reduced microbial diversity and increased pathogenic bacteria, exacerbating inflammatory responses. The integration of multi-omics data allows for the identification of novel biomarkers and therapeutic targets, enabling precision diagnostics and personalized treatments. Therefore, this review highlights the critical importance of multi-omics approaches in deepening our understanding of DED's complex molecular mechanisms and their potential to transform clinical management and therapeutic innovations in this challenging field.

Preferred practice guidelines and narrative review on infectious keratitis in ocular surface diseases

Ocular surface disease (OSD) encompasses a variety of additional factors in the natural history of infectious keratitis like disruption of the normal tear film, altered ocular microbiome, adnexal inflammation, de-epithelization of the cornea due to anatomical factors like trichiasis, lid margin keratinization, presence of limbal stem cell deficiency, and other lid related problems. These cases need special attention with respect to lower threshold for inpatient admission and care along with examination and careful corneal scraping to avoid any perforation. The preferable practice patterns in these include documenting epithelial defects using fluorescein stain in the presence of cobalt blue filter, use of preservative-free monotherapy drops in mild to moderate corneal ulcers, quantification of corneal thinning and depth of infiltrate using anterior segment optical coherence tomography, and early tapering of epithelia-toxic drugs with judicious addition of lubricants and steroids. The changes in surgical management involve adopting a lower threshold for procedures that can enhance healing, such as amniotic membrane grafting, electrolysis of trichiasis, and punctal occlusion for severe dry eye disease. Conversely, a higher threshold for therapeutic keratoplasty is preferable as postoperative healing is a major challenge in eyes with OSD. A closer follow-up is vital as healing is slower and risk of reinfection is higher. The long-term management of corneal opacity in OSD is also complex as first-stage ocular surface stabilization is essential prior to keratoplasty.

The microbiome and the eye: a new era in ophthalmology

The human microbiome has progressively been recognised for its role in various disease processes. In ophthalmology, complex interactions between the gut and distinct ocular microbiota within each structure and microenvironment of the eye has advanced our knowledge on the multi-directional relationships of these ecosystems. Increasingly, studies have shown that modulation of the microbiome can be achieved through faecal microbiota transplantation and synbiotics producing favourable outcomes for ophthalmic diseases. As ophthalmologists, we are obliged to educate our patients on measures to cultivate a healthy gut microbiome through a range of holistic measures. Further integrative studies combining microbial metagenomics, metatranscriptomics and metabolomics are necessary to fully characterise the human microbiome and enable targeted therapeutic interventions.

From Dysbiosis to Disease: The Microbiome's Influence on Uveitis Pathogenesis

The microbiome, comprising the diverse microbial communities inhabiting the human body, has emerged as a critical factor in regulating immune function and inflammation. The relationship between the microbiome and uveitis represents a promising frontier in ophthalmological research, with the microbiome increasingly implicated in disease onset and progression. Research has predominantly focused on the gut microbiome, with animal studies providing evidence that dysbiosis is a key factor in autoimmunity. As the understanding of the microbiome increases, so does the potential for developing innovative treatments that leverage the microbiome's impact on immune and inflammatory processes. Future research will be crucial for deciphering the complexities of the interaction between the microbiome and immune system and for creating effective microbiome-based therapies for those with uveitis. Incorporating microbiome research into clinical practice could transform how uveitis is managed, leading to better and more individualized approaches for management. This review discusses the current understanding of the microbiome-uveitis axis, the promise of microbiome-based diagnostics and therapeutics, and the critical need for large-scale, longitudinal studies. Unlocking the potential of microbiome-targeted approaches may revolutionize the management of uveitis and other inflammatory diseases.

The Effect of Face Mask Wear on the Ocular Surface and Contact Lens Microbiome

OBJECTIVES

As face mask wear can result in the redirection of nasal and oral exhalation toward the ocular region, this study investigated the impact of face mask wear on the conjunctiva, eyelid margin, and contact lens (CL) surface microbiome.

METHODS

In this prospective, cross-over study, experienced CL wearers (N=20) were randomized to wear a face mask for 6 hr/day (minimum) for a week or no mask for a week. The conjunctiva, eyelid, and CLs were then sampled. After a 1-week washout period, participants were crossed over into the alternate treatment for 1 week and sampling was repeated. Sampling was bilateral and randomly assigned to be processed for culturing or 16S ribosomal(r) RNA gene sequencing.

RESULTS

Culturing showed no effect of mask wear on the average number of bacterial colonies isolated on the conjunctiva, eyelid, or CL, but there was increased isolation of Staphylococcus capitis on CL samples with mask wear ( P =0.040). Culture-independent sequencing found differences in the taxonomic complexity and bacterial composition between the three sites ( P <0.001), but there was no effect of bacterial diversity within and between sites. Mask wear did not impact dry eye or CL discomfort, but increased ocular surface staining was reported ( P =0.035).

CONCLUSIONS

Mask wear did not substantially alter the microbiome of the conjunctiva, eyelid margin, or CL surfaces in uncompromised healthy eyes.

Pharmacogenomic Analysis of Response to Topical Tumor Necrosis Factor α Antagonist Licaminlimab (OCS-02) in Dry Eye Disease [RETRACTED]

PURPOSE

The purpose of this study was to evaluate the pharmacogenomics of response to topical ocular tumor necrosis factor α (TNFα) inhibitor licaminlimab in patients with DED.

METHODS

Three single-nucleotide polymorphisms (SNPs) associated with Sjögren syndrome, 3 in the TNFα gene and 1 in the TNF receptor 1 (TNFR1) gene, were assessed for association with response to licaminlimab in participants from a randomized, vehicle-controlled, Phase 2 study in which adults with DED and severe ocular discomfort persisting despite treatment with artificial tears received licaminlimab or vehicle for 6 weeks. Response was assessed for change from baseline in Global Ocular Discomfort score at Day 29 of treatment. The pharmacogenomic analysis was a prospectively specified exploratory objective of the study. mRNA expression for TNFα, interleukin (IL) 1β, and IL8 in conjunctival epithelium cells was determined. The relationship between SNPs and response to licaminlimab was assessed using a mixed model repeated measures analysis.

RESULTS

SNP rs1800693 in the TNFR1 gene showed a significant effect on response to licaminlimab ( P < 0.0001, initial association test); no effect was seen for any of the other SNPs tested. The CC genotype of rs1800693 was associated with much greater response to licaminlimab than the CT or TT genotypes: LS mean changes from baseline to Day 29 in Global Ocular Discomfort score were -29.5, -0.09, and -3.90, in patients with the CC, CT, and TT genotypes, respectively ( P < 0.0001). No significant effect was observed in vehicle-treated patients. Improvements from baseline were seen in 3/4 licaminlimab-treated participants with the CC genotype. Conjunctival epithelium cell levels of mRNA for TNFα, IL1β, and IL8 decreased from baseline in participants with the CC genotype, but not with the CT or TT genotypes. Between-genotype differences in mRNA levels were not observed in participants receiving vehicle.

CONCLUSIONS

The CC genotype of rs1800693, relatively common in patients with DED, was strongly associated with response to licaminlimab and decreased inflammatory cytokine gene expression in ocular surface cells during treatment. This study is one of the first to our knowledge to investigate pharmacogenomics in the treatment of DED.

Whole genome sequencing and characterization of Corynebacterium isolated from the healthy and dry eye ocular surface

BACKGROUND

The purpose of this study was to characterize Corynebacterium isolated from the ocular surface of dry eye disease patients and healthy controls. We aimed to investigate the pathogenic potential of these isolates in relation to ocular surface health. To this end, we performed whole genome sequencing in combination with biochemical, enzymatic, and antibiotic susceptibility tests. In addition, we employed deferred growth inhibition assays to examine how Corynebacterium isolates may impact the growth of potentially competing microorganisms including the ocular pathogens Pseudomonas aeruginosa and Staphylococcus aureus, as well as other Corynebacterium present on the eye.

RESULTS

The 23 isolates were found to belong to 8 different species of Corynebacterium with genomes ranging from 2.12 mega base pairs in a novel Corynebacterium sp. to 2.65 mega base pairs in C. bovis. Whole genome sequencing revealed the presence of a range of antimicrobial targets present in all isolates. Pangenome analysis showed the presence of 516 core genes and that the pangenome is open. Phenotypic characterization showed variously urease, lipase, mucinase, protease and DNase activity in some isolates. Attention was particularly drawn to a potentially new or novel Corynebacterium species which had the smallest genome, and which produced a range of hydrolytic enzymes. Strikingly the isolate inhibited in vitro the growth of a range of possible pathogenic bacteria as well as other Corynebacterium isolates. The majority of Corynebacterium species included in this study did not seem to possess canonical pathogenic activity.

CONCLUSIONS

This study is the first reported genomic and biochemical characterization of ocular Corynebacterium. A number of potential virulence factors were identified which may have direct relevance for ocular health and contribute to the finding of our previous report on the ocular microbiome, where it was shown that DNA libraries were often dominated by members of this genus. Particularly interesting in this regard was the observation that some Corynebacterium, particularly new or novel Corynebacterium sp. can inhibit the growth of other ocular Corynebacterium as well as known pathogens of the eye.

Androgen Deprivation Therapy and the Risk of Newly Developed Dry Eye Syndrome in Patients with Prostate Cancer: A Nationwide Nested Case-Control Study in the Republic of Korea

Background: We aimed to evaluate the association between androgen deprivation therapy (ADT) and newly developed dry eye syndrome (DES) in patients with prostate cancer. Methods: A nested case-control study was conducted. From the nationwide claims database of the Republic of Korea, 125,005 patients were included in the final analysis. Cases were defined as those newly diagnosed with DES during follow-up, and 12,654 patients were identified. The cases were matched with controls in a ratio of 1:4. Odds ratios (ORs) for newly developed DES associated with ADT were estimated using conditional logistic regression. Results: After matching, 7499 cases and 29,996 controls were selected. ADT was associated with a reduced risk of newly developed DES in patients with prostate cancer compared to no ADT (OR = 0.875; 95% confidence interval, 0.825-0.927; p < 0.0001). An accumulated dose of ADT < 1 year was associated with a reduced risk of incidental DES (OR = 0.811; 95% CI, 0.751-0.875; p < 0.0001), and a duration of 1-2 years was also associated with a reduced risk (OR = 0.890; 95% CI, 0.802-0.986; p = 0.026). No association was observed with an ADT duration of ≥2 years. Conclusions: The use of ADT, especially for shorter durations (<2 years), was associated with a reduced risk of newly developed DES in S. Korean patients with prostate cancer.

Dual Role of Cutibacterium acnes: Commensal Bacterium and Pathogen in Ocular Diseases

Microbiota present around the ocular surface, encompassing the eyelid skin, the conjunctival sac, and the meibomian glands, play a significant role in various inflammatory conditions associated with the ocular surface. Cutibacterium acnes (C. acnes), formerly, Propionibacterium acnes, is one of the most predominant commensal bacteria and its relative abundance declines with aging. However, it can act as both an infectious and an immunogenic pathogen. As an infectious pathogen, C. acnes has been reported to cause late onset endophthalmitis post-cataract surgery and infectious keratitis. On the other hand, it can trigger immune responses resulting in conditions such as phlyctenules in the cornea, chalazion in the meibomian glands, and granuloma formation in ocular sarcoidosis. This review explores the role of C. acnes in ocular inflammation, specifically highlighting its implications for diagnosis and management.

Changes in the ocular surface microbiome of patients with coronavirus disease 2019 (COVID-19)

Purpose

To elucidate the reasons behind the increased incidence of ocular disease in patients with coronavirus disease 2019 (COVID-19), this study delved deeper into the specific effects of COVID-19 on patients' ocular surface microbiome (OSM) and investigated its relationship with the increased incidence of ocular disease.

Methods

In this study, conjunctival sac swabs were collected from 43 participants for 16S rRNA amplicon sequencing. The participants were categorized into three groups based on their COVID-19 status: the control group (C group) consisted of 15 participants who showed no evidence of COVID-19, the experimental group (E group) included 15 participants who tested positive for COVID-19, and the COVID-19 recovery period group (R group) comprised 13 participants.

Results

In the comparison of alpha diversity, group E had a higher Shannon, Chao1 and Goods coverage index. When comparing beta diversity, groups E and R were more similar to each other. At the phylum level, although the OSM of the three groups was dominated by Proteobacteria, Actinobacteriota, Bacteroidota and Firmicutes, the compositional proportions were significantly different. At the genus level, the dominant species in the three OSM groups were significantly different, with Pseudomonas becoming the dominant genus in groups E and R compared to group C, and the abundance of Ralstonia decreasing significantly.

Conclusion

This study provides additional evidence supporting the association between the OSM and COVID-19, which contributes to our understanding of the potential mechanisms underlying ocular symptoms and complications associated with COVID-19 in the future.

Culture- and non-culture-based approaches reveal unique features of the ocular microbiome in dry eye patients

PURPOSE

The purpose of this study was to investigate the ocular microbiome in individuals with dry eye disease and to identify features of their ocular microbiome of possible health and diagnostic significance.

METHODS

Conjunctival samples were collected from both eyes in duplicate from 91 individuals (61 dry eye, 30 healthy) and used for both culture-dependent and culture-independent analyses. Samples were either analysed using next generation sequencing (V3-V4 16S rDNA) or inoculated on a wide range of agar types and grown under a broad range of conditions to maximize recovery. Isolates were identified by partial sequencing of the 16S rDNA and rpoB genes and tested for antibiotic susceptibility. We applied a L2-regularized logistic regression model on the next generation sequencing data to investigate any potential association between severe dry eye disease and the ocular microbiome.

RESULTS

Culture-dependent analysis showed the highest number of colony forming units in healthy individuals. The majority of isolates recovered from the samples were Corynebacterium, Micrococcus sp., Staphylococcus epidermidis, and Cutibacterium acnes. Culture independent analysis revealed 24 phyla, of which Actinobacteria, Firmicutes and Proteobacteria were the most abundant. Over 405 genera were detected of which Corynebacterium was the most dominant, followed by Staphylococcus and Cutibacterium. The L2-regularized logistic regression model indicated that Blautia and Corynebacterium sp. may be associated with severe DED.

CONCLUSIONS

Our study indicates that the ocular microbiome has characteristic features in severe DED patients. Certain Corynebacterium species and Blautia are of particular interest for future studies.

Tear and Saliva Metabolomics in Evaporative Dry Eye Disease in Females

Accurate diagnosis of dry eye disease (DED) is challenging, and even today there is no gold standard biomarker of DED. Hypothesis-free global metabolomic studies of tears from DED patients have great potential to discover metabolites and pathways affected in the pathophysiology of DED, and to identify possible future biomarkers. These metabolites and biomarkers could be important for diagnosing and monitoring disease as well as for new therapeutic targets and strategies. As DED is associated with dry mouth, this study aimed to perform metabolomic analyses of tears and saliva from patients with decreased tear film break-up time but normal Schirmer test, and age-matched controls with both tear production and stability within physiological range. We applied strict inclusion criteria to reduce sampling bias in the metabolomic analyses and selected only age-matched females with Schirmer test values between 10-15 mm/5 min. The tear film analysis arm included 19 patients (with tear film break-up time 0-5 s) and 12 controls (with tear film break-up time 10-30 s), while the salivary analysis arm consisted of a subset which included 18 patients and six controls. Metabolomic analyses were performed using liquid chromatography and high-resolution mass spectrometry. Analyses using a global database search detected a total of 56 metabolites in tear samples that were significantly different between the groups. Of these, several have known associations with DED. These metabolites are present in meibum and have anti-oxidative characteristics or associations with the ocular microbiome, and altered concentrations suggest that they may play a significant role in DED associated with decreased tear film stability. In saliva, hypotaurine levels were lower among patients with tear film instability. In this pilot study, we found different levels of several metabolites in patients with decreased tear film break-up time that may have associations with DED. Future studies are required to replicate our findings and clarify the exact roles of these metabolites.