Alterations in the Ocular Surface Microbiome in Traumatic Corneal Ulcer Patients

Advanced bioengineering strategies broaden the therapeutic landscape for corneal failure

The cornea acts as the eye foremost protective layer and is essential for its focusing power. Corneal blindness may arise from physical trauma or conditions like dystrophies, keratitis, keratoconus, or ulceration. While conventional treatments involve medical therapies and donor allografts-sometimes supplemented with keratoprostheses-these options are not suitable for all corneal defects. Consequently, the development of bioartificial corneal tissue has emerged as a critical research area, aiming to address the global shortage of human cornea donors. Bioengineered corneas hold considerable promise as substitutes, with the potential to replace either specific layers or the entire thickness of damaged corneas. This review first delves into the structural anatomy of the human cornea, identifying key attributes necessary for successful corneal tissue bioengineering. It then examines various corneal pathologies, current treatments, and their limitations. Finally, the review outlines the primary approaches in corneal tissue engineering, exploring cell-free, cell-based, and scaffold-based options as three emerging strategies to address corneal failure.

Oxford Nanopore Technology-Based Identification of an Acanthamoeba castellanii Endosymbiosis in Microbial Keratitis

(1) Background: Microbial keratitis is a serious eye infection that carries a significant risk of vision loss. Acanthamoeba spp. are known to cause keratitis and their bacterial endosymbionts can increase virulence and/or treatment resistance and thus significantly worsen the course of the disease. (2) Methods and Results: In a suspected case of Acanthamoeba keratitis, in addition to Acanthamoeba spp., an endosymbiont of acanthamoebae belonging to the taxonomic order of Holosporales was detected by chance in a bacterial 16S rDNA-based pan-PCR and subsequently classified as Candidatus Paracaedibacter symbiosus through an analysis of an enlarged 16S rDNA region. We used Oxford Nanopore Technology to evaluate the usefulness of whole-genome sequencing (WGS) as a one-step diagnostics method. Here, Acanthamoeba castellanii and the endosymbiont Candidatus Paracaedibacter symbiosus could be directly detected at the species level. No other microbes were identified in the specimen. (3) Conclusions: We recommend the introduction of WGS as a diagnostic approach for keratitis to replace the need for multiple species-specific qPCRs in future routine diagnostics and to enable an all-encompassing characterisation of the polymicrobial community in one step.

Macrophage Membrane-Coated Nanoparticles for the Delivery of Natamycin Exhibit Increased Antifungal and Anti-Inflammatory Activities in Fungal Keratitis

This study aims to explore the efficacy and safety of macrophage membrane-coated nanoparticles for the delivery of natamycin (NAT) in the therapy of fungal keratitis (FK). Macrophage membranes were isolated and identified by immunofluorescence staining (IFS). NAT was encapsulated into poly(lactic-co-glycolic acid) (PLGA). Fungal stimulated macrophage membranes (M1) or unstimulated membranes (M) were separately mixed and sonicated with PLGA nanoparticles. The biocompatible nanoparticles (PLGA-NAT, PLGA-NAT@M, and PLGA-NAT@M1) were characterized with zeta-sizer analysis, transmission electron microscopy (TEM), and Western blot. Drug encapsulation and loading efficiency and the release of NAT in the nanoparticles were detected by ultraviolet spectrophotometry. The cytotoxicity, ocular surface toxicity and irritability, and systemic safety of nanoparticles with different concentrations were assessed. In vitro, we examined the antifungal properties of the nanoparticles. The eye surface retention time, drug release, and curative effects on FK were evaluated in vitro and in vivo. IFS results showed the separation of the macrophage membrane and nucleus. The prepared nanoparticles had a typical "core-shell" structure and uniform nanometer size, and the membrane proteins were retained on the membrane allowing to exert functional effects of macrophage. The loading efficiencies of PLGA-NAT@M and PLGA-NAT@M1 were 7.6 and 6.7%, respectively. The encapsulation efficiencies of PLGA-NAT@M and PLGA-NAT@M1 were 51.2 and 41.5%, respectively. PLGA-NAT@M and PLGA-NAT@M1 could gradually release NAT and reduce the clearance of the ocular surface. Macrophage membranes enhanced the antifungal activity of PLGA-NAT. Furthermore, the membrane coated with macrophage increased the biocompatibility and decreased the corneal toxicity of nanoparticles. In vivo, PLGA-NAT@M1 significantly alleviated the severity of FK. In vitro, PLGA@M and PLGA@M1 reduced the protein levels of inflammatory cytokines after fungal stimulation. The prepared PLGA-NAT@M1 has good physical properties and biosafety. It could evade ocular surface clearance, release NAT gradually, and achieve high antifungal and anti-inflammatory efficiencies to FK. Macrophage membrane-coated nanoparticles clinically have high application potential to the treatment of FK.

The Role of Pseudomonas aeruginosa in the Pathogenesis of Corneal Ulcer, Its Associated Virulence Factors, and Suggested Novel Treatment Approaches

BACKGROUND

Pseudomonas aeruginosa (P. aeruginosa), is a diverse Gram-negative pathogen commonly associated with a wide spectrum of infections. It is indicated to be the most prevalent causative agent in the development of bacterial keratitis linked with the use of contact lens. Corneal infections attributed to P. aeruginosa frequently have poor clinical outcomes necessitating lengthy and costly therapies. Therefore, this review looks at the aetiology of P. aeruginosa bacterial keratitis as well as the bacterial drivers of its virulence and the potential therapeutics on the horizon.

METHOD

A literature review with the articles used for the review searched for and retrieved from PubMed, Scopus, and Google Scholar (date last accessed 1 April 2024). The keywords used for the search criteria were "Pseudomonas and keratitis, biofilm and cornea as well as P. aeruginosa".

RESULTS

P. aeruginosa is implicated in the pathogenesis of bacterial keratitis associated with contact lens usage. To reduce the potential seriousness of these infections, a variety of contact lens-cleaning options are available. However, continuous exposure to a range of antibiotics doses, from sub-inhibitory to inhibitory, has been shown to lead to the development of resistance to both antibiotics and disinfectant. Generally, there is a global public health concern regarding the rise of difficult-to-treat infections, particularly in the case of P. aeruginosa virulence in ocular infections. This study of the basic pathogenesis of a prevalent P. aeruginosa strain is therefore implicated in keratitis. To this effect, anti-virulence methods and phage therapy are being researched and developed in response to increasing antibiotic resistance.

CONCLUSION

This review has shown P. aeruginosa to be a significant cause of bacterial keratitis, particularly among users of contact lens. It also revealed treatment options, their advantages, and their drawbacks, including prospective candidates.

Glaucoma and the Human Microbiome

PURPOSE OF REVIEW

To explore a view of the human microbiome as an interconnected, functional, dynamic system that may be linked to the pathogenesis and progression of glaucoma.

METHODS

A literature review was undertaken that included publications from 1966 to 2023.

RESULTS

Bacterial lipopolysaccharides (LPS) activate toll-like receptors (TLR) and mediate the human immune response. The LPS-TLR4 pathway is a potential avenue for the ocular, gut, and oral microbiomes to interface and/or influence ocular disease. Studies of gut dysbiosis have shown that alterations in the healthy microbiota can predispose the host to immune-mediated inflammatory and neurodegenerative conditions, while oral and ocular surface dysbiosis has been correlated with glaucoma. While developmental exposure to commensal microflora has shown to be necessary for the autoimmune and neurodegenerative responses to elevated intraocular pressure to take place, commensal bacterial products like short-chain fatty acids have regulatory effects protective against glaucoma.

SUMMARY

Alterations to human microbiotas have been associated with changes in intestinal permeability, gene regulation, immune cell differentiation, and neural functioning, which may predispose the host to glaucoma. Select microbes have been highlighted for their potential contributions to glaucoma disease progression or protection, raising the potential for microbiota-based treatment modalities. Current topical glaucoma treatments may disrupt the ocular surface microbiota, potentially having ramifications on host health. Further study of the relationships between human microbiome and glaucoma is needed.

Unique composition of ocular surface microbiome in the old patients with dry eye and diabetes mellitus in a community from Shanghai, China

BACKGROUND

This study investigates the variations in microbiome abundance and diversity on the ocular surfaces of diabetic patients suffering from dry eye within a community setting. The goal is to offer theoretical insights for the community-level prevention and treatment of dry eye in diabetic cohorts.

METHODS

Dry eye screening was performed in the Shanghai Cohort Study of Diabetic Eye Disease (SCODE) from July 15, 2021, to August 15, 2021, in the Xingjing community; this study included both a population with diabetes and a normal population. The population with diabetes included a dry eye group (DM-DE, n = 40) and a non-dry eye group (DM-NoDE, n = 39). The normal population included a dry eye group (NoDM-DE, n = 40) and a control group (control, n = 39). High-throughput sequencing of the 16 S rRNA V3-V4 region was performed on conjunctival swab from both eyes of each subject, and the composition of microbiome on the ocular surface of each group was analyzed.

RESULTS

Significant statistical differences were observed in both α and β diversity of the ocular surface microbiome among the diabetic dry eye, diabetic non-dry eye, non-diabetic dry eye, and normal control groups (P < 0.05).

CONCLUSIONS

The study revealed distinct microecological compositions on the ocular surfaces between the diabetic dry eye group and other studied groups. Firmicutes and Anoxybacillus were unique bacterial phyla and genera in the dry eye with DM group, while Actinobacteria and Corynebacterium were unique bacterial phyla and genera in the normal control group.

Longitudinal Changes of Ocular Surface Microbiome in Patients Undergoing Hemopoietic Stem Cell Transplant (HSCT)

PURPOSE

To evaluate changes in the ocular surface microbiome (OSM) between pre- and post-haemopoietic stem cell transplant (HSCT) in the same patient, and to assess the potential impact of these changes in ocular graft-versus-host disease (o)GVHD development.

METHODS

Lower fornix conjunctival swabs of 24 patients were obtained before and after HSCT and subjected to DNA extraction for amplification and sequencing of the V3-V4 regions of the bacterial 16S rRNA gene. The obtained reads were reconstructed, filtered, and clustered into zero-radius operational taxonomic units (zOTUs) at 97% identity level before taxonomic assignment, and biodiversity indexes were calculated. Transplant characteristics were recorded, and dry eye was diagnosed and staged 1-4 according to the Dry Eye WorkShop (DEWS) score.

RESULTS

No significant difference in OSM alpha diversity between pre- and post-transplant was found. A significant difference in beta diversity was observed between patients with a DEWS score of 1 versus 3 (p = 0.035). Increased corneal damage between pre- and post-HSCT was significantly associated with a decrease in alpha diversity. The changes in OSM were not associated with oGVHD, nor with any transplant parameter.

CONCLUSIONS

This preliminary study is the first study to analyse changes in the OSM before and after HSCT longitudinally. No trend in OSM biodiversity, microbial profile, or overall composition changes before and after HSCT was significant or associated with oGVHD onset. The great variability in the observed OSM profiles seems to suggest the absence of a patient-specific OSM "signature".

Temporal dynamics and composition of ocular surface microbiota in C57BL/6J mice: uncovering a 12h ultradian rhythm

Purpose

This study aimed to investigate the presence of rhythmic fluctuations in the composition, abundance, and functions of commensal core bacteria on the ocular surface of C57BL/6J mice.

Methods

Male C57BL/6J mice, aged 12 weeks, were subjected to a 12-hour light/12-hour dark cycle. Ocular surface tissue samples were collected at four time points (ZT) over a 24-hour period at six-hour intervals. The core ocular surface microbiota's oscillation cycles and frequencies were assessed using 16S rRNA gene sequencing targeting the V3-V4 region, along with the JTK_CYCLE algorithm. Functional predictions of these bacteria were conducted using PICRUSt2.

Results

Deep sequencing of the ocular surface microbiota highlighted the high abundance of commensal bacteria, with Proteobacteria, Actinobacteriota, and Firmicutes collectively constituting over 90% of the total sample abundance. Among the 22 core bacterial genera, 11 exhibited robust 12-hour rhythms, including Halomonas, Pelagibacterium, Pseudomonas, Nesterenkonia, norank_f_Hyphomonadaceae, Stenotrophomonas, Anoxybacillus, Acinetobacter, Zoogloea, Brevibacillus, and Ralstonia. Further taxonomic analysis indicated significant intra-cluster similarities and inter-cluster differences at the order, family, and genus levels during ZT0/12 and ZT6/18. Community interaction networks and functional prediction analyses revealed synchronized 12-hour rhythmic oscillations in neural, immune, metabolic, and other pathways associated with symbiotic bacteria.

Conclusion

This study demonstrates the presence of ultradian rhythmic oscillations in commensal bacteria on the ocular surface of normal C57BL/6J mice, with a 12-hour cycle. These findings suggest a crucial role for ultradian rhythms in maintaining ocular surface homeostasis in the host.

Alterations of the bacterial ocular surface microbiome are found in both eyes of horses with unilateral ulcerative keratitis

Next generation sequencing (NGS) studies in healthy equine eyes have shown a more diverse ocular surface microbiota compared to culture-based techniques. This study aimed to compare the bacterial ocular surface microbiota in both eyes of horses with unilateral ulcerative keratitis (UK) with controls free of ocular disease. Conjunctival swabs were obtained from both ulcerated eyes and unaffected eyes of 15 client-owned horses with unilateral UK following informed consent, as well as from one eye of 15 healthy horses. Genomic DNA was extracted from the swabs and sequenced on an Illumina platform using primers that target the V4 region of bacterial 16S rRNA. Data were analyzed using Quantitative Insights Into Molecular Ecology (QIIME2). The ocular surface of ulcerated eyes had significantly decreased species richness compared with unaffected fellow eyes (Chao1 q = 0.045, Observed ASVs p = 0.045) with no differences in evenness of species (Shannon q = 0.135). Bacterial community structure was significantly different between either eye of horses with UK and controls (unweighted UniFrac: control vs. unaffected, p = 0.03; control vs. ulcerated, p = 0.003; unaffected vs. ulcerated, p = 0.016). Relative abundance of the gram-positive taxonomic class, Bacilli, was significantly increased in ulcerated eyes compared with controls (q = 0.004). Relative abundance of the taxonomic family Staphylococcaceae was significantly increased in ulcerated and unaffected eyes compared with controls (q = 0.030). The results suggest the occurrence of dysbiosis in infected eyes and reveal alterations in beta diversity and taxa of unaffected fellow eyes. Further investigations are necessary to better understand the role of the microbiome in the pathophysiology of ocular surface disease.

Comparison of Conjunctival Sac Microbiome between Low and High Myopic Eyes

Microbial communities played a vital role in maintaining homeostasis of ocular surface. However, no studies explored the myopia-associated conjunctiva microbiota changes until now. In this study, conjunctival sac swab specimens were collected from 12 eyes of low myopia (LM), and 14 eyes of high myopia (HM) patients. The V3-V4 region of the 16S rRNA gene was amplified and then sequenced. Statistical analysis was performed to investigate differences in the taxonomy and diversity between two groups. Compared to LM, higher Ocular Surface Disease Index (OSDI) scores were observed in HM group. The Shannon index of the HM was lower than that of the LM group (P = 0.017). Principle coordinate analysis and Partial Least Squares Discrimination Analysis showed distinct microbiome composition between two groups. At the phylum level, there were higher relative abundances of Proteobacteria (68.27% vs 38.51%) and lower abundances of Actinobacteria (3.71% vs 9.19%) in HM, compared to LM group (P = 0.031, 0.010, respectively). At the genus level, the abundances of Acinetobacter in HM (18.16%) were significantly higher than the LM (6.52%) group (P = 0.011). Actinobacteria levels were negatively correlated with the myopic spherical equivalent and OSDI scores. Moreover, positive correlations were found between Proteobacteria levels and OSDI scores, Acinetobacter levels were positively correlated with myopic spherical equivalent and OSDI scores. In conclusion, HM Patients have bacterial microbiota imbalance in the conjunctival sac, compared with LM patients. Proteobacteria, Actinobacteria, Acinetobacter may play roles in the HM associated ocular surface irritation.

An Update on the Ocular Surface Bacterial Microbiota in Small Animals

High-throughput sequencing (HTS) techniques have revolutionized the way we understand microbial communities in both research and clinical settings and are bringing new insights into what constitutes a healthy ocular surface (and a diseased one). As more diagnostic laboratories incorporate HTS into their technique repertoire, practitioners can expect this technology to become increasingly accessible for clinical practice, potentially becoming the new standard. However, particularly regarding ophthalmic microbiota, considerable research remains to render HTS accessible and applicable.

Significantly different results in the ocular surface microbiome detected by tear paper and conjunctival swab

BACKGROUND

Great variation has been observed in the composition of the normal microbiota of the ocular surface, and therefore, in addition to differences in detection techniques, the method of collecting ocular surface specimens has a significant impact on the test results.The goal of this study is to ascertain whether the eye surface microbial communities detected by two different sampling methods are consistent and hence explore the feasibility of using tear test paper instead of conjunctival swabs to collect eye surface samples for microbial investigation.

MATERIALS AND METHODS

From July 15, 2021, to July 30, 2021, nonirritating tear test strips and conjunctival swabs of both eyes were used in 158 elderly people (> 60 years old) (79 diabetic and 79 nondiabetic adults) in Xinjing Community for high-throughput sequencing of the V3-V4 region of the 16S rRNA gene. The composition of the microbial communities in tear test paper and conjunctival swab samples was analyzed.

RESULTS

There was no statistically significant difference in Alpha diversity of ocular surface microorganisms represented by tear strip and conjunctival swab in diabetic group (P > 0.05), but there was statistically significant difference in Alpha diversity of ocular surface microorganisms detected by tear strip and conjunctival swab in nondiabetic group (P < 0.05). There were statistically significant differences in Beta diversity of ocular surface microorganisms detected by two sampling methods between diabetic group and nondiabetic group (P < 0.05). There were statistically significant differences in ocular surface microorganisms detected by tear strip method between diabetic group and nondiabetic group (P < 0.05), but there was no statistically significant difference in conjunctival swab method (P > 0.05).

CONCLUSIONS

Tear test paper and conjunctival swabs detect different compositions of microbes through two different techniques of eye surface microbe sampling. Tear test paper cannot completely replace conjunctival swab specimens for the study of microbes related to eye surface diseases.

Shotgun metagenomic sequencing analysis of ocular surface microbiome in Singapore residents with mild dry eye

The ocular surface microbiome has implications for ocular surface inflammation and immunology. Previous shotgun metagenomics analyses were performed in China, showing results that differed according to environment and age. Patients with Sjogren's syndrome were reported to have altered conjunctival microbiome, but such studies have not been done in milder dry eye. The aim of this study is to describe the conjunctival microbiome in people with mild dry eye in Singapore. Samples were collected from 14 participants with mild dry eye and 10 age-matched comparison participants recruited from Singapore National Eye Centre (SNEC) clinics. Shotgun metagenomic sequencing analysis was employed to evaluate the conjunctival microbiome composition. Proteobacteria formed the predominant phylum in the conjunctiva. As in a study from a coastal city in China, Achromobacter spp. was numerically most abundant. Compared to age-matched controls, the conjunctival microbial composition in mild dry eye was similar. Several microorganisms, including Streptococcus spp. increased in representation with age, and the abundance of Staphylococcus correlated with Schirmer readings. In addition, when cultured corneal epithelial cells were exposed to three strains of Achromobacter xylosoxidans, cytokines such as TNF-α and IL-6 were upregulated in the cell lysates and supernatants. Ourresults suggest that age is an important factor that affects composition of the conjunctival microbiome, and relative abundance of specific microorganism may vary according to the environment of the human host.

Ocular surface microbiota: Ophthalmic infectious disease and probiotics

Recently, increasing studies have emphasized the importance of commensal bacteria in humans, including microbiota in the oral cavity, gut, vagina, or skin. Ocular surface microbiota (OSM) is gaining great importance as new methodologies for bacteria DNA sequencing have been published. This review outlines the current understanding and investigation of OSM and introduces the new concept of the gut–eye axis. Moreover, we have collected current studies that focus on the relationship between ophthalmic infectious disease and alterations in the OSM or human gut microbiota. Finally, we discuss the current application of probiotics in ophthalmic infectious disease, its limitations to date, and futural directions.

Topical Glaucoma Therapy Is Associated With Alterations of the Ocular Surface Microbiome

Purpose

To investigate the ocular surface microbiome of patients with unilateral or asymmetric glaucoma being treated with topical ophthalmic medications in one eye and to determine whether microbial community changes were related to measures of ocular surface disease.

Methods

V3-V4 16S rRNA sequencing was conducted on ocular surface swabs collected from both eyes of 17 subjects: 10 patients with asymmetric/unilateral glaucoma using topical glaucoma therapy on only one eye and seven age-matched, healthy controls with no history of ocular disease or eyedrop use. Samples were categorized into three groups: patients’ glaucomatous eye treated with eyedrops, patients’ contralateral eye without eyedrops, and healthy control eyes. Comparisons were made for microbial diversity and composition, with differences in composition tested for association with ocular surface disease measures including tear meniscus height, tear break-up time, and Dry Eye Questionnaire.

Results

Samples obtained from the patients’ treated and untreated eyes both had significantly greater alpha-diversity and relative abundance of gram-negative organisms compared to healthy controls. The microbial composition of patient eyes was associated with decreased tear meniscus height and tear break-up time, whereas metagenomic predictions, based on 16S rRNA data, suggested increased synthesis of lipopolysaccharide.

Conclusions

The ocular surface microbiome of patients taking unilateral preserved glaucoma drops is characterized by a highly diverse array of gram-negative bacteria that is significantly different from the predominantly gram-positive microbes detected on healthy control eyes. These compositional differences were associated with decreased tear film measures and distinct inferred protein synthesis pathways, suggesting a potential link between microbial alterations and ocular surface inflammation.

Comparison of the ocular surface microbiota between thyroid-associated ophthalmopathy patients and healthy subjects

Purpose

Thyroid-associated ophthalmopathy (TAO) is a chronic autoimmune disease. In this study, high-throughput sequencing was used to investigate the diversity and composition of the ocular microbiota in patients with TAO.

Methods

Patients with TAO did not receive treatment for the disease and did not have exposed keratitis. Patients with TAO (TAO group) and healthy individuals (control group) were compared. All samples were swabbed at the conjunctival vault of the lower eyelid. The V3 to V4 region of the 16S rDNA was amplified using polymerase chain reaction and sequenced on the Illumina HiSeq 2500 Sequencing Platform. Statistical analysis was performed to analyze the differences between the groups and the correlation between ocular surface microbiota and the disease. The ocular surface microbiota of patients and healthy individuals were cultured.

Results

The ocular surface microbiota structure of TAO patients changed significantly. The average relative abundance of Bacillus and Brevundimonas increased significantly in the TAO group. Corynebacterium had a significantly decreased relative abundance (P<0.05). Paracoccus, Haemophilus, Lactobacillus, and Bifidobacterium were positively correlated with the severity of clinical manifestations or disease activity (P<0.05). Bacillus cereus and other opportunistic pathogens were obtained by culture from TAO patients.

Conclusions

This study found that the composition of ocular microbiota in patients with TAO was significantly different from that in healthy individuals. The ocular surface opportunistic pathogens, such as Bacillus, Brevundimonas, Paracoccus, and Haemophilus in TAO patients, increase the potential risk of ocular surface infection. The findings of this study provide a new avenue of research into the mechanism of ocular surface in TAO patients.

Clinicopathological Correlation of Microbial Keratitis and Ahead: Is There a Corneal Sepsis?

Microbial, infectious keratitis is a relevant indication for penetrating keratoplasty. The requirement for transplantation results in histopathological examination of the entire thickness of the cornea. Although the clinical diagnosis is not always possible to confirm, pathology can support diagnostic evidence of clinical presentation and pathogenesis. This is achieved with multiple methods from cytology, histochemistry, immunohistology, molecular pathology and in rare cases electron microscopy. These allow tissue-based detection of previous and parallel diseases and the responsible pathogens. The failure of satisfactory clinicopathological correlation raises the question whether a suspected pathogen was not ultimately responsible for destroyed corneal tissue. The pathogenesis of keratitis requiring transplantation is not yet completely understood, also on the experimental level. The development of such a keratitis can lead to a clinical symptomatology which can be described as "threatening organ dysfunction", a term used in sepsis research. Considering recent literature, possible correlations between sepsis and microbial keratitis and their relation to histopathology are discussed.

Effects of Sodium Hyaluronate Eye Drops With or Without Preservatives on Ocular Surface Bacterial Microbiota

Purpose

This study aimed to determine the composition and diversity of bacterial communities on the ocular surface before and after the intervention with sodium hyaluronate eye drops (with or without preservatives) using 16S rRNA gene amplicon sequencing.

Methods

Sixteen healthy adults were randomly divided into two groups and treated with sodium hyaluronate eye drops with or without preservatives for 2 weeks. The individuals used the same artificial tears in both eyes. The microbial samples from the conjunctival sac of each participant were collected at baseline and 2 weeks after intervention. The diversity and taxonomic differences among different groups before and after intervention were compared by sequencing the V3–V4 region of the 16S rRNA gene.

Results

The similarity in the binocular microbial community was high in 1 of the 16 volunteers (Bray-Curtis dissimilarity score < 0.3). At the genus level, 11 bacteria were detected in all samples with an average relative abundance of more than 1%. The bacterial community changed significantly after the use of sodium hyaluronate eye drops (with or without preservatives), whether within individuals or between individuals in different groups (P < 0.05, PERMANOVA). Different dosage forms of sodium hyaluronate eye drops significantly decreased the relative abundance of Flavobacterium caeni and Deinococcus antarcticus, respectively (P < 0.05).

Conclusions

Healthy people had a rich diversity of the bacterial microbiota on the ocular surface, but the bacterial communities between the eyes were not completely similar. Irrespective of containing benzalkonium chloride (BAC), sodium hyaluronate eye drops can change the bacterial community on the ocular surface.

Bacterial keratitis: identifying the areas of clinical uncertainty

Bacterial keratitis is a common corneal infection that is treated with topical antimicrobials. By the time of presentation there may already be severe visual loss from corneal ulceration and opacity, which may persist despite treatment. There are significant differences in the associated risk factors and the bacterial isolates between high income and low- or middle-income countries, so that general management guidelines may not be appropriate. Although the diagnosis of bacterial keratitis may seem intuitive there are multiple uncertainties about the criteria that are used, which impacts the interpretation of investigations and recruitment to clinical studies. Importantly, the concept that bacterial keratitis can only be confirmed by culture ignores the approximately 50% of cases clinically consistent with bacterial keratitis in which investigations are negative. The aetiology of these culture-negative cases is unknown. Currently, the estimation of bacterial susceptibility to antimicrobials is based on data from systemic administration and achievable serum or tissue concentrations, rather than relevant corneal concentrations and biological activity in the cornea. The provision to the clinician of minimum inhibitory concentrations of the antimicrobials for the isolated bacteria would be an important step forward. An increase in the prevalence of antimicrobial resistance is a concern, but the effect this has on disease outcomes is yet unclear. Virulence factors are not routinely assessed although they may affect the pathogenicity of bacteria within species and affect outcomes. New technologies have been developed to detect and kill bacteria, and their application to bacterial keratitis is discussed. In this review we present the multiple areas of clinical uncertainty that hamper research and the clinical management of bacterial keratitis, and we address some of the assumptions and dogma that have become established in the literature.

Conjunctival Microbiota in Patients With Type 2 Diabetes Mellitus and Influences of Perioperative Use of Topical Levofloxacin in Ocular Surgery

Background: Patients with type 2 diabetes mellitus (T2DM) are prone to ocular surface infections. We therefore characterized the conjunctival microbiome of T2DM patients and the influence of topical levofloxacin to investigate whether a dysbiosis is associated with this phenomenon.

Methods: Conjunctival microbiome of 79 T2DM patients and 113 non-diabetic controls was profiled using the 16S rDNA sequencing approach. Furthermore, 21 T2DM and 14 non-diabetic patients who underwent cataract surgeries were followed up perioperatively and the influence of pre- and post-operative levofloxacin on the conjunctival microbiome was further investigated prospectively and compared longitudinally.

Results: The α-diversity of the conjunctival microbiota was significantly higher in T2DM patients than in controls (P < 0.05). Significant differences in both composition and function of the conjunctival microbiome were identified on the ocular surface of T2DM patients as compared to non-diabetic controls. Particularly, phylum Bacteroidetes and Fusobacteria, genus Pseudomonas, Haemophilus, and Empedobacter were enriched, while genus Streptococcus was reduced on the T2DM ocular surface. Microbial genes functioning of bacterial chemotaxis was elevated in the conjunctival microbiome of T2DM patients. Furthermore, compared to the initial status, several genera including Staphylococcus were more abundant in the conjunctival microbiome of T2DM patients after 3-days use of preoperative levofloxacin topically, while no genus was more abundant in the non-diabetic follow-up group. No difference was observed between initial status and 7 days after ceasing all postoperative medications in both diabetic and non-diabetic follow-up groups.

Conclusions: The conjunctival microbiome of T2DM patients was more complex and may respond differently to topical antibiotics.

Intracellular Microbiome Profiling of the Acanthamoeba Clinical Isolates from Lens Associated Keratitis

Acanthamoeba act as hosts for various microorganisms and pathogens, causing Acanthamoeba Keratitis (AK). To investigate the association between endosymbionts and AK progression, we performed a metagenomics study to characterize the intracellular microbiome from five lenses associated with AK isolates and standard strains to characterize the role of ocular flora in AK progression. The used clinical isolates were axenic cultured from lenses associated with AK patients. AK isolates and standard controls such as 16S ribosomal RNA sequencing techniques were used for analysis. The microbiome compositions and relative abundance values were compared. The orders of Clostridiales and Bacteroidales presented major populations of intracellular microbes belonging to all isolates. Comparison of the different source isolates showed that most of the abundance in keratitis isolates came from Ruminococcus gnavus (121.0 folds), Eubacterium dolichum (54.15 folds), Roseburia faecis (24.51 folds), and Blautia producta (3.15 folds). Further analysis of the relative abundance data from keratitis isolates showed that Blautia producta was positively correlated with the disease course. In contrast, Bacteroides ovatus was found to be abundant in early-stage keratitis isolates. This study reveals the abundant anaerobic Gram-positive rods present in severe keratitis isolate and characterize the association between Acanthamoeba and ocular flora in AK progression.

Strain heterogeneity, cooccurrence network, taxonomic composition and functional profile of the healthy ocular surface microbiome

BACKGROUND

There is growing evidence indicating that the microbial communities that dwell on the human ocular surface are crucially important for ocular surface health and disease. Little is known about interspecies interactions, functional profiles, and strain heterogeneity across individuals in healthy ocular surface microbiomes.

METHODS

To comprehensively characterize the strain heterogeneity, cooccurrence network, taxonomic composition and functional profile of the healthy ocular surface microbiome, we performed shotgun metagenomics sequencing on ocular surface mucosal membrane swabs of 17 healthy volunteers.

RESULTS

The healthy ocular surface microbiome was classified into 12 phyla, 70 genera, and 140 species. The number of species in each healthy ocular surface microbiome ranged from 6 to 47, indicating differences in microbial diversity among individuals. The species with high relative abundances and high positivity rates were Streptococcus pyogenes, Staphylococcus epidermidis, Propionibacterium acnes, Corynebacterium accolens, and Enhydrobacter aerosaccus. A correlation network analysis revealed a competitive interaction of Staphylococcus epidermidis with Streptococcus pyogenes in ocular surface microbial ecosystems. Staphylococcus epidermidis and Streptococcus pyogenes revealed phylogenetic diversity among different individuals. At the functional level, the pathways related to transcription were the most abundant. We also found that there were abundant lipid and amino acid metabolism pathways in the healthy ocular surface microbiome.

CONCLUSION

This study explored the strain heterogeneity, cooccurrence network, taxonomic composition, and functional profile of the healthy ocular surface microbiome. These findings have important significance for the future development of probiotic-based eye therapeutic drugs.

Current ocular microbiome investigations limit reproducibility and reliability: Critical review and opportunities

Enthusiasm for research describing microbial communities using next-generation sequencing (NGS) has outpaced efforts to standardize methodology. Without consistency in the way research is carried out in this field, the comparison of data between studies is near impossible and the utility of results remains limited. This holds true for bacterial microbiome research of the ocular surface, and other sites, in both humans and animals. In addition, the ocular surface remains under-explored when compared to other mucosal sites. Low bacterial biomass samples from the ocular surface lead to further technical challenges. Taken together, two major problems were identified: (1) Normalization of the workflow in studies utilizing NGS to investigate the ocular surface bacteriome is necessary in order to propel the field forward and improve research impact through cross-study comparisons. (2) Current microbiome profiling technology was developed for high bacterial biomass samples (such as feces or soil), posing a challenge for analyses of samples with low bacterial load such as the ocular surface. This article reviews the challenges and limitations currently facing ocular microbiome research and provides recommendations for minimum reporting standards for veterinary ophthalmologists and clinician scientists to limit inter-study variation, improve reproducibility, and ultimately render results from these studies more impactful. The move toward normalization of methodology will expedite and maximize the potential for microbiome research to translate into meaningful discovery and tangible clinical applications.