Alterations in the Ocular Surface Fungal Microbiome in Fungal Keratitis Patients

Prashanthi, Gumpili Sai; Jayasudha, Rajagopalaboopathi; Chakravarthy, Sama Kalyana; Padakandla, Shalem Raj; SaiAbhilash, Chinthala Reddy; Sharma, Savitri; Bagga, Bhupesh; Murthy, Somasheila I; Garg, Prashant; Shivaji, Sisinthy

doi:10.3390/microorganisms7090309

Cited by 47 publications

(53 citation statements)

References 50 publications

(73 reference statements)

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“…Studies based on 16S RNA sequencing and traditional culture methods have found that human OSs are colonized by a wide variety of microorganisms. Although recent studies have investigated the composition and changes in conjunctival microbiome profiles of individuals with fungal keratitis and bacterial keratitis, 12,13 a comprehensive study of OS microbiome changes associated with keratitis using shotgun metagenomics is lacking. Whether the ocular microbiome is associated with OS infections also remains unknown.…”

Section: Discussionmentioning

confidence: 99%

“…Although the composition of the ocular microbiome is still under dispute, data have become available to indicate the distribution characteristics of OS microbial communities in health and disease states. Recent studies have demonstrated the potential relationship between changes in the OS microbiome and some conditions, such as trachoma, 11 fungal keratitis, 12,13 ulcerative bacterial keratitis, 14 conjunctivitis, 15 dry eye, 16 mesangial gland dysfunction, 17,18 blepharitis, 19 and contact lens wearing. 20,21 However, all of these studies were based on 16S rRNA gene sequencing, which, despite contributing to understanding the potential diversity of the OS bacterial flora, has limited ability to characterize nonbacterial components and functional profiles of the OS microbiome.…”

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confidence: 99%

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Alterations in the Ocular Surface Microbiome in Traumatic Corneal Ulcer Patients

Kang

Zhang

et al. 2020

Invest. Ophthalmol. Vis. Sci.

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PURPOSE. Corneal ulcers are a common eye inflammatory disease that can cause visual impairment or even blindness if not treated promptly. Ocular trauma is a major risk factor for corneal ulcers, and corneal trauma in agricultural work can rapidly progress to corneal ulcers. This study aims to evaluate the changes in the ocular surface (OS) microbiome of patients with traumatic corneal ulcer (TCU). METHODS. Among 20 healthy control (HC) subjects and 22 patients with TCU, 42 eyes were examined to investigate the OS microbial flora using metagenomic shotgun sequencing. RESULTS. At the taxonomic composition level, our findings showed that dysbiosis (alterations in richness and community structure) occurs in the OS microbiome of patients with TCU. Notably, Pseudomonas was present at a greater than 30% relative abundance in all individuals in the TCU group. At the species level, the abundance of Pseudomonas fluorescens and Pseudomonas aeruginosa was significantly elevated in the TCU group compared to the HC group. At the functional level, we identified significant differences in the HC and TCU groups. We observed that inflammation-related pathways involved in bacterial chemotaxis, flagellar assembly, and biofilm formation were significantly more abundant in the TCU group. Besides, the pathways related to biosynthesis, degradation, and metabolism were also increased significantly in the TCU group. CONCLUSIONS. These findings indicate an altered OS microbiome in the affected eyes of patients with TCU. Further research is needed to determine whether these alterations contribute to the pathogenesis of TCU or impact disease progression.

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Section: Discussionmentioning

confidence: 99%

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confidence: 99%

Alterations in the Ocular Surface Microbiome in Traumatic Corneal Ulcer Patients

Kang

Zhang

et al. 2020

Invest. Ophthalmol. Vis. Sci.

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“…Therefore analysis of the ocular surface mycobiome from all the participants may be required for comparison with vitreous. Since in the present study the ocular surface samples were not collected, the data of the present study was compared with the ocular surface mycobiome from published literature [9][10][11]. The mycobiome from blood in control and PFR group participants could have enhanced the understanding of the mycobiome penetration into the eye.…”

Section: Plos Onementioning

confidence: 99%

Mycobiome changes in the vitreous of post fever retinitis patients

et al. 2020

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Fungi have been associated with various diseases of the eye like keratitis, uveitis and endophthalmitis. Despite this fact, fungal microbiome (mycobiome) studies compared to the bacterial microbiome studies have remained neglected. In the present study, using metagenomic sequencing, the mycobiomes of the vitreous of healthy control individuals (VC, n = 15) and individuals with post fever retinitis + non-PFR uveitis (PFR+, n = 9) were analysed and compared. The results indicated that Ascomycota was the most predominant phylum in both VC and PFR+ groups. Further, at the genera level it was observed that the abundance of 17 fungal genera were significantly different in post fever retinitis (PFR, n = 6) group compared to control group. Of these 17 genera, it was observed that 14 genera were relatively more abundant in PFR group and the remaining 3 genera in the VC group. Genus Saccharomyces, a commensal of the gut and skin, was predominantly present in the vitreous of both the cohorts, however it was significantly less abundant in PFR group. Further, significant increase in the genera that have a pathogenic interaction with the host were observed in PFR group. On the whole the mycobiome in both the groups differed significantly and formed two distinct clusters in the heatmap and Principal co-ordinate analysis. These results demonstrate significant changes in the mycobiome from the vitreous of post fever retinitis patients compared to healthy controls thus implying that dysbiotic changes in the fungal vitreous microbiome are associated with PFR.

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“…Negative correlations between OTUs occur is all groups at time T1, but they are remarkably more frequent in both selection regimes within the skin microbiome networks. In many studies, the increase of negative correlations in networks was associated to microbiota dysbiosis in several contexts of human lung infectious diseases [63][64][65], in dog's gut (Vázquez-Baeza et al 2016) and macaque model of tuberculosis for instance. Furthermore, network connectivity under stress was maintained by rare OTUs, while abundant OTUs were mainly composed of opportunistic invaders such as Mycoplasma and other genera related to sh pathogens like Aeromonas, Pseudomonas and Flavobacterium [66,67].…”

Section: Discussionmentioning

confidence: 99%

The yellow perch (Perca flavescens) microbiome revealed resistance to colonisation mostly associated with neutralism driven by rare taxa under cadmium disturbance

Cheaib

Seghouani

Llewellyn

et al. 2020

Preprint

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Background: Disentangling the dynamics of microbial interactions within communities improves our comprehension of metacommunity assembly of microbiota during host development and under perturbations. To assess the impact of stochastic variation of neutral processes on microbiota structure and composition under disturbance, two types of microbial habitats, free-living (water), and host-associated (skin and gut) were experimentally exposed to either a constant or gradual selection regime exerted by two sublethal cadmium chloride dosages (CdCl2). Yellow Perch (Perca flavescens) was used as a piscivorous ecotoxicological model. Using 16S rDNA gene based metataxonomics, quantitative diversity metrics of water, skin and gut microbial communities were characterized along with development and across experimental conditions. Results: After 30 days, constant and gradual selection regimes drove a significant alpha diversity increase for both skin and gut microbiota. In the skin, pervasive negative correlations between taxa in both selection regimes in addition to the taxonomic convergence with the environmental bacterial community, suggest a loss of colonisation resistance resulting in the dysbiosis of yellow perch microbiota. Furthermore, the network connectivity in gut microbiome was exclusively maintained by rare (low abundance) OTUs, while most abundant OTUs were mainly composed of opportunistic invaders such as Mycoplasma and other genera related to fish pathogens such as Flavobacterium. Finally, the mathematical modelling of community assembly using both non-linear least squares models (NLS) based estimates of migration rates and normalized stochasticity ratios (NST) based beta-diversity distances suggested neutral processes drove by taxonomic drift in host and water communities for almost all treatments. The NLS models predicted higher demographic stochasticity in the cadmium-free host and water microbiomes, however, NST models suggested higher ecological stochasticity under perturbations. Conclusions: Neutral models agree that water and host-microbiota assembly promoted by rare taxa have evolved predominantly under neutral processes with potential involvement of deterministic forces sourced from host filtering and cadmium selection. The early signals of perturbations in the skin microbiome revealed antagonistic interactions by a preponderance of negative correlations in the co-abundance networks. Our findings enhance our understanding of community assembly host-associated and free-living under anthropogenic selective pressure.

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Alterations in the Ocular Surface Fungal Microbiome in Fungal Keratitis Patients

Cited by 47 publications

References 50 publications

Alterations in the Ocular Surface Microbiome in Traumatic Corneal Ulcer Patients

Alterations in the Ocular Surface Microbiome in Traumatic Corneal Ulcer Patients

Mycobiome changes in the vitreous of post fever retinitis patients

The yellow perch (Perca flavescens) microbiome revealed resistance to colonisation mostly associated with neutralism driven by rare taxa under cadmium disturbance

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