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Objective <p>The understanding of the ocular microbiota, particularly in fungal keratitis (FK), is evolving with advancements in high-throughput sequencing technologies. Traditional culture-based methods may not fully capture the microbial diversity present in keratitis, highlighting the need for more comprehensive approaches to explore microbial dysbiosis in corneal infections. This study aimed to reveal the dysbacteriosis of the ocular fungal microbiome associated with FK.</p> Methods <p>We analysed 105 samples, including conjunctival swabs from healthy eyes (HE) and conjunctival swabs (SW), as well as corneal scrapings (SC), from FK eyes. Positive results were observed in 58 samples, and detailed taxonomic categorization was carried out across multiple levels—phylum, class, order, family, and genus—using high-throughput ITS sequencing. Alpha and beta diversity indices were computed, and interaction networks at the genus level were predicted to elucidate changes in microbial communities. The analyses also included assessments of functional groups within the fungal microbiome.</p> Results <p>Among the samples, the HE, SW, and SC groups presented differences in positivity rates and diversity indices. Compared with HE eyes, infected eyes (SW and SC) presented significantly greater Good’s coverage estimator and lower Chao1, Shannon, and Simpson diversity indices, indicating reduced species richness and evenness. At multiple taxonomic levels, various taxa were significantly downregulated in the FK eyes. Functional analyses revealed differences, notably, an increase in the number of litter saprotrophs in FK eyes. <i>Ascomycota</i> and <i>Basidiomycota</i> were identified as core phyla in the ocular microbiota interaction network.</p> Conclusion <p>Fungal keratitis significantly alters the ocular surface microbiome, which is characterized by decreased microbial richness and evenness. High-throughput sequencing revealed a complex interaction network with significant variability between healthy and infected eyes. Additionally, these findings suggest potential benefits from early and aggressive debridement in managing FK due to its impact on functional microbial groups.</p>

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Alterations in ocular fungal microbiota in patients with fungal keratitis: a comparative study from coastal regions of Eastern China

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年5月27日

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  • Xudong Zhao,
  • Zhichao Ren,
  • Wenfeng Li,
  • Qing Liu,
  • Yanling Dong,
  • Yusen Huang

摘要

Objective

The understanding of the ocular microbiota, particularly in fungal keratitis (FK), is evolving with advancements in high-throughput sequencing technologies. Traditional culture-based methods may not fully capture the microbial diversity present in keratitis, highlighting the need for more comprehensive approaches to explore microbial dysbiosis in corneal infections. This study aimed to reveal the dysbacteriosis of the ocular fungal microbiome associated with FK.

Methods

We analysed 105 samples, including conjunctival swabs from healthy eyes (HE) and conjunctival swabs (SW), as well as corneal scrapings (SC), from FK eyes. Positive results were observed in 58 samples, and detailed taxonomic categorization was carried out across multiple levels—phylum, class, order, family, and genus—using high-throughput ITS sequencing. Alpha and beta diversity indices were computed, and interaction networks at the genus level were predicted to elucidate changes in microbial communities. The analyses also included assessments of functional groups within the fungal microbiome.

Results

Among the samples, the HE, SW, and SC groups presented differences in positivity rates and diversity indices. Compared with HE eyes, infected eyes (SW and SC) presented significantly greater Good’s coverage estimator and lower Chao1, Shannon, and Simpson diversity indices, indicating reduced species richness and evenness. At multiple taxonomic levels, various taxa were significantly downregulated in the FK eyes. Functional analyses revealed differences, notably, an increase in the number of litter saprotrophs in FK eyes. Ascomycota and Basidiomycota were identified as core phyla in the ocular microbiota interaction network.

Conclusion

Fungal keratitis significantly alters the ocular surface microbiome, which is characterized by decreased microbial richness and evenness. High-throughput sequencing revealed a complex interaction network with significant variability between healthy and infected eyes. Additionally, these findings suggest potential benefits from early and aggressive debridement in managing FK due to its impact on functional microbial groups.