Overview of Microorganisms: Bacterial Microbiome, Mycobiome, Virome Identified Using Next-Generation Sequencing, and Their Application to Ophthalmic Diseases
This review outlines technological advances in pathogen identification and describes the development and evolution of next-generation sequencers that can be applied to the ocular microbiome. Traditional methods such as culture and PCR have limitations in detecting the full spectrum of resident micro...
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MDPI AG
2025-06-01
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| Online Access: | https://www.mdpi.com/2076-2607/13/6/1300 |
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| author | Kazunobu Asao Noriyasu Hashida |
| author_facet | Kazunobu Asao Noriyasu Hashida |
| author_sort | Kazunobu Asao |
| collection | DOAJ |
| description | This review outlines technological advances in pathogen identification and describes the development and evolution of next-generation sequencers that can be applied to the ocular microbiome. Traditional methods such as culture and PCR have limitations in detecting the full spectrum of resident microorganisms, prompting a transition toward metagenomic analysis. As microbiome research expands across body systems, the comprehensive identification of ocular bacteria, fungi, and viruses has become possible. The commensal ocular microbiome may influence disease development through changes in the immune system and ocular environment. Next-generation sequencing enables detailed microbial profiling, aiding in disease diagnosis and treatment selection. Alterations in the microbiome may also induce metabolic changes, offering insights into novel treatment methods. This review outlines the evolution of next-generation sequencing technology, summarizes current knowledge of microorganisms found on the ocular surface and in intraocular fluid, and discusses future challenges and prospects. However, the large volume of microbiome data obtained must be interpreted with caution due to possible analytical biases. Furthermore, determining whether the microbiome is truly pathogenic requires comprehensive interpretation beyond the clinical findings and results of traditional identification methods. |
| format | Article |
| id | doaj-art-65e6fcdb755c42529eb8bb8d62202e2b |
| institution | DOAJ |
| issn | 2076-2607 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj-art-65e6fcdb755c42529eb8bb8d62202e2b2025-08-20T03:16:23ZengMDPI AGMicroorganisms2076-26072025-06-01136130010.3390/microorganisms13061300Overview of Microorganisms: Bacterial Microbiome, Mycobiome, Virome Identified Using Next-Generation Sequencing, and Their Application to Ophthalmic DiseasesKazunobu Asao0Noriyasu Hashida1Department of Ophthalmology, Osaka University Graduate School of Medicine, Osaka 565-0871, JapanDepartment of Ophthalmology, Osaka University Graduate School of Medicine, Osaka 565-0871, JapanThis review outlines technological advances in pathogen identification and describes the development and evolution of next-generation sequencers that can be applied to the ocular microbiome. Traditional methods such as culture and PCR have limitations in detecting the full spectrum of resident microorganisms, prompting a transition toward metagenomic analysis. As microbiome research expands across body systems, the comprehensive identification of ocular bacteria, fungi, and viruses has become possible. The commensal ocular microbiome may influence disease development through changes in the immune system and ocular environment. Next-generation sequencing enables detailed microbial profiling, aiding in disease diagnosis and treatment selection. Alterations in the microbiome may also induce metabolic changes, offering insights into novel treatment methods. This review outlines the evolution of next-generation sequencing technology, summarizes current knowledge of microorganisms found on the ocular surface and in intraocular fluid, and discusses future challenges and prospects. However, the large volume of microbiome data obtained must be interpreted with caution due to possible analytical biases. Furthermore, determining whether the microbiome is truly pathogenic requires comprehensive interpretation beyond the clinical findings and results of traditional identification methods.https://www.mdpi.com/2076-2607/13/6/1300ocularmicrobiomemycobiomeviromenext-generation sequencinginfectious diseases |
| spellingShingle | Kazunobu Asao Noriyasu Hashida Overview of Microorganisms: Bacterial Microbiome, Mycobiome, Virome Identified Using Next-Generation Sequencing, and Their Application to Ophthalmic Diseases Microorganisms ocular microbiome mycobiome virome next-generation sequencing infectious diseases |
| title | Overview of Microorganisms: Bacterial Microbiome, Mycobiome, Virome Identified Using Next-Generation Sequencing, and Their Application to Ophthalmic Diseases |
| title_full | Overview of Microorganisms: Bacterial Microbiome, Mycobiome, Virome Identified Using Next-Generation Sequencing, and Their Application to Ophthalmic Diseases |
| title_fullStr | Overview of Microorganisms: Bacterial Microbiome, Mycobiome, Virome Identified Using Next-Generation Sequencing, and Their Application to Ophthalmic Diseases |
| title_full_unstemmed | Overview of Microorganisms: Bacterial Microbiome, Mycobiome, Virome Identified Using Next-Generation Sequencing, and Their Application to Ophthalmic Diseases |
| title_short | Overview of Microorganisms: Bacterial Microbiome, Mycobiome, Virome Identified Using Next-Generation Sequencing, and Their Application to Ophthalmic Diseases |
| title_sort | overview of microorganisms bacterial microbiome mycobiome virome identified using next generation sequencing and their application to ophthalmic diseases |
| topic | ocular microbiome mycobiome virome next-generation sequencing infectious diseases |
| url | https://www.mdpi.com/2076-2607/13/6/1300 |
| work_keys_str_mv | AT kazunobuasao overviewofmicroorganismsbacterialmicrobiomemycobiomeviromeidentifiedusingnextgenerationsequencingandtheirapplicationtoophthalmicdiseases AT noriyasuhashida overviewofmicroorganismsbacterialmicrobiomemycobiomeviromeidentifiedusingnextgenerationsequencingandtheirapplicationtoophthalmicdiseases |