Characterization of Ocular Surface Microbial Profiles Revealed Discrepancies between Conjunctival and Corneal Microbiota
The ocular microbiome composition has only been partially characterized. Here, we used RNA-sequencing (RNA-Seq) data to assess microbial diversity in human corneal tissue. Additionally, conjunctival swab samples were examined to characterize ocular surface microbiota. Short RNA-Seq reads, obtained f...
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MDPI AG
2021-03-01
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| Series: | Pathogens |
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| Online Access: | https://www.mdpi.com/2076-0817/10/4/405 |
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| author | Anna Matysiak Michal Kabza Justyna A. Karolak Marcelina M. Jaworska Malgorzata Rydzanicz Rafal Ploski Jacek P. Szaflik Marzena Gajecka |
| author_facet | Anna Matysiak Michal Kabza Justyna A. Karolak Marcelina M. Jaworska Malgorzata Rydzanicz Rafal Ploski Jacek P. Szaflik Marzena Gajecka |
| author_sort | Anna Matysiak |
| collection | DOAJ |
| description | The ocular microbiome composition has only been partially characterized. Here, we used RNA-sequencing (RNA-Seq) data to assess microbial diversity in human corneal tissue. Additionally, conjunctival swab samples were examined to characterize ocular surface microbiota. Short RNA-Seq reads, obtained from a previous transcriptome study of 50 corneal tissues, were mapped to the human reference genome GRCh38 to remove sequences of human origin. The unmapped reads were then used for taxonomic classification by comparing them with known bacterial, archaeal, and viral sequences from public databases. The components of microbial communities were identified and characterized using both conventional microbiology and polymerase chain reaction (PCR) techniques in 36 conjunctival swabs. The majority of ocular samples examined by conventional and molecular techniques showed very similar microbial taxonomic profiles, with most of the microorganisms being classified into <i>Proteobacteria</i>, <i>Firmicutes</i>, and <i>Actinobacteria</i> phyla. Only 50% of conjunctival samples exhibited bacterial growth. The PCR detection provided a broader overview of positive results for conjunctival materials. The RNA-Seq assessment revealed significant variability of the corneal microbial communities, including fastidious bacteria and viruses. The use of the combined techniques allowed for a comprehensive characterization of the eye microbiome’s elements, especially in aspects of microbiota diversity. |
| first_indexed | 2024-03-10T12:45:48Z |
| format | Article |
| id | doaj.art-b3636329dc434f1e926db4b8a9a4a091 |
| institution | Directory Open Access Journal |
| issn | 2076-0817 |
| language | English |
| last_indexed | 2024-03-10T12:45:48Z |
| publishDate | 2021-03-01 |
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| record_format | Article |
| series | Pathogens |
| spelling | doaj.art-b3636329dc434f1e926db4b8a9a4a0912023-11-21T13:29:20ZengMDPI AGPathogens2076-08172021-03-0110440510.3390/pathogens10040405Characterization of Ocular Surface Microbial Profiles Revealed Discrepancies between Conjunctival and Corneal MicrobiotaAnna Matysiak0Michal Kabza1Justyna A. Karolak2Marcelina M. Jaworska3Malgorzata Rydzanicz4Rafal Ploski5Jacek P. Szaflik6Marzena Gajecka7Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 60-781 Poznan, PolandChair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 60-781 Poznan, PolandChair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 60-781 Poznan, PolandChair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 60-781 Poznan, PolandDepartment of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, PolandDepartment of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, PolandDepartment of Ophthalmology, Medical University of Warsaw, 00-576 Warsaw, PolandChair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 60-781 Poznan, PolandThe ocular microbiome composition has only been partially characterized. Here, we used RNA-sequencing (RNA-Seq) data to assess microbial diversity in human corneal tissue. Additionally, conjunctival swab samples were examined to characterize ocular surface microbiota. Short RNA-Seq reads, obtained from a previous transcriptome study of 50 corneal tissues, were mapped to the human reference genome GRCh38 to remove sequences of human origin. The unmapped reads were then used for taxonomic classification by comparing them with known bacterial, archaeal, and viral sequences from public databases. The components of microbial communities were identified and characterized using both conventional microbiology and polymerase chain reaction (PCR) techniques in 36 conjunctival swabs. The majority of ocular samples examined by conventional and molecular techniques showed very similar microbial taxonomic profiles, with most of the microorganisms being classified into <i>Proteobacteria</i>, <i>Firmicutes</i>, and <i>Actinobacteria</i> phyla. Only 50% of conjunctival samples exhibited bacterial growth. The PCR detection provided a broader overview of positive results for conjunctival materials. The RNA-Seq assessment revealed significant variability of the corneal microbial communities, including fastidious bacteria and viruses. The use of the combined techniques allowed for a comprehensive characterization of the eye microbiome’s elements, especially in aspects of microbiota diversity.https://www.mdpi.com/2076-0817/10/4/405corneaeye microbiomecorneal microbiotaconjunctival microbiotaRNA-Seqhost–pathogen interactions |
| spellingShingle | Anna Matysiak Michal Kabza Justyna A. Karolak Marcelina M. Jaworska Malgorzata Rydzanicz Rafal Ploski Jacek P. Szaflik Marzena Gajecka Characterization of Ocular Surface Microbial Profiles Revealed Discrepancies between Conjunctival and Corneal Microbiota Pathogens cornea eye microbiome corneal microbiota conjunctival microbiota RNA-Seq host–pathogen interactions |
| title | Characterization of Ocular Surface Microbial Profiles Revealed Discrepancies between Conjunctival and Corneal Microbiota |
| title_full | Characterization of Ocular Surface Microbial Profiles Revealed Discrepancies between Conjunctival and Corneal Microbiota |
| title_fullStr | Characterization of Ocular Surface Microbial Profiles Revealed Discrepancies between Conjunctival and Corneal Microbiota |
| title_full_unstemmed | Characterization of Ocular Surface Microbial Profiles Revealed Discrepancies between Conjunctival and Corneal Microbiota |
| title_short | Characterization of Ocular Surface Microbial Profiles Revealed Discrepancies between Conjunctival and Corneal Microbiota |
| title_sort | characterization of ocular surface microbial profiles revealed discrepancies between conjunctival and corneal microbiota |
| topic | cornea eye microbiome corneal microbiota conjunctival microbiota RNA-Seq host–pathogen interactions |
| url | https://www.mdpi.com/2076-0817/10/4/405 |
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