Relative and Quantitative Characterization of the Bovine Bacterial Ocular Surface Microbiome in the Context of Suspected Ocular Squamous Cell Carcinoma
The ocular surface microbiome is altered in certain disease states. The aim of this study was to characterize the bovine bacterial ocular surface microbiome (BBOSM) in the context of ocular squamous cell carcinoma (OSCC). The conjunctiva of normal (<i>n</i> = 28) and OSCC (<i>n<...
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MDPI AG
2023-06-01
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| Online Access: | https://www.mdpi.com/2076-2615/13/12/1976 |
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| author | Hannah B. Gafen Chin-Chi Liu Nikole E. Ineck Clare M. Scully Melanie A. Mironovich Lauren Guarneri Christopher M. Taylor Meng Luo Marina L. Leis Erin M. Scott Renee T. Carter Andrew C. Lewin |
| author_facet | Hannah B. Gafen Chin-Chi Liu Nikole E. Ineck Clare M. Scully Melanie A. Mironovich Lauren Guarneri Christopher M. Taylor Meng Luo Marina L. Leis Erin M. Scott Renee T. Carter Andrew C. Lewin |
| author_sort | Hannah B. Gafen |
| collection | DOAJ |
| description | The ocular surface microbiome is altered in certain disease states. The aim of this study was to characterize the bovine bacterial ocular surface microbiome (BBOSM) in the context of ocular squamous cell carcinoma (OSCC). The conjunctiva of normal (<i>n</i> = 28) and OSCC (<i>n</i> = 10) eyes of cows aged 2 to 13 years from two farms in Louisiana and Wyoming were sampled using individual sterile swabs. DNA extraction followed by 16S ribosomal ribonucleic acid (rRNA) gene sequencing and real-time polymerase chain reaction (RT-PCR) were performed to, respectively, assess the relative and absolute BBOSM. Discriminant analysis (DA) was performed using RT-PCR data, and relative abundance analysis was performed using 16S rRNA gene sequencing data. The 11 most abundant phyla in both normal and OSCC-affected cows were identified using 16S rRNA gene sequencing analysis. The relative abundance of Euryarchaeota was found to be significantly lower (<i>p</i> = 0.0372) in OSCC eyes compared to normal eyes. Relative abundance differences within and between geographic locations were also identified. Quadratic DA categorized samples as OSCC or normal with 100% sensitivity and 83.3–100% specificity. Relative abundance analysis identified relative BBOSM phylum alterations in OSCC. Quadratic DA can be used to accurately categorize BBOSM from normal and OSCC ocular surface samples. |
| first_indexed | 2024-03-11T02:51:02Z |
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| institution | Directory Open Access Journal |
| issn | 2076-2615 |
| language | English |
| last_indexed | 2024-03-11T02:51:02Z |
| publishDate | 2023-06-01 |
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| series | Animals |
| spelling | doaj.art-bed096d5be024f19af1b33d801747f7e2023-11-18T08:58:51ZengMDPI AGAnimals2076-26152023-06-011312197610.3390/ani13121976Relative and Quantitative Characterization of the Bovine Bacterial Ocular Surface Microbiome in the Context of Suspected Ocular Squamous Cell CarcinomaHannah B. Gafen0Chin-Chi Liu1Nikole E. Ineck2Clare M. Scully3Melanie A. Mironovich4Lauren Guarneri5Christopher M. Taylor6Meng Luo7Marina L. Leis8Erin M. Scott9Renee T. Carter10Andrew C. Lewin11Department of Veterinary Clinical Sciences, Louisiana State University, Baton Rouge, LA 70803, USADepartment of Veterinary Clinical Sciences, Louisiana State University, Baton Rouge, LA 70803, USADepartment of Veterinary Clinical Sciences, Louisiana State University, Baton Rouge, LA 70803, USADepartment of Veterinary Clinical Sciences, Louisiana State University, Baton Rouge, LA 70803, USADepartment of Veterinary Clinical Sciences, Louisiana State University, Baton Rouge, LA 70803, USADepartment of Pathobiological Sciences, Louisiana State University, Baton Rouge, LA 70803, USADepartment of Microbiology, Immunology, and Parasitology, School of Medicine, Louisiana State University, New Orleans, LA 70112, USADepartment of Microbiology, Immunology, and Parasitology, School of Medicine, Louisiana State University, New Orleans, LA 70112, USADepartment of Small Animal Clinical Sciences, Western College of Veterinary Medicine, Saskatoon, SK S7N 5B4, CanadaDepartment of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USADepartment of Veterinary Clinical Sciences, Louisiana State University, Baton Rouge, LA 70803, USADepartment of Veterinary Clinical Sciences, Louisiana State University, Baton Rouge, LA 70803, USAThe ocular surface microbiome is altered in certain disease states. The aim of this study was to characterize the bovine bacterial ocular surface microbiome (BBOSM) in the context of ocular squamous cell carcinoma (OSCC). The conjunctiva of normal (<i>n</i> = 28) and OSCC (<i>n</i> = 10) eyes of cows aged 2 to 13 years from two farms in Louisiana and Wyoming were sampled using individual sterile swabs. DNA extraction followed by 16S ribosomal ribonucleic acid (rRNA) gene sequencing and real-time polymerase chain reaction (RT-PCR) were performed to, respectively, assess the relative and absolute BBOSM. Discriminant analysis (DA) was performed using RT-PCR data, and relative abundance analysis was performed using 16S rRNA gene sequencing data. The 11 most abundant phyla in both normal and OSCC-affected cows were identified using 16S rRNA gene sequencing analysis. The relative abundance of Euryarchaeota was found to be significantly lower (<i>p</i> = 0.0372) in OSCC eyes compared to normal eyes. Relative abundance differences within and between geographic locations were also identified. Quadratic DA categorized samples as OSCC or normal with 100% sensitivity and 83.3–100% specificity. Relative abundance analysis identified relative BBOSM phylum alterations in OSCC. Quadratic DA can be used to accurately categorize BBOSM from normal and OSCC ocular surface samples.https://www.mdpi.com/2076-2615/13/12/1976squamous cell carcinomamicrobiomereal-time PCRsequencingbovinediscriminant analysis |
| spellingShingle | Hannah B. Gafen Chin-Chi Liu Nikole E. Ineck Clare M. Scully Melanie A. Mironovich Lauren Guarneri Christopher M. Taylor Meng Luo Marina L. Leis Erin M. Scott Renee T. Carter Andrew C. Lewin Relative and Quantitative Characterization of the Bovine Bacterial Ocular Surface Microbiome in the Context of Suspected Ocular Squamous Cell Carcinoma Animals squamous cell carcinoma microbiome real-time PCR sequencing bovine discriminant analysis |
| title | Relative and Quantitative Characterization of the Bovine Bacterial Ocular Surface Microbiome in the Context of Suspected Ocular Squamous Cell Carcinoma |
| title_full | Relative and Quantitative Characterization of the Bovine Bacterial Ocular Surface Microbiome in the Context of Suspected Ocular Squamous Cell Carcinoma |
| title_fullStr | Relative and Quantitative Characterization of the Bovine Bacterial Ocular Surface Microbiome in the Context of Suspected Ocular Squamous Cell Carcinoma |
| title_full_unstemmed | Relative and Quantitative Characterization of the Bovine Bacterial Ocular Surface Microbiome in the Context of Suspected Ocular Squamous Cell Carcinoma |
| title_short | Relative and Quantitative Characterization of the Bovine Bacterial Ocular Surface Microbiome in the Context of Suspected Ocular Squamous Cell Carcinoma |
| title_sort | relative and quantitative characterization of the bovine bacterial ocular surface microbiome in the context of suspected ocular squamous cell carcinoma |
| topic | squamous cell carcinoma microbiome real-time PCR sequencing bovine discriminant analysis |
| url | https://www.mdpi.com/2076-2615/13/12/1976 |
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