Infectious Keratitis : Characterization of Microbial Diversity through Species Richness and Shannon Diversity Index

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dc.contributor.authorSchiano-Lomoriello, Domenico
dc.contributor.authorAbicca, Irene
dc.contributor.authorContento, Laura
dc.contributor.authorGabrielli, Federico
dc.contributor.authorAlfonsi, Cinzia
dc.contributor.authorDi Pietro, Fabio
dc.contributor.authorPapa, Filomena Tiziana
dc.contributor.authorBallesteros-Sánchez, Antonio
dc.contributor.authorSánchez-González, José María
dc.contributor.authorRocha-De-Lossada, Carlos
dc.contributor.authorMazzotta, Cosimo
dc.contributor.authorGiannaccare, Giuseppe
dc.contributor.authorBonzano, Chiara
dc.contributor.authorBorroni, Davide
dc.contributor.institutionDepartment of Ophthalmology
dc.date.accessioned2025-01-02T09:25:02Z
dc.date.available2025-01-02T09:25:02Z
dc.date.issued2024-04
dc.descriptionPublisher Copyright: © 2024 by the authors.
dc.description.abstractPurpose: To characterize microbial keratitis diversity utilizing species richness and Shannon Diversity Index. Methods: Corneal impression membrane was used to collect samples. All swabs were processed and analyzed by Biolab Laboratory (level V—SSN Excellence: ISO 9001:2015), Biolab Srl (Ascoli Piceno, Italy). DNA extraction, library preparation, and sequencing were performed in all samples. After sequencing, low-quality and polyclonal sequences were filtered out by the Ion software. At this point, we employed Kraken2 for microbial community analysis in keratitis samples. Nuclease-free water and all the reagents included in the experiment were used as a negative control. The primary outcome was the reduction in bacterial DNA (microbial load) at T1, expressed as a percentage of the baseline value (T0). Richness and Shannon alpha diversity metrics, along with Bray–Curtis beta diversity values, were calculated using the phyloseq package in R. Principal coordinate analysis was also conducted to interpret these metrics. Results: 19 samples were included in the study. The results exhibited a motley species richness, with the highest recorded value surpassing 800 species. Most of the samples displayed richness values ranging broadly from under 200 to around 600, indicating considerable variability in species count among the keratitis samples. Conclusions: A significant presence of both typical and atypical bacterial phyla in keratitis infections, underlining the complexity of the disease’s microbial etiology.en
dc.description.statusPeer reviewed
dc.format.extent892348
dc.identifier.citationSchiano-Lomoriello, D, Abicca, I, Contento, L, Gabrielli, F, Alfonsi, C, Di Pietro, F, Papa, F T, Ballesteros-Sánchez, A, Sánchez-González, J M, Rocha-De-Lossada, C, Mazzotta, C, Giannaccare, G, Bonzano, C & Borroni, D 2024, 'Infectious Keratitis : Characterization of Microbial Diversity through Species Richness and Shannon Diversity Index', Biomolecules, vol. 14, no. 4, 389. https://doi.org/10.3390/biom14040389
dc.identifier.doi10.3390/biom14040389
dc.identifier.issn2218-273X
dc.identifier.urihttps://dspace.rsu.lv/jspui/handle/123456789/16991
dc.identifier.urlhttp://www.scopus.com/inward/record.url?scp=85191310765&partnerID=8YFLogxK
dc.language.isoeng
dc.relation.ispartofBiomolecules
dc.rightsinfo:eu-repo/semantics/openAccess
dc.subjectmetagenomics
dc.subjectmicrobial diversity
dc.subjectmicrobial keratitis
dc.subjectmicrobiome
dc.subjectProteobacteria
dc.subject3.2 Clinical medicine
dc.subject1.1. Scientific article indexed in Web of Science and/or Scopus database
dc.subjectBiochemistry
dc.subjectMolecular Biology
dc.titleInfectious Keratitis : Characterization of Microbial Diversity through Species Richness and Shannon Diversity Indexen
dc.type/dk/atira/pure/researchoutput/researchoutputtypes/contributiontojournal/article

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