TY - JOUR
T1 - Infectious Keratitis
T2 - Characterization of Microbial Diversity through Species Richness and Shannon Diversity Index
AU - Schiano-Lomoriello, Domenico
AU - Abicca, Irene
AU - Contento, Laura
AU - Gabrielli, Federico
AU - Alfonsi, Cinzia
AU - Di Pietro, Fabio
AU - Papa, Filomena Tiziana
AU - Ballesteros-Sánchez, Antonio
AU - Sánchez-González, José María
AU - Rocha-De-Lossada, Carlos
AU - Mazzotta, Cosimo
AU - Giannaccare, Giuseppe
AU - Bonzano, Chiara
AU - Borroni, Davide
N1 - Publisher Copyright:
© 2024 by the authors.
PY - 2024/4
Y1 - 2024/4
N2 - Purpose: 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.
AB - Purpose: 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.
KW - metagenomics
KW - microbial diversity
KW - microbial keratitis
KW - microbiome
KW - Proteobacteria
UR - http://www.scopus.com/inward/record.url?scp=85191310765&partnerID=8YFLogxK
U2 - 10.3390/biom14040389
DO - 10.3390/biom14040389
M3 - Article
C2 - 38672407
AN - SCOPUS:85191310765
SN - 2218-273X
VL - 14
JO - Biomolecules
JF - Biomolecules
IS - 4
M1 - 389
ER -