PDF(Pubmed)
Abstract：
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.
摘要：
目的：利用物种丰富度和香农多样性指数表征微生物角膜炎的多样性。方法:采用角膜印模膜采集标本。所有拭子均由Biolab实验室处理和分析（V-SSN卓越级：ISO9001：2015），BiolabSrl(AscoliPiceno，意大利）。DNA提取,图书馆准备,并对所有样品进行测序。测序后，低质量和多克隆序列被Ion软件过滤掉。在这一点上,我们使用Kraken2进行角膜炎样品中的微生物群落分析。将不含核酸酶的水和实验中包含的所有试剂用作阴性对照。主要结果是T1时细菌DNA（微生物负荷）的减少，以基线值（T0）的百分比表示。丰富度和香农α多样性指标，还有Bray-Curtisβ多样性值,使用R中的phyloseq包计算。还进行了主坐标分析来解释这些指标。结果:19个样本被纳入研究。结果显示杂色物种丰富，最高记录价值超过800种。大多数样品显示的丰富度值广泛地从低于200到约600，表明角膜炎样品之间的物种计数差异很大。结论：在角膜炎感染中明显存在典型和非典型细菌门，强调了该病微生物病因学的复杂性。
