Comparative analysis of ocular surface tissue microbiome in human, mouse, rabbit, and guinea pig
Comparative analysis of ocular surface tissue microbiome in human, mouse, rabbit, and guinea pig
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DOI：
10.1016/j.exer.2021.108609
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发表时间：
2021-05-03
影响因子：
3.4
通讯作者：
Willcox, Mark
中科院分区：
文献类型：
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作者：
Ozkan, Jerome;Majzoub, Marwan E.;Willcox, Mark
动物模型是眼表研究的关键因素，用于研究治疗滴剂、外科植入物和感染研究。本研究对比分析了几种常用实验动物（BALB/c小鼠、新西兰大白兔和IMVS有色豚鼠）与人类结膜组织样本的微生物群落。从结膜组织中提取总DNA，利用Illumina MiSeq平台对16s rRNA基因进行测序，分析微生物群落。使用USEARCH中的UNOISE管道对序列进行质量过滤，使用GTDB数据库对序列进行分类。在下游分析之前，用decontam R软件包去除与空白提取和采样阴性对照相关的序列。人类与家兔的多样性丰富度测量值（P = 0.0124）和Shannon指数（P = 0.0002）存在差异，而人类、小鼠和豚鼠之间没有差异。人和动物的细菌群落结构存在差异（P = 0.006）。人和小鼠样品的细菌组成具有较高的相似性，均以变形菌门和厚壁菌门为主。由于细菌群落结构和组成与人类更相似，使用小鼠模型可能更适合研究由于抗生素应用等干预措施而导致的眼部微生物组变化。
Animal models are a critical element of ocular surface research for investigating therapeutic drops, surgical implants, and infection research. This study was a comparative analysis of the microbial communities on conjunctival tissue samples from humans compared to several commonly used laboratory animals (BALB/c mice, New Zealand white rabbits and IMVS colored stock guinea pigs). Microbial communities were analyzed by extracting total DNA from conjunctival tissue and sequencing the 16 S rRNA gene using the Illumina MiSeq platform. Sequences were quality filtered using the UNOISE pipeline in USEARCH and taxonomically classified using GTDB database. Sequences associated with blank extraction and sampling negative controls were removed with the decontam R software package prior to downstream analysis. There was a difference in the diversity measures of richness (P = 0.0124) and Shannon index (P = 0.0002) between humans and rabbits but not between human, mouse and guinea pigs. There was a difference between the human and any animal for bacterial community structure (P = 0.006). There was a higher degree of similarity between the bacterial composition of the human and mouse samples with each dominated by the phyla Proteobacteria and Firmicutes. The use of mouse models may be more appropriate for studies investigating changes to the ocular microbiome due to interventions such as application of antibiotics due to greater similarities in bacterial community structure and composition to humans.