This study aimed to characterize the taxonomic composition of intraradicular multispecies biofilms (IMBs) formed in situ in a model to reproduce clinical conditions. Twelve palatal roots of maxillary molars had its canals prepared. Two roots were randomly selected to sterility control. Ten intraoral prosthetic appliances with lateral slots were fabricated. The roots were positioned in the slots with the canal access open to the oral cavity. Eight volunteers wore the appliance for 21 days, and two wore it at two different time points. One root from each appliance was removed and stored at −20°C until DNA extraction and sequencing (n = 10). Biofilm was analyzed using next‐generation sequencing and bioinformatics. The V4 hyper‐variable region of the 16SrRNA gene was amplified and sequenced. For data analyses, the mothur pipeline was used for 16SrRNA processing, and subsequent analyses of the sequence dataset were performed in R using the MicrobiomeAnalyst R package. The taxonomy‐based analysis of bacterial communities identified 562 operational taxonomic units (OTUs), which belonged to 93 genera, 44 families, and 8 phyla. Bacterial colonization was different for each biofilm, and samples did not have the same group of bacteria. Alpha and beta diversity analysis revealed some general patterns of sample clustering. A core microbiome of prevalent OTUs and genera was identified. IMBs were heterogeneous when analyzed individually, but some diversity patterns were found after sample clustering. The experimental model seemed to reproduce the actual biofilm composition in endodontic infections, which suggests that it may be used to evaluate disinfection protocols.

中文翻译：

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原位形成的根内生物膜的微生物组成和多样性：基于下一代测序的新概念

本研究旨在表征在重现临床状况的模型中原位形成的根内多物种生物膜（IMB）的分类组成。上颌磨牙的十二根腭根已准备好根管。随机选择两个根进行不育控制。制造了十个带有侧槽的口内假肢矫治器。将根部放置在槽中，使根管进入口腔。八名志愿者佩戴该设备 21 天，其中两名志愿者在两个不同的时间点佩戴该设备。从每个器具中取出一根根并储存在-20°C，直到 DNA 提取和测序（n= 10）。使用下一代测序和生物信息学对生物膜进行分析。 16SrRNA 基因的 V4 高变区被扩增并测序。对于数据分析，mothur 管道用于 16SrRNA 处理，随后使用 MicrobiomeAnalyst R 软件包在 R 中对序列数据集进行分析。基于分类学的细菌群落分析确定了 562 个操作分类单元 (OTU)，分别属于 93 个属、44 个科和 8 个门。每个生物膜的细菌定植都不同，并且样品中不存在同一组细菌。 Alpha 和 Beta 多样性分析揭示了样本聚类的一些一般模式。确定了流行 OTU 和属的核心微生物组。单独分析时，IMB 是异质的，但样本聚类后发现了一些多样性模式。该实验模型似乎再现了牙髓感染中的实际生物膜成分，这表明它可用于评估消毒方案。