High-Resolution Differentiation of Enteric Bacteria in Premature Infant Fecal Microbiomes Using a Novel rRNA Amplicon.
High-Resolution Differentiation of Enteric Bacteria in Premature Infant Fecal Microbiomes Using a Novel rRNA Amplicon.
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DOI：
10.1128/mbio.03656-20
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发表时间：
2021-02-16
期刊：
影响因子：
6.4
通讯作者：
Matson AP
中科院分区：
文献类型：
--
作者：
Graf J;Ledala N;Caimano MJ;Jackson E;Gratalo D;Fasulo D;Driscoll MD;Coleman S;Matson AP
随着微生物组的进化，识别和跟踪微生物菌株是微生物组研究领域的主要挑战。我们使用了一种新的测序试剂盒，该试剂盒将DNA提取与rRNA操纵子大区域的PCR扩增和下游生物信息学数据分析相结合。来自两个不同新生儿重症监护病房（NICU）的双胞胎的纵向微生物组样本使用跨越16 S和23 S rRNA基因的2,500个碱基的扩增子进行分析，并映射到一个新的定制16 S-23 S rRNA数据库。使用DADA 2推断的扩增子序列变体（ASV）为区分来自密切相关但先前未测序的克雷伯菌属、大肠杆菌属和肠杆菌属菌株的rRNA变体提供了足够的分辨率，这些菌株是进入NICU后在这些婴儿肠道定植的第一批细菌。随着时间的推移，在同时入院的双胞胎之间监测不同的ASV组（指纹），这表明有可能跟踪病原体和病原体的来源和传播。从长扩增子测序获得的高分辨率分类法使得能够在医院环境中建立婴儿微生物组时在时间和空间上跟踪菌株。
Identifying and tracking microbial strains as microbiomes evolve are major challenges in the field of microbiome research. We utilized a new sequencing kit that combines DNA extraction with PCR amplification of a large region of the rRNA operon and downstream bioinformatic data analysis. Longitudinal microbiome samples of coadmitted twins from two different neonatal intensive care units (NICUs) were analyzed using an ∼2,500-base amplicon that spans the 16S and 23S rRNA genes and mapped to a new, custom 16S-23S rRNA database. Amplicon sequence variants (ASVs) inferred using DADA2 provided sufficient resolution for the differentiation of rRNA variants from closely related but not previously sequenced Klebsiella, Escherichia coli, and Enterobacter strains, among the first bacteria colonizing the gut of these infants after admission to the NICU. Distinct ASV groups (fingerprints) were monitored between coadmitted twins over time, demonstrating the potential to track the source and spread of both commensals and pathogens. The high-resolution taxonomy obtained from long amplicon sequencing enables the tracking of strains temporally and spatially as microbiomes are established in infants in the hospital environment.
影响因子：
4.2
作者：
Tazumi A;Kakinuma Y;Misawa N;Moore JE;Millar BC;Matsuda M
通讯作者：
Matsuda M