Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota.
Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota.
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DOI：
10.1371/journal.pone.0237556
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发表时间：
2021
期刊：
影响因子：
3.7
通讯作者：
Robeson MS 2nd
中科院分区：
文献类型：
--
作者：
Shibata T;Nakagawa M;Coleman HN;Owens SM;Greenfield WW;Sasagawa T;Robeson MS 2nd
宫颈微生物群（CM）被认为是影响宫颈上皮内瘤变（CIN）进展的重要因素，并与人乳头瘤病毒（HPV）的持续存在有关。液基细胞学（LBC）样本的收集是宫颈癌筛查和HPV基因分型的常规方法，可用于长期细胞生物库。我们试图确定是否有可能从LBC标本中获取微生物DNA，并比较了四种不同提取方案的性能：（ZymoBIOMICS DNA Miniprep试剂盒; QIAamp PowerFecal Pro DNA试剂盒; QIAamp DNA Mini试剂盒;和IndiSpin病原体试剂盒）及其从LBC标本中捕获CM多样性的能力。将CIN值为2或3的20例患者的LBC标本（储存716 ± 105天）分别等分用于4种试剂盒中的每一种。由于缺乏新鲜LBC样品，无法评估长期LBC储存造成的微生物多样性损失。未与其他类型的宫颈取样进行比较。我们观察到，所有DNA提取试剂盒对储存的LBC样本中的宫颈微生物DNA提供了等同的可及性。在所有的DNA提取方案中，大约80%的微生物属是共享的。还观察到潜在的试剂盒污染物。个体之间的变化是一个显着更大的影响所观察到的微生物组成比DNA提取的方法。我们还观察到HPV 16与不以惰性乳杆菌为主的群落类型显著相关。
Cervical microbiota (CM) are considered an important factor affecting the progression of cervical intraepithelial neoplasia (CIN) and are implicated in the persistence of human papillomavirus (HPV). Collection of liquid-based cytology (LBC) samples is routine for cervical cancer screening and HPV genotyping and can be used for long-term cytological biobanking. We sought to determine whether it is possible to access microbial DNA from LBC specimens, and compared the performance of four different extraction protocols: (ZymoBIOMICS DNA Miniprep Kit; QIAamp PowerFecal Pro DNA Kit; QIAamp DNA Mini Kit; and IndiSpin Pathogen Kit) and their ability to capture the diversity of CM from LBC specimens. LBC specimens from 20 patients (stored for 716 ± 105 days) with CIN values of 2 or 3 were each aliquoted for each of the four kits. Loss of microbial diversity due to long-term LBC storage could not be assessed due to lack of fresh LBC samples. Comparisons with other types of cervical sampling were not performed. We observed that all DNA extraction kits provided equivalent accessibility to the cervical microbial DNA within stored LBC samples. Approximately 80% microbial genera were shared among all DNA extraction protocols. Potential kit contaminants were observed as well. Variation between individuals was a significantly greater influence on the observed microbial composition than was the method of DNA extraction. We also observed that HPV16 was significantly associated with community types that were not dominated by Lactobacillus iners.
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影响因子：
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作者：
Bardou P;Mariette J;Escudié F;Djemiel C;Klopp C
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影响因子：
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Callahan BJ;McMurdie PJ;Rosen MJ;Han AW;Johnson AJ;Holmes SP
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影响因子：
3.7
作者：
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通讯作者：
Vereecken AJ
DOI：
10.1073/pnas.1502875112
发表时间：
2015-09-01
影响因子：
11.1
作者：
DiGiulio, Daniel B.;Callahan, Benjamin J.;Relman, David A.
通讯作者：
Relman, David A.