Effects of variation in sample storage conditions and swab order on 16S vaginal microbiome analyses.
Effects of variation in sample storage conditions and swab order on 16S vaginal microbiome analyses.
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DOI：
10.1128/spectrum.03712-23
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发表时间：
2024-01-11
影响因子：
3.7
通讯作者：
中科院分区：
文献类型：
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作者：
技术偏差是微生物组研究中的一个紧迫问题，从样本收集到图形生成的任何阶段都可能引入变异性。在这项研究中，我们的目标是通过使用阴道拭子生成的 16S rRNA 基因扩增子测序数据来检查样本存储缓冲液和多次拭子事件的影响，从而减少研究人类阴道微生物组的偏差。我们证明 AssayAssure Genelock 是一种临床相关的尿液样本防腐剂，可有效保存用于微生物组研究的阴道样本。当将 Genelock 与 95%（体积/体积）乙醇和无防腐剂（仅空气）进行比较时，宿主变异性解释了加权和未加权 UniFrac 测量值比保存方法更大的差异。我们进一步研究了三个连续的自我擦拭事件的影响，因为阴道样本相对较低的生物量本质上可能会引入偏差。重要的是要知道采集多个拭子是否可以提供可复制的结果，从而允许额外的技术复制和增加样本量。我们发现，在检查类群是否存在时，最多三个拭子事件不会引入偏差，但可以解释计算的类群数量的 3% 的变异性。有必要进行一项有更多参与者的研究来进一步验证这些发现，但在进行这项试点研究时，我们的目标是继续奠定基础，以便创建普遍标准化和可访问的研究。人类阴道微生物群的组成与多种疾病有关，包括酵母菌感染、细菌性阴道病和性传播感染。人们越来越认识到阴道微生物组是个人健康的关键因素，因此必须建立利用自我采集技术收集和处理准确样本的方法，以进行大规模的基于人群的研究。在本研究中，我们调查使用 AssayAssure Genelock（一种核酸防腐剂）是否会在自行采集的阴道样本中引入微生物偏差。据我们所知，我们还提供了一些关于在一个时间点采集多个拭子的影响的初步证据。阴道样本的生物量相对较低，因此一次从特定参与者收集多个拭子的能力将大大提高可重复性和可用于未来研究的数据。这有望为更完整、更准确地了解阴道微生物组奠定基础。
Technical bias is a pressing issue in microbiome research, and variability can be introduced at any stage from sample collection to figure generation. In this study, we aim to reduce biases in studying the human vaginal microbiome by examining the impact of sample storage buffer and multiple swabbing events using 16S rRNA gene amplicon sequencing data generated from vaginal swabs. We show that AssayAssure Genelock, a clinically relevant preservative for urine samples, is effective in preserving vaginal samples for microbiome studies. When comparing Genelock to 95% (vol/vol) ethanol and no preservative (air only), host variability explained more variance in both weighted and unweighted UniFrac measurements than the preservation method. We further examined the impact of three successive self-swabbing events, as the relatively low biomass nature of vaginal samples can inherently introduce bias. It is important to know if taking multiple swabs can provide replicable results and thus allow for additional technical replicates and an increased sample size. We found that up to three swabbing events do not introduce bias when examining the presence or absence of taxa but can explain 3% of the variability in the amount of taxa calculated. A study with more participants is warranted to provide further validation of these findings, but in producing this pilot study, we aim to continue laying the groundwork so that universally standardized and accessible studies can be created. The composition of the human vaginal microbiome has been linked to a variety of medical conditions including yeast infection, bacterial vaginosis, and sexually transmitted infection. The vaginal microbiome is becoming increasingly acknowledged as a key factor in personal health, and it is essential to establish methods to collect and process accurate samples with self-collection techniques to allow large, population-based studies. In this study, we investigate if using AssayAssure Genelock, a nucleic acid preservative, introduces microbial biases in self-collected vaginal samples. To our knowledge, we also contribute some of the first evidence regarding the impacts of multiple swabs taken at one time point. Vaginal samples have relatively low biomass, so the ability to collect multiple swabs from a unique participant at a single time would greatly improve the replicability and data available for future studies. This will hopefully lay the groundwork to gain a more complete and accurate understanding of the vaginal microbiome.
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影响因子：
11.3
作者：
d'Enfert C;Kaune AK;Alaban LR;Chakraborty S;Cole N;Delavy M;Kosmala D;Marsaux B;Fróis-Martins R;Morelli M;Rosati D;Valentine M;Xie Z;Emritloll Y;Warn PA;Bequet F;Bougnoux ME;Bornes S;Gresnigt MS;Hube B;Jacobsen ID;Legrand M;Leibundgut-Landmann S;Manichanh C;Munro CA;Netea MG;Queiroz K;Roget K;Thomas V;Thoral C;Van den Abbeele P;Walker AW;Brown AJP
通讯作者：
Brown AJP
影响因子：
6.4
作者：
Marotz C;Cavagnero KJ;Song SJ;McDonald D;Wandro S;Humphrey G;Bryant M;Ackermann G;Diaz E;Knight R
通讯作者：
Knight R
影响因子：
1.3
作者：
King, JR;Porter, SD
通讯作者：
Porter, SD
影响因子：
6.4
作者：
Mayer, Bryan T.;Srinivasan, Sujatha;Schiffer, Joshua T.
通讯作者：
Schiffer, Joshua T.
影响因子：
1.8
作者：
Komesu, Yuko M.;Richter, Holly E.;Gantz, Marie
通讯作者：
Gantz, Marie