Comparison of storage conditions for human vaginal microbiome studies.
Comparison of storage conditions for human vaginal microbiome studies.
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DOI：
10.1371/journal.pone.0036934
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Brotman RM
中科院分区：
文献类型：
--
作者：
Bai G;Gajer P;Nandy M;Ma B;Yang H;Sakamoto J;Blanchard MH;Ravel J;Brotman RM
储存条件对人类生物样本微生物组和代谢物组成的影响尚未作为潜在的偏差来源进行彻底研究。我们使用条形码 16S rRNA 基因测序的焦磷酸测序和 1H-NMR 分析，评估了临床试验中使用的两种常见储存条件对阴道微生物群的细菌和代谢物组成的影响。招募了八名女性，医生从每位女性身上采集了四份阴道中部拭子。样品要么立即处理，在-80°C 下保存 4 周，要么在 -20°C 下保存 1 周，然后在分析前转移至 -80°C 再保存 4 周。统计方法，包括Kolmogorovo-Smirnov和Wilcoxon检验，用于评估不同条件下储存的样本之间阴道细菌群落组成和代谢物的差异。结果表明，采集后立即处理的样品或保存不同时间的样品之间没有显着差异。对阴道分泌物中小分子代谢物的 1H-NMR 分析表明，高水平的乳酸与乳杆菌占主导地位的群落有关。乳酸的相对丰度似乎与单个乳杆菌属的相对丰度没有相关性。在这个有限的样本中，尽管当 L.gasseri 占优势时观察到乳酸水平较低，这表明看似相似的群落的代谢输出存在差异。这些发现有利于阴道微生物群的大规模、现场微生物组和代谢组学研究。
The effect of storage conditions on the microbiome and metabolite composition of human biological samples has not been thoroughly investigated as a potential source of bias. We evaluated the effect of two common storage conditions used in clinical trials on the bacterial and metabolite composition of the vaginal microbiota using pyrosequencing of barcoded 16S rRNA gene sequencing and 1H-NMR analyses. Eight women were enrolled and four mid-vaginal swabs were collected by a physician from each woman. The samples were either processed immediately, stored at −80°C for 4 weeks or at −20°C for 1 week followed by transfer to −80°C for another 4 weeks prior to analysis. Statistical methods, including Kolmogorovo-Smirnov and Wilcoxon tests, were performed to evaluate the differences in vaginal bacterial community composition and metabolites between samples stored under different conditions. The results showed that there were no significant differences between samples processed immediately after collection or stored for varying durations. 1H-NMR analysis of the small molecule metabolites in vaginal secretions indicated that high levels of lactic acid were associated with Lactobacillus-dominated communities. Relative abundance of lactic acid did not appear to correlate with relative abundance of individual Lactobacillus sp. in this limited sample, although lower levels of lactic acid were observed when L. gasseri was dominant, indicating differences in metabolic output of seemingly similar communities. These findings benefit large-scale, field-based microbiome and metabolomic studies of the vaginal microbiota.
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DOI：
10.1086/657320
发表时间：
2010-12-15
期刊：
The Journal of infectious diseases
影响因子：
--
作者：
Brotman RM;Klebanoff MA;Nansel TR;Yu KF;Andrews WW;Zhang J;Schwebke JR
通讯作者：
Schwebke JR
影响因子：
9.4
作者：
Forney, Larry J.;Gajer, Pawel;Ravel, Jacques
通讯作者：
Ravel, Jacques
影响因子：
6.1
作者：
Boskey, ER;Cone, RA;Moench, TR
通讯作者：
Moench, TR
影响因子：
2.1
作者：
Lauber CL;Zhou N;Gordon JI;Knight R;Fierer N
通讯作者：
Fierer N
影响因子：
5.4
作者：
Lai, Samuel K.;Hida, Kaoru;Hanes, Justin
通讯作者：
Hanes, Justin