Influence of fecal sample storage on bacterial community diversity.
Influence of fecal sample storage on bacterial community diversity.
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DOI：
10.2174/1874285800903010040
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发表时间：
2009
期刊：
影响因子：
--
通讯作者：
Triplett EW
中科院分区：
文献类型：
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作者：
Roesch LF;Casella G;Simell O;Krischer J;Wasserfall CH;Schatz D;Atkinson MA;Neu J;Triplett EW
先前的研究已经确定了特定粪便细菌菌株与某些自身免疫性疾病之间的相关性，无论是阳性还是阴性。这些相互冲突的数据可能与样本采集有关。本工作的目的是评估收集参数的时间和温度对细菌群落组成的影响。样本取自健康儿童，并立即分为5个子样本。将一个样品立即在-80 ° C下冷冻，而将其他等分试样在12、24、48和72小时后冷冻，将从每个样品提取的DNA用于用条形码引物扩增16 S rRNA。将扩增产物合并，并通过焦磷酸测序获得部分16 S rRNA序列。社区多样性的人与人之间的差异很大。为每个个体列出了至少占群落1%的分类群。这些都不是在所有的人都大量存在。拟杆菌在四个科目中的三个中以最高丰度存在。共获得23，701个16 S rRNA序列，每个样品平均1，185个读数，平均长度为200个碱基。尽管扩增的16 S rRNA的焦磷酸测序鉴定了群落组成随时间的变化（~10%），但在12小时（3.06%）观察到很少的多样性变化，在收集后24小时（8.61%）、48小时（9.72%）和72小时（10.14%）后发生逐渐变化。
Previous studies have identified a correlation, either positive or negative, between specific stool bacteria strains and certain autoimmune diseases. These conflicting data may relate to sample collection. The aim of this work was to evaluate the influence of the collection parameters of time and temperature on bacterial community composition. Samples were taken from healthy children and immediately divided in 5 sub-samples. One sample was frozen immediately at -80°C, while the other aliquots were frozen 12, 24, 48, and 72h later DNA extracted from each sample was used to amplify the 16S rRNA with barcoded primers. The amplified products were pooled and partial 16S rRNA sequences were obtained by pyrosequencing. Person-to-person variability in community diversity was high. A list of those taxa that comprise at least 1% of the community was made for each individual. None of these were present in high numbers in all individuals. The Bacteroides were present in the highest abundance in three of four subjects. A total of 23,701 16S rRNA sequences were obtained with an average of 1,185 reads per sample with an average length of 200 bases. Although pyrosequencing of amplified 16S rRNA identified changes in community composition over time (~10%), little diversity change was observed at 12 hours (3.06%) with gradual changes occurring after 24 (8.61%), 48 (9.72%), and 72 h (10.14%), post collection.