Differential effects of frozen storage on the molecular detection of bacterial taxa that inhabit the nasopharynx.
Differential effects of frozen storage on the molecular detection of bacterial taxa that inhabit the nasopharynx.
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DOI：
10.1186/1472-6890-11-2
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发表时间：
2011-01-24
影响因子：
--
通讯作者：
Antonio M
中科院分区：
文献类型：
--
作者：
Kwambana BA;Mohammed NI;Jeffries D;Barer M;Adegbola RA;Antonio M
冷冻储存通常先于生物样品的宏基因组分析;然而，冷冻过程可能对微生物组成产生不利影响。研究了冷冻对婴儿鼻咽部细菌检测的影响，鼻咽部是细菌病原体的主要储存库。16 S核糖体RNA（rRNA）基因为基础的末端限制性片段长度多态性（T-RFLP）分析的鼻咽（NP）拭子从12冈比亚婴儿。在采集后数小时内分析NP拭子，然后在-70 ° C下储存30天后进行分析。在冷冻对检测到的操作分类单位（OTU）数量的影响方面，受试者之间存在实质性异质性。然而，OTU的平均数量在冷冻储存后下降，并且72%的OTU的相对丰度在深度冷冻储存后变化小于0.5%。与莫拉氏菌属物种匹配的OTU的检测几率和相对丰度存在差异，嗜血杆菌属/伯克霍尔德氏菌属，发现性别与冷冻效果之间存在强烈的相互作用，因此在冷冻储存后，男性未观察到显著变化，而女性婴儿中OTU的平均数量显著下降。虽然生物样品的冷冻储存往往是必要的存档和物流目的，微生物群落研究中检测到的类群（组成）的数量的潜在影响是显着的，不应被忽视。此外，性别等遗传因素可能会影响冷冻过程中核酸的完整性。
Frozen storage often precedes metagenomic analysis of biological samples; however, the freezing process can have adverse effects on microbial composition. The effect of freezing on the detection of bacteria inhabiting the infant nasopharynx, a major reservoir of bacterial pathogens, was investigated. 16S ribosomal RNA (rRNA) gene-based terminal restriction fragment length polymorphism (T-RFLP) analysis of nasopharyngeal (NP) swabs from twelve Gambian infants was employed. NP swabs were analysed within hours of collection and then after 30 days of storage at -70°C. There was substantial heterogeneity among subjects with respect to the effect of freezing on the number of operational taxonomic units (OTUs) detected. Nevertheless, the mean number of OTUs decreased after frozen storage and the relative abundance for 72% of the OTUs changed by less than 0.5% after deep frozen storage. There were differences in the odds of detection and relative abundance of OTUs matched with Moraxella sp., Haemophilus sp./Burkholderia sp., and Pseudomonas sp. A strong interaction between sex and the effect of freezing was found, whereby there was no significant change observed for males while the mean number of OTUs significantly declined among female infants following frozen storage. Although frozen storage of biological samples is often necessary for archiving and logistic purposes, the potential effects on the number of taxa (composition) detected in microbial community studies are significant and should not be overlooked. Moreover, genetic factors such as sex may influence the integrity of nucleic acids during the freezing process.
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影响因子：
14.2
作者：
Guevara, M.;Barricarte, A.;Castilla, J.
通讯作者：
Castilla, J.
影响因子：
2.1
作者：
Grahn, N;Olofsson, M;Jonasson, J
通讯作者：
Jonasson, J
影响因子：
9.4
作者：
Abdullahi, Osman;Wanjiru, Eva;Scott, J. Anthony G.
通讯作者：
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影响因子：
9.4
作者：
Moreno, J;Hernández, E;Castañeda, E
通讯作者：
Castañeda, E
影响因子：
5
作者：
Carrigg, Cora;Rice, Olivia;O'Flaherty, Vincent
通讯作者：
O'Flaherty, Vincent