Evaluation of microbiome enrichment and host DNA depletion in human vaginal samples using Oxford Nanopore's adaptive sequencing.
Evaluation of microbiome enrichment and host DNA depletion in human vaginal samples using Oxford Nanopore's adaptive sequencing.
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使用Oxford Nanopore的自适应测序评估人类阴道样品中微生物组富集和宿主DNA耗竭的评估。
DOI：
10.1038/s41598-022-08003-8
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发表时间：
2022-03-07
影响因子：
4.6
通讯作者：
Brandt C
中科院分区：
文献类型：
--
作者：
Marquet M;Zöllkau J;Pastuschek J;Viehweger A;Schleußner E;Makarewicz O;Pletz MW;Ehricht R;Brandt C
宏基因组测序有望用于临床应用，以研究与疾病或患者结局有关的微生物组成。阴道微生物组的改变与不良妊娠结局有关，如早产胎膜早破和早产。在方法学上，这些样品通常必须处理相对低量的原核DNA和高量的宿主DNA（> 90%），从而降低了总体微生物分辨率。Nanopore的自适应采样方法提供了选择性的DNA耗尽或目标富集，以在测序过程中直接拒绝或接受DNA分子，而无需专门的样品制备。在这里，我们证明了选择性的“人类宿主耗竭”如何导致总测序深度增加1.70倍（± 0.27倍），从而提供更高的分类学分析灵敏度。同时，微生物组成与对照实验保持一致。完全去除所有人类宿主序列尚不可能，应考虑作为伦理批准声明可能仍然是必要的。自适应采样增加了所有15个测序的临床常规阴道样本中的微生物测序产率，使其成为临床监测和基于医学的研究的有价值的工具，除了测序前的其他宿主消耗方法之外，还可以使用。
Metagenomic sequencing is promising for clinical applications to study microbial composition concerning disease or patient outcomes. Alterations of the vaginal microbiome are associated with adverse pregnancy outcomes, like preterm premature rupture of membranes and preterm birth. Methodologically these samples often have to deal with low relative amounts of prokaryotic DNA and high amounts of host DNA (> 90%), decreasing the overall microbial resolution. Nanopore's adaptive sampling method offers selective DNA depletion or target enrichment to directly reject or accept DNA molecules during sequencing without specialized sample preparation. Here, we demonstrate how selective ‘human host depletion’ resulted in a 1.70 fold (± 0.27 fold) increase in total sequencing depth, providing higher taxonomic profiling sensitivity. At the same time, the microbial composition remains consistent with the control experiments. The complete removal of all human host sequences is not yet possible and should be considered as an ethical approval statement might still be necessary. Adaptive sampling increased microbial sequencing yield in all 15 sequenced clinical routine vaginal samples, making it a valuable tool for clinical surveillance and medical-based research, which can be used in addition to other host depletion methods before sequencing.
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影响因子：
14.9
作者：
Klindworth A;Pruesse E;Schweer T;Peplies J;Quast C;Horn M;Glöckner FO
通讯作者：
Glöckner FO
影响因子：
10.5
作者：
Ma B;Forney LJ;Ravel J
通讯作者：
Ravel J
影响因子：
4.4
作者：
Acinas, SG;Sarma-Rupavtarm, R;Polz, MF
通讯作者：
Polz, MF
影响因子：
9.2
作者：
Nicholls, Samuel M.;Quick, Joshua C.;Loman, Nicholas J.
通讯作者：
Loman, Nicholas J.
影响因子：
5.8
作者：
Li, Heng
通讯作者：
Li, Heng