Technical note: overcoming host contamination in bovine vaginal metagenomic samples with nanopore adaptive sequencing.
Technical note: overcoming host contamination in bovine vaginal metagenomic samples with nanopore adaptive sequencing.
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DOI：
10.1093/jas/skab344
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发表时间：
2022-01-01
影响因子：
3.3
通讯作者：
Tabor AE
中科院分区：
文献类型：
--
作者：
Ong CT;Ross EM;Boe-Hansen GB;Turni C;Hayes BJ;Tabor AE
动物宏基因组学研究，其中主机相关的微生物组的概况，是一个越来越重要的贡献，我们了解的生理功能，健康和疾病的牲畜的易感性。这些研究中的主要挑战之一是宿主DNA污染，这限制了宏基因组内容的测序能力并降低了宏基因组分析的准确性。这是第一项比较不同测序方法对牛阴道宏基因组样本进行分析的有效性的研究。我们将牛津纳米孔技术（ONT）适应性测序的新方法（可用于靶向或消除定义的基因序列）与标准ONT测序、Illumina 16 S rDNA扩增子测序和Illumina鸟枪测序进行了比较。评估了每种方法在恢复宏基因组数据和回忆宏基因组谱中的效率。ONT自适应测序产生的宏基因组数据量高于其他方法每1Gb的序列数据。ONT适应性测序的增加的测序效率因此减少了为具有高宿主与微生物DNA比率的宏基因组样品提供足够覆盖所需的原始数据量。此外，ONT自适应测序产生的长读段保留了读段信息的连续性，这有利于宏基因组的分类学和功能概况的深入注释。不同的方法导致了不同分类群的鉴定。当使用16 S rDNA扩增子测序方法时，以低丰度鉴定并归类于“未分类梭菌目”的梭菌属，当使用其他三种方法测序时，被鉴定为样品中的优势属。此外，用ONT适应性测序鉴定了更多数量的注释基因，这也在大多数常见注释基因上产生了高覆盖率。这项研究说明了ONT自适应测序在提高来源于具有高宿主-微生物DNA比的微生物组样品的宏基因组数据量方面的优势，以及长读段在保留完整信息以进行准确注释方面的优势。
Animal metagenomic studies, in which host-associated microbiomes are profiled, are an increasingly important contribution to our understanding of the physiological functions, health and susceptibility to diseases of livestock. One of the major challenges in these studies is host DNA contamination, which limits the sequencing capacity for metagenomic content and reduces the accuracy of metagenomic profiling. This is the first study comparing the effectiveness of different sequencing methods for profiling bovine vaginal metagenomic samples. We compared the new method of Oxford Nanopore Technologies (ONT) adaptive sequencing, which can be used to target or eliminate defined genetic sequences, to standard ONT sequencing, Illumina 16S rDNA amplicon sequencing, and Illumina shotgun sequencing. The efficiency of each method in recovering the metagenomic data and recalling the metagenomic profiles was assessed. ONT adaptive sequencing yielded a higher amount of metagenomic data than the other methods per 1 Gb of sequence data. The increased sequencing efficiency of ONT adaptive sequencing consequently reduced the amount of raw data needed to provide sufficient coverage for the metagenomic samples with high host-to-microbe DNA ratio. Additionally, the long reads generated by ONT adaptive sequencing retained the continuity of read information, which benefited the in-depth annotations for both taxonomical and functional profiles of the metagenome. The different methods resulted in the identification of different taxa. Genera Clostridium, which was identified at low abundances and categorized under Order “Unclassified Clostridiales” when using the 16S rDNA amplicon sequencing method, was identified to be the dominant genera in the sample when sequenced with the three other methods. Additionally, higher numbers of annotated genes were identified with ONT adaptive sequencing, which also produced high coverage on most of the commonly annotated genes. This study illustrates the advantages of ONT adaptive sequencing in improving the amount of metagenomic data derived from microbiome samples with high host-to-microbe DNA ratio and the advantage of long reads in preserving intact information for accurate annotations.
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影响因子：
14.9
作者：
Haft DH;Selengut JD;Richter RA;Harkins D;Basu MK;Beck E
通讯作者：
Beck E
影响因子：
5.9
作者：
Gupta, Shashank;Mortensen, Martin S.;Sorensen, Soren J.
通讯作者：
Sorensen, Soren J.
影响因子：
5.2
作者：
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通讯作者：
Myer PR
影响因子：
1.4
作者：
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通讯作者：
Hoffmann, Aline Rodrigues
影响因子：
3.7
作者：
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通讯作者：
Strous, Marc