Benchmarking second and third-generation sequencing platforms for microbial metagenomics.
Benchmarking second and third-generation sequencing platforms for microbial metagenomics.
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DOI：
10.1038/s41597-022-01762-z
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发表时间：
2022-11-11
期刊：
影响因子：
9.8
通讯作者：
Almeida, Mathieu
中科院分区：
文献类型：
--
作者：
Meslier, Victoria;Quinquis, Benoit;Da Silva, Kevin;Plaza Onate, Florian;Pons, Nicolas;Roume, Hugo;Podar, Mircea;Almeida, Mathieu
鸟枪式元基因组测序是研究复杂微生物群落的分类多样性和代谢潜力的常用方法。目前的方法主要使用第二代短读测序，然而第三代长读技术的进步提供了克服短读测序的一些限制的机会。在这里，我们比较了七个平台，包括第二代测序仪(Illumina HiSeq 300、MGI DNBSEQ-G400和DNBSEQ-T7、ThermoFisher Ion GeneStudio S5和Ion Proton P1)和第三代测序仪(牛津纳米孔技术公司Minion R9和太平洋生物科学续集II)。我们构建了三个不均匀的合成微生物群落，每个模拟由多达87个基因组微生物菌株DNA组成，跨越29个细菌和古菌门，代表了用于测序技术比较的最复杂和最多样化的合成群落。我们的结果表明，第三代测序在分析复杂微生物群落方面比第二代平台具有优势，但需要仔细的测序文库准备才能进行最佳的定量元基因组分析。我们的测序数据也为元基因组学生物信息学软件的测试和基准测试提供了宝贵的资源。
Shotgun metagenomic sequencing is a common approach for studying the taxonomic diversity and metabolic potential of complex microbial communities. Current methods primarily use second generation short read sequencing, yet advances in third generation long read technologies provide opportunities to overcome some of the limitations of short read sequencing. Here, we compared seven platforms, encompassing second generation sequencers (Illumina HiSeq 300, MGI DNBSEQ-G400 and DNBSEQ-T7, ThermoFisher Ion GeneStudio S5 and Ion Proton P1) and third generation sequencers (Oxford Nanopore Technologies MinION R9 and Pacific Biosciences Sequel II). We constructed three uneven synthetic microbial communities composed of up to 87 genomic microbial strains DNAs per mock, spanning 29 bacterial and archaeal phyla, and representing the most complex and diverse synthetic communities used for sequencing technology comparisons. Our results demonstrate that third generation sequencing have advantages over second generation platforms in analyzing complex microbial communities, but require careful sequencing library preparation for optimal quantitative metagenomic analysis. Our sequencing data also provides a valuable resource for testing and benchmarking bioinformatics software for metagenomics.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
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作者：
Almeida M;Hébert A;Abraham AL;Rasmussen S;Monnet C;Pons N;Delbès C;Loux V;Batto JM;Leonard P;Kennedy S;Ehrlich SD;Pop M;Montel MC;Irlinger F;Renault P
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作者：
Costea, Paul I.;Zeller, Georg;Bork, Peer
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