Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27, Singapore, 637551, Singapore.
Department of Computer Science, University of Tübingen, Sand 14, Tübingen, 72076, Germany.
Microbiome. 2019 Apr 16;7(1):61. doi: 10.1186/s40168-019-0665-y.
Short-read sequencing technologies have long been the work-horse of microbiome analysis. Continuing technological advances are making the application of long-read sequencing to metagenomic samples increasingly feasible.
We demonstrate that whole bacterial chromosomes can be obtained from an enriched community, by application of MinION sequencing to a sample from an EBPR bioreactor, producing 6 Gb of sequence that assembles into multiple closed bacterial chromosomes. We provide a simple pipeline for processing such data, which includes a new approach to correcting erroneous frame-shifts.
Advances in long-read sequencing technology and corresponding algorithms will allow the routine extraction of whole chromosomes from environmental samples, providing a more detailed picture of individual members of a microbiome.
短读测序技术长期以来一直是微生物组分析的主力军。不断的技术进步使得长读测序在宏基因组样本中的应用越来越可行。
我们通过将 MinION 测序应用于 EBPR 生物反应器中的样本，证明了从富集群落中可以获得完整的细菌染色体，产生了 6Gb 的序列，这些序列组装成多个闭合的细菌染色体。我们提供了一个简单的处理此类数据的管道，其中包括一种新的纠正错误框架移位的方法。
长读测序技术和相应算法的进步将允许从环境样本中常规提取完整的染色体，从而更详细地了解微生物组的各个成员。
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