Binning and Hybrid assembly of synthetic microbial communities

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 HiSeq300, 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.

霰弹枪宏基因组测序（Shotgun metagenomic sequencing）是研究复杂微生物群落分类多样性与代谢潜能的常用研究手段。当前主流方法多采用第二代短读长测序技术，而第三代长读长测序技术的发展为突破短读长测序的部分局限提供了全新机遇。本研究比对了七种测序平台，涵盖第二代测序仪：因美纳（Illumina）HiSeq300、华大智造（MGI）DNBSEQ-G400与DNBSEQ-T7、赛默飞世尔科技（ThermoFisher）Ion GeneStudio S5及Ion Proton P1，以及第三代测序仪：牛津纳米孔科技（Oxford Nanopore Technologies）MinION R9与太平洋生物科学（Pacific Biosciences）Sequel II。我们构建了三组非均匀合成微生物群落，每个模拟群落最多包含87株微生物菌株的基因组DNA，覆盖29个细菌与古菌门，是目前用于测序技术性能比对的最复杂、最多样化的合成群落。研究结果表明，在分析复杂微生物群落时，第三代测序技术相较于第二代平台具备显著优势，但为实现最优的定量宏基因组分析效果，需谨慎开展测序文库制备工作。本研究产生的测序数据同时为宏基因组学生物信息学软件的测试与基准测试提供了极具价值的科研资源。