Shotgun metagenomic sequencing provides valuable insights into microbial communities, but the high cost of library preparation with standard kits and protocols is a barrier for many. New methods such as Hackflex use diluted commercially available reagents to greatly reduce library preparation costs. However, these methods have not been systematically validated for metagenomic sequencing. Here, we evaluate Hackflex performance by sequencing metagenomic libraries from known mock communities as well as mouse fecal samples prepared by Hackflex, Illumina DNA Prep, and Illumina TruSeq methods. Hackflex successfully recovered all members of the Zymo mock community, performing best for samples with DNA concentrations <1 ng/uL. Furthermore, Hackflex was able to delineate microbiota of individual inbred mice from the same breeding stock at the same mouse facility, and statistical modeling indicated that mouse ID explained a greater fraction of the variance in metagenomic composition than did library preparation method. These results show that Hackflex is suitable for generating inventories of bacterial communities through metagenomic sequencing.

中文翻译：

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Hackflex 文库制备可实现低成本宏基因组分析

鸟枪法宏基因组测序为微生物群落提供了宝贵的见解，但使用标准试剂盒和方案进行文库制备的高昂成本对许多人来说是一个障碍。 Hackflex等新方法使用稀释的市售试剂来大大降低文库制备成本。然而，这些方法尚未针对宏基因组测序进行系统验证。在这里，我们通过对已知模拟群落的宏基因组文库以及通过 Hackflex、Illumina DNA Prep 和 Illumina TruSeq 方法制备的小鼠粪便样本进行测序来评估 Hackflex 的性能。 Hackflex 成功恢复了 Zymo 模拟社区的所有成员，对于 DNA 浓度 <1 ng/uL 的样品表现最佳。此外，Hackflex 能够描绘来自同一小鼠设施的同一种种的个体近交小鼠的微生物群，并且统计模型表明，与文库制备方法相比，小鼠 ID 解释了宏基因组组成中更大比例的差异。这些结果表明 Hackflex 适合通过宏基因组测序生成细菌群落清单。