Horizontal gene transfer (HGT) plays a central role in microbial evolution. Our understanding of the mechanisms, frequency, and taxonomic range of HGT in polymicrobial environments is limited, as we currently rely on historical HGT events inferred from genome sequencing and studies involving cultured microorganisms. We lack approaches to observe ongoing HGT in microbial communities. To address this knowledge gap, we developed a DNA sequencing-based “transductomics” approach that detects and characterizes microbial DNA transferred via transduction. We validated our approach using model systems representing a range of transduction modes and show that we can detect numerous classes of transducing DNA. Additionally, we show that we can use this methodology to obtain insights into DNA transduction among all major taxonomic groups of the intestinal microbiome. The transductomics approach that we present here allows for the detection and characterization of genes that are potentially transferred between microbes in complex microbial communities at the time of measurement and thus provides insights into real-time ongoing horizontal gene transfer. This work extends the genomic toolkit for the broader study of mobile DNA within microbial communities and could be used to understand how phenotypes spread within microbiomes.

中文翻译：

---

转导组学：基于测序的纯培养物和微生物群落中转导 DNA 的检测和分析


水平基因转移（HGT）在微生物进化中发挥着核心作用。我们对多微生物环境中 HGT 的机制、频率和分类范围的了解是有限的，因为我们目前依赖于基因组测序和涉及培养微生物的研究推断出的历史 HGT 事件。我们缺乏观察微生物群落中持续 HGT 的方法。为了解决这一知识差距，我们开发了一种基于 DNA 测序的“转导组学”方法，可检测和表征通过转导转移的微生物 DNA。我们使用代表一系列转导模式的模型系统验证了我们的方法，并表明我们可以检测多种类型的转导 DNA。此外，我们表明我们可以使用这种方法来深入了解肠道微生物组所有主要分类群之间的 DNA 转导。我们在这里介绍的转导组学方法可以在测量时检测和表征复杂微生物群落中微生物之间可能转移的基因，从而提供对实时持续水平基因转移的见解。这项工作扩展了基因组工具包，用于更广泛地研究微生物群落内的移动 DNA，并可用于了解表型如何在微生物组内传播。