The effect of the microbiota on its human host is driven, at least in part, by small-molecule and protein effectors it produces. Here, we report on the use of functional multigenomic screening to identify microbiota-encoded effectors. In this study, genomic DNA from 116 human-associated bacteria was cloned en masse, and the resulting multigenomic library was screened using a nuclear factor-κB reporter (NF-κB) assay. Functional multigenomics builds on the concept of functional metagenomics but takes advantage of increasing advances in cultivating and sequencing human-associated bacteria. Effector genes found to confer NF-κB-inducing activity to Escherichia coli encode proteins in four general categories: cell wall hydrolases, membrane transporters, lipopolysaccharide biosynthetic enzymes, and proteins of unknown function. The compact nature of multigenomic libraries, which results from the ability to normalize input DNA ratios, should simplify screening of libraries using diverse heterologous hosts and reporter assays, increasing the rate of discovery of novel effector genes.IMPORTANCE Human-associated bacteria are thought to encode bioactive small molecules and proteins that play an intimate role in human health and disease. Here, we report on the creation and functional screening of a multigenomic library constructed using genomic DNA from 116 bacteria found at diverse sites across the human body. Individual clones were screened for genes capable of conferring NF-κB-inducing activity to Escherichia coli NF-κB is a useful reporter for a range of cellular processes related to immunity, pathogenesis, and inflammation. Compared to the screening of metagenomic libraries, the ability to normalize input DNA ratios when constructing a multigenomic library should facilitate the more efficient examination of commensal bacteria for diverse bioactivities. Multigenomic screening takes advantage of the growing available resources in culturing and sequencing the human microbiota and generates starting points for more in-depth studies on the mechanisms by which commensal bacteria interact with their human host.

中文翻译：

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对人类相关细菌进行 NF-κB 诱导生物活性效应器的功能性多基因组筛选。

微生物群对其人类宿主的影响至少部分是由其产生的小分子和蛋白质效应子驱动的。在这里，我们报告了使用功能性多基因组筛选来识别微生物编码的效应物。在这项研究中，来自 116 种人类相关细菌的基因组 DNA 被大量克隆，并使用核因子-κB 报告基因 (NF-κB) 测定筛选所得的多基因组文库。功能多基因组学建立在功能宏基因组学的概念之上，但利用了人类相关细菌培养和测序方面不断进步的优势。被发现赋予大肠杆菌 NF-κB 诱导活性的效应基因编码四大类蛋白质：细胞壁水解酶、膜转运蛋白、脂多糖生物合成酶和未知功能的蛋白质。多基因组文库的紧凑性源于标准化输入 DNA 比率的能力，应简化使用不同异源宿主和报告基因检测的文库筛选，从而提高新效应基因的发现率。 重要性 人类相关细菌被认为编码生物活性小分子和蛋白质在人类健康和疾病中发挥着密切作用。在这里，我们报告了使用来自人体不同部位的 116 种细菌的基因组 DNA 构建的多基因组文库的创建和功能筛选。筛选出能够赋予大肠杆菌 NF-κB 诱导活性的基因的各个克隆。NF-κB 是与免疫、发病机制和炎症相关的一系列细胞过程的有用报告基因。与宏基因组文库的筛选相比，构建多基因组文库时标准化输入 DNA 比率的能力应有助于更有效地检查共生细菌的不同生物活性。多基因组筛选利用不断增长的可用资源来培养和测序人类微生物群，并为更深入地研究共生细菌与其人类宿主相互作用的机制提供起点。