摘要
      功能宏基因组学是鉴定环境中抗生素抗性基因（ARGs）的强大实验工具，但合适的宿主细菌种类范围有限。这一限制影响了已鉴定ARGs的范围及其临床相关性的解释。在这里，我们提出了一个功能宏基因组学管道，称为重编程噬菌体颗粒辅助多物种功能宏基因组（DEEPMINE）。这种方法结合并改进了T7噬菌体与交换尾纤维和靶向诱变的使用，以扩大噬菌体宿主的特异性和功能宏基因组学的效率。这些修饰的噬菌体颗粒被用于将大型宏基因组质粒文库引入临床相关的细菌病原体中。通过在土壤和肠道微生物群以及临床基因组中针对13种抗生素筛选ARGs，我们证明这种方法大大扩大了已鉴定的ARGs的范围。许多ARGs对抗性具有物种特异性影响；它们在一个细菌物种中提供高水平的抗性，但在相关物种中产生非常有限的抗性。最后，我们确定了目前正在临床开发或最近获得批准的针对抗生素的移动ARG。总的来说，DEEPMINE扩展了用于研究微生物群落的功能宏基因组学工具箱。
Abstract
Functional metagenomics is a powerful experimental tool to identify antibiotic resistance genes (ARGs) in the environment, but the range of suitable host bacterial species is limited. This limitation affects both the scope of the identified ARGs and the interpretation of their clinical relevance. Here we present a functional metagenomics pipeline called Reprogrammed Bacteriophage Particle Assisted Multi-species Functional Metagenomics (DEEPMINE). This approach combines and improves the use of T7 bacteriophage with exchanged tail fibres and targeted mutagenesis to expand phage host-specificity and efficiency for functional metagenomics. These modified phage particles were used to introduce large metagenomic plasmid libraries into clinically relevant bacterial pathogens. By screening for ARGs in soil and gut microbiomes and clinical genomes against 13 antibiotics, we demonstrate that this approach substantially expands the list of identified ARGs. Many ARGs have species-specific effects on resistance; they provide a high level of resistance in one bacterial species but yield very limited resistance in a related species. Finally, we identified mobile ARGs against antibiotics that are currently under clinical development or have recently been approved. Overall, DEEPMINE expands the functional metagenomics toolbox for studying microbial communities.

https://www.nature.com/articles/s41564-023-01320-2