Mi Kai, Xu Rui, Liu Xingyin
Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine and Offspring Health, Key Laboratory of Pathogen of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing 211166, China.
Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine and Offspring Health, Key Laboratory of Pathogen of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing 211166, China; The Second Affiliated Hospital of Nanjing Medical University, Nanjing 211166, China.
Cell Rep Methods. 2024 Dec 16;4(12):100932. doi: 10.1016/j.crmeth.2024.100932. Epub 2024 Dec 10.
Functional profiling of whole-metagenome shotgun sequencing (WMS) enables our understanding of microbe-host interactions. We demonstrate microbial functional information loss by current annotation methods at both the taxon and community levels, particularly at lower read depths. To address information loss, we develop a framework, RFW (reference-based functional profile inference on WMS), that utilizes information from genome functional annotations and taxonomic profiles to infer microbial function abundances from WMS. Furthermore, we provide an algorithm for absolute abundance change quantification between groups as part of the RFW framework. By applying RFW to several datasets related to autism spectrum disorder and colorectal cancer, we show that RFW augments downstream analyses, such as differential microbial function identification and association analysis between microbial function and host phenotype. RFW is open source and freely available at https://github.com/Xingyinliu-Lab/RFW.
全基因组鸟枪法测序（WMS）的功能分析有助于我们理解微生物与宿主之间的相互作用。我们证明了当前注释方法在分类单元和群落水平上都会导致微生物功能信息丢失，尤其是在较低读取深度时。为了解决信息丢失问题，我们开发了一个框架RFW（基于参考的WMS功能谱推断），该框架利用来自基因组功能注释和分类谱的信息从WMS推断微生物功能丰度。此外，作为RFW框架的一部分，我们提供了一种用于量化组间绝对丰度变化的算法。通过将RFW应用于几个与自闭症谱系障碍和结直肠癌相关的数据集，我们表明RFW增强了下游分析，如差异微生物功能识别以及微生物功能与宿主表型之间的关联分析。RFW是开源的，可在https://github.com/Xingyinliu-Lab/RFW上免费获取。
