Guild-level signature of gut microbiome for diabetic kidney disease

作者：Shasha Tang, Guojun Wu, Yalei Liu, Binghua Xue, Shihan Zhang, Weiwei Zhang, Yifan Jia, Qinyuan Xie, Chenghong Liang, Limin Wang, Hongyan Heng, Wei Wei, Xiaoyang Shi, Yimeng Hu, Junpeng Yang, Lingyun Zhao, Xiaobing Wang, Liping Zhao, Huijuan Yuan · 发表于：mBio · 年份：2024 · DOI：10.1128/mbio.00735-24 · 被引用次数：11 · 研究领域：Gut microbiota and health、Dialysis and Renal Disease Management、Oral microbiology and periodontitis research

Current microbiome signatures for chronic diseases such as diabetic kidney disease (DKD) are mainly based on low-resolution taxa such as genus or phyla and are often inconsistent among studies. In microbial ecosystems, bacterial functions are strain specific, and taxonomically different bacteria tend to form co-abundance functional groups called guilds. Here, we identified guild-level signatures for DKD by performing in-depth metagenomic sequencing and conducting genome-centric and guild-based analysis on fecal samples from 116 DKD patients and 91 healthy subjects. Redundancy analysis on 1,543 high-quality metagenome-assembled genomes (HQMAGs) identified 54 HQMAGs that were differentially distributed among the young healthy control group, elderly healthy control group, early-stage DKD patients (EDG), and late-stage DKD patients (LDG). Co-abundance network analysis classified the 54 HQMAGs into two guilds. Compared to guild 2, guild 1 contained more short-chain fatty acid biosynthesis genes and fewer genes encoding uremic toxin indole biosynthesis, antibiotic resistance, and virulence factors. Guild indices, derived from the total abundance of guild members and their diversity, delineated DKD patients from healthy subjects and between different severities of DKD. Age-adjusted partial Spearman correlation analysis showed that the guild indices were correlated with DKD disease progression and with risk indicators of poor prognosis. We further validated that the random forest cla...