Gut microbial genomes with paired isolates from China illustrate probiotic and cardiometabolic effects

• Published in: Cell genomics 2024-06, Vol.4 (6), p.100559, Article 100559
• Main Authors: Huang, Pan, Dong, Quanbin, Wang, Yifeng, Tian, Yunfan, Wang, Shunhe, Zhang, Chengcheng, Yu, Leilei, Tian, Fengwei, Gao, Xiaoxiang, Guo, Hang, Yi, Shanrong, Li, Mingyang, Liu, Yang, Zhang, Qingsong, Lu, Wenwei, Wang, Gang, Yang, Bo, Cui, Shumao, Hua, Dongxu, Wang, Xiuchao, Jiao, Yuwen, Liu, Lu, Deng, Qiufeng, Ma, Beining, Wu, Tingting, Zou, Huayiyang, Shi, Jing, Zhang, Haifeng, Fan, Daming, Sheng, Yanhui, Zhao, Jianxin, Tang, Liming, Zhang, Hao, Sun, Wei, Chen, Wei, Kong, Xiangqing, Chen, Lianmin, Zhai, Qixiao
• Format: Article
• Language: English
• ISSN: 2666-979X; 2666-979X
• DOI: 10.1016/j.xgen.2024.100559

The gut microbiome displays genetic differences among populations, and characterization of the genomic landscape of the gut microbiome in China remains limited. Here, we present the Chinese Gut Microbial Reference (CGMR) set, comprising 101,060 high-quality metagenomic assembled genomes (MAGs) of 3,707 nonredundant species from 3,234 fecal samples across primarily rural Chinese locations, 1,376 live isolates mainly from lactic acid bacteria, and 987 novel species relative to worldwide databases. We observed region-specific coexisting MAGs and MAGs with probiotic and cardiometabolic functionalities. Preliminary mouse experiments suggest a probiotic effect of two Faecalibacillus intestinalis isolates in alleviating constipation, cardiometabolic influences of three Bacteroides fragilis_A isolates in obesity, and isolates from the genera Parabacteroides and Lactobacillus in host lipid metabolism. Our study expands the current microbial genomes with paired isolates and demonstrates potential host effects, contributing to the mechanistic understanding of host-microbe interactions. [Display omitted] •101,060 assemblies paired with 1,376 isolates from Chinese gut metagenomes•987 novel species relative to worldwide databases improve mappability•Microbial genomes show regional specificity and are associated with host phenotypes•Potential probiotic and cardiometabolic effects of isolates are validated with mice Huang et al. introduced the CGMR catalog, comprising 101,060 high-quality assemblies of 3,707 nonredundant species from a nationwide collection of 3,234 Chinese gut metagenomes. They reconstructed 987 novel species relative to worldwide databases, enhancing mappability. Associations with host phenotypes further demonstrate their probiotic and cardiometabolic effects, validated with mouse experiments.