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

Pan Huang; Quanbin Dong; Yifeng Wang; Yunfan Tian; Shunhe Wang; Chengcheng Zhang; Leilei Yu; Fengwei Tian; Xiaoxiang Gao; Hang Guo; Shanrong Yi; Mingyang Li; Yang Liu; Qingsong Zhang; Wenwei Lu; Gang Wang; Bo Yang; Shumao Cui; Dongxu Hua; Xiuchao Wang; Yuwen Jiao; Lu Liu; Qiufeng Deng; Beining Ma; Tingting Wu; Huayiyang Zou; Jing Shi; Haifeng Zhang; Daming Fan; Yanhui Sheng; Jianxin Zhao; Liming Tang; Hao Zhang; Wei Sun; CGMR Consortium; Wei Chen; Xiangqing Kong; Lianmin Chen; Qixiao Zhai

doi:10.1016/j.xgen.2024.100559

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

Cell Genom. 2024 May 12:100559. doi: 10.1016/j.xgen.2024.100559. Online ahead of print.

Authors

Pan Huang¹, Quanbin Dong², Yifeng Wang³, Yunfan Tian⁴, Shunhe Wang¹, Chengcheng Zhang¹, Leilei Yu¹, Fengwei Tian¹, Xiaoxiang Gao¹, Hang Guo¹, Shanrong Yi¹, Mingyang Li¹, Yang Liu¹, Qingsong Zhang¹, Wenwei Lu¹, Gang Wang¹, Bo Yang¹, Shumao Cui¹, Dongxu Hua⁴, Xiuchao Wang⁴, Yuwen Jiao⁵, Lu Liu⁴, Qiufeng Deng⁴, Beining Ma⁴, Tingting Wu⁴, Huayiyang Zou⁴, Jing Shi⁴, Haifeng Zhang⁶, Daming Fan¹, Yanhui Sheng⁶, Jianxin Zhao¹, Liming Tang⁵, Hao Zhang¹, Wei Sun⁴; CGMR Consortium; Wei Chen¹, Xiangqing Kong⁷, Lianmin Chen⁸, Qixiao Zhai⁹

Affiliations

¹ State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China.
² Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China; Department of Gastroenterology, Changzhou Medical Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Nanjing Medical University, Changzhou, China.
³ Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China; Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China.
⁴ Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China.
⁵ Department of Gastroenterology, Changzhou Medical Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Nanjing Medical University, Changzhou, China.
⁶ Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China.
⁷ Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China; Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China. Electronic address: kongxq@njmu.edu.cn.
⁸ Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China; Department of Gastroenterology, Changzhou Medical Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Nanjing Medical University, Changzhou, China. Electronic address: lianminchen@njmu.edu.cn.
⁹ State Key Laboratory of Food Science and Resources & School of Food Science and Technology, Jiangnan University, Wuxi, China. Electronic address: zhaiqixiao@jiangnan.edu.cn.

PMID: 38740021
DOI: 10.1016/j.xgen.2024.100559

Abstract

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.