PT  - JOURNAL ARTICLE
AU  - Guojun Wu
AU  - Ting Xu
AU  - Naisi Zhao
AU  - Yan Y. Lam
AU  - Xiaoying Ding
AU  - Dongqin Wei
AU  - Jian Fan
AU  - Yajuan Shi
AU  - Xiaofeng Li
AU  - Mi Li
AU  - Shenjie Ji
AU  - Xuejiao Wang
AU  - Huaqing Fu
AU  - Feng Zhang
AU  - Yongde Peng
AU  - Yu Shi
AU  - Chenhong Zhang
AU  - Liping Zhao
TI  - Two Competing Guilds as a Core Microbiome Signature for Chronic Diseases
AID  - 10.1101/2022.05.02.490290
DP  - 2022 Jan 01
TA  - bioRxiv
PG  - 2022.05.02.490290
4099  - http://biorxiv.org/content/early/2022/05/02/2022.05.02.490290.short
4100  - http://biorxiv.org/content/early/2022/05/02/2022.05.02.490290.full
AB  - Gut microbiota may work as an essential organ and its members interact closely with each other and form a higher-level organization called guilds. How such guild-level structure supports the gut microbiota to stably provide essential health-relevant functions to the host remains elusive. With high quality metagenome-assembled genomes as network nodes, here we identified a core microbiome signature made up of two robust competing guilds that together correlate with a wide range of host health conditions. Genomes in these two guilds kept their ecological relationship unchanged despite experiencing profound abundance changes during a 3-month high fiber intervention and 1-year follow-up in patients with type 2 diabetes. The genomes of one guild harbored more genes for plant polysaccharide degradation and butyrate production, while the other guild had more genes for virulence or antibiotic resistance. A Random Forest regression model showed that the abundance distributions of these genomes were associated with 41 out of 43 bio-clinical parameters in the study cohort. With these genomes as reference, Random Forest modeling successfully classified case and control of 8 chronic diseases in 12 independent metagenomic datasets from 1,816 participants across ethnicity and geography. This core microbiome signature may facilitate ecological management of chronic diseases.Competing Interest StatementLiping Zhao is a co-founder of Notitia Biotechnologies Company.