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Two Competing Guilds as a Core Microbiome Signature for Chronic Diseases

Guojun Wu, Ting Xu, Naisi Zhao, Yan Y. Lam, Xiaoying Ding, Dongqin Wei, Jian Fan, Yajuan Shi, Xiaofeng Li, Mi Li, Shenjie Ji, Xuejiao Wang, Huaqing Fu, Feng Zhang, Yongde Peng, Yu Shi, Chenhong Zhang, Liping Zhao
doi: https://doi.org/10.1101/2022.05.02.490290
Guojun Wu
2Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences and Center for Microbiome, Nutrition, and Health, New Jersey Institute for Food, Nutrition, and Health, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
3Rutgers-Jiaotong Joint Laboratory for Microbiome and Human Health, New Brunswick, NJ, USA
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Ting Xu
1State Key Laboratory of Microbial Metabolism and Ministry of Education Key Laboratory of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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Naisi Zhao
6Department of Public Health and Community Medicine, School of Medicine, Tufts University, Boston, MA, 02111, USA
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Yan Y. Lam
7Gut Microbiota and Metabolism Group, Centre for Chinese Herbal Medicine Drug Development, School of Chinese Medicine, Hong Kong Baptist University, Units 201-207, Building 15W, 15 Science Park West Avenue, Pak Shek Kok, N.T., Hong Kong, China
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Xiaoying Ding
5Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
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Dongqin Wei
4Department of Endocrinology and Metabolism, Qidong People’s Hospital, Jiangsu 226200, China
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Jian Fan
4Department of Endocrinology and Metabolism, Qidong People’s Hospital, Jiangsu 226200, China
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Yajuan Shi
4Department of Endocrinology and Metabolism, Qidong People’s Hospital, Jiangsu 226200, China
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Xiaofeng Li
4Department of Endocrinology and Metabolism, Qidong People’s Hospital, Jiangsu 226200, China
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Mi Li
4Department of Endocrinology and Metabolism, Qidong People’s Hospital, Jiangsu 226200, China
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Shenjie Ji
4Department of Endocrinology and Metabolism, Qidong People’s Hospital, Jiangsu 226200, China
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Xuejiao Wang
5Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
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Huaqing Fu
1State Key Laboratory of Microbial Metabolism and Ministry of Education Key Laboratory of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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Feng Zhang
8Nutrition Department (Clinical Study Center of Functional Food), The Affiliated Hospital of Jiangnan University Wuxi, Jiangsu 214122, China
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Yongde Peng
5Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
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  • For correspondence: liping.zhao@rutgers.edu
Yu Shi
4Department of Endocrinology and Metabolism, Qidong People’s Hospital, Jiangsu 226200, China
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  • For correspondence: liping.zhao@rutgers.edu
Chenhong Zhang
1State Key Laboratory of Microbial Metabolism and Ministry of Education Key Laboratory of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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  • For correspondence: liping.zhao@rutgers.edu
Liping Zhao
1State Key Laboratory of Microbial Metabolism and Ministry of Education Key Laboratory of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
2Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences and Center for Microbiome, Nutrition, and Health, New Jersey Institute for Food, Nutrition, and Health, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
3Rutgers-Jiaotong Joint Laboratory for Microbiome and Human Health, New Brunswick, NJ, USA
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  • For correspondence: liping.zhao@rutgers.edu
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Summary Paragraph

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 Statement

Liping Zhao is a co-founder of Notitia Biotechnologies Company.

Footnotes

  • ↵* co-first author

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted May 02, 2022.
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Two Competing Guilds as a Core Microbiome Signature for Chronic Diseases
Guojun Wu, Ting Xu, Naisi Zhao, Yan Y. Lam, Xiaoying Ding, Dongqin Wei, Jian Fan, Yajuan Shi, Xiaofeng Li, Mi Li, Shenjie Ji, Xuejiao Wang, Huaqing Fu, Feng Zhang, Yongde Peng, Yu Shi, Chenhong Zhang, Liping Zhao
bioRxiv 2022.05.02.490290; doi: https://doi.org/10.1101/2022.05.02.490290
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Two Competing Guilds as a Core Microbiome Signature for Chronic Diseases
Guojun Wu, Ting Xu, Naisi Zhao, Yan Y. Lam, Xiaoying Ding, Dongqin Wei, Jian Fan, Yajuan Shi, Xiaofeng Li, Mi Li, Shenjie Ji, Xuejiao Wang, Huaqing Fu, Feng Zhang, Yongde Peng, Yu Shi, Chenhong Zhang, Liping Zhao
bioRxiv 2022.05.02.490290; doi: https://doi.org/10.1101/2022.05.02.490290

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