TY - JOUR
T1 - Compositional and genetic alterations in Graves’ disease gut microbiome reveal specific diagnostic biomarkers
AU - Zhu, Qiyun
AU - Hou, Qiangchuan
AU - Huang, Shi
AU - Ou, Qianying
AU - Huo, Dongxue
AU - Vázquez-Baeza, Yoshiki
AU - Cen, Chaoping
AU - Cantu, Victor
AU - Estaki, Mehrbod
AU - Chang, Haibo
AU - Belda-Ferre, Pedro
AU - Kim, Ho Cheol
AU - Chen, Kaining
AU - Knight, Rob
AU - Zhang, Jiachao
N1 - Funding Information:
Acknowledgements We sincerely thank all of the volunteers for their participation. This research was supported by the Key Research and Development Project of Hainan Province (No. ZDYF2018111 and ZDYF2019150) (JZ). This work was also supported by the National Science Foundation (grant no. 2038509) (RK). This work was also supported by IBM Research through the AI Horizons Network, UC San Diego AI for Healthy Living program in partnership with the UC San Diego Center for Microbiome Innovation.
Publisher Copyright:
© 2021, The Author(s).
PY - 2021/11
Y1 - 2021/11
N2 - Graves’ Disease is the most common organ-specific autoimmune disease and has been linked in small pilot studies to taxonomic markers within the gut microbiome. Important limitations of this work include small sample sizes and low-resolution taxonomic markers. Accordingly, we studied 162 gut microbiomes of mild and severe Graves’ disease (GD) patients and healthy controls. Taxonomic and functional analyses based on metagenome-assembled genomes (MAGs) and MAG-annotated genes, together with predicted metabolic functions and metabolite profiles, revealed a well-defined network of MAGs, genes and clinical indexes separating healthy from GD subjects. A supervised classification model identified a combination of biomarkers including microbial species, MAGs, genes and SNPs, with predictive power superior to models from any single biomarker type (AUC = 0.98). Global, cross-disease multi-cohort analysis of gut microbiomes revealed high specificity of these GD biomarkers, notably discriminating against Parkinson’s Disease, and suggesting that non-invasive stool-based diagnostics will be useful for these diseases.
AB - Graves’ Disease is the most common organ-specific autoimmune disease and has been linked in small pilot studies to taxonomic markers within the gut microbiome. Important limitations of this work include small sample sizes and low-resolution taxonomic markers. Accordingly, we studied 162 gut microbiomes of mild and severe Graves’ disease (GD) patients and healthy controls. Taxonomic and functional analyses based on metagenome-assembled genomes (MAGs) and MAG-annotated genes, together with predicted metabolic functions and metabolite profiles, revealed a well-defined network of MAGs, genes and clinical indexes separating healthy from GD subjects. A supervised classification model identified a combination of biomarkers including microbial species, MAGs, genes and SNPs, with predictive power superior to models from any single biomarker type (AUC = 0.98). Global, cross-disease multi-cohort analysis of gut microbiomes revealed high specificity of these GD biomarkers, notably discriminating against Parkinson’s Disease, and suggesting that non-invasive stool-based diagnostics will be useful for these diseases.
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U2 - 10.1038/s41396-021-01016-7
DO - 10.1038/s41396-021-01016-7
M3 - Article
C2 - 34079079
AN - SCOPUS:85107305303
SN - 1751-7362
VL - 15
SP - 3399
EP - 3411
JO - ISME Journal
JF - ISME Journal
IS - 11
ER -