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PsycGM: a comprehensive database for associations between gut microbiota and psychiatric disorders

Molecular Psychiatry (2025)Cite this article

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Abstract

Psychiatric disorders pose substantial global burdens on public health, yet therapeutic options remain limited. Recently, gut microbiota is in the spotlight of new research on psychiatric disorders, as emerging discoveries have highlighted the importance of gut microbiome in the regulation of central nervous system via mediating the gut-brain-axis bidirectional communication. While metagenomics studies have accumulated for psychiatric disorders, few systematic efforts were dedicated to integrating these high-throughput data across diverse phenotypes, interventions, geographical regions, and biological species. To present a panoramic view of global data and provide a comprehensive resource for investigating the gut microbiota dysbiosis in psychiatric disorders, we developed the PsycGM, a manually curated and well-annotated database that provides the literature-supported associations between gut microbiota and psychiatric disorders or intervention measures. In total, PsycGM incorporated 559 studies from 31 countries worldwide, encompassing research involving humans, rats, mice, and non-human primates. PsycGM documented 8907 curated associations between 1514 gut microbial taxa and 11 psychiatric disorders, as well as 4050 associations between 869 taxa and 232 microbiota-based and non-microbiota-based interventions. Moreover, PsycGM provided a user-friendly web interface with comprehensive information, enabling browsing, retrieving and downloading of all entries. In the application of PsycGM, we panoramically depicted the intestinal microecological imbalance in depression. Additionally, we identified 9 microbial taxa consistently altered in patients with depression, with the most common dysregulations observed for Parabacteroides, Alistipes, and Faecalibacterium; in animal models of depression, consistent changes were observed in 21 microbial taxa, most frequently reported as Helicobacter, Lactobacillus, Roseburia, and the ratio of Firmicutes/Bacteroidetes. PsycGM is a comprehensive resource for future investigations on the role of gut microbiota in mental and brain health, and for therapeutic target innovations based on modifications of gut microbiota. PsycGM is freely accessed at http://psycgmomics.info.

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Fig. 1: Summary of the data composition in PsycGM.
Fig. 2: The numbers of reported entries for the most frequently reported microbial taxa at genus level in different psychiatric disorders in separate settings.
Fig. 3: Web interface of PsycGM.
Fig. 4: Differential microbial taxa reported by ≥2 human or animal studies on depression.
Fig. 5: Plots for data integration in a case study for the alteration of gut microbiota in depression.
Fig. 6: Overview of PsycGM database.

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Data availability

PsycGM is freely available at http://psycgmomics.info. All data sources analyzed in this study are included in the Supplementary Information. Supplementary information is available at MP’s website.

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Acknowledgements

This study was supported by the Joint Project of Chongqing Municipal Science and Technology Bureau and Chongqing Health Commission (2023CCXM003), the Natural Science Foundation of Chongqing (CSTB2024NSCQ-MSX1027), the Fund of Moutaintop Plan Project in the First Affiliated Hospital of Chongqing Medical University (cyyy-xkdfjh-lcyj-202301), the Natural Science Foundation Project of China (82371526), and the Natural Science Foundation Project of Chongqing (cstc2022ycjh-bgzxm0033). We thank Zhixin Chen for optimizing and beautifying the webpage of this database.

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Author notes

  1. These authors contributed equally: Dongfang Wang, Siwen Gui, Juncai Pu.

Authors and Affiliations

  1. Department of Neurology, NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China

    Dongfang Wang, Siwen Gui, Juncai Pu, Xiaogang Zhong, Zhuocan Li, Xiangkun Tao, Dan Yang, Haipeng Zhou, Renjie Qiao, Hanping Zhang, Xiangyu Cheng, Yi Ren, Weiyi Chen, Xiaopeng Chen, Wei Tao, Yue Chen, Xiang Chen, Yiyun Liu & Peng Xie

  2. Jinfeng Laboratory, Chongqing, 401329, China

    Dongfang Wang, Siwen Gui, Xiaogang Zhong, Yiyun Liu & Peng Xie

  3. Chongqing Institute for Brain and Intelligence, Chongqing, 400064, China

    Dongfang Wang, Siwen Gui, Xiaogang Zhong, Yiyun Liu & Peng Xie

  4. School of Medical Information, Chongqing Medical University, Chongqing, 400042, China

    Li Yan

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Contributions

Xie P and Liu YY conceptualized and designed the study. Wang DF was responsible for the literature search. Wang DF, Gui SW, Pu JC, Yan L, Li ZC, Tao XK were responsible for the study selection. Wang DF, Gui SW, Pu JC, Zhong XG, Yan L, Li ZC, Tao XK, Yang D, Zhou HP, and Qiao RJ were responsible for the data extraction, data curation, and quality assessment. Wang DF, Gui SW, and Pu JC wrote the original draft. Zhang HP, Cheng XY, Ren Y, Chen WY, Chen XP, Tao W, Chen Y, Chen X, Liu YY, and Xie P commented on and revised the manuscript. Xie P and Liu YY reviewed, edited, and made the final version. All authors contributed to the final draft of the manuscript.

Corresponding authors

Correspondence to Yiyun Liu or Peng Xie.

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The authors declare no competing interests.

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All methods were performed in accordance with the relevant guidelines and regulations. This study was approved by The Ethics Committee of Chongqing Medical University (IACUC-CQMU-2024-0115). The datasets generated in the current study were collected from publicly available literature or reports, therefore informed consent forms are not applicable.

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Wang, D., Gui, S., Pu, J. et al. PsycGM: a comprehensive database for associations between gut microbiota and psychiatric disorders. Mol Psychiatry (2025). https://doi.org/10.1038/s41380-025-03000-5

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