1
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Wang Y, Wan L, Li Y, Qu Y, Qu L, Ma X, Yu Y, Wang X, Nie Z. Profiling of carbonyl metabolic fingerprints in urine of Graves' disease patients based on atmospheric ionization mass spectrometry. Talanta 2024; 277:126329. [PMID: 38815320 DOI: 10.1016/j.talanta.2024.126329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/22/2024] [Accepted: 05/25/2024] [Indexed: 06/01/2024]
Abstract
Graves' disease (GD) is considered among the organ autoimmune diseases and is somewhat linked to other autoimmune and secondary diseases. Commonly used detection methods rely on identifying characteristic clinical features and abnormal biochemical markers, but they have certain limitations and may be affected by patient medication. In this study, a desorption separation ionization (DSI) device coupled with a linear ion trap mass spectrometer is introduced for effective detection and screening of urine from GD patients. To enhance the sensitivity of MS analysis, derivatization reagent is utilized as a labeling method. The MS signal is used for metabolic profiling, through which differential metabolites and pathways are identified. Subsequently, processing the acquired spectra with a machine learning algorithm enables successful differentiation of GD patients and healthy individuals. This method is believed to provide versatile and powerful technical support for effective detection on the scene. Notably, this method offers the advantage of achieving early and rapid diagnosis of thyroid-related diseases.
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Affiliation(s)
- Yiran Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Wan
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Yuze Li
- State Key Laboratory of High-efficiency Utilization of Coal and Green Chemical Engineering, College of Chemistry and Chemical Engineering, Ningxia University, Yinchuan, 750021, China
| | - Yijiao Qu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liangliang Qu
- School of Life Sciences, Nanchang University, Nanchang, 330031, China
| | - Xiaobing Ma
- Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing, 100094, China
| | - Yang Yu
- Department of Endocrinology, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoxia Wang
- Department of Endocrinology, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.
| | - Zongxiu Nie
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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2
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Ludgate ME, Masetti G, Soares P. The relationship between the gut microbiota and thyroid disorders. Nat Rev Endocrinol 2024:10.1038/s41574-024-01003-w. [PMID: 38906998 DOI: 10.1038/s41574-024-01003-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/21/2024] [Indexed: 06/23/2024]
Abstract
Disorders of the thyroid gland are common, more prevalent in women than in men, and range from inflammatory to neoplastic lesions. Autoimmune thyroid diseases (AITD) affect 2-5% of the population, while thyroid cancer is the most frequent endocrine malignancy. Treatment for AITD is still restricted to management rather than prevention or cure. Progress has been made in identifying genetic variants that predispose to AITD and thyroid cancer, but the increasing prevalence of all thyroid disorders indicates that factors other than genes are involved. The gut microbiota, which begins to develop before birth, is highly sensitive to diet and the environment, providing a potential mechanism for non-communicable diseases to become communicable. Its functions extend beyond maintenance of gut integrity: the gut microbiota regulates the immune system, contributes to thyroid hormone metabolism and can generate or catabolize carcinogens, all of which are relevant to AITD and thyroid cancer. Observational and interventional studies in animal models support a role for the gut microbiota in AITD, which has been confirmed in some reports from human cohorts, although considerable geographic variation is apparent. Reports of a role for the microbiota in thyroid cancer are more limited, but evidence supports a relationship between gut dysbiosis and thyroid cancer.
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Affiliation(s)
| | | | - Paula Soares
- Faculty of Medicine of the University of Porto (FMUP), Porto, Portugal
- Instituto de Investigação e Inovação em Saúde da Universidade do Porto (I3S), Porto, Portugal
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3
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Yan Q, Li S, Yan Q, Huo X, Wang C, Wang X, Sun Y, Zhao W, Yu Z, Zhang Y, Guo R, Lv Q, He X, Yao C, Li Z, Chen F, Ji Q, Zhang A, Jin H, Wang G, Feng X, Feng L, Wu F, Ning J, Deng S, An Y, Guo DA, Martin FM, Ma X. A genomic compendium of cultivated human gut fungi characterizes the gut mycobiome and its relevance to common diseases. Cell 2024; 187:2969-2989.e24. [PMID: 38776919 DOI: 10.1016/j.cell.2024.04.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 02/17/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
The gut fungal community represents an essential element of human health, yet its functional and metabolic potential remains insufficiently elucidated, largely due to the limited availability of reference genomes. To address this gap, we presented the cultivated gut fungi (CGF) catalog, encompassing 760 fungal genomes derived from the feces of healthy individuals. This catalog comprises 206 species spanning 48 families, including 69 species previously unidentified. We explored the functional and metabolic attributes of the CGF species and utilized this catalog to construct a phylogenetic representation of the gut mycobiome by analyzing over 11,000 fecal metagenomes from Chinese and non-Chinese populations. Moreover, we identified significant common disease-related variations in gut mycobiome composition and corroborated the associations between fungal signatures and inflammatory bowel disease (IBD) through animal experimentation. These resources and findings substantially enrich our understanding of the biological diversity and disease relevance of the human gut mycobiome.
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Affiliation(s)
- Qiulong Yan
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China; Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China; College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Shenghui Li
- Puensum Genetech Institute, Wuhan 430076, China; Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100091, China
| | - Qingsong Yan
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Xiaokui Huo
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Chao Wang
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China; Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China; First Affiliated Hospital, Dalian Medical University, Dalian 116044, China.
| | - Xifan Wang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100091, China; Department of Obstetrics and Gynecology, Columbia University, New York, NY 10027, USA
| | - Yan Sun
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Wenyu Zhao
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Zhenlong Yu
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan 430076, China
| | - Ruochun Guo
- Puensum Genetech Institute, Wuhan 430076, China
| | - Qingbo Lv
- Puensum Genetech Institute, Wuhan 430076, China
| | - Xin He
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China; Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China
| | - Changliang Yao
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China
| | | | - Fang Chen
- College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Qianru Ji
- Puensum Genetech Institute, Wuhan 430076, China
| | - Aiqin Zhang
- Puensum Genetech Institute, Wuhan 430076, China
| | - Hao Jin
- Puensum Genetech Institute, Wuhan 430076, China
| | - Guangyang Wang
- College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Xiaoying Feng
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Lei Feng
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Fan Wu
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Jing Ning
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Sa Deng
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Yue An
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - De-An Guo
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China.
| | - Francis M Martin
- Université de Lorraine, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux 54280, France; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100091, China.
| | - Xiaochi Ma
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China; Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China.
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4
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Jeong C, Baek H, Bae J, Hwang N, Ha J, Cho YS, Lim DJ. Gut microbiome in the Graves' disease: Comparison before and after anti-thyroid drug treatment. PLoS One 2024; 19:e0300678. [PMID: 38820506 PMCID: PMC11142679 DOI: 10.1371/journal.pone.0300678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 03/01/2024] [Indexed: 06/02/2024] Open
Abstract
While several studies have proposed a connection between the gut microbiome and the pathogenesis of Graves's disease (GD), there has been a lack of reports on alteration in microbiome following using anti-thyroid drug treatment (ATD) to treat GD. Stool samples were collected from newly diagnosed GD patients provided at baseline and after 6 months of ATD treatment. The analysis focused on investigating the association between the changes in the gut microbiome and parameter including thyroid function, thyroid-related antibodies, and the symptom used to assess hyperthyroidism before and after treatment. A healthy control (HC) group consisting of data from 230 healthy subjects (110 males and 120 females) sourced from the open EMBL Nucleotide Sequence Database was included. Twenty-nine GD patients (14 males and 15 females) were enrolled. The analysis revealed a significant reduction of alpha diversity in GD patients. However, after ATD treatment, alpha diversity exhibited a significant increase, restored to levels comparable to the HC levels. Additionally, GD patients displayed lower levels of Firmicutes and higher levels of Bacteroidota. Following treatment, there was an increased in Firmicutes and a decrease in Bacteroidota, resembling levels found in the HC levels. The symptoms of hyperthyroidism were negatively associated with Firmicutes and positively associated with Bacteroidota. GD had significantly lower levels of Roseburia, Lachnospiraceaea, Sutterella, Escherichia-shigella, Parasuterella, Akkermansia, and Phascolarctobacterium compared to HC (all p < 0.05). Post-treatment, Subdoligranulum increased (p = 0.010), while Veillonella and Christensenellaceaea R-7 group decreased (p = 0.023, p = 0.029, respectively). Anaerostipes showed a significant association with both higher smoking pack years and TSHR-Ab levels, with greater abundantce observed in smokers among GD (p = 0.16). Although reduced ratio of Firmicutes/Bacteroidetes was evident in GD, this ratio recovered after treatment. This study postulates the involvement of the gut microbiome in the pathogenesis of GD, suggesting potential restoration after treatment.
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Affiliation(s)
- Chaiho Jeong
- Division of Endocrinology and Metabolism, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hansang Baek
- Division of Endocrinology and Metabolism, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jaewoong Bae
- R&D Institute, BioEleven Co., Ltd., Seoul, Republic of Korea
| | - Nakwon Hwang
- R&D Institute, BioEleven Co., Ltd., Seoul, Republic of Korea
| | - Jeonghoon Ha
- Division of Endocrinology and Metabolism, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Young-Seok Cho
- Division of Gastroenterology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Dong-Jun Lim
- Division of Endocrinology and Metabolism, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
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5
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Seida I, Al Shawaf M, Mahroum N. Fecal microbiota transplantation in autoimmune diseases - An extensive paper on a pathogenetic therapy. Autoimmun Rev 2024:103541. [PMID: 38593970 DOI: 10.1016/j.autrev.2024.103541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/31/2024] [Accepted: 04/04/2024] [Indexed: 04/11/2024]
Abstract
The role of infections in the pathogenesis of autoimmune diseases has long been recognized and reported. In addition to infectious agents, the internal composition of the "friendly" living bacteria, (microbiome) and its correlation to immune balance and dysregulation have drawn the attention of researchers for decades. Nevertheless, only recently, scientific papers regarding the potential role of transferring microbiome from healthy donor subjects to patients with autoimmune diseases has been proposed. Fecal microbiota transplantation or FMT, carries the logic of transferring microorganisms responsible for immune balance from healthy donors to individuals with immune dysregulation or more accurately for our paper, autoimmune diseases. Viewing the microbiome as a pathogenetic player allows us to consider FMT as a pathogenetic-based treatment. Promising results alongside improved outcomes have been demonstrated in patients with different autoimmune diseases following FMT. Therefore, in our current extensive review, we aimed to highlight the implication of FMT in various autoimmune diseases, such as inflammatory bowel disease, autoimmune thyroid and liver diseases, systemic lupus erythematosus, and type 1 diabetes mellitus, among others. Presenting all the aspects of FMT in more than 12 autoimmune diseases in one paper, to the best of our knowledge, is the first time presented in medical literature. Viewing FMT as such could contribute to better understanding and newer application of the model in the therapy of autoimmune diseases, indeed.
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Affiliation(s)
- Isa Seida
- International School of Medicine, Istanbul Medipol University, Istanbul, Turkey
| | - Maisam Al Shawaf
- International School of Medicine, Istanbul Medipol University, Istanbul, Turkey
| | - Naim Mahroum
- International School of Medicine, Istanbul Medipol University, Istanbul, Turkey.
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6
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Teniou A, Rhouati A, Marty JL. Recent Advances in Biosensors for Diagnosis of Autoimmune Diseases. SENSORS (BASEL, SWITZERLAND) 2024; 24:1510. [PMID: 38475046 DOI: 10.3390/s24051510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 02/01/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024]
Abstract
Over the last decade, autoimmune diseases (ADs) have undergone a significant increase because of genetic and/or environmental factors; therefore, their simple and fast diagnosis is of high importance. The conventional diagnostic techniques for ADs require tedious sample preparation, sophisticated instruments, a dedicated laboratory, and qualified personnel. For these reasons, biosensors could represent a useful alternative to these methods. Biosensors are considered to be promising tools that can be used in clinical analysis for an early diagnosis due to their high sensitivity, simplicity, low cost, possible miniaturization (POCT), and potential ability for real-time analysis. In this review, recently developed biosensors for the detection of autoimmune disease biomarkers are discussed. In the first part, we focus on the main AD biomarkers and the current methods of their detection. Then, we discuss the principles and different types of biosensors. Finally, we overview the characteristics of biosensors based on different bioreceptors reported in the literature.
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Affiliation(s)
- Ahlem Teniou
- Bioengineering Laboratory, Higher National School of Biotechnology, Constantine 25100, Algeria
| | - Amina Rhouati
- Bioengineering Laboratory, Higher National School of Biotechnology, Constantine 25100, Algeria
| | - Jean-Louis Marty
- Laboratoire BAE, Université de Perpignan through Domitia, 66860 Perpignan, France
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7
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Geng X, Liu Y, Xu W, Li G, Xue B, Feng Y, Tang S, Wei W, Yuan H. Eukaryotes may play an important ecological role in the gut microbiome of Graves' disease. Front Immunol 2024; 15:1334158. [PMID: 38455050 PMCID: PMC10917987 DOI: 10.3389/fimmu.2024.1334158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 02/05/2024] [Indexed: 03/09/2024] Open
Abstract
The prevalence of autoimmune diseases worldwide has risen rapidly over the past few decades. Increasing evidence has linked gut dysbiosis to the onset of various autoimmune diseases. Thanks to the significant advancements in high-throughput sequencing technology, the number of gut microbiome studies has increased. However, they have primarily focused on bacteria, so our understanding of the role and significance of eukaryotic microbes in the human gut microbial ecosystem remains quite limited. Here, we selected Graves' disease (GD) as an autoimmune disease model and investigated the gut multi-kingdom (bacteria, fungi, and protists) microbial communities from the health control, diseased, and medication-treated recovered patients. The results showed that physiological changes in GD increased homogenizing dispersal processes for bacterial community assembly and increased homogeneous selection processes for eukaryotic community assembly. The recovered patients vs. healthy controls had similar bacterial and protistan, but not fungal, community assembly processes. Additionally, eukaryotes (fungi and protists) may play a more significant role in gut ecosystem functions than bacteria. Overall, this study gives brief insights into the potential contributions of eukaryotes to gut and immune homeostasis in humans and their potential influence in relation to therapeutic interventions.
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Affiliation(s)
- Xiwen Geng
- Department of the Clinical Research Center, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yalei Liu
- Department of Endocrinology, Henan Provincial Key Medicine Laboratory of Intestinal Microecology and Diabetes, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Wenbo Xu
- Department of Clinical Microbiology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Gefei Li
- Department of Blood Transfusion, Henan Provincial People's Hospital, Department of Blood Transfusion of Central China Fuwai Hospital, Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Binghua Xue
- Department of Endocrinology, Henan Provincial Key Medicine Laboratory of Intestinal Microecology and Diabetes, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yu Feng
- Department of Endocrinology, Henan Provincial Key Medicine Laboratory of Intestinal Microecology and Diabetes, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Shasha Tang
- Department of Endocrinology, Henan Provincial Key Medicine Laboratory of Intestinal Microecology and Diabetes, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Wei Wei
- Department of Endocrinology, Henan Provincial Key Medicine Laboratory of Intestinal Microecology and Diabetes, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Huijuan Yuan
- Department of Endocrinology, Henan Provincial Key Medicine Laboratory of Intestinal Microecology and Diabetes, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
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8
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Wu J, Singleton SS, Bhuiyan U, Krammer L, Mazumder R. Multi-omics approaches to studying gastrointestinal microbiome in the context of precision medicine and machine learning. Front Mol Biosci 2024; 10:1337373. [PMID: 38313584 PMCID: PMC10834744 DOI: 10.3389/fmolb.2023.1337373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/27/2023] [Indexed: 02/06/2024] Open
Abstract
The human gastrointestinal (gut) microbiome plays a critical role in maintaining host health and has been increasingly recognized as an important factor in precision medicine. High-throughput sequencing technologies have revolutionized -omics data generation, facilitating the characterization of the human gut microbiome with exceptional resolution. The analysis of various -omics data, including metatranscriptomics, metagenomics, glycomics, and metabolomics, holds potential for personalized therapies by revealing information about functional genes, microbial composition, glycans, and metabolites. This multi-omics approach has not only provided insights into the role of the gut microbiome in various diseases but has also facilitated the identification of microbial biomarkers for diagnosis, prognosis, and treatment. Machine learning algorithms have emerged as powerful tools for extracting meaningful insights from complex datasets, and more recently have been applied to metagenomics data via efficiently identifying microbial signatures, predicting disease states, and determining potential therapeutic targets. Despite these rapid advancements, several challenges remain, such as key knowledge gaps, algorithm selection, and bioinformatics software parametrization. In this mini-review, our primary focus is metagenomics, while recognizing that other -omics can enhance our understanding of the functional diversity of organisms and how they interact with the host. We aim to explore the current intersection of multi-omics, precision medicine, and machine learning in advancing our understanding of the gut microbiome. A multidisciplinary approach holds promise for improving patient outcomes in the era of precision medicine, as we unravel the intricate interactions between the microbiome and human health.
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Affiliation(s)
- Jingyue Wu
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, United States
| | - Stephanie S. Singleton
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, United States
| | - Urnisha Bhuiyan
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, United States
| | - Lori Krammer
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, United States
- Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
| | - Raja Mazumder
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, United States
- The McCormick Genomic and Proteomic Center, The George Washington University, Washington, DC, United States
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9
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Shu Q, Kang C, Li J, Hou Z, Xiong M, Wang X, Peng H. Effect of probiotics or prebiotics on thyroid function: A meta-analysis of eight randomized controlled trials. PLoS One 2024; 19:e0296733. [PMID: 38206993 PMCID: PMC10783727 DOI: 10.1371/journal.pone.0296733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 12/18/2023] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Microbiome-directed therapies are increasingly utilized to optimize thyroid function in both healthy individuals and those with thyroid disorders. However, recent doubts have been raised regarding the efficacy of probiotics, prebiotics, and synbiotics in improving thyroid function. This systematic review aimed to investigate the potential relationship between probiotics/prebiotics and thyroid function by analyzing the impact on thyroid hormone levels. METHODS We conducted a comprehensive systematic review and meta-analysis of randomized controlled trials that investigated the effects of probiotics, prebiotics, and synbiotics on free triiodothyronine (fT3), free thyroxine (fT4), thyroid stimulating hormone (TSH), and thyroid stimulating hormone receptor antibody (TRAb) levels. We searched for articles from PubMed, Scopus, Web of Science, and Embase up until April 1st, 2023, without any language restriction. Quantitative data analysis was performed using a random-effects model, with standardized mean difference (SMD) and 95% confidence interval as summary statistics. The methods and results were reported according to the PRISMA2020 statement. RESULTS A total of eight articles were included in this review. The meta-analysis showed no significant alterations in TSH (SMD: -0.01, 95% CI: -0.21, 0.20, P = 0.93; I2: 0.00%), fT4 (SMD: 0.04, 95% CI: -0.29, 0.21, P = 0.73; I2: 0.00%) or fT3 (SMD: 0.45, 95% CI: -0.14, 1.03, P = 0.43; I2: 78.00%), while a significant reduction in TRAb levels was observed (SMD: -0.85, 95% CI: -1.54, -0.15, P = 0.02; I2: 18.00%) following probiotics/prebiotics supplementation. No indication of publication bias was found. CONCLUSIONS Probiotics/prebiotics supplementation does not influence thyroid hormone levels, but may modestly reduce TRAb levels in patients with Graves' disease.
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Affiliation(s)
- Qinxi Shu
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan Province, China
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan Province, China
| | - Chao Kang
- Department of Nutriology of the General Hospital of Western Theater Command, Chengdu, Sichuan Province, China
| | - Jiaxin Li
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan Province, China
| | - Zhenzhu Hou
- Department of Emergency Medicine, No. 922 Hospital of the Joint Service Support Force of the PLA, Hengyang, Hunan Province, China
| | - Minfen Xiong
- Department of Critical Care Medicine, No. 922 Hospital of the Joint Service Support Force of the PLA, Hengyang, Hunan Province, China
| | - Xingang Wang
- Department of Health Medicine, No. 922 Hospital of the Joint Service Support Force of the PLA, Hengyang, Hunan Province, China
| | - Hongyan Peng
- Department of Critical Care Medicine, No. 922 Hospital of the Joint Service Support Force of the PLA, Hengyang, Hunan Province, China
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10
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Ma C, Zhang Y, Jiang S, Teng F, Huang S, Zhang J. Cross-cohort single-nucleotide-variant profiling of gut microbiota suggests a novel gut-health assessment approach. mSystems 2023; 8:e0082823. [PMID: 37905808 PMCID: PMC10734426 DOI: 10.1128/msystems.00828-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/21/2023] [Indexed: 11/02/2023] Open
Abstract
IMPORTANCE Most studies focused much on the change in abundance and often failed to explain the microbiome variation related to disease conditions, Herein, we argue that microbial genetic changes can precede the ecological changes associated with the host physiological changes and, thus, would offer a new information layer from metagenomic data for predictive modeling of diseases. Interestingly, we preliminarily found a few genetic biomarkers on SCFA production can cover most chronic diseases involved in the meta-analysis. In the future, it is of both scientific and clinical significance to further explore the dynamic interactions between adaptive evolution and ecology of gut microbiota associated with host health status.
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Affiliation(s)
- Chenchen Ma
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, School of Food Science and Engineering, Hainan University, Haikou, China
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Yufeng Zhang
- Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| | - Shuaiming Jiang
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, School of Food Science and Engineering, Hainan University, Haikou, China
| | - Fei Teng
- Qingdao Stomatological Hospital Affiliated to Qingdao University, Qingdao, China
| | - Shi Huang
- Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| | - Jiachao Zhang
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, School of Food Science and Engineering, Hainan University, Haikou, China
- One Health Institute, Hainan University, Haikou, Hainan, China
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11
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Gao W, Gao X, Zhu L, Gao S, Sun R, Feng Z, Wu D, Liu Z, Zhu R, Jiao N. Multimodal metagenomic analysis reveals microbial single nucleotide variants as superior biomarkers for early detection of colorectal cancer. Gut Microbes 2023; 15:2245562. [PMID: 37635357 PMCID: PMC10464540 DOI: 10.1080/19490976.2023.2245562] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/29/2023] Open
Abstract
Microbial signatures show remarkable potentials in predicting colorectal cancer (CRC). This study aimed to evaluate the diagnostic powers of multimodal microbial signatures, multi-kingdom species, genes, and single-nucleotide variants (SNVs) for detecting precancerous adenomas. We performed cross-cohort analyses on whole metagenome sequencing data of 750 samples via xMarkerFinder to identify adenoma-associated microbial multimodal signatures. Our data revealed that fungal species outperformed species from other kingdoms with an area under the ROC curve (AUC) of 0.71 in distinguishing adenomas from controls. The microbial SNVs, including dark SNVs with synonymous mutations, displayed the strongest diagnostic capability with an AUC value of 0.89, sensitivity of 0.79, specificity of 0.85, and Matthews correlation coefficient (MCC) of 0.74. SNV biomarkers also exhibited outstanding performances in three independent validation cohorts (AUCs = 0.83, 0.82, 0.76; sensitivity = 1.0, 0.72, 0.93; specificity = 0.67, 0.81, 0.67, MCCs = 0.69, 0.83, 0.72) with high disease specificity for adenoma. In further support of the above results, functional analyses revealed more frequent inter-kingdom associations between bacteria and fungi, and abnormalities in quorum sensing, purine and butanoate metabolism in adenoma, which were validated in a newly recruited cohort via qRT-PCR. Therefore, these data extend our understanding of adenoma-associated multimodal alterations in the gut microbiome and provide a rationale of microbial SNVs for the early detection of CRC.
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Affiliation(s)
- Wenxing Gao
- Department of Gastroenterology, the Shanghai Tenth People’s Hospital, School of Medicine, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
| | - Xiang Gao
- Department of Gastroenterology, the Shanghai Tenth People’s Hospital, School of Medicine, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
| | - Lixin Zhu
- Guangdong Institute of Gastroenterology; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases; Biomedical Innovation Center, Sun Yat-Sen University, Guangzhou, P. R. China
- Department of General Surgery, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, P. R. China
| | - Sheng Gao
- Department of Gastroenterology, the Shanghai Tenth People’s Hospital, School of Medicine, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
| | - Ruicong Sun
- Department of Gastroenterology, the Shanghai Tenth People’s Hospital, School of Medicine, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
| | - Zhongsheng Feng
- Department of Gastroenterology, the Shanghai Tenth People’s Hospital, School of Medicine, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
| | - Dingfeng Wu
- National Clinical Research Center for Child Health, the Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, P. R. China
| | - Zhanju Liu
- Center for IBD Research, Department of Gastroenterology, the Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, P. R. China
| | - Ruixin Zhu
- Department of Gastroenterology, the Shanghai Tenth People’s Hospital, School of Medicine, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
- Research Institute, GloriousMed Clinical Laboratory Co, Ltd, Shanghai, P. R. China
| | - Na Jiao
- National Clinical Research Center for Child Health, the Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, P. R. China
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12
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Fenneman AC, van der Spek AH, Hartstra A, Havik S, Salonen A, de Vos WM, Soeters MR, Saeed P, Nieuwdorp M, Rampanelli E. Intestinal permeability is associated with aggravated inflammation and myofibroblast accumulation in Graves' orbitopathy: the MicroGO study. Front Endocrinol (Lausanne) 2023; 14:1173481. [PMID: 38107520 PMCID: PMC10724020 DOI: 10.3389/fendo.2023.1173481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 06/20/2023] [Indexed: 12/19/2023] Open
Abstract
Background Graves' disease (GD) and Graves' orbitopathy (GO) result from ongoing stimulation of the TSH receptor due to autoantibodies acting as persistent agonists. Orbital pre-adipocytes and fibroblasts also express the TSH receptor, resulting in expanded retro-orbital tissue and causing exophthalmos and limited eye movement. Recent studies have shown that GD/GO patients have a disturbed gut microbiome composition, which has been associated with increased intestinal permeability. This study hypothesizes that enhanced intestinal permeability may aggravate orbital inflammation and, thus, increase myofibroblast differentiation and the degree of fibrosis. Methods Two distinct cohorts of GO patients were studied, one of which was a unique cohort consisting of blood, fecal, and retro-orbital tissue samples. Intestinal permeability was assessed by measuring serum lipopolysaccharide-binding protein (LBP), zonulin, TLR5, and TLR9 ligands. The influx of macrophages and accumulation of T-cells and myofibroblast were quantified in orbital connective tissue. The NanoString immune-oncology RNA targets panel was used to determine the transcriptional profile of active fibrotic areas within orbital sections. Results GO patients displayed significantly higher LBP serum concentrations than healthy controls. Within the MicroGO cohort, patients with high serum LBP levels also showed higher levels of zonulin and TLR5 and TLR9 ligands in their circulation. The increased intestinal permeability was accompanied by augmented expression of genes marking immune cell infiltration and encoding key proteins for immune cell adhesion, antigen presentation, and cytokine signaling in the orbital tissue. Macrophage influx was positively linked to the extent of T cell influx and fibroblast activation within GO-affected orbital tissues. Moreover, serum LBP levels significantly correlated with the abundance of specific Gram-negative gut bacteria, linking the gut to local orbital inflammation. Conclusion These results indicate that GO patients have enhanced intestinal permeability. The subsequent translocation of bacterial compounds to the systemic circulation may aggravate inflammatory processes within the orbital tissue and, as a consequence, augment the proportion of activated myofibroblasts, which actively secrete extracellular matrix leading to retro-orbital tissue expansion. These findings warrant further exploration to assess the correlation between specific inflammatory pathways in the orbital tissue and the gut microbiota composition and may pave the way for new microbiota-targeting therapies.
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Affiliation(s)
- Aline C. Fenneman
- Department of (Experimental) Vascular Medicine, Amsterdam Cardiovascular Sciences (ACS), Amsterdam University Medical Centre (UMC), University of Amsterdam, Amsterdam, Netherlands
- Department of Endocrinology and Metabolism, Amsterdam Gastroenterology Endocrinology & Metabolism (AGEM), Amsterdam University Medical Centre (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Anne H. van der Spek
- Department of Endocrinology and Metabolism, Amsterdam Gastroenterology Endocrinology & Metabolism (AGEM), Amsterdam University Medical Centre (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Annick Hartstra
- Department of (Experimental) Vascular Medicine, Amsterdam Cardiovascular Sciences (ACS), Amsterdam University Medical Centre (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Stefan Havik
- Department of (Experimental) Vascular Medicine, Amsterdam Cardiovascular Sciences (ACS), Amsterdam University Medical Centre (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Anne Salonen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Willem M. de Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Maarten R. Soeters
- Department of Endocrinology and Metabolism, Amsterdam Gastroenterology Endocrinology & Metabolism (AGEM), Amsterdam University Medical Centre (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Peeroz Saeed
- Department of Ophthalmology, Amsterdam University Medical Centre (UMC), Amsterdam, Netherlands
| | - Max Nieuwdorp
- Department of (Experimental) Vascular Medicine, Amsterdam Cardiovascular Sciences (ACS), Amsterdam University Medical Centre (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Elena Rampanelli
- Department of (Experimental) Vascular Medicine, Amsterdam Cardiovascular Sciences (ACS), Amsterdam University Medical Centre (UMC), University of Amsterdam, Amsterdam, Netherlands
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13
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Yang F, Gao R, Luo X, Liu R, Xiong D. Berberine influences multiple diseases by modifying gut microbiota. Front Nutr 2023; 10:1187718. [PMID: 37599699 PMCID: PMC10435753 DOI: 10.3389/fnut.2023.1187718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 07/17/2023] [Indexed: 08/22/2023] Open
Abstract
Berberine (BBR) is an isoquinoline alkaloid that is widely distributed in the plant kingdom and is commonly found in Coptis chinensis Franch. It has low bioavailability, but it can interact with gut microbiota and affect a variety of diseases. The effects of BBR in diabetes, hyperlipidemia, atherosclerosis, liver diseases, intestinal diseases, mental disorders, autoimmune diseases, and other diseases are all thought to be related to gut microbiota. This review systematically and comprehensively summarize these interactions and their effects, and describes the changes of gut microbiota after the intervention of different doses of berberine and its potential clinical consequences, in order to provide a basis for the rational application of BBR in the future clinical treatment.
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Affiliation(s)
- Fujie Yang
- Department of Laboratory Medicine, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Rongmao Gao
- Department of ICU, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiaoxiu Luo
- Department of ICU, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Rongan Liu
- Department of ICU, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Daqian Xiong
- Department of Laboratory Medicine, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
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14
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Zhang XY, Xu JD, Wang Y, Wu CY, Zhou J, Shen H, Zou YT, Zhu JH, Zhou SS, Li SL, Xu J, Long F. Comparing steamed and wine-stewed Rehmanniae Radix in terms of Yin-nourishing effects via metabolomics and microbiome analysis. JOURNAL OF ETHNOPHARMACOLOGY 2023; 311:116424. [PMID: 37003400 DOI: 10.1016/j.jep.2023.116424] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 03/02/2023] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Rehmanniae Radix Praeparata (RRP), the processed root of Rehmannia glutinosa, has been widely used to treat Yin deficiency syndrome in traditional Chinese medicine. RRP is available in two forms: processed by steaming with water (SRR) or processed by stewing with yellow rice wine (WRR). Previous work has documented chemical differences in the secondary metabolomes and glycomes of SRR and WRR. AIM OF THE STUDY This study aimed to compare SRR and WRR in terms of Yin-nourishing effects via metabolomics and microbiome analysis. MATERIALS AND METHODS ICR mice were orally administered with thyroxine for 14 d to induce Yin deficiency. Changes in biochemical indices and histopathology were detected. Serum metabolomics analysis and microbial 16S rRNA sequencing were performed to compare the therapeutic effects and mechanisms between SRR and WRR in treating thyroxine-induced Yin deficiency. RESULTS Both SRR and WRR decreased serum T3, T4 and MDA levels, and increased SOD activity. SRR more effectively decreased serum Cr, and ameliorated kidney injury, while WRR showed better regulation on ratio of cAMP/cGMP and serum TSH, and relieved thyroid injury. Both SRR and WRR regulated tyrosine, glycerophospholipid, and linoleic acid metabolism and the citric acid cycle. Additionally, SRR regulated fatty acid metabolism, while WRR influenced alanine, aspartate and glutamate metabolism, and bile acid biosynthesis. SRR significantly enriched the genera Staphylococcus and Bifidobacterium in the gut microbiome, while WRR significantly enriched the genera Akkermansia, Bacteroides and Parabacteroides, and decreased the abundance of Lactobacillus. CONCLUSIONS SRR displayed better protective effects on kidney, while WRR showed stronger effects on thyroid in thyroxine-induced Yin deficient mice. These differences might be due to different regulating effects of SRR and WRR on the metabolome and gut microbiota.
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Affiliation(s)
- Xiao-Ya Zhang
- Department of Pharmaceutical Analysis, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, China
| | - Jin-Di Xu
- Department of Pharmaceutical Analysis, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, China; Department of Metabolomics, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, China
| | - Yao Wang
- Department of Pharmaceutical Analysis, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, China
| | - Cheng-Ying Wu
- Department of Metabolomics, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, China
| | - Jing Zhou
- Department of Metabolomics, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, China
| | - Hong Shen
- Department of Metabolomics, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, China
| | - Ye-Ting Zou
- Department of Pharmaceutical Analysis, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, China
| | - Jin-Hao Zhu
- Department of Pharmaceutical Analysis, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, China
| | - Shan-Shan Zhou
- Department of Metabolomics, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, China
| | - Song-Lin Li
- Department of Pharmaceutical Analysis, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, China; Department of Metabolomics, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, 210028, China.
| | - Jun Xu
- Department of Pharmaceutical Analysis, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, China; School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, 999077, Hong Kong, China.
| | - Fang Long
- Department of Pharmaceutical Analysis, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, China; Department of Respiratory Medicine, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, China.
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15
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Mendoza-León MJ, Mangalam AK, Regaldiz A, González-Madrid E, Rangel-Ramírez MA, Álvarez-Mardonez O, Vallejos OP, Méndez C, Bueno SM, Melo-González F, Duarte Y, Opazo MC, Kalergis AM, Riedel CA. Gut microbiota short-chain fatty acids and their impact on the host thyroid function and diseases. Front Endocrinol (Lausanne) 2023; 14:1192216. [PMID: 37455925 PMCID: PMC10349397 DOI: 10.3389/fendo.2023.1192216] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 05/23/2023] [Indexed: 07/18/2023] Open
Abstract
Thyroid disorders are clinically characterized by alterations of L-3,5,3',5'-tetraiodothyronine (T4), L-3,5,3'-triiodothyronine (T3), and/or thyroid-stimulating hormone (TSH) levels in the blood. The most frequent thyroid disorders are hypothyroidism, hyperthyroidism, and hypothyroxinemia. These conditions affect cell differentiation, function, and metabolism. It has been reported that 40% of the world's population suffers from some type of thyroid disorder and that several factors increase susceptibility to these diseases. Among them are iodine intake, environmental contamination, smoking, certain drugs, and genetic factors. Recently, the intestinal microbiota, composed of more than trillions of microbes, has emerged as a critical player in human health, and dysbiosis has been linked to thyroid diseases. The intestinal microbiota can affect host physiology by producing metabolites derived from dietary fiber, such as short-chain fatty acids (SCFAs). SCFAs have local actions in the intestine and can affect the central nervous system and immune system. Modulation of SCFAs-producing bacteria has also been connected to metabolic diseases, such as obesity and diabetes. In this review, we discuss how alterations in the production of SCFAs due to dysbiosis in patients could be related to thyroid disorders. The studies reviewed here may be of significant interest to endocrinology researchers and medical practitioners.
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Affiliation(s)
- María José Mendoza-León
- Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | | | - Alejandro Regaldiz
- Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
- Facultad de Medicina Veterinaria y Agronomía, Instituto de Ciencias Naturales, Universidad de las Américas, Santiago, Chile
| | - Enrique González-Madrid
- Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Ma. Andreina Rangel-Ramírez
- Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Oscar Álvarez-Mardonez
- Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Omar P. Vallejos
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
- Millennium Institute of Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Constanza Méndez
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
- Millennium Institute of Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Susan M. Bueno
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
- Millennium Institute of Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Felipe Melo-González
- Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Yorley Duarte
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Ma. Cecilia Opazo
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
- Facultad de Medicina Veterinaria y Agronomía, Instituto de Ciencias Naturales, Universidad de las Américas, Santiago, Chile
| | - Alexis M. Kalergis
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
- Millennium Institute of Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Claudia A. Riedel
- Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
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16
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Ferreiro AL, Choi J, Ryou J, Newcomer EP, Thompson R, Bollinger RM, Hall-Moore C, Ndao IM, Sax L, Benzinger TLS, Stark SL, Holtzman DM, Fagan AM, Schindler SE, Cruchaga C, Butt OH, Morris JC, Tarr PI, Ances BM, Dantas G. Gut microbiome composition may be an indicator of preclinical Alzheimer's disease. Sci Transl Med 2023; 15:eabo2984. [PMID: 37315112 PMCID: PMC10680783 DOI: 10.1126/scitranslmed.abo2984] [Citation(s) in RCA: 61] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/26/2023] [Indexed: 06/16/2023]
Abstract
Alzheimer's disease (AD) pathology is thought to progress from normal cognition through preclinical disease and ultimately to symptomatic AD with cognitive impairment. Recent work suggests that the gut microbiome of symptomatic patients with AD has an altered taxonomic composition compared with that of healthy, cognitively normal control individuals. However, knowledge about changes in the gut microbiome before the onset of symptomatic AD is limited. In this cross-sectional study that accounted for clinical covariates and dietary intake, we compared the taxonomic composition and gut microbial function in a cohort of 164 cognitively normal individuals, 49 of whom showed biomarker evidence of early preclinical AD. Gut microbial taxonomic profiles of individuals with preclinical AD were distinct from those of individuals without evidence of preclinical AD. The change in gut microbiome composition correlated with β-amyloid (Aβ) and tau pathological biomarkers but not with biomarkers of neurodegeneration, suggesting that the gut microbiome may change early in the disease process. We identified specific gut bacterial taxa associated with preclinical AD. Inclusion of these microbiome features improved the accuracy, sensitivity, and specificity of machine learning classifiers for predicting preclinical AD status when tested on a subset of the cohort (65 of the 164 participants). Gut microbiome correlates of preclinical AD neuropathology may improve our understanding of AD etiology and may help to identify gut-derived markers of AD risk.
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Affiliation(s)
- Aura L. Ferreiro
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - JooHee Choi
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jian Ryou
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Erin P. Newcomer
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Regina Thompson
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rebecca M. Bollinger
- Program in Occupational Therapy, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Carla Hall-Moore
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - I. Malick Ndao
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Laurie Sax
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Tammie L. S. Benzinger
- Department of Radiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Charles F. and Joanne Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Susan L. Stark
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Program in Occupational Therapy, Washington University School of Medicine, St. Louis, MO 63110, USA
- Charles F. and Joanne Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David M. Holtzman
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Charles F. and Joanne Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Anne M. Fagan
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Charles F. and Joanne Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Suzanne E. Schindler
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Charles F. and Joanne Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Carlos Cruchaga
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Omar H. Butt
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - John C. Morris
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Charles F. and Joanne Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Phillip I. Tarr
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Beau M. Ances
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Radiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Charles F. and Joanne Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Gautam Dantas
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
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17
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Rasouli-Saravani A, Jahankhani K, Moradi S, Gorgani M, Shafaghat Z, Mirsanei Z, Mehmandar A, Mirzaei R. Role of microbiota short-chain fatty acid chains in the pathogenesis of autoimmune diseases. Biomed Pharmacother 2023; 162:114620. [PMID: 37004324 DOI: 10.1016/j.biopha.2023.114620] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
There is emerging evidence that microbiota and its metabolites play an important role in helath and diseases. In this regard, gut microbiota has been found as a crucial component that influences immune responses as well as immune-related disorders such as autoimmune diseases. Gut bacterial dysbiosis has been shown to cause disease and altered microbiota metabolite synthesis, leading to immunological and metabolic dysregulation. Of note, microbiota in the gut produce short-chain fatty acids (SCFAs) such as acetate, butyrate, and propionate, and remodeling in these microbiota metabolites has been linked to the pathophysiology of a number of autoimmune disorders such as type 1 diabetes, multiple sclerosis, inflammatory bowel disease, rheumatoid arthritis, celiac disease, and systemic lupus erythematosus. In this review, we will address the most recent findings from the most noteworthy studies investigating the impact of microbiota SCFAs on various autoimmune diseases.
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Affiliation(s)
- Ashkan Rasouli-Saravani
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kasra Jahankhani
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shadi Moradi
- Department of Immunology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Melika Gorgani
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Zahra Shafaghat
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Zahra Mirsanei
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amirreza Mehmandar
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Rasoul Mirzaei
- Venom and Biotherapeutics Molecules Lab, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
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Cao J, Wang N, Luo Y, Ma C, Chen Z, Chenzhao C, Zhang F, Qi X, Xiong W. A cause-effect relationship between Graves' disease and the gut microbiome contributes to the thyroid-gut axis: A bidirectional two-sample Mendelian randomization study. Front Immunol 2023; 14:977587. [PMID: 36865531 PMCID: PMC9974146 DOI: 10.3389/fimmu.2023.977587] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 01/23/2023] [Indexed: 02/16/2023] Open
Abstract
Background An association between Graves' disease (GD) and the gut microbiome has been identified, but the causal effect between them remains unclear. Methods Bidirectional two-sample Mendelian randomization (MR) analysis was used to detect the causal effect between GD and the gut microbiome. Gut microbiome data were derived from samples from a range of different ethnicities (18,340 samples) and data on GD were obtained from samples of Asian ethnicity (212,453 samples). Single nucleotide polymorphisms (SNPs) were selected as instrumental variables according to different criteria. They were used to evaluate the causal effect between exposures and outcomes through inverse-variance weighting (IVW), weighted median, weighted mode, MR-Egger, and simple mode methods. F-statistics and sensitivity analyses were performed to evaluate bias and reliability. Results In total, 1,560 instrumental variables were extracted from the gut microbiome data (p< 1 × 105). The classes Deltaproteobacteria [odds ratio (OR) = 3.603] and Mollicutes, as well as the genera Ruminococcus torques group, Oxalobacter, and Ruminococcaceae UCG 011 were identified as risk factors for GD. The family Peptococcaceae and the genus Anaerostipes (OR = 0.489) were protective factors for GD. In addition, 13 instrumental variables were extracted from GD (p< 1 × 10-8), causing one family and eight genera to be regulated. The genus Clostridium innocuum group (p = 0.024, OR = 0.918) and Anaerofilum (p = 0.049, OR = 1.584) had the greatest probability of being regulated. Significant bias, heterogeneity, and horizontal pleiotropy were not detected. Conclusion A causal effect relationship exists between GD and the gut microbiome, demonstrating regulatory activity and interactions, and thus providing evidence supporting the involvement of a thyroid-gut axis.
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Affiliation(s)
- Jiamin Cao
- Department of Ophthalmology, The Third Xiangya Hospital, Central South University, Hunan, China
| | - Nuo Wang
- Department of Ophthalmology, The Third Xiangya Hospital, Central South University, Hunan, China
| | - Yong Luo
- Department of Ophthalmology, The Third Xiangya Hospital, Central South University, Hunan, China
| | - Chen Ma
- Department of Ophthalmology, The Third Xiangya Hospital, Central South University, Hunan, China
| | - Zhuokun Chen
- Department of Ophthalmology, The Third Xiangya Hospital, Central South University, Hunan, China
| | - Changci Chenzhao
- Department of Ophthalmology, The Third Xiangya Hospital, Central South University, Hunan, China
| | - Feng Zhang
- Department of Ophthalmology, The Third Xiangya Hospital, Central South University, Hunan, China
| | - Xin Qi
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Hunan, China
| | - Wei Xiong
- Department of Ophthalmology, The Third Xiangya Hospital, Central South University, Hunan, China
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19
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Fenneman AC, Bruinstroop E, Nieuwdorp M, van der Spek AH, Boelen A. A Comprehensive Review of Thyroid Hormone Metabolism in the Gut and Its Clinical Implications. Thyroid 2023; 33:32-44. [PMID: 36322786 DOI: 10.1089/thy.2022.0491] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Background: The gut is a target organ of thyroid hormone (TH) that exerts its action via the nuclear thyroid hormone receptor α1 (TRα1) expressed in intestinal epithelial cells. THs are partially metabolized via hepatic sulfation and glucuronidation, resulting in the production of conjugated iodothyronines. Gut microbiota play an important role in peripheral TH metabolism as they produce and secrete enzymes with deconjugation activity (β-glucuronidase and sulfatase), via which TH can re-enter the enterohepatic circulation. Summary: Intestinal epithelium homeostasis (the finely tuned balance between cell proliferation and differentiation) is controlled by the crosstalk between triiodothyronine and TRα1 and the presence of specific TH transporters and TH-activating and -inactivating enzymes. Patients and experimental murine models with a dominant-negative mutation in the TRα exhibit gross abnormalities in the morphology of the intestinal epithelium and suffer from severe symptoms of a dysfunctional gastrointestinal tract. Over the past decade, gut microbiota has been identified as an essential factor in health and disease, depending on its compositional and functional profile. This has led to a renewed interest in the so-called gut-thyroid axis. Disruption of gut microbial homeostasis (dysbiosis) is associated with autoimmune thyroid disease (AITD), including Hashimoto's thyroiditis, Graves' disease, and Graves' orbitopathy. These studies reviewed here provide new insights into the gut microbiota roles in thyroid disease pathogenesis and may be an initial step toward microbiota-based therapies in AITD. However, it should be noted that cause-effect mechanisms remain to be proven, for which prospective cohort studies, randomized clinical trials, and experimental studies are needed. Conclusion: This review aims at providing a comprehensive insight into the interplay between TH metabolism and gut homeostasis.
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Affiliation(s)
- Aline C Fenneman
- Department of Vascular Medicine, Amsterdam Cardiovascular Sciences (ACS), Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Endocrinology and Metabolism, Amsterdam Gastroenterology Endocrinology & Metabolism (AGEM), Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Eveline Bruinstroop
- Department of Endocrinology and Metabolism, Amsterdam Gastroenterology Endocrinology & Metabolism (AGEM), Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Max Nieuwdorp
- Department of Vascular Medicine, Amsterdam Cardiovascular Sciences (ACS), Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Anne H van der Spek
- Department of Endocrinology and Metabolism, Amsterdam Gastroenterology Endocrinology & Metabolism (AGEM), Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Anita Boelen
- Endocrine Laboratory, Department of Clinical Chemistry, Amsterdam Gastroenterology, Endocrinology & Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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20
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Stramazzo I, Capriello S, Filardo S, Centanni M, Virili C. Microbiota and Thyroid Disease: An Updated Systematic Review. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023. [DOI: 10.1007/5584_2023_770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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21
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Belvoncikova P, Maronek M, Gardlik R. Gut Dysbiosis and Fecal Microbiota Transplantation in Autoimmune Diseases. Int J Mol Sci 2022; 23:ijms231810729. [PMID: 36142642 PMCID: PMC9503867 DOI: 10.3390/ijms231810729] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Gut microbiota dysbiosis has recently been reported in a number of clinical states, including neurological, psychiatric, cardiovascular, metabolic and autoimmune disorders. Yet, it is not completely understood how colonizing microorganisms are implicated in their pathophysiology and molecular pathways. There are a number of suggested mechanisms of how gut microbiota dysbiosis triggers or sustains extraintestinal diseases; however, none of these have been widely accepted as part of the disease pathogenesis. Recent studies have proposed that gut microbiota and its metabolites could play a pivotal role in the modulation of immune system responses and the development of autoimmunity in diseases such as rheumatoid arthritis, multiple sclerosis or type 1 diabetes. Fecal microbiota transplantation (FMT) is a valuable tool for uncovering the role of gut microbiota in the pathological processes. This review aims to summarize the current knowledge about gut microbiota dysbiosis and the potential of FMT in studying the pathogeneses and therapies of autoimmune diseases. Herein, we discuss the extraintestinal autoimmune pathologies with at least one published or ongoing FMT study in human or animal models.
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22
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Huang S, Zhang C, Xu T, Shaukat A, He Y, Chen P, Lin L, Yue K, Cao Q, Tong X. Integrated Fecal Microbiome and Metabolomics Reveals a Novel Potential Biomarker for Predicting Tibial Dyschondroplasia in Chickens. Front Physiol 2022; 13:887207. [PMID: 35634144 PMCID: PMC9133743 DOI: 10.3389/fphys.2022.887207] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/19/2022] [Indexed: 12/12/2022] Open
Abstract
Tibial dyschondroplasia (TD) is a metabolic tibial-tarsal disorder occurring in fast-growing poultry, and its diagnosis is mainly based on an invasive method. Here, we profiled the fecal gut microbiome and metabolome of broilers with and without TD to identify potential non-invasive and non-stress biomarkers of TD. First, TD broilers with the most pronounced clinical signs during the experiment were screened and faecal samples were collected for integrated microbiome and metabolomics analysis. Moreover, the diagnostic potential of identified biomarkers was further validated throughout the experiment. It was noted that the microbial and metabolic signatures of TD broilers differed from those of normal broilers. TD broilers were characterized by enriched bacterial OTUs of the genus Klebsiella, and depleted genera [Ruminococcus], Dorea, Ruminococcus, Oscillospira, Ochrobactrum, and Sediminibacterium. In addition, a total of 189 fecal differential metabolites were identified, mainly enriched in the purine, vitamin and amino acid metabolism, which were closely associated with differential microbiota and tibia-related indicators. Furthermore, three fecal metabolites were screened, including 4-hydroxybenzaldehyde, which distinguished TD from normal broilers with extremely high specificity and was superior to serum bone markers. These results indicated that gut microbiota equilibrium might influence the pathogenesis of TD by modulating host metabolism, and the identified fecal metabolite 4-hydroxybenzaldehyde might be a potential and non-invasive biomarker for predicting TD in chickens.
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Affiliation(s)
- Shucheng Huang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
- *Correspondence: Shucheng Huang,
| | - Chaodong Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Tingting Xu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Aftab Shaukat
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Huazhong Agricultural University, Wuhan, China
| | - Yanfeng He
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Pan Chen
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Luxi Lin
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Ke Yue
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Qinqin Cao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Xishuai Tong
- Institutes of Agricultural Science and Technology Development (Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China)/College of Veterinary Medicine, Yangzhou University, Yangzhou, China
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23
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Li C, Luan Z, Zhao Y, Chen J, Yang Y, Wang C, Jing Y, Qi S, Li Z, Guo H, Xu W, Zhao B, Wu C, Wang S, Yang Y, Sun G. Deep insights into the gut microbial community of extreme longevity in south Chinese centenarians by ultra-deep metagenomics and large-scale culturomics. NPJ Biofilms Microbiomes 2022; 8:28. [PMID: 35440640 PMCID: PMC9019030 DOI: 10.1038/s41522-022-00282-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 03/03/2022] [Indexed: 12/22/2022] Open
Abstract
The gut microbes play important roles in human longevity and the gut microbiota profile of centenarians shows some unique features from young adults. Nowadays, most microbial studies on longevity are commonly based on metagenomic sequencing which may lose information about the functional microbes with extremely low abundance. Here, we combined in-depth metagenomic sequencing and large-scale culturomics to reveal the unique gut microbial structure of a Chinese longevity population, and to explore the possible relationship between intestinal microbes and longevity. Twenty-five healthy Hainan natives were enrolled in the study, including 12 centenarians and 13 senior neighbors. An average of 51.1 Gb raw sequencing data were obtained from individual fecal sample. We assembled 1778 non-redundant metagenomic assembled genomes (MAGs), 33.46% of which cannot be classified into known species. Comparison with the ordinary people in Hainan province, the longevous cohort displayed significantly decreased abundance of butyrate-producing bacteria and largely increased proportion of Escherichia coli, Desulfovibrio piger and Methanobrevibacter smithii. These species showed a constant change with aging. We also isolated 8,030 strains from these samples by large-scale culturomics, most of which belonged to 203 known species as identified by MALDI-TOF. Surprisingly, only 42.17% of the isolated species were also detected by metagenomics, indicating obvious complementarity between these two approaches. Combination of two complement methods, in-depth metagenomic sequencing and culturomics, provides deeper insights into the longevity-related gut microbiota. The uniquely enriched gut microbes in Hainan extreme decades population may help to promote health and longevity.
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Affiliation(s)
- Congyong Li
- Sixth Health Care Department, Second Medical Center of PLA General Hospital, 100853, Beijing, China
| | - Zhe Luan
- Department of Gastroenterology and Hepatology, First Medical Center of PLA General Hospital, 100853, Beijing, China
| | - Yiming Zhao
- Department of Gastroenterology and Hepatology, Hainan Hospital of PLA General Hospital, 572013, Sanya, China
| | - Jun Chen
- Unit 91917, 102401, Beijing, China
| | - Yanan Yang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, 301617, Tianjin, China
| | - Cong Wang
- Department of Gastroenterology and Hepatology, First Medical Center of PLA General Hospital, 100853, Beijing, China
| | - Yujia Jing
- Department of Gastroenterology and Hepatology, First Medical Center of PLA General Hospital, 100853, Beijing, China
| | - Shirui Qi
- Emergency Department, Tianjin First Central Hospital, 300192, Tianjin, China
| | - Zhuanyu Li
- Beijing QuantiHealth Technology Co., Ltd, 100070, Beijing, China
| | - Hao Guo
- Beijing QuantiHealth Technology Co., Ltd, 100070, Beijing, China
| | - Wenyi Xu
- Beijing QuantiHealth Technology Co., Ltd, 100070, Beijing, China
| | - Bowen Zhao
- Beijing QuantiHealth Technology Co., Ltd, 100070, Beijing, China
| | - Chongming Wu
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, 301617, Tianjin, China.
| | - Shufang Wang
- Department of Gastroenterology and Hepatology, First Medical Center of PLA General Hospital, 100853, Beijing, China.
| | - Yunsheng Yang
- Department of Gastroenterology and Hepatology, First Medical Center of PLA General Hospital, 100853, Beijing, China.
| | - Gang Sun
- Department of Gastroenterology and Hepatology, First Medical Center of PLA General Hospital, 100853, Beijing, China.
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Liu H, Liu H, Liu C, Shang M, Wei T, Yin P. Gut Microbiome and the Role of Metabolites in the Study of Graves’ Disease. Front Mol Biosci 2022; 9:841223. [PMID: 35252357 PMCID: PMC8889015 DOI: 10.3389/fmolb.2022.841223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/31/2022] [Indexed: 12/12/2022] Open
Abstract
Graves’ disease (GD) is an autoimmune thyroid disease (AITD), which is one of the most common organ-specific autoimmune disorders with an increasing prevalence worldwide. But the etiology of GD is still unclear. A growing number of studies show correlations between gut microbiota and GD. The dysbiosis of gut microbiota may be the reason for the development of GD by modulating the immune system. Metabolites act as mediators or modulators between gut microbiota and thyroid. The purpose of this review is to summarize the correlations between gut microbiota, microbial metabolites and GD. Challenges in the future study are also discussed. The combination of microbiome and metabolome may provide new insight for the study and put forward the diagnosis, treatment, prevention of GD in the future.
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Affiliation(s)
- Haihua Liu
- Clinical Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, China
- Institute of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Huiying Liu
- Clinical Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, China
- Institute of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Chang Liu
- Clinical Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, China
- Institute of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Mengxue Shang
- Clinical Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, China
- Institute of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Tianfu Wei
- Clinical Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, China
- Institute of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Peiyuan Yin
- Clinical Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, China
- *Correspondence: Peiyuan Yin, ,
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Human gut bacterial metabolism drives Th17 activation and colitis. Cell Host Microbe 2022; 30:17-30.e9. [PMID: 34822777 PMCID: PMC8785648 DOI: 10.1016/j.chom.2021.11.001] [Citation(s) in RCA: 85] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 10/21/2021] [Accepted: 11/03/2021] [Indexed: 01/14/2023]
Abstract
Bacterial activation of T helper 17 (Th17) cells exacerbates mouse models of autoimmunity, but how human-associated bacteria impact Th17-driven disease remains elusive. We show that human gut Actinobacterium Eggerthella lenta induces intestinal Th17 activation by lifting inhibition of the Th17 transcription factor Rorγt through cell- and antigen-independent mechanisms. E. lenta is enriched in inflammatory bowel disease (IBD) patients and worsens colitis in a Rorc-dependent manner in mice. Th17 activation varies across E. lenta strains, which is attributable to the cardiac glycoside reductase 2 (Cgr2) enzyme. Cgr2 is sufficient to induce interleukin (IL)-17a, a major Th17 cytokine. cgr2+ E. lenta deplete putative steroidal glycosides in pure culture; related compounds are negatively associated with human IBD severity. Finally, leveraging the sensitivity of Cgr2 to dietary arginine, we prevented E. lenta-induced intestinal inflammation in mice. Together, these results support a role for human gut bacterial metabolism in driving Th17-dependent autoimmunity.
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Ma C, Zhang C, Chen D, Jiang S, Shen S, Huo D, Huang S, Zhai Q, Zhang J. Probiotic consumption influences universal adaptive mutations in indigenous human and mouse gut microbiota. Commun Biol 2021; 4:1198. [PMID: 34663913 PMCID: PMC8523657 DOI: 10.1038/s42003-021-02724-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 09/21/2021] [Indexed: 11/30/2022] Open
Abstract
The adaptive evolution in indigenous intestinal microbes derived from probiotics is critical to safety and efficacy evaluation of probiotics, yet it is still largely underexplored. Here, through 11 publicly accessible datasets, we demonstrated that probiotic consumption can lead to widespread single-nucleotide variants (SNVs) in the native microbiota. Interestingly, the same probiotic strains introduced far more SNVs in mouse gut than humans. Furthermore, the pattern of probiotics-induced SNVs was highly probiotic-strain specific, and 17 common SNVs in Faecalibacterium prausnitzii genome were identified cross studies, which might lead to changes in bacterial protein structure. Further, nearly 50% of F. prausnitzii SNVs can be inherited for six months in an independent human cohort, whereas the other half only transiently occurred. Collectively, our study substantially extended our understanding of co-evolution of the probiotics and the indigenous gut microbiota, highlighting the importance of assessment of probiotics efficacy and safety in an integrated manner. Chenchen Ma, Chengcheng Zhang, and Denghui Chen et al. examine how probiotic consumption impacts gut microbiota composition in human and mice through a global, cross-cohort metagenomic analysis. Their results suggest that probiotic consumption may result in widespread variation among the native microbiota in both the human and mouse gut.
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Affiliation(s)
- Chenchen Ma
- College of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, 570228, Haikou, China
| | - Chengcheng Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, 214122, Wuxi, China
| | - Denghui Chen
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Shuaiming Jiang
- College of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, 570228, Haikou, China
| | - Siyuan Shen
- College of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, 570228, Haikou, China
| | - Dongxue Huo
- College of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, 570228, Haikou, China
| | - Shi Huang
- Department of Pediatrics and Center for Microbiome Innovation at Jacobs School of Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, 214122, Wuxi, China.
| | - Jiachao Zhang
- College of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, 570228, Haikou, China.
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27
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Zheng D, Liao H, Chen S, Liu X, Mao C, Zhang C, Meng M, Wang Z, Wang Y, Jiang Q, Xue Y, Zhou L, Chen Y. Elevated Levels of Circulating Biomarkers Related to Leaky Gut Syndrome and Bacterial Translocation Are Associated With Graves' Disease. Front Endocrinol (Lausanne) 2021; 12:796212. [PMID: 34975767 PMCID: PMC8716831 DOI: 10.3389/fendo.2021.796212] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 11/29/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND A growing number of studies have found dysbiosis of the intestinal microbiota in patients with Graves' disease (GD). The intestinal epithelial barrier serves as the first line of defense, protecting the immune system from excessive stimulation of microbiota and toxins. Most autoimmune diseases are associated with a gut barrier dysfunction (leaky gut) which allows bacterial translocation. However, to date, potential correlations between intestinal barrier dysfunction and GD have not been explored. METHODS Serum lipopolysaccharide (LPS), intestinal fatty acid-binding protein (I-FABP), zonulin, D-lactate, and diamine oxidase (DAO) were measured to assess barrier integrity in 91 patients with GD (61 initial GD and 30 euthyroid GD) and 44 healthy controls. The quality of life (QOL) of patients with GD was assessed using the thyroid-specific patient-reported outcome (ThyPRO-39) questionnaire. RESULTS The serum levels of LPS, I-FABP, zonulin, and D-lactate were significantly higher in patients with initial GD than in healthy controls. Logistic regression analysis revealed that zonulin and D-lactate were independently associated with risk for GD and circulating zonulin could effectively distinguish patients with initial GD from healthy controls. Correlation analyses showed that I-FABP, LPS, and D-lactate were positively associated with FT4 and negatively associated with TSH. In addition, circulating LPS, zonulin, and D-lactate levels were all independent predictors of TRAb levels. Moreover, higher circulating LPS levels in patients with GD were associated with more severe hyperthyroidism (higher concentrations of FT3, FT4, and TRAb and lower TSH concentrations) and worse scores of hyperthyroid and eye symptoms. CONCLUSION Patients with initial GD show a disrupted intestinal barrier, characterized by elevated levels of leaky gut biomarkers. Increased intestinal permeability and bacterial translocation were associated with TRAb levels and hyperthyroidism in GD. Further research is required to elucidate the underlying mechanisms.
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Affiliation(s)
- Dekai Zheng
- Guangdong Provincial Key Laboratory of Gastroenterology, State Key Laboratory of Organ Failure Research, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Integrative Clinical Center of Microecology, Department of Gastroenterology, Shenzhen Hospital, Southern Medical University, Guangzhou, China
| | - Huimin Liao
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Shuze Chen
- Guangdong Provincial Key Laboratory of Gastroenterology, State Key Laboratory of Organ Failure Research, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Integrative Clinical Center of Microecology, Department of Gastroenterology, Shenzhen Hospital, Southern Medical University, Guangzhou, China
| | - Xiuying Liu
- Guangdong Provincial Key Laboratory of Gastroenterology, State Key Laboratory of Organ Failure Research, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Chuyin Mao
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Cangui Zhang
- Guangdong Provincial Key Laboratory of Gastroenterology, State Key Laboratory of Organ Failure Research, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Min Meng
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zhi Wang
- Guangdong Provincial Key Laboratory of Gastroenterology, State Key Laboratory of Organ Failure Research, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ying Wang
- Guangdong Provincial Key Laboratory of Gastroenterology, State Key Laboratory of Organ Failure Research, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qinrui Jiang
- Guangdong Provincial Key Laboratory of Gastroenterology, State Key Laboratory of Organ Failure Research, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yaoming Xue
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Lin Zhou
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Ye Chen, ; Lin Zhou,
| | - Ye Chen
- Guangdong Provincial Key Laboratory of Gastroenterology, State Key Laboratory of Organ Failure Research, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Integrative Clinical Center of Microecology, Department of Gastroenterology, Shenzhen Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Ye Chen, ; Lin Zhou,
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