1
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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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2
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An K, Jia Y, Xie B, Gao J, Chen Y, Yuan W, Zhong J, Su P, Liu X. Alterations in the gut mycobiome with coronary artery disease severity. EBioMedicine 2024; 103:105137. [PMID: 38703606 PMCID: PMC11087906 DOI: 10.1016/j.ebiom.2024.105137] [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: 07/02/2023] [Revised: 04/08/2024] [Accepted: 04/16/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Coronary artery disease (CAD) is a prevalent cardiovascular condition, and numerous studies have linked gut bacterial imbalance to CAD. However, the relationship of gut fungi, another essential component of the intestinal microbiota, with CAD remains poorly understood. METHODS In this cross-sectional study, we analyzed fecal samples from 132 participants, split into 31 healthy controls and 101 CAD patients, further categorized into stable CAD (38), unstable angina (41), and acute myocardial infarction (22) groups. We conducted internal transcribed spacer 1 (ITS1) and 16S sequencing to examine gut fungal and bacterial communities. FINDINGS Based on ITS1 analyses, Ascomycota and Basidiomycota were the dominant fungal phyla in all the groups. The α diversity of gut mycobiome remained unaltered among the control group and CAD subgroups; however, the structure and composition of the mycobiota differed significantly with the progression of CAD. The abundances of 15 taxa gradually changed with the occurrence and progression of the disease and were significantly correlated with major CAD risk factor indicators. The mycobiome changes were closely linked to gut microbiome dysbiosis in patients with CAD. Furthermore, disease classifiers based on gut fungi effectively identified subgroups with different degrees of CAD. Finally, the FUNGuild analysis further categorized these fungi into distinct ecological guilds. INTERPRETATION In conclusion, the structure and composition of the gut fungal community differed from healthy controls to various subtypes of CAD, revealing key fungi taxa alterations linked to the onset and progression of CAD. Our study highlights the potential role of gut fungi in CAD and may facilitate the development of novel biomarkers and therapeutic targets for CAD. FUNDING This work was supported by the grants from the National Natural Science Foundation of China (No. 82170302, 92168117, 82370432), National clinical key specialty construction project- Cardiovascular Surgery, the Reform and Development Program of Beijing Institute of Respiratory Medicine (No. Ggyfz202417, Ggyfz202308), the Beijing Natural Science Foundation (No. 7222068); and the Clinical Research Incubation Program of Beijing Chaoyang Hospital Affiliated to Capital Medical University (No. CYFH202209).
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Affiliation(s)
- Kun An
- Department of Cardiac Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China; Heart Center and Beijing Key Laboratory of Hypertension, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Yanxiong Jia
- Department of Cardiac Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China; Heart Center and Beijing Key Laboratory of Hypertension, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Boqia Xie
- Department of Cardiac Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China; Heart Center and Beijing Key Laboratory of Hypertension, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Jie Gao
- Department of Cardiac Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China; Heart Center and Beijing Key Laboratory of Hypertension, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Yihang Chen
- Heart Center and Beijing Key Laboratory of Hypertension, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China; Department of Cardiology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Wen Yuan
- Medical Research Center, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Jiuchang Zhong
- Heart Center and Beijing Key Laboratory of Hypertension, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China; Department of Cardiology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China.
| | - Pixiong Su
- Department of Cardiac Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China; Heart Center and Beijing Key Laboratory of Hypertension, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China.
| | - Xiaoyan Liu
- Heart Center and Beijing Key Laboratory of Hypertension, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China; Department of Cardiology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China; Medical Research Center, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China.
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3
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Gu P, Liu R, Yang Q, Xie L, Wei R, Li J, Mei F, Chen T, Zeng Z, He Y, Zhou H, Peng H, Nandakumar KS, Chu H, Jiang Y, Gong W, Chen Y, Schnabl B, Chen P. A metabolite from commensal Candida albicans enhances the bactericidal activity of macrophages and protects against sepsis. Cell Mol Immunol 2023; 20:1156-1170. [PMID: 37553429 PMCID: PMC10541433 DOI: 10.1038/s41423-023-01070-5] [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: 04/18/2023] [Accepted: 07/14/2023] [Indexed: 08/10/2023] Open
Abstract
The gut microbiome is recognized as a key modulator of sepsis development. However, the contribution of the gut mycobiome to sepsis development is still not fully understood. Here, we demonstrated that the level of Candida albicans was markedly decreased in patients with bacterial sepsis, and the supernatant of Candida albicans culture significantly decreased the bacterial load and improved sepsis symptoms in both cecum ligation and puncture (CLP)-challenged mice and Escherichia coli-challenged pigs. Integrative metabolomics and the genetic engineering of fungi revealed that Candida albicans-derived phenylpyruvate (PPA) enhanced the bactericidal activity of macrophages and reduced organ damage during sepsis. Mechanistically, PPA directly binds to sirtuin 2 (SIRT2) and increases reactive oxygen species (ROS) production for eventual bacterial clearance. Importantly, PPA enhanced the bacterial clearance capacity of macrophages in sepsis patients and was inversely correlated with the severity of sepsis in patients. Our findings highlight the crucial contribution of commensal fungi to bacterial disease modulation and expand our understanding of the host-mycobiome interaction during sepsis development.
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Affiliation(s)
- Peng Gu
- Department of Gastroenterology, Shenzhen Hospital, Southern Medical University, Shenzhen, China
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Ruofan Liu
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Qin Yang
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Department of Gastroenterology, The Seventh Affiliated Hospital of Southern Medical University, Foshan, China
| | - Li Xie
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Rongjuan Wei
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Jiaxin Li
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Fengyi Mei
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Tao Chen
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Zhenhua Zeng
- Department of Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yan He
- Microbiome Medicine Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Hongwei Zhou
- Microbiome Medicine Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Hongjuan Peng
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Kutty Selva Nandakumar
- Department of Environment and Biosciences, School of Business, Innovation and Sustainability, Halmstad University, Halmstad, Sweden
| | - Huikuan Chu
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yong Jiang
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Wei Gong
- Department of Gastroenterology, Shenzhen Hospital, Southern Medical University, Shenzhen, China.
| | - Ye Chen
- Department of Gastroenterology, Shenzhen Hospital, Southern Medical University, Shenzhen, China.
| | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Peng Chen
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.
- Microbiome Medicine Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
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4
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Ouyang J, Yan J, Zhou X, Isnard S, Tang S, Costiniuk CT, Chen Y, Routy JP, Chen Y. The Influence of Oral Terbinafine on Gut Fungal Microbiome Composition and Microbial Translocation in People Living with HIV Treated for Onychomycosis. J Fungi (Basel) 2023; 9:963. [PMID: 37888218 PMCID: PMC10607585 DOI: 10.3390/jof9100963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/19/2023] [Accepted: 09/19/2023] [Indexed: 10/28/2023] Open
Abstract
People living with HIV (PLWH) display altered gut epithelium that allows for the translocation of microbial products, contributing to systemic immune activation. Although there are numerous studies which examine the gut bacterial microbiome in PLWH, few studies describing the fungal microbiome, or the mycobiome, have been reported. Like the gut bacterial microbiome, the fungal microbiome and its by-products play a role in maintaining the body's homeostasis and modulating immune function. We conducted a prospective study to assess the effects of oral terbinafine, an antifungal agent widely used against onychomycosis, on gut permeability and microbiome composition in ART-treated PLWH (trial registration: ChiCTR2100043617). Twenty participants completed all follow-up visits. During terbinafine treatment, the levels of the intestinal fatty acid binding protein (I-FABP) significantly increased, and the levels of interleukin-6 (IL-6) significantly decreased, from baseline to week 12. Both markers subsequently returned to pre-treatment levels after terbinafine discontinuation. After terbinafine treatment, the abundance of fungi decreased significantly, while the abundance of the bacteria did not change. After terbinafine discontinuation, the abundance of fungi returned to the levels observed pre-treatment. Moreover, terbinafine treatment induced only minor changes in the composition of the gut bacterial and fungal microbiome. In summary, oral terbinafine decreases fungal microbiome abundance while only slightly influencing gut permeability and microbial translocation in ART-treated PLWH. This study's findings should be validated in larger and more diverse studies of ART-treated PLWH; our estimates of effect size can be used to inform optimal sample sizes for future studies.
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Affiliation(s)
- Jing Ouyang
- Clinical Research Center, Chongqing Public Health Medical Center, Chongqing 400036, China; (J.O.); (Y.C.)
| | - Jiangyu Yan
- Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing 400036, China; (J.Y.); (S.T.)
| | - Xin Zhou
- Department of Pharmacy, Chongqing Public Health Medical Center, Chongqing 400036, China;
| | - Stéphane Isnard
- Infectious Diseases and Immunity in Global Health Program, Research Institute, McGill University Health Centre, Montréal, QC H4A 3J1, Canada; (S.I.); (C.T.C.)
- Chronic Viral Illness Service, McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Shengquan Tang
- Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing 400036, China; (J.Y.); (S.T.)
| | - Cecilia T. Costiniuk
- Infectious Diseases and Immunity in Global Health Program, Research Institute, McGill University Health Centre, Montréal, QC H4A 3J1, Canada; (S.I.); (C.T.C.)
- Chronic Viral Illness Service, McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Yaling Chen
- Clinical Research Center, Chongqing Public Health Medical Center, Chongqing 400036, China; (J.O.); (Y.C.)
| | - Jean-Pierre Routy
- Infectious Diseases and Immunity in Global Health Program, Research Institute, McGill University Health Centre, Montréal, QC H4A 3J1, Canada; (S.I.); (C.T.C.)
- Chronic Viral Illness Service, McGill University Health Centre, Montreal, QC H4A 3J1, Canada
- Division of Hematology, McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Yaokai Chen
- Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing 400036, China; (J.Y.); (S.T.)
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5
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Yu H, Xu H, Yang X, Zhang Z, Hu J, Lu J, Fu J, Bu M, Zhang H, Zhai Z, Wang J, Jiang J, Wang Y. Gut microbiota-based pharmacokinetic-pharmacodynamic study and molecular mechanism of specnuezhenide in the treatment of colorectal cancer targeting carboxylesterase. J Pharm Anal 2023; 13:1024-1040. [PMID: 37842660 PMCID: PMC10568112 DOI: 10.1016/j.jpha.2023.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 06/15/2023] [Accepted: 06/25/2023] [Indexed: 10/17/2023] Open
Abstract
Specnuezhenide (SNZ) is among the main components of Fructus Ligustri Lucidi, which has anti-inflammation, anti-oxidation, and anti-tumor effect. The low bioavailability makes it difficult to explain the mechanism of pharmacological effect of SNZ. In this study, the role of the gut microbiota in the metabolism and pharmacokinetics characteristics of SNZ as well as the pharmacological meaning were explored. SNZ can be rapidly metabolized by the gut microbiome, and two intestinal bacterial metabolites of SNZ, salidroside and tyrosol, were discovered. In addition, carboxylesterase may be the main intestinal bacterial enzyme that mediates its metabolism. At the same time, no metabolism was found in the incubation system of SNZ with liver microsomes or liver homogenate, indicating that the gut microbiota is the main part involved in the metabolism of SNZ. In addition, pharmacokinetic studies showed that salidroside and tyrosol can be detected in plasma in the presence of gut microbiota. Interestingly, tumor development was inhibited in a colorectal tumor mice model administered orally with SNZ, which indicated that SNZ exhibited potential to inhibit tumor growth, and tissue distribution studies showed that salidroside and tyrosol could be distributed in tumor tissues. At the same time, SNZ modulated the structure of gut microbiota and fungal group, which may be the mechanism governing the antitumoral activity of SNZ. Furthermore, SNZ stimulates the secretion of short-chain fatty acids by intestinal flora in vitro and in vivo. In the future, targeting gut microbes and the interaction between natural products and gut microbes could lead to the discovery and development of new drugs.
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Affiliation(s)
| | | | - Xinyu Yang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, 100050, China
| | - Zhengwei Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, 100050, China
| | - Jiachun Hu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, 100050, China
| | - Jinyue Lu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, 100050, China
| | - Jie Fu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, 100050, China
| | - Mengmeng Bu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, 100050, China
| | - Haojian Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, 100050, China
| | - Zhao Zhai
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, 100050, China
| | - Jingyue Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, 100050, China
| | - Jiandong Jiang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, 100050, China
| | - Yan Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, 100050, China
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6
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Yeasts and Yeast-based Products in Poultry Nutrition. J APPL POULTRY RES 2023. [DOI: 10.1016/j.japr.2023.100345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
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7
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Roles of the gut virome and mycobiome in faecal microbiota transplantation. Lancet Gastroenterol Hepatol 2022; 7:472-484. [DOI: 10.1016/s2468-1253(21)00303-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/02/2021] [Accepted: 08/10/2021] [Indexed: 12/16/2022]
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8
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Zheng L, Wen XL, Duan SL. Role of metabolites derived from gut microbiota in inflammatory bowel disease. World J Clin Cases 2022; 10:2660-2677. [PMID: 35434116 PMCID: PMC8968818 DOI: 10.12998/wjcc.v10.i9.2660] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/12/2021] [Accepted: 02/27/2022] [Indexed: 02/06/2023] Open
Abstract
Over the past two decades, it is improved gut microbiota plays an important role in the health and disease pathogenesis. Metabolites, small molecules produced as intermediate or end products of microbial metabolism, is considered as one of the major interaction way for gut microbiota with the host. Bacterial metabolisms of dietary substrates, modification of host molecules or bacteria are the major source of metabolites. Signals from microbial metabolites affect immune maturation and homeostasis, host energy metabolism as well as mucosal integrity maintenance. Based on many researches, the composition and function of the microbiota can be changed, which is also seen in the metabolite profiles of patients with inflammatory bowel disease (IBD). Additionally, some specific classes of metabolites also can trigger IBD. In this paper, definition of the key classes of microbial-derived metabolites which are changed in IBD, description of the pathophysiological basis of association and identification of the precision therapeutic modulation in the future are the major contents.
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Affiliation(s)
- Lie Zheng
- Department of Gastroenterology, Shaanxi Hospital of Traditional Chinese Medicine, Xi’an 710003, Shaanxi Province, China
| | - Xin-Li Wen
- Department of Gastroenterology, Shaanxi Hospital of Traditional Chinese Medicine, Xi’an 710003, Shaanxi Province, China
| | - Sheng-Lei Duan
- Department of Gastroenterology, Shaanxi Hospital of Traditional Chinese Medicine, Xi’an 710003, Shaanxi Province, China
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9
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Zheng L, Wen XL, Duan SL. Role of metabolites derived from gut microbiota in inflammatory bowel disease. World J Clin Cases 2022; 10:2658-2675. [DOI: 10.12998/wjcc.v10.i9.2658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Over the past two decades, it is improved gut microbiota plays an important role in the health and disease pathogenesis. Metabolites, small molecules produced as intermediate or end products of microbial metabolism, is considered as one of the major interaction way for gut microbiota with the host. Bacterial metabolisms of dietary substrates, modification of host molecules or bacteria are the major source of metabolites. Signals from microbial metabolites affect immune maturation and homeostasis, host energy metabolism as well as mucosal integrity maintenance. Based on many researches, the composition and function of the microbiota can be changed, which is also seen in the metabolite profiles of patients with inflammatory bowel disease (IBD). Additionally, some specific classes of metabolites also can trigger IBD. In this paper, definition of the key classes of microbial-derived metabolites which are changed in IBD, description of the pathophysiological basis of association and identification of the precision therapeutic modulation in the future are the major contents.
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Affiliation(s)
- Lie Zheng
- Department of Gastroenterology, Shaanxi Hospital of Traditional Chinese Medicine, Xi’an 710003, Shaanxi Province, China
| | - Xin-Li Wen
- Department of Gastroenterology, Shaanxi Hospital of Traditional Chinese Medicine, Xi’an 710003, Shaanxi Province, China
| | - Sheng-Lei Duan
- Department of Gastroenterology, Shaanxi Hospital of Traditional Chinese Medicine, Xi’an 710003, Shaanxi Province, China
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10
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Begum N, Harzandi A, Lee S, Uhlen M, Moyes DL, Shoaie S. Host-mycobiome metabolic interactions in health and disease. Gut Microbes 2022; 14:2121576. [PMID: 36151873 PMCID: PMC9519009 DOI: 10.1080/19490976.2022.2121576] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/31/2022] [Accepted: 08/31/2022] [Indexed: 02/04/2023] Open
Abstract
Fungal communities (mycobiome) have an important role in sustaining the resilience of complex microbial communities and maintenance of homeostasis. The mycobiome remains relatively unexplored compared to the bacteriome despite increasing evidence highlighting their contribution to host-microbiome interactions in health and disease. Despite being a small proportion of the total species, fungi constitute a large proportion of the biomass within the human microbiome and thus serve as a potential target for metabolic reprogramming in pathogenesis and disease mechanism. Metabolites produced by fungi shape host niches, induce immune tolerance and changes in their levels prelude changes associated with metabolic diseases and cancer. Given the complexity of microbial interactions, studying the metabolic interplay of the mycobiome with both host and microbiome is a demanding but crucial task. However, genome-scale modelling and synthetic biology can provide an integrative platform that allows elucidation of the multifaceted interactions between mycobiome, microbiome and host. The inferences gained from understanding mycobiome interplay with other organisms can delineate the key role of the mycobiome in pathophysiology and reveal its role in human disease.
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Affiliation(s)
- Neelu Begum
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London, UK
| | - Azadeh Harzandi
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London, UK
| | - Sunjae Lee
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London, UK
| | - Mathias Uhlen
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
| | - David L. Moyes
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London, UK
| | - Saeed Shoaie
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London, UK
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
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11
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Wu X, Xia Y, He F, Zhu C, Ren W. Intestinal mycobiota in health and diseases: from a disrupted equilibrium to clinical opportunities. MICROBIOME 2021; 9:60. [PMID: 33715629 PMCID: PMC7958491 DOI: 10.1186/s40168-021-01024-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/04/2021] [Indexed: 05/08/2023]
Abstract
Bacteria, viruses, protozoa, and fungi establish a complex ecosystem in the gut. Like other microbiota, gut mycobiota plays an indispensable role in modulating intestinal physiology. Notably, the most striking characteristics of intestinal fungi are their extraintestinal functions. Here, we provide a comprehensive review of the importance of gut fungi in the regulation of intestinal, pulmonary, hepatic, renal, pancreatic, and brain functions, and we present possible opportunities for the application of gut mycobiota to alleviate/treat human diseases. Video Abstract.
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Affiliation(s)
- Xiaoyan Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China
| | - Yaoyao Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China
| | - Fang He
- College of Animal Science and Technology, Southwest University, Chongqing, 400716 China
| | - Congrui Zhu
- College of Veterinary Medicine, Kansas State University, Manhattan, KS USA
| | - Wenkai Ren
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China
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12
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Mycobiome in the Gut: A Multiperspective Review. Mediators Inflamm 2020; 2020:9560684. [PMID: 32322167 PMCID: PMC7160717 DOI: 10.1155/2020/9560684] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 02/23/2020] [Accepted: 03/17/2020] [Indexed: 12/13/2022] Open
Abstract
Human gut is home to a diverse and complex microbial ecosystem encompassing bacteria, viruses, parasites, fungi, and other microorganisms that have an undisputable role in maintaining good health for the host. Studies on the interplay between microbiota in the gut and various human diseases remain the key focus among many researchers. Nevertheless, advances in sequencing technologies and computational biology have helped us to identify a diversity of fungal community that reside in the gut known as the mycobiome. Although studies on gut mycobiome are still in its infancy, numerous sources have reported its potential role in host homeostasis and disease development. Nonetheless, the actual mechanism of its involvement remains largely unknown and underexplored. Thus, in this review, we attempt to discuss the recent advances in gut mycobiome research from multiple perspectives. This includes understanding the composition of fungal communities in the gut and the involvement of gut mycobiome in host immunity and gut-brain axis. Further, we also discuss on multibiome interactions in the gut with emphasis on fungi-bacteria interaction and the influence of diet in shaping gut mycobiome composition. This review also highlights the relation between fungal metabolites and gut mycobiota in human homeostasis and the role of gut mycobiome in various human diseases. This multiperspective review on gut mycobiome could perhaps shed new light for future studies in the mycobiome research area.
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Abstract
Microbiome dysbiosis is strongly associated with alcoholic liver disease (ALD). Recent studies on comprehensive analyses of microbiome compositional and functional changes have begun to uncover the mechanistic relation between microbiome and the pathogenesis of ALD. Importantly, targeting the microbiome has become a potential strategy for the prevention and treatment of ALD. In this review, we summarize the clinical evidence of microbiome dysbiosis in ALD patients, and experimental advances in microbiome and metabolomic functional changes in animals with different species and genetic backgrounds in ALD. We also summarize the studies in humanized intestinal microbiome and fecal microbiota transplantation in mice. We introduce new developments in the studies on the role of the circulating bacterial microbiome, oral bacterial microbiome and fungal microbiome in the development of ALD. We highlight the potential mechanisms by which microbiome dysbiosis contributes to ALD, including short chain fatty acid changes, bile acid metabolism, intestinal barrier function, release of bacterial and fungal products, and inflammation. In addition, we summarize the recent developments targeting the microbiome in prevention and treatment of ALD, including dietary nutrient interference, herbal medicine, antibiotics, anti-fungal agents, probiotics, engineered bacterial therapy, fecal transplantation and oral hygiene. Although recent preclinical studies have advanced our understanding of the microbiome and ALD, clinical studies, especially prospective studies with large samples, are needed to better understand the cause-effect of microbiome dysbiosis in ALD. Identifying new precision-based strategies targeting the microbiome are expected to be developed as more effective therapies in ALD.
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