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Wei G. Insights into gut fungi in pigs: A comprehensive review. J Anim Physiol Anim Nutr (Berl) 2024. [PMID: 39154229 DOI: 10.1111/jpn.14036] [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: 10/10/2023] [Revised: 06/17/2024] [Accepted: 08/04/2024] [Indexed: 08/19/2024]
Abstract
Fungi in the gut microbiota of mammals play a crucial role in host physiological regulation, including intestinal homeostasis and host immune regulation. However, our understanding of gut fungi in mammals remains limited, especially in economically valuable animals, such as pigs. Therefore, this review first describes the classification and characterisation of fungi, provides insights into the methods used to study gut fungi, and summarises the recent progress on pig gut fungi. Additionally, it discusses the challenges in the study of pig gut fungi and highlights potential perspectives. The aim of this review is to serve as a valuable reference for advancing our knowledge of gut fungi in animals.
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Affiliation(s)
- Guanyue Wei
- National Key Laboratory of Pig Genetic Improvement and Germplasm Innovation, Jiangxi Agricultural University, Nanchang, China
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2
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Pu L, Pang S, Mu W, Chen X, Zou Y, Wang Y, Ding Y, Yan Q, Huang Y, Chen X, Peng T, Luo W, Wang S. The gut mycobiome signatures in long-lived populations. iScience 2024; 27:110412. [PMID: 39081291 PMCID: PMC11284699 DOI: 10.1016/j.isci.2024.110412] [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: 02/22/2024] [Revised: 04/22/2024] [Accepted: 06/26/2024] [Indexed: 08/02/2024] Open
Abstract
Long-lived individuals have been extensively studied as a model to investigate the role of the gut microbiota in aging, but their gut fungi remain almost unexplored. Here, we recruited a community-dwelling cohort of 251 participants (24-108 years, including 47 centenarians) from Guangxi in China to characterize the gut mycobiome signatures. We found gut mycobiome markedly varied during aging and determined aging as a predominant factor driving these variations. For long-lived individuals, core taxa, including Penicillium and Aspergillus, were maintained and Candida enterotype was enriched when compared with old counterparts. Individuals with this enterotype were more likely to possess Bacteroides enterotype enriched in young and centenarians. Moreover, the drivers from Candida enterotype were positively linked with the bacteria components dominated in Bacteroides enterotype. We also identified potentially beneficial yeasts-enriched features to differentiate long-lived individuals from others. Our findings suggest that the gut mycobiome develops with aging, and long-lived individuals possess unique fungal signatures.
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Affiliation(s)
- Lixia Pu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Shifu Pang
- AIage Life Science Corporation Ltd., Guangxi Free Trade Zone Aisheng Biotechnology Corporation Ltd., Nanning, Guangxi, China
| | - Wenjie Mu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Xiaodong Chen
- AIage Life Science Corporation Ltd., Guangxi Free Trade Zone Aisheng Biotechnology Corporation Ltd., Nanning, Guangxi, China
- Guangxi Key Laboratory of Longevity Science and Technology, AIage Life Science Corporation Ltd., Nanning, Guangxi, China
| | - Yang Zou
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Yugui Wang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Yingying Ding
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Qi Yan
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Yu Huang
- AIage Life Science Corporation Ltd., Guangxi Free Trade Zone Aisheng Biotechnology Corporation Ltd., Nanning, Guangxi, China
| | - Xiaochun Chen
- AIage Life Science Corporation Ltd., Guangxi Free Trade Zone Aisheng Biotechnology Corporation Ltd., Nanning, Guangxi, China
- Guangxi Key Laboratory of Longevity Science and Technology, AIage Life Science Corporation Ltd., Nanning, Guangxi, China
| | - Tao Peng
- Guangxi Key Laboratory of Enhanced Recovery After Surgery for Gastrointestinal Cancer, Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Weifei Luo
- AIage Life Science Corporation Ltd., Guangxi Free Trade Zone Aisheng Biotechnology Corporation Ltd., Nanning, Guangxi, China
- Guangxi Key Laboratory of Longevity Science and Technology, AIage Life Science Corporation Ltd., Nanning, Guangxi, China
| | - Shuai Wang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
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Estrada R, Romero Y, Quilcate C, Dipaz D, Alejos-Asencio CS, Leon S, Alvarez-García WY, Rojas D, Alvarado W, Maicelo JL, Arbizu CI. Age-Dependent Changes in Protist and Fungal Microbiota in a Peruvian Cattle Genetic Nucleus. Life (Basel) 2024; 14:1010. [PMID: 39202752 PMCID: PMC11355802 DOI: 10.3390/life14081010] [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: 06/27/2024] [Revised: 07/21/2024] [Accepted: 08/13/2024] [Indexed: 09/03/2024] Open
Abstract
In this research, the connection between age and microbial diversity in cattle was explored, revealing significant changes in both protist diversity and fungal microbiota composition with age. Using fecal samples from 21 Simmental cattle, microbial communities were analyzed through 18S rRNA gene sequencing. Results indicated significant differences in alpha protist diversity among the three age groups, while fungal composition varied notably with age and was linked to hematological parameters. Despite the stability of fungal alpha diversity, compositional changes suggest the gut as a stable niche for microbial colonization influenced by diet, clinical parameters, and microbial interactions. All cattle were maintained on a consistent diet, tailored to meet the specific nutritional needs of each age group. These findings emphasize the importance of understanding age-related microbial dynamics to enhance livestock management and animal health, contributing to broader ecological and biomedical research. This study was limited by the lack of comprehensive metabolic analyses correlating microbiota changes with specific age-related variations, indicating a need for further research in this area.
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Affiliation(s)
- Richard Estrada
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Lima 15024, Peru; (R.E.); (Y.R.); (C.Q.); (D.D.); (C.S.A.-A.); (S.L.); (W.Y.A.-G.); (D.R.)
| | - Yolanda Romero
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Lima 15024, Peru; (R.E.); (Y.R.); (C.Q.); (D.D.); (C.S.A.-A.); (S.L.); (W.Y.A.-G.); (D.R.)
| | - Carlos Quilcate
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Lima 15024, Peru; (R.E.); (Y.R.); (C.Q.); (D.D.); (C.S.A.-A.); (S.L.); (W.Y.A.-G.); (D.R.)
| | - Deisy Dipaz
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Lima 15024, Peru; (R.E.); (Y.R.); (C.Q.); (D.D.); (C.S.A.-A.); (S.L.); (W.Y.A.-G.); (D.R.)
| | - Carol S. Alejos-Asencio
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Lima 15024, Peru; (R.E.); (Y.R.); (C.Q.); (D.D.); (C.S.A.-A.); (S.L.); (W.Y.A.-G.); (D.R.)
| | - Silvia Leon
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Lima 15024, Peru; (R.E.); (Y.R.); (C.Q.); (D.D.); (C.S.A.-A.); (S.L.); (W.Y.A.-G.); (D.R.)
| | - Wuesley Yusmein Alvarez-García
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Lima 15024, Peru; (R.E.); (Y.R.); (C.Q.); (D.D.); (C.S.A.-A.); (S.L.); (W.Y.A.-G.); (D.R.)
| | - Diorman Rojas
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Lima 15024, Peru; (R.E.); (Y.R.); (C.Q.); (D.D.); (C.S.A.-A.); (S.L.); (W.Y.A.-G.); (D.R.)
| | - Wigoberto Alvarado
- Facultad de Ingeniería Zootecnista, Agronegocios y Biotecnología, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas (UNTRM), Cl. Higos Urco 342, Chachapoyas 01001, Peru; (W.A.)
| | - Jorge L. Maicelo
- Facultad de Ingeniería Zootecnista, Agronegocios y Biotecnología, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas (UNTRM), Cl. Higos Urco 342, Chachapoyas 01001, Peru; (W.A.)
| | - Carlos I. Arbizu
- Facultad de Ingeniería y Ciencias Agrarias, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas (UNTRM), Cl. Higos Urco 342, Chachapoyas 01001, Peru
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Han Z, Ran Y, Li J, Zhang X, Yang H, Liu J, Dong S, Jia H, Yang Z, Li Y, Guo L, Zhou S, Bao S, Yuan W, Wang B, Zhou L. Association of gut microbiota with lactose intolerance and coeliac disease: a two-sample Mendelian randomization study. Front Nutr 2024; 11:1395801. [PMID: 39166131 PMCID: PMC11333455 DOI: 10.3389/fnut.2024.1395801] [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: 03/04/2024] [Accepted: 07/23/2024] [Indexed: 08/22/2024] Open
Abstract
Background and objectives Lactose intolerance and coeliac disease are common clinical nutrient malabsorption disorders, with an unclear pathogenesis and limited therapeutic options. It is widely believed that the gut microbiota plays an important role in many digestive disorders, but its role in lactose intolerance and coeliac disease is not yet clear. This study aimed to investigate the correlation between gut microbiota and lactose intolerance and coeliac disease. Materials and methods This study utilized the genome-wide association study database to investigate the association between gut microbiota and lactose intolerance and coeliac disease using Mendelian randomization (MR). The robustness of our findings was confirmed through subsequent analyses including Cochrane's Q statistic, MR-Egger Intercept Regression, MR-PRESSO Global Test and Leave-one-out methods. Results By employing the inverse variance weighted method, we identified that family Veillonellaceae, genus Oxalobacter and Senegalimassilia were protective against lactose intolerance, whereas genus Anaerotruncus, Eubacterium rectale group and Ruminococcus2 were found to be risk factors for lactose intolerance. Regarding coeliac disease, class Bacilli and Gammaproteobacteria, family FamilyXIII and Veillonellaceae, genus Eisenbergiella, Lachnoclostridium, RuminococcaceaeUCG014 and Ruminococcus2 were identified as protective factors, while class Betaproteobacteria, genus Eubacterium xylanophilum group and Blautia were risk factors. Furthermore, reverse the MR analysis did not reveal any evidence of a causal relationship between lactose intolerance or coeliac disease and the bacteria identified in our study. Conclusion This study provides novel insights into exploring the role of gut microbiota in lactose intolerance and coeliac disease; however, further experiments investigations are required to elucidate the specific underlying mechanisms.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Lu Zhou
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China
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Wei X, Yao C, He X, Li J, Wang Y, Wang C, Chen Q, Ma X, Guo DA. Biotransformation of chenodeoxycholic acid by human intestinal fungi and the agonistic effects on FXR. PHYTOCHEMISTRY 2024; 224:114162. [PMID: 38797255 DOI: 10.1016/j.phytochem.2024.114162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/13/2024] [Accepted: 05/24/2024] [Indexed: 05/29/2024]
Abstract
Bile acids play a vital role in modulating host metabolism, with chenodeoxycholic acid (CDCA) standing out as a primary bile acid that naturally activates farnesoid X receptor (FXR). In this study, we investigated the microbial transformations of CDCA by seven human intestinal fungal species. Our findings revealed that hydroxylation and dehydrogenation were the most prevalent metabolic pathways. Incubation of CDCA with Rhizopus microspores (PT2906) afforded eight undescribed compounds (6-13) alongside five known analogs (1-5) which were elucidated by HRESI-MS and NMR data. Notably, compounds 8, 12 and 13 exhibited an inhibitory effect on FXR in contrast to the FXR activation observed with CDCA in vitro assays. This study shone a light on the diverse transformations of CDCA by intestinal fungi, unveiling potential modulators of FXR activity with implications for host metabolism.
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Affiliation(s)
- Xuemei Wei
- National Engineering Research Center of TCM Standardization Technology, Shanghai Research Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmaceutical Sciences, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Changliang Yao
- National Engineering Research Center of TCM Standardization Technology, Shanghai Research Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xin He
- National Engineering Research Center of TCM Standardization Technology, Shanghai Research Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Jiayuan Li
- National Engineering Research Center of TCM Standardization Technology, Shanghai Research Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yulu Wang
- National Engineering Research Center of TCM Standardization Technology, Shanghai Research Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Chao Wang
- College of Integrative Medicine, College of Pharmacy, Dalian Medical University, Dalian, 116044, China
| | - Qinhua Chen
- Shenzhen Baoan Authentic TCM Therapy Hospital, Shenzhen, 518101, China
| | - Xiaochi Ma
- College of Integrative Medicine, College of Pharmacy, Dalian Medical University, Dalian, 116044, China.
| | - De-An Guo
- National Engineering Research Center of TCM Standardization Technology, Shanghai Research Center for Modernization of Traditional Chinese Medicine, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmaceutical Sciences, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China.
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Deng K, Gupta DK, Shu XO, Lipworth L, Zheng W, Cai H, Cai Q, Yu D. Circulating Metabolite Profiles and Risk of Coronary Heart Disease Among Racially and Geographically Diverse Populations. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2024; 17:e004437. [PMID: 38950084 PMCID: PMC11335450 DOI: 10.1161/circgen.123.004437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 05/17/2024] [Indexed: 07/03/2024]
Abstract
BACKGROUND Metabolomics may reveal novel biomarkers for coronary heart disease (CHD). We aimed to identify circulating metabolites and construct a metabolite risk score (MRS) associated with incident CHD among racially and geographically diverse populations. METHODS Untargeted metabolomics was conducted using baseline plasma samples from 900 incident CHD cases and 900 age-/sex-/race-matched controls (300 pairs of Black Americans, White Americans, and Chinese adults, respectively), which detected 927 metabolites with known identities among ≥80% of samples. After quality control, 896 case-control pairs remained and were randomly divided into discovery (70%) and validation (30%) sets within each race. In the discovery set, conditional logistic regression and least absolute shrinkage and selection operator over 100 subsamples were applied to identify metabolites robustly associated with CHD risk and construct the MRS. The MRS-CHD association was evaluated using conditional logistic regression and the C-index. Mediation analysis was performed to examine if MRS mediated associations between conventional risk factors and incident CHD. The results from the validation set were presented as the main findings. RESULTS Twenty-four metabolites selected in ≥90% of subsamples comprised the MRS, which was significantly associated with incident CHD (odds ratio per 1 SD, 2.21 [95% CI, 1.62-3.00] after adjusting for sociodemographics, lifestyles, family history, and metabolic health status). MRS could distinguish incident CHD cases from matched controls (C-index, 0.69 [95% CI, 0.63-0.74]) and improve CHD risk prediction when adding to conventional risk factors (C-index, 0.71 [95% CI, 0.65-0.76] versus 0.67 [95% CI, 0.61-0.73]; P<0.001). The odds ratios and C-index were similar across subgroups defined by race, sex, socioeconomic status, lifestyles, metabolic health, family history, and follow-up duration. The MRS mediated large portions (46.0%-74.2%) of the associations for body mass index, smoking, diabetes, hypertension, and dyslipidemia with incident CHD. CONCLUSIONS In a diverse study sample, we identified 24 circulating metabolites that, when combined into an MRS, were robustly associated with incident CHD and modestly improved CHD risk prediction beyond conventional risk factors.
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Affiliation(s)
- Kui Deng
- Vanderbilt Epidemiology Center, Division of Epidemiology, Dept of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Deepak K. Gupta
- Vanderbilt Translational and Clinical Cardiovascular Research Center & Division of Cardiovascular Medicine, Dept of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Xiao-Ou Shu
- Vanderbilt Epidemiology Center, Division of Epidemiology, Dept of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Loren Lipworth
- Vanderbilt Epidemiology Center, Division of Epidemiology, Dept of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Wei Zheng
- Vanderbilt Epidemiology Center, Division of Epidemiology, Dept of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Hui Cai
- Vanderbilt Epidemiology Center, Division of Epidemiology, Dept of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Qiuyin Cai
- Vanderbilt Epidemiology Center, Division of Epidemiology, Dept of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Danxia Yu
- Vanderbilt Epidemiology Center, Division of Epidemiology, Dept of Medicine, Vanderbilt University Medical Center, Nashville, TN
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Sey EA, Warris A. The gut-lung axis: the impact of the gut mycobiome on pulmonary diseases and infections. OXFORD OPEN IMMUNOLOGY 2024; 5:iqae008. [PMID: 39193472 PMCID: PMC11316619 DOI: 10.1093/oxfimm/iqae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 06/12/2024] [Accepted: 06/13/2024] [Indexed: 08/29/2024] Open
Abstract
The gastrointestinal tract contains a diverse microbiome consisting of bacteria, fungi, viruses and archaea. Although these microbes usually reside as commensal organisms, it is now well established that higher abundance of specific bacterial or fungal species, or loss of diversity in the microbiome can significantly affect development, progression and outcomes in disease. Studies have mainly focused on the effects of bacteria, however, the impact of other microbes, such as fungi, has received increased attention in the last few years. Fungi only represent around 0.1% of the total gut microbial population. However, key fungal taxa such as Candida, Aspergillus and Wallemia have been shown to significantly impact health and disease. The composition of the gut mycobiome has been shown to affect immunity at distal sites, such as the heart, lung, brain, pancreas, and liver. In the case of the lung this phenomenon is referred to as the 'gut-lung axis'. Recent studies have begun to explore and unveil the relationship between gut fungi and lung immunity in diseases such as asthma and lung cancer, and lung infections caused by viruses, bacteria and fungi. In this review we will summarize the current, rapidly growing, literature describing the impact of the gut mycobiome on respiratory disease and infection.
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Affiliation(s)
- Emily A Sey
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, EX4 4QD, UK
| | - Adilia Warris
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, EX4 4QD, UK
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Fu Y, Gou W, Wu P, Lai Y, Liang X, Zhang K, Shuai M, Tang J, Miao Z, Chen J, Yuan J, Zhao B, Yang Y, Liu X, Hu Y, Pan A, Pan XF, Zheng JS. Landscape of the gut mycobiome dynamics during pregnancy and its relationship with host metabolism and pregnancy health. Gut 2024; 73:1302-1312. [PMID: 38724219 PMCID: PMC11287620 DOI: 10.1136/gutjnl-2024-332260] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 04/23/2024] [Indexed: 07/13/2024]
Abstract
OBJECTIVE The remodelling of gut mycobiome (ie, fungi) during pregnancy and its potential influence on host metabolism and pregnancy health remains largely unexplored. Here, we aim to examine the characteristics of gut fungi in pregnant women, and reveal the associations between gut mycobiome, host metabolome and pregnancy health. DESIGN Based on a prospective birth cohort in central China (2017 to 2020): Tongji-Huaxi-Shuangliu Birth Cohort, we included 4800 participants who had available ITS2 sequencing data, dietary information and clinical records during their pregnancy. Additionally, we established a subcohort of 1059 participants, which included 514 women who gave birth to preterm, low birthweight or macrosomia infants, as well as 545 randomly selected controls. In this subcohort, a total of 750, 748 and 709 participants had ITS2 sequencing data, 16S sequencing data and serum metabolome data available, respectively, across all trimesters. RESULTS The composition of gut fungi changes dramatically from early to late pregnancy, exhibiting a greater degree of variability and individuality compared with changes observed in gut bacteria. The multiomics data provide a landscape of the networks among gut mycobiome, biological functionality, serum metabolites and pregnancy health, pinpointing the link between Mucor and adverse pregnancy outcomes. The prepregnancy overweight status is a key factor influencing both gut mycobiome compositional alteration and the pattern of metabolic remodelling during pregnancy. CONCLUSION This study provides a landscape of gut mycobiome dynamics during pregnancy and its relationship with host metabolism and pregnancy health, which lays the foundation of the future gut mycobiome investigation for healthy pregnancy.
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Affiliation(s)
- Yuanqing Fu
- Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, China
| | - Wanglong Gou
- Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, China
| | - Ping Wu
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuwei Lai
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xinxiu Liang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, China
| | - Ke Zhang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, China
| | - Menglei Shuai
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, China
| | - Jun Tang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, China
| | - Zelei Miao
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, China
| | - Jieteng Chen
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, China
| | - Jiaying Yuan
- Department of Science and Education, Shuangliu Maternal and Child Health Hospital, Chengdu, China
| | - Bin Zhao
- Antenatal Care Clinics, Shuangliu Maternal and Child Health Hospital, Chengdu, China
| | - Yunhaonan Yang
- Section of Epidemiology and Population Health & Department of Obstetrics and Gynecology, Ministry of Education Key Laboratory of Birth Defects and Related Diseases of Women and Children & National Medical Products Administration Key Laboratory for Technical Research on Drug Products In Vitro and In Vivo Correlation, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Xiaojuan Liu
- Department of Laboratory Medicine, Ministry of Education Key Laboratory of Birth Defects and Related Diseases of Women and Children, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Yayi Hu
- Department of Obstetrics and Gynecology, Ministry of Education Key Laboratory of Birth Defects and Related Diseases of Women and Children, West China Second University Hospital, Sichuan University, Chengdu, China
| | - An Pan
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiong-Fei Pan
- Section of Epidemiology and Population Health & Department of Obstetrics and Gynecology, Ministry of Education Key Laboratory of Birth Defects and Related Diseases of Women and Children & National Medical Products Administration Key Laboratory for Technical Research on Drug Products In Vitro and In Vivo Correlation, West China Second University Hospital, Sichuan University, Chengdu, China
- Shuangliu Institute of Women's and Children's Health, Shuangliu Maternal and Child Health Hospital, Chengdu, China
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China
| | - Ju-Sheng Zheng
- Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
- Zhejiang Key Laboratory of Multi-Omics in Infection and Immunity, Center for Infectious Disease Research, School of Medicine, Westlake University, Hangzhou, China
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Naik B, Sasikumar J, Das SP. From Skin and Gut to the Brain: The Infectious Journey of the Human Commensal Fungus Malassezia and Its Neurological Consequences. Mol Neurobiol 2024:10.1007/s12035-024-04270-w. [PMID: 38871941 DOI: 10.1007/s12035-024-04270-w] [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: 01/12/2024] [Accepted: 05/27/2024] [Indexed: 06/15/2024]
Abstract
The human mycobiome encompasses diverse communities of fungal organisms residing within the body and has emerged as a critical player in shaping health and disease. While extensive research has focused on the skin and gut mycobiome, recent investigations have pointed toward the potential role of fungal organisms in neurological disorders. Among those fungal organisms, the presence of the commensal fungus Malassezia in the brain has created curiosity because of its commensal nature and primary association with the human skin and gut. This budding yeast is responsible for several diseases, such as Seborrheic dermatitis, Atopic dermatitis, Pityriasis versicolor, Malassezia folliculitis, dandruff, and others. However recent findings surprisingly show the presence of Malassezia DNA in the brain and have been linked to diseases like Alzheimer's disease, Parkinson's disease, Multiple sclerosis, and Amyotrophic lateral sclerosis. The exact role of Malassezia in these disorders is unknown, but its ability to infect human cells, travel through the bloodstream, cross the blood-brain barrier, and reside along with the lipid-rich neuronal cells are potential mechanisms responsible for pathogenesis. This also includes the induction of pro-inflammatory cytokines, disruption of the blood-brain barrier, gut-microbe interaction, and accumulation of metabolic changes in the brain environment. In this review, we discuss these key findings from studies linking Malassezia to neurological disorders, emphasizing the complex and multifaceted nature of these cases. Furthermore, we discuss potential mechanisms through which Malassezia might contribute to the development of neurological conditions. Future investigations will open up new avenues for our understanding of the fungal gut-brain axis and how it influences human behavior. Collaborative research efforts among microbiologists, neuroscientists, immunologists, and clinicians hold promise for unraveling the enigmatic connections between human commensal Malassezia and neurological disorders.
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Affiliation(s)
- Bharati Naik
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Jayaprakash Sasikumar
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Shankar Prasad Das
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India.
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10
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Van Syoc E, Nixon MP, Silverman JD, Luo Y, Gonzalez FJ, Elbere I, Klovins J, Patterson AD, Rogers CJ, Ganda E. Changes in the type 2 diabetes gut mycobiome associate with metformin treatment across populations. mBio 2024; 15:e0016924. [PMID: 38767350 PMCID: PMC11237675 DOI: 10.1128/mbio.00169-24] [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: 01/18/2024] [Accepted: 04/08/2024] [Indexed: 05/22/2024] Open
Abstract
The human gut teems with a diverse ecosystem of microbes, yet non-bacterial portions of that community are overlooked in studies of metabolic diseases firmly linked to gut bacteria. Type 2 diabetes mellitus (T2D) is associated with compositional shifts in the gut bacterial microbiome and the mycobiome, the fungal portion of the microbiome. However, whether T2D and/or metformin treatment underpins fungal community changes is unresolved. To differentiate these effects, we curated a gut mycobiome cohort spanning 1,000 human samples across five countries and validated our findings in a murine experimental model. We use Bayesian multinomial logistic normal models to show that T2D and metformin both associate with shifts in the relative abundance of distinct gut fungi. T2D is associated with shifts in the Saccharomycetes and Sordariomycetes fungal classes, while the genera Fusarium and Tetrapisipora most consistently associate with metformin treatment. We confirmed the impact of metformin on individual gut fungi by administering metformin to healthy mice. Thus, metformin and T2D account for subtle, but significant and distinct variation in the gut mycobiome across human populations. This work highlights for the first time that metformin can confound associations of gut fungi with T2D and warrants the need to consider pharmaceutical interventions in investigations of linkages between metabolic diseases and gut microbial inhabitants. IMPORTANCE This is the largest to-date multi-country cohort characterizing the human gut mycobiome, and the first to investigate potential perturbations in gut fungi from oral pharmaceutical treatment. We demonstrate the reproducible effects of metformin treatment on the human and murine gut mycobiome and highlight a need to consider metformin as a confounding factor in investigations between type 2 diabetes mellitus and the gut microbial ecosystem.
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Affiliation(s)
- Emily Van Syoc
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Animal Science, The Pennsylvania State University, University Park, Pennsylvania, USA
- One Health Microbiome Center, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Michelle Pistner Nixon
- College of Information Sciences and Technology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Justin D. Silverman
- One Health Microbiome Center, The Pennsylvania State University, University Park, Pennsylvania, USA
- College of Information Sciences and Technology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Statistics, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Medicine, The Pennsylvania State University, Hershey, Pennsylvania, USA
| | - Yuhong Luo
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Frank J. Gonzalez
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Ilze Elbere
- Latvian Biomedical Research and Study Center, Riga, Latvia
| | - Janis Klovins
- Latvian Biomedical Research and Study Center, Riga, Latvia
| | - Andrew D. Patterson
- One Health Microbiome Center, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Connie J. Rogers
- Department of Nutritional Sciences, University of Georgia, Athens, Georgia, USA
| | - Erika Ganda
- Department of Animal Science, The Pennsylvania State University, University Park, Pennsylvania, USA
- One Health Microbiome Center, The Pennsylvania State University, University Park, Pennsylvania, USA
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11
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Iacucci M, Santacroce G, Majumder S, Morael J, Zammarchi I, Maeda Y, Ryan D, Di Sabatino A, Rescigno M, Aburto MR, Cryan JF, Ghosh S. Opening the doors of precision medicine: novel tools to assess intestinal barrier in inflammatory bowel disease and colitis-associated neoplasia. Gut 2024:gutjnl-2023-331579. [PMID: 38851294 DOI: 10.1136/gutjnl-2023-331579] [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] [Received: 04/19/2024] [Accepted: 05/18/2024] [Indexed: 06/10/2024]
Abstract
Mounting evidence underscores the pivotal role of the intestinal barrier and its convoluted network with diet and intestinal microbiome in the pathogenesis of inflammatory bowel disease (IBD) and colitis-associated colorectal cancer (CRC). Moreover, the bidirectional association of the intestinal barrier with the liver and brain, known as the gut-brain axis, plays a crucial role in developing complications, including extraintestinal manifestations of IBD and CRC metastasis. Consequently, barrier healing represents a crucial therapeutic target in these inflammatory-dependent disorders, with barrier assessment predicting disease outcomes, response to therapy and extraintestinal manifestations.New advanced technologies are revolutionising our understanding of the barrier paradigm, enabling the accurate assessment of the intestinal barrier and aiding in unravelling the complexity of the gut-brain axis. Cutting-edge endoscopic imaging techniques, such as ultra-high magnification endocytoscopy and probe-based confocal laser endomicroscopy, are new technologies allowing real-time exploration of the 'cellular' intestinal barrier. Additionally, novel advanced spatial imaging technology platforms, including multispectral imaging, upconversion nanoparticles, digital spatial profiling, optical spectroscopy and mass cytometry, enable a deep and comprehensive assessment of the 'molecular' and 'ultrastructural' barrier. In this promising landscape, artificial intelligence plays a pivotal role in standardising and integrating these novel tools, thereby contributing to barrier assessment and prediction of outcomes.Looking ahead, this integrated and comprehensive approach holds the promise of uncovering new therapeutic targets, breaking the therapeutic ceiling in IBD. Novel molecules, dietary interventions and microbiome modulation strategies aim to restore, reinforce, or modulate the gut-brain axis. These advancements have the potential for transformative and personalised approaches to managing IBD.
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Affiliation(s)
- Marietta Iacucci
- APC Microbiome Ireland, College of Medicine and Health, University College Cork, Cork, Ireland
| | - Giovanni Santacroce
- APC Microbiome Ireland, College of Medicine and Health, University College Cork, Cork, Ireland
| | - Snehali Majumder
- APC Microbiome Ireland, College of Medicine and Health, University College Cork, Cork, Ireland
| | - Jennifer Morael
- APC Microbiome Ireland, Department of Anatomy and Neuroscience, School of Medicine, University College Cork, Cork, Ireland
| | - Irene Zammarchi
- APC Microbiome Ireland, College of Medicine and Health, University College Cork, Cork, Ireland
| | - Yasuharu Maeda
- APC Microbiome Ireland, College of Medicine and Health, University College Cork, Cork, Ireland
| | - David Ryan
- Department of Radiology, School of Medicine, University College Cork, Cork, Ireland
| | - Antonio Di Sabatino
- Department of Internal Medicine and Medical Therapeutics, University of Pavia, Pavia, Italy
- First Department of Internal Medicine, San Matteo Hospital Foundation, Pavia, Italy
| | - Maria Rescigno
- IRCSS Humanitas Research Hospital, Milan, Italy; Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Maria R Aburto
- APC Microbiome Ireland, Department of Anatomy and Neuroscience, School of Medicine, University College Cork, Cork, Ireland
| | - John F Cryan
- APC Microbiome Ireland, Department of Anatomy and Neuroscience, School of Medicine, University College Cork, Cork, Ireland
| | - Subrata Ghosh
- APC Microbiome Ireland, College of Medicine and Health, University College Cork, Cork, Ireland
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12
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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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13
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Zhu C, Zhang C, Wang S, Xun Z, Zhang D, Lan Z, Zhang L, Chao J, Liang Y, Pu Z, Ning C, Sang X, Yang X, Wang H, Jiang X, Zhao H. Characterizations of multi-kingdom gut microbiota in immune checkpoint inhibitor-treated hepatocellular carcinoma. J Immunother Cancer 2024; 12:e008686. [PMID: 38844407 PMCID: PMC11163665 DOI: 10.1136/jitc-2023-008686] [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] [Accepted: 05/17/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND The association between gut bacteria and the response to immune checkpoint inhibitors (ICI) in hepatocellular carcinoma (HCC) has been studied; however, multi-kingdom gut microbiome alterations and interactions in ICI-treated HCC cohorts are not fully understood. METHODS From November 2018 to April 2022, patients receiving ICI treatment for advanced HCC were prospectively enrolled. Herein, we investigated the multi-kingdom microbiota characterization of the gut microbiome, mycobiome, and metabolome using metagenomic, ITS2, and metabolomic data sets of 80 patients with ICI-treated HCC. RESULTS Our findings demonstrated that bacteria and metabolites differed significantly between the durable clinical benefit (DCB) and non-durable clinical benefit (NDB) groups, whereas the differences were smaller for fungi. The overall diversity of bacteria and fungi before treatment was higher in the DCB group than in the NDB group, and the difference in diversity began to change with the use of immunotherapy after 6-8 weeks. We also explored the alterations of gut microbes in the DCB and NDB groups, established 18 bacterial species models as predictive biomarkers for predicting whether immunotherapy is of sustained benefit (area under the curve=75.63%), and screened two species of bacteria (Actinomyces_sp_ICM47, and Senegalimassilia_anaerobia) and one metabolite (galanthaminone) as prognostic biomarkers for predicting survival in patients with HCC treated with ICI. CONCLUSIONS In this study, the status and characterization of the multi-kingdom microbiota, including gut bacteria, fungi, and their metabolites, were described by multiomics sequencing for the first time in patients with HCC treated with ICI. Our findings demonstrate the potential of bacterial taxa as predictive biomarkers of ICI clinical efficacy, and bacteria and their metabolites as prognostic biomarkers.
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Affiliation(s)
- Chengpei Zhu
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
- Department of General Surgery Center, Beijing Youan Hospital, Clinical Center for Liver Cancer, Capital Medical University, Beijing, China
| | - Chenchen Zhang
- Microbiome Research Center, Moon (Guangzhou) Biotech Ltd, Guangzhou, China
| | - Shanshan Wang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Ziyu Xun
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Dongya Zhang
- Microbiome Research Center, Moon (Guangzhou) Biotech Ltd, Guangzhou, China
| | - Zhou Lan
- Microbiome Research Center, Moon (Guangzhou) Biotech Ltd, Guangzhou, China
| | - Longhao Zhang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Jiashuo Chao
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Yajun Liang
- Microbiome Research Center, Moon (Guangzhou) Biotech Ltd, Guangzhou, China
| | - Zilun Pu
- Microbiome Research Center, Moon (Guangzhou) Biotech Ltd, Guangzhou, China
| | - Cong Ning
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Xinting Sang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Xiaobo Yang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Hanping Wang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
- Department of Pulmonary and Critical Care Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Xianzhi Jiang
- Microbiome Research Center, Moon (Guangzhou) Biotech Ltd, Guangzhou, China
| | - Haitao Zhao
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
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14
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Ling CW, Zhong H, Zeng FF, Chen G, Fu Y, Wang C, Zhang ZQ, Cao WT, Sun TY, Ding D, Liu YH, Dong HL, Jing LP, Ling W, Zheng JS, Chen YM. Cohort Profile: Guangzhou Nutrition and Health Study (GNHS): A Population-based Multi-omics Study. J Epidemiol 2024; 34:301-306. [PMID: 37813622 PMCID: PMC11078596 DOI: 10.2188/jea.je20230108] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023] Open
Abstract
BACKGROUND The Guangzhou Nutrition and Health Study (GNHS) aims to assess the determinants of metabolic disease in nutritional aspects, as well as other environmental and genetic factors, and explore possible biomarkers and mechanisms with multi-omics integration. METHODS The population-based sample of adults in Guangzhou, China (baseline: 40-83 years old; n = 5,118) was followed up about every 3 years. All are tracked via on-site follow-up and health information systems. We assessed detailed information on lifestyle factors, physical activities, dietary assessments, psychological health, cognitive function, body measurements, and muscle function. Instrument tests included dual-energy X-ray absorptiometry scanning, carotid artery and liver ultrasonography evaluations, vascular endothelial function evaluation, upper-abdomen and brain magnetic resonance imaging, and 14-day real-time continuous glucose monitoring tests. We also measured multi-omics, including host genome-wide genotyping, serum metabolome and proteome, gut microbiome (16S rRNA sequencing, metagenome, and internal transcribed spacer 2 sequencing), and fecal metabolome and proteome. RESULTS The baseline surveys were conducted from 2008 to 2015. Now, we have completed 3 waves. The 3rd and 4th follow-ups have started but have yet to end. A total of 5,118 participants aged 40-83 took part in the study. The median age at baseline was approximately 59.0 years and the proportion of female participants was about 69.4%. Among all the participants, 3,628 (71%) completed at least one on-site follow-up, with a median duration of 9.48 years. CONCLUSION The cohort will provide data that will be influential in establishing the role of nutrition in metabolic diseases with multi-omics.
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Affiliation(s)
- Chu-Wen Ling
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-Sen University
| | - Haili Zhong
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-Sen University
| | - Fang-Fang Zeng
- Department of Epidemiology, School of Medicine, Jinan University
| | - Gengdong Chen
- Department of Obstetrics, Foshan Institute of Fetal Medicine, Southern Medical University Affiliated Maternal & Child Health Hospital of Foshan
| | - Yuanqing Fu
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University
| | - Cheng Wang
- Department of Clinical Nutrition, Sun Yat-sen Memorial Hospital
| | - Zhe-Qing Zhang
- Department of Nutrition and Food Hygiene, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University
| | - Wen-Ting Cao
- International School of Public Health and One Health, Hainan Medical University
| | - Ting-Yu Sun
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-Sen University
| | - Ding Ding
- Global Health Research Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences
| | - Yan-Hua Liu
- Department of Nutrition, the First Affiliated Hospital of Zhengzhou University
| | - Hong-Li Dong
- Scientific Education Section and Department of Child Healthcare, Affiliated Maternity & Child Health Care Hospital of Nantong University
| | - Li-Peng Jing
- Department of Epidemiology, School of Public Health, Lanzhou University
| | - Wenhua Ling
- Department of Nutrition, School of Public Health, Sun Yat-sen University
| | - Ju-Sheng Zheng
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University
| | - Yu-Ming Chen
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-Sen University
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15
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Zhou S, Zhou H, Qian J, Han J, Zhang Y, Li Y, Zhang M, Cong J. Compound prebiotics as prophylactic and adjunctive treatments ameliorate DSS-induced colitis through gut microbiota modulation effects. Int J Biol Macromol 2024; 270:132362. [PMID: 38750864 DOI: 10.1016/j.ijbiomac.2024.132362] [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: 01/02/2024] [Revised: 04/29/2024] [Accepted: 05/11/2024] [Indexed: 05/19/2024]
Abstract
The prophylactic and adjunctive impacts of compound prebiotics (CP), comprising galacto-oligosaccharides, fructo-oligosaccharides, and isomalto-oligosaccharides, on colitis remain unclear. This study aimed to elucidate the effects of CP on dextran sodium sulfate (DSS)-induced colitis via modulation of the gut microbiota. Mice received prophylactic CP (PCP) for three weeks and DSS in the second week. In the third week, therapeutic CP, mesalazine, and a combination of CP and mesalazine (CPM) were administered to mice with DSS-induced colitis. The administration of PCP and CPM was found to ameliorate colitis, as evidenced by increases in body weight and colon length, elevation of the anti-inflammatory cytokine IL-10, and reductions in the disease activity index, histological scores, and levels of pro-inflammatory cytokines in mice with DSS-induced colitis on days 14 or 21. Furthermore, an increase in the relative abundance of probiotics (Ligilactobacillus, Bifidobacterium, and Limosilactobacillus), alpha diversity indices, short-chain fatty acids (SCFA) contents, and microbial network complexity was observed following PCP or CPM treatment. Correlation analysis revealed positive associations between these probiotics and both SCFA and IL-10, and negative associations with pro-inflammatory cytokines. This study highlighted the potential of CP as novel prophylactic and adjunctive treatments for alleviating DSS-induced intestinal inflammation and maintaining gut microbiota homeostasis.
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Affiliation(s)
- Siyu Zhou
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266000, China
| | - Hongxia Zhou
- Department of Cardiology, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, China
| | - Jia Qian
- Department of Oncology, Qingdao Central Hospital, University of Health and Rehabilitation Sciences, Qingdao 266000, China
| | - Jiaqi Han
- Department of Cardiology, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, China
| | - Yun Zhang
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266000, China
| | - Ying Li
- Shanxi Zhendong Wuhe Medical Care Hall Co., Changzhi, Shanxi, China
| | - Meiping Zhang
- Shanxi Zhendong Wuhe Medical Care Hall Co., Changzhi, Shanxi, China
| | - Jing Cong
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266000, China.
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16
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Dalamaga M. Clinical metabolomics: Useful insights, perspectives and challenges. Metabol Open 2024; 22:100290. [PMID: 39011161 PMCID: PMC11247213 DOI: 10.1016/j.metop.2024.100290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024] Open
Abstract
Metabolomics, a cutting-edge omics technique, is a rapidly advancing field in biomedical research, concentrating on the elucidation of pathogenetic mechanisms and the discovery of novel metabolite signatures predictive of disease risk, aiding in earlier disease detection, prognosis and prediction of treatment response. The capacity of this omics approach to simultaneously quantify thousands of metabolites, i.e. small molecules less than 1500 Da in samples, positions it as a promising tool for research and clinical applications in personalized medicine. Clinical metabolomics studies have proven valuable in understanding cardiometabolic disorders, potentially uncovering diagnostic biomarkers predictive of disease risk. Liquid chromatography-mass spectrometry is the predominant analytical method used in metabolomics, particularly untargeted. Metabolomics combined with extensive genomic data, proteomics, clinical chemistry data, imaging, health records, and other pertinent health-related data may yield significant advances beneficial for both public health initiatives, clinical applications and precision medicine, particularly in rare disorders and multimorbidity. This special issue has gathered original research articles in topics related to clinical metabolomics as well as research articles, reviews, perspectives and highlights in the broader field of translational and clinical metabolic research. Additional research is necessary to identify which metabolites consistently enhance clinical risk prediction across various populations and are causally linked to disease progression.
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Affiliation(s)
- Maria Dalamaga
- Department of Biological Chemistry, School of Medicine, National and Kapodistrian University of Athens, 75 Mikras Asias, 11527, Athens, Greece
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17
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Liang Y, Jiang Z, Fu Y, Lu S, Miao Z, Shuai M, Liang X, Gou W, Zhang K, Shi RQ, Gao C, Shi MQ, Wang XH, Hu WS, Zheng JS. Cross-Sectional and Prospective Association of Serum 25-Hydroxyvitamin D with Gut Mycobiota during Pregnancy among Women with Gestational Diabetes. Mol Nutr Food Res 2024; 68:e2400022. [PMID: 38763911 DOI: 10.1002/mnfr.202400022] [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: 01/08/2024] [Revised: 04/30/2024] [Indexed: 05/21/2024]
Abstract
SCOPE Little is known about the effect of blood vitamin D status on the gut mycobiota (i.e., fungi), a crucial component of the gut microbial ecosystem. The study aims to explore the association between 25-hydroxyvitamin D [25(OH)D] and gut mycobiota and to investigate the link between the identified mycobial features and blood glycemic traits. METHODS AND RESULTS The study examines the association between serum 25(OH)D levels and the gut mycobiota in the Westlake Precision Birth Cohort, which includes pregnant women with gestational diabetes mellitus (GDM). The study develops a genetic risk score (GRS) for 25(OH)D to validate the observational results. In both the prospective and cross-sectional analyses, the vitamin D is associated with gut mycobiota diversity. Specifically, the abundance of Saccharomyces is significantly lower in the vitamin D-sufficient group than in the vitamin D-deficient group. The GRS of 25(OH)D is inversely associated with the abundance of Saccharomyces. Moreover, the Saccharomyces is positively associated with blood glucose levels. CONCLUSION Blood vitamin D status is associated with the diversity and composition of gut mycobiota in women with GDM, which may provide new insights into the mechanistic understanding of the relationship between vitamin D levels and metabolic health.
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Affiliation(s)
- Yuhui Liang
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310030, China
| | - Zengliang Jiang
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310030, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, 310024, China
| | - Yuanqing Fu
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310030, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, 310024, China
| | - Sha Lu
- Department of Obstetrics and Gynecology, Hangzhou Women's Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, 310012, China
- Department of Obstetrics and Gynecology, The Affiliated Hangzhou Women's Hospital of Hangzhou Normal University, Hangzhou, 310012, China
| | - Zelei Miao
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310030, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, 310024, China
| | - Menglei Shuai
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310030, China
| | - Xinxiu Liang
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310030, China
| | - Wanglong Gou
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310030, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, 310024, China
| | - Ke Zhang
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310030, China
| | - Rui-Qi Shi
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310030, China
| | - Chang Gao
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310030, China
| | - Mei-Qi Shi
- Department of Nutrition, Hangzhou Women's Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, 310012, China
| | - Xu-Hong Wang
- Department of Nutrition, Hangzhou Women's Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, 310012, China
| | - Wen-Sheng Hu
- Department of Obstetrics and Gynecology, Hangzhou Women's Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, 310012, China
- Department of Obstetrics and Gynecology, The Affiliated Hangzhou Women's Hospital of Hangzhou Normal University, Hangzhou, 310012, China
| | - Ju-Sheng Zheng
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310030, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, 310024, China
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18
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Qiao Y, Tang X, Liu Z, Ocansey DKW, Zhou M, Shang A, Mao F. Therapeutic Prospects of Mesenchymal Stem Cell and Their Derived Exosomes in the Regulation of the Gut Microbiota in Inflammatory Bowel Disease. Pharmaceuticals (Basel) 2024; 17:607. [PMID: 38794176 PMCID: PMC11124012 DOI: 10.3390/ph17050607] [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: 04/04/2024] [Revised: 05/05/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
Mesenchymal stem cells (MSCs) have shown great potential in the treatment of several inflammatory diseases due to their immunomodulatory ability, which is mediated by exosomes secreted by MSCs (MSC-Exs). The incidence of inflammatory bowel disease (IBD) is increasing globally, but there is currently no long-term effective treatment. As an emerging therapy, MSC-Exs have proven to be effective in alleviating IBD experimentally, and the specific mechanism continues to be explored. The gut microbiota plays an important role in the occurrence and development of IBD, and MSCs and MSC-Exs can effectively regulate gut microbiota in animal models of IBD, but the mechanism involved and whether the outcome can relieve the characteristic dysbiosis necessary to alleviate IBD still needs to be studied. This review provides current evidence on the effective modulation of the gut microbiota by MSC-Exs, offering a basis for further research on the pathogenic mechanism of IBD and MSC-Ex treatments through the improvement of gut microbiota.
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Affiliation(s)
- Yaru Qiao
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Y.Q.); (Z.L.); (D.K.W.O.); (M.Z.)
- Department of Laboratory Medicine, Lianyungang Clinical College, Jiangsu University, Lianyungang 222006, China;
| | - Xiaohua Tang
- The People’s Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Zhenjiang 212300, China;
| | - Ziyue Liu
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Y.Q.); (Z.L.); (D.K.W.O.); (M.Z.)
| | - Dickson Kofi Wiredu Ocansey
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Y.Q.); (Z.L.); (D.K.W.O.); (M.Z.)
- Department of Medical Laboratory Science, School of Allied Health Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast CC0959347, Ghana
| | - Mengjiao Zhou
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Y.Q.); (Z.L.); (D.K.W.O.); (M.Z.)
| | - Anquan Shang
- Department of Laboratory Medicine, Lianyungang Clinical College, Jiangsu University, Lianyungang 222006, China;
| | - Fei Mao
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Y.Q.); (Z.L.); (D.K.W.O.); (M.Z.)
- Department of Laboratory Medicine, Lianyungang Clinical College, Jiangsu University, Lianyungang 222006, China;
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19
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Liu T, Asif IM, Chen Y, Zhang M, Li B, Wang L. The Relationship between Diet, Gut Mycobiome, and Functional Gastrointestinal Disorders: Evidence, Doubts, and Prospects. Mol Nutr Food Res 2024; 68:e2300382. [PMID: 38659179 DOI: 10.1002/mnfr.202300382] [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: 06/08/2023] [Revised: 12/11/2023] [Indexed: 04/26/2024]
Abstract
Gut fungi are important parts of intestinal microbes. Dietary ingredients have the potential to regulate the structure of gut fungi in different directions and modulate mycobiome composition by changing dietary patterns, which have been applied to neurological disorders. Emerging pieces of evidence have revealed the regulatory functions of gut mycobiome in gastrointestinal diseases, but the relationships between gut fungi and functional gastrointestinal disorders (FGIDs) are ignored in the past. This review discusses the impact of dietary nutrients and patterns on mycobiome, and the possible ways in which gut fungi are involved in the pathogenesis of FGIDs. Besides affecting host immunity, intestinal fungi can be involved in the pathogenesis of FGIDs by endosymbiosis or bidirectional regulation with gut bacteria as well. In addition, the Mediterranean diet may be the most appropriate dietary pattern for subjects with FGIDs. A full understanding of these associations may have important implications for the pathogenesis and treatment of FGIDs.
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Affiliation(s)
- Tianxu Liu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Key Laboratory of Environment Correlative Dietology (Huazhong Agricultural University), Ministry of Education, Wuhan, Hubei, 430070, China
| | - Ismail Muhammad Asif
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Key Laboratory of Environment Correlative Dietology (Huazhong Agricultural University), Ministry of Education, Wuhan, Hubei, 430070, China
| | - Yan Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Key Laboratory of Environment Correlative Dietology (Huazhong Agricultural University), Ministry of Education, Wuhan, Hubei, 430070, China
| | - Meixue Zhang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Key Laboratory of Environment Correlative Dietology (Huazhong Agricultural University), Ministry of Education, Wuhan, Hubei, 430070, China
| | - Bin Li
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Key Laboratory of Environment Correlative Dietology (Huazhong Agricultural University), Ministry of Education, Wuhan, Hubei, 430070, China
| | - Ling Wang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Key Laboratory of Environment Correlative Dietology (Huazhong Agricultural University), Ministry of Education, Wuhan, Hubei, 430070, China
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20
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Wu D, Guan YX, Li CH, Zheng Q, Yin ZJ, Wang H, Liu NN. "Nutrient-fungi-host" tripartite interaction in cancer progression. IMETA 2024; 3:e170. [PMID: 38882486 PMCID: PMC11170973 DOI: 10.1002/imt2.170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 06/18/2024]
Abstract
The human microbiome exhibits a profound connection with the cancer development, progression, and therapeutic response, with particular emphasis on its components of the mycobiome, which are still in the early stages of research. In this review, we comprehensively summarize cancer-related symbiotic and pathogenic fungal genera. The intricate mechanisms through which fungi impact cancer as an integral member of both gut and tissue-resident microbiomes are further discussed. In addition, we shed light on the pivotal physiological roles of various nutrients, including cholesterol, carbohydrates, proteins and minerals, in facilitating the growth, reproduction, and invasive pathogenesis of the fungi. While our exploration of the interplay between nutrients and cancer, mediated by the mycobiome, is ongoing, the current findings have yet to yield conclusive results. Thus, delving into the relationship between nutrients and fungal pathogenesis in cancer development and progression would provide valuable insights into anticancer therapy and foster precision nutrition and individualized treatments that target fungi from bench to bedside.
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Affiliation(s)
- Di Wu
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Yun-Xuan Guan
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Chen-Hao Li
- Institute of Computing Technology Chinese Academy of Sciences Beijing China
| | - Quan Zheng
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Zuo-Jing Yin
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Hui Wang
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Ning-Ning Liu
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health Shanghai Jiao Tong University School of Medicine Shanghai China
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21
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Guo J, Shi W, Li X, Yang B, Qin C, Su L. Comparative Analysis of Gut Microbiomes in Laboratory Chinchillas, Ferrets, and Marmots: Implications for Pathogen Infection Research. Microorganisms 2024; 12:646. [PMID: 38674591 PMCID: PMC11051751 DOI: 10.3390/microorganisms12040646] [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: 02/20/2024] [Revised: 03/17/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
Gut microbes play a vital role in the health and disease of animals, especially in relation to pathogen infections. Chinchillas, ferrets, and marmots are commonly used as important laboratory animals for infectious disease research. Here, we studied the bacterial and fungal microbiota and discovered that chinchillas had higher alpha diversity and a higher abundance of bacteria compared to marmots and ferrets by using the metabarcoding of 16S rRNA genes and ITS2, coupled with co-occurrence network analysis. The dominant microbes varied significantly among the three animal species, particularly in the gut mycobiota. In the ferrets, the feces were dominated by yeast such as Rhodotorula and Kurtzmaniella, while in the chinchillas, we found Teunomyces and Penicillium dominating, and Acaulium, Piromyces, and Kernia in the marmots. Nevertheless, the dominant bacterial genera shared some similarities, such as Clostridium and Pseudomonas across the three animal species. However, there were significant differences observed, such as Vagococcus and Ignatzschineria in the ferrets, Acinetobacter and Bacteroides in the chinchillas, and Bacteroides and Cellvibrio in the marmots. Additionally, our differential analysis revealed significant differences in classification levels among the three different animal species, as well as variations in feeding habitats that resulted in distinct contributions from the host microbiome. Therefore, our data are valuable for monitoring and evaluating the impacts of the microbiome, as well as considering potential applications.
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Affiliation(s)
| | | | | | | | | | - Lei Su
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, International Center for Technology and Innovation of Animal Model, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Comparative Medicine Center, Peking Union Medical College (PUMC), Beijing 100021, China; (J.G.); (W.S.); (X.L.); (B.Y.); (C.Q.)
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22
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Mok K, Poolsawat T, Somnuk S, Wanikorn B, Patumcharoenpol P, Nitisinprasert S, Vongsangnak W, Nakphaichit M. Preliminary characterization of gut mycobiome enterotypes reveals the correlation trends between host metabolic parameter and diet: a case study in the Thai Cohort. Sci Rep 2024; 14:5805. [PMID: 38461361 PMCID: PMC10924899 DOI: 10.1038/s41598-024-56585-2] [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: 10/08/2023] [Accepted: 03/08/2024] [Indexed: 03/11/2024] Open
Abstract
The association between the gut mycobiome and its potential influence on host metabolism in the Thai Cohort was assessed. Two distinct predominant enterotypes, Saccharomyces (Sa) and Aspergillus/Penicillium (Ap/Pe) showed differences in gut mycobiota diversity and composition. Notably, the Sa enterotype exhibited lower evenness and richness, likely due to the prevalence of Saccharomyces, while both enterotypes displayed unique metabolic behaviors related to nutrient metabolism and body composition. Fiber consumption was positively correlated with adverse body composition and fasting glucose levels in individuals with the Sa enterotype, whereas in the Ap/Pe enterotype it was positively correlated with fat and protein intake. The metabolic functional analysis revealed the Sa enterotype associated with carbohydrate metabolism, while the Ap/Pe enterotype involved in lipid metabolism. Very interestingly, the genes involved in the pentose and glucuronate interconversion pathway, such as polygalacturonase and L-arabinose-isomerase, were enriched in the Sa enterotype signifying a metabolic capacity for complex carbohydrate degradation and utilization of less common sugars as energy sources. These findings highlight the interplay between gut mycobiome composition, dietary habits, and metabolic outcomes within the Thai cohort studies.
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Affiliation(s)
- Kevin Mok
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, 10900, Thailand
- Specialized Research Unit: Probiotics and Prebiotics for Health, Faculty of Agro-Industry, Kasetsart University, Bangkok, 10900, Thailand
| | - Thitirat Poolsawat
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, 10900, Thailand
- Specialized Research Unit: Functional Food and Human Health Laboratory, Faculty of Agro-Industry, Kasetsart University, Bangkok, 10900, Thailand
| | - Surasawadee Somnuk
- Department of Sports and Health Sciences, Faculty of Sport Science, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand
| | - Bandhita Wanikorn
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, 10900, Thailand
- Specialized Research Unit: Functional Food and Human Health Laboratory, Faculty of Agro-Industry, Kasetsart University, Bangkok, 10900, Thailand
| | - Preecha Patumcharoenpol
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok, 10900, Thailand
| | - Sunee Nitisinprasert
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, 10900, Thailand
- Specialized Research Unit: Probiotics and Prebiotics for Health, Faculty of Agro-Industry, Kasetsart University, Bangkok, 10900, Thailand
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok, 10900, Thailand
| | - Massalin Nakphaichit
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, 10900, Thailand.
- Specialized Research Unit: Probiotics and Prebiotics for Health, Faculty of Agro-Industry, Kasetsart University, Bangkok, 10900, Thailand.
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23
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Rizzello F, Viciani E, Gionchetti P, Filippone E, Imbesi V, Melotti L, Dussias NK, Salice M, Santacroce B, Padella A, Velichevskaya A, Marcante A, Castagnetti A. Signatures of disease outcome severity in the intestinal fungal and bacterial microbiome of COVID-19 patients. Front Cell Infect Microbiol 2024; 14:1352202. [PMID: 38510960 PMCID: PMC10952111 DOI: 10.3389/fcimb.2024.1352202] [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: 12/07/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024] Open
Abstract
Background COVID-19, whose causative pathogen is the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), was declared a pandemic in March 2020. The gastrointestinal tract is one of the targets of this virus, and mounting evidence suggests that gastrointestinal symptoms may contribute to disease severity. The gut-lung axis is involved in the immune response to SARS-CoV-2; therefore, we investigated whether COVID-19 patients' bacterial and fungal gut microbiome composition was linked to disease clinical outcome. Methods In May 2020, we collected stool samples and patient records from 24 hospitalized patients with laboratory-confirmed SARS-CoV-2 infection. Fungal and bacterial gut microbiome was characterized by amplicon sequencing on the MiSeq, Illumina's integrated next generation sequencing instrument. A cohort of 201 age- and sex-matched healthy volunteers from the project PRJNA661289 was used as a control group for the bacterial gut microbiota analysis. Results We observed that female COVID-19 patients had a lower gut bacterial microbiota richness than male patients, which was consistent with a different latency in hospital admittance time between the two groups. Both sexes in the COVID-19 patient study group displayed multiple positive associations with opportunistic bacterial pathogens such as Enterococcus, Streptococcus, and Actinomyces. Of note, the Candida genus dominated the gut mycobiota of COVID-19 patients, and adult patients showed a higher intestinal fungal diversity than elderly patients. We found that Saccharomycetales unassigned fungal genera were positively associated with bacterial short-chain fatty acid (SCFA) producers and negatively associated with the proinflammatory genus Bilophila in COVID-19 patients, and we observed that none of the patients who harbored it were admitted to the high-intensity unit. Conclusions COVID-19 was associated with opportunistic bacterial pathogens, and Candida was the dominant fungal taxon in the intestine. Together, we found an association between commensal SCFA-producers and a fungal genus that was present in the intestines of patients who did not experience the most severe outcome of the disease. We believe that this taxon could have played a role in the disease outcome, and that further studies should be conducted to understand the role of fungi in gastrointestinal and health protection.
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Affiliation(s)
- Fernando Rizzello
- IBD Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, University of Bologna, Bologna, Italy
- Department of Medical and Surgical and Sciences, University of Bologna, Bologna, Italy
| | | | - Paolo Gionchetti
- IBD Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, University of Bologna, Bologna, Italy
- Department of Medical and Surgical and Sciences, University of Bologna, Bologna, Italy
| | - Eleonora Filippone
- IBD Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, University of Bologna, Bologna, Italy
- Department of Medical and Surgical and Sciences, University of Bologna, Bologna, Italy
| | - Veronica Imbesi
- IBD Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, University of Bologna, Bologna, Italy
| | - Laura Melotti
- IBD Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, University of Bologna, Bologna, Italy
- Department of Medical and Surgical and Sciences, University of Bologna, Bologna, Italy
| | - Nikolas Konstantine Dussias
- IBD Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, University of Bologna, Bologna, Italy
- Department of Medical and Surgical and Sciences, University of Bologna, Bologna, Italy
| | - Marco Salice
- IBD Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, University of Bologna, Bologna, Italy
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24
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Gaire TN, Scott HM, Noyes NR, Ericsson AC, Tokach MD, William H, Menegat MB, Vinasco J, Nagaraja TG, Volkova VV. Temporal dynamics of the fecal microbiome in female pigs from early life through estrus, parturition, and weaning of the first litter of piglets. Anim Microbiome 2024; 6:7. [PMID: 38383422 PMCID: PMC10882843 DOI: 10.1186/s42523-024-00294-8] [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: 09/09/2023] [Accepted: 02/07/2024] [Indexed: 02/23/2024] Open
Abstract
BACKGROUND Age-associated changes in the gastrointestinal microbiome of young pigs have been robustly described; however, the temporal dynamics of the fecal microbiome of the female pig from early life to first parity are not well understood. Our objective was to describe microbiome and antimicrobial resistance dynamics of the fecal microbiome of breeding sows from early life through estrus, parturition and weaning of the first litter of piglets (i.e., from 3 to 53 weeks of age). RESULTS Our analysis revealed that fecal bacterial populations in developing gilts undergo changes consistent with major maturation milestones. As the pigs progressed towards first estrus, the fecal bacteriome shifted from Rikenellaceae RC9 gut group- and UCG-002-dominated enterotypes to Treponema- and Clostridium sensu stricto 1-dominated enterotypes. After first estrus, the fecal bacteriome stabilized, with minimal changes in enterotype transition and associated microbial diversity from estrus to parturition and subsequent weaning of first litter piglets. Unlike bacterial communities, fecal fungal communities exhibited low diversity with high inter- and intra-pig variability and an increased relative abundance of certain taxa at parturition, including Candida spp. Counts of resistant fecal bacteria also fluctuated over time, and were highest in early life and subsequently abated as the pigs progressed to adulthood. CONCLUSIONS This study provides insights into how the fecal microbial community and antimicrobial resistance in female pigs change from three weeks of age throughout their first breeding lifetime. The fecal bacteriome enterotypes and diversity are found to be age-driven and established by the time of first estrus, with minimal changes observed during subsequent physiological stages, such as parturition and lactation, when compared to the earlier age-related shifts. The use of pigs as a model for humans is well-established, however, further studies are needed to understand how our results compare to the human microbiome dynamics. Our findings suggest that the fecal microbiome exhibited consistent changes across individual pigs and became more diverse with age, which is a beneficial characteristic for an animal model system.
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Affiliation(s)
- Tara N Gaire
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
| | - H Morgan Scott
- Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Noelle R Noyes
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Aaron C Ericsson
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA
| | - Michael D Tokach
- Department of Animal Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS, 66506, USA
| | - Hayden William
- Department of Animal Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS, 66506, USA
| | - Mariana B Menegat
- Department of Animal Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS, 66506, USA
| | - Javier Vinasco
- Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - T G Nagaraja
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA.
| | - Victoriya V Volkova
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
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McGuinness AJ, Loughman A, Foster JA, Jacka F. Mood Disorders: The Gut Bacteriome and Beyond. Biol Psychiatry 2024; 95:319-328. [PMID: 37661007 DOI: 10.1016/j.biopsych.2023.08.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/09/2023] [Accepted: 08/29/2023] [Indexed: 09/05/2023]
Abstract
Knowledge of the microbiome-gut-brain axis has revolutionized the field of psychiatry. It is now well recognized that the gut bacteriome is associated with, and likely influences, the pathogenesis of mental disorders, including major depressive disorder and bipolar disorder. However, while substantial advances in the field of microbiome science have been made, we have likely only scratched the surface in our understanding of how these ecosystems might contribute to mental disorder pathophysiology. Beyond the gut bacteriome, research into lesser explored components of the gut microbiome, including the gut virome, mycobiome, archaeome, and parasitome, is increasingly suggesting relevance in psychiatry. The contribution of microbiomes beyond the gut, including the oral, lung, and small intestinal microbiomes, to human health and pathology should not be overlooked. Increasing both our awareness and understanding of these less traversed fields of research are critical to improving the therapeutic benefits of treatments targeting the gut microbiome, including fecal microbiome transplantation, postbiotics and biogenics, and dietary intervention. Interdisciplinary collaborations integrating systems biology approaches are required to fully elucidate how these different microbial components and distinct microbial niches interact with each other and their human hosts. Excitingly, we may be at the start of the next microbiome revolution and thus one step closer to informing the field of precision psychiatry to improve outcomes for those living with mental illness.
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Affiliation(s)
- Amelia J McGuinness
- Food and Mood Centre, Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin University, Geelong, Australia.
| | - Amy Loughman
- Food and Mood Centre, Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin University, Geelong, Australia
| | - Jane A Foster
- Center for Depression Research and Clinical Care, Department of Psychiatry, UT Southwestern Medical Center, Dallas, Texas
| | - Felice Jacka
- Food and Mood Centre, Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin University, Geelong, Australia; Centre for Adolescent Health, Murdoch Children's Research Institute, Melbourne, Victoria, Australia; College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
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26
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Lu Y, Zhou X, Wu Y, Cui Q, Tian X, Yi H, Gong P, Zhang L. Metabolites 13,14-Dihydro-15-keto-PGE2 Participates in Bifidobacterium animalis F1-7 to Alleviate Opioid-Induced Constipation by 5-HT Pathway. Mol Nutr Food Res 2024; 68:e2200846. [PMID: 38054625 DOI: 10.1002/mnfr.202200846] [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: 12/03/2022] [Revised: 07/13/2023] [Indexed: 12/07/2023]
Abstract
SCOPE People suffer from constipation caused by many factors, including constipation (Opioid-Induced Constipation, OIC) during analgesic treatment. Microorganisms may be a potent solution to this problem, but the mechanism is still unclear. METHODS AND RESULTS Based on models in vivo and in vitro, the potential mechanism involving Bifidobacterium animalis F1-7 (B. animalis F1-7), screened in the previous studies, is explored through non-targeted metabonomics, electrophysiological experiment and molecular level docking. The results showed that B. animalis F1-7 effectively alleviates OIC and promotes the expression of chromogranin A (CGA) and 5-hydroxytryptamine (5-HT). The metabolite 13,14-dihydro-15-keto-PGE2 related to B. animalis F1-7 is found, which has a potential improvement effect on OIC at 20 mg kg BW-1 in vivo. At 30 ng mL-1 it effectively stimulates secretion of CGA/5-HT (408.95 ± 1.18 ng mL-1 ) by PC-12 cells and changes the membrane potential potassium ion current without affecting the sodium ion current in vitro. It upregulates the target of free fatty acid receptor-4 protein(FFAR4/β-actin, 0.81 ± 0.02). CONCLUSION The results demonstrate that metabolite 13,14-dihydro-15-keto-PGE2 participated in B. animalis F1-7 to alleviate OIC via the 5-HT pathway.
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Affiliation(s)
- Youyou Lu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Environment Correlative Dietology, Ministry of Education (Huazhong Agricultural University), China
| | | | - Yeting Wu
- College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qingyu Cui
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266000, China
| | - Xiaoying Tian
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266000, China
| | - Huaxi Yi
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266000, China
| | - Pimin Gong
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266000, China
| | - Lanwei Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266000, China
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Park G, Munley JA, Kelly LS, Kannan KB, Mankowski RT, Sharma A, Upchurch G, Casadesus G, Chakrabarty P, Wallet SM, Maile R, Bible LE, Wang B, Moldawer LL, Mohr AM, Efron PA, Nagpal R. Gut mycobiome dysbiosis after sepsis and trauma. Crit Care 2024; 28:18. [PMID: 38212826 PMCID: PMC10785534 DOI: 10.1186/s13054-023-04780-4] [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: 11/15/2023] [Accepted: 12/14/2023] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Sepsis and trauma are known to disrupt gut bacterial microbiome communities, but the impacts and perturbations in the fungal (mycobiome) community after severe infection or injury, particularly in patients experiencing chronic critical illness (CCI), remain unstudied. METHODS We assess persistence of the gut mycobiome perturbation (dysbiosis) in patients experiencing CCI following sepsis or trauma for up to two-to-three weeks after intensive care unit hospitalization. RESULTS We show that the dysbiotic mycobiome arrays shift toward a pathobiome state, which is more susceptible to infection, in CCI patients compared to age-matched healthy subjects. The fungal community in CCI patients is largely dominated by Candida spp; while, the commensal fungal species are depleted. Additionally, these myco-pathobiome arrays correlate with alterations in micro-ecological niche involving specific gut bacteria and gut-blood metabolites. CONCLUSIONS The findings reveal the persistence of mycobiome dysbiosis in both sepsis and trauma settings, even up to two weeks post-sepsis and trauma, highlighting the need to assess and address the increased risk of fungal infections in CCI patients.
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Affiliation(s)
- Gwoncheol Park
- Department of Health, Nutrition, and Food Sciences, Florida State University, Tallahassee, FL, 32306, USA
| | - Jennifer A Munley
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, FL, 32611, USA
| | - Lauren S Kelly
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, FL, 32611, USA
| | - Kolenkode B Kannan
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, FL, 32611, USA
| | - Robert T Mankowski
- Department of Aging and Geriatric Research, University of Florida College of Medicine, Gainesville, FL, 32611, USA
| | - Ashish Sharma
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, FL, 32611, USA
| | - Gilbert Upchurch
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, FL, 32611, USA
| | - Gemma Casadesus
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, FL, 32611, USA
| | - Paramita Chakrabarty
- Department of Neuroscience, University of Florida College of Medicine, Gainesville, FL, 32611, USA
| | - Shannon M Wallet
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, FL, 32611, USA
| | - Robert Maile
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, FL, 32611, USA
| | - Letitia E Bible
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, FL, 32611, USA
| | - Bo Wang
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL, 32901, USA
| | - Lyle L Moldawer
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, FL, 32611, USA
| | - Alicia M Mohr
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, FL, 32611, USA
| | - Philip A Efron
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, FL, 32611, USA
| | - Ravinder Nagpal
- Department of Health, Nutrition, and Food Sciences, Florida State University, Tallahassee, FL, 32306, USA.
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Yang Z, Yang M, Deehan EC, Cai C, Madsen KL, Wine E, Li G, Li J, Liu J, Zhang Z. Dietary fiber for the prevention of childhood obesity: a focus on the involvement of the gut microbiota. Gut Microbes 2024; 16:2387796. [PMID: 39163556 PMCID: PMC11340751 DOI: 10.1080/19490976.2024.2387796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/22/2024] Open
Abstract
Given the worldwide epidemic of overweight and obesity among children, evidence-based dietary recommendations are fundamentally important for obesity prevention. Although the significance of the human gut microbiome in shaping the physiological effects of diet and obesity has been widely recognized, nutritional therapeutics for the mitigation of pediatric obesity globally are only just starting to leverage advancements in the nutritional microbiology field. In this review, we extracted data from PubMed, EMBASE, Scopus, Web of Science, Google Scholar, CNKI, Cochrane Library and Wiley online library that focuses on the characterization of gut microbiota (including bacteria, fungi, viruses, and archaea) in children with obesity. We further review host-microbe interactions as mechanisms mediating the physiological effects of dietary fibers and how fibers alter the gut microbiota in children with obesity. Contemporary nutritional recommendations for the prevention of pediatric obesity are also discussed from a gut microbiological perspective. Finally, we propose an experimental framework for integrating gut microbiota into nutritional interventions for children with obesity and provide recommendations for the design of future studies on precision nutrition for pediatric obesity.
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Affiliation(s)
- Zhongmin Yang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian, China
| | - Mingyue Yang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian, China
| | - Edward C. Deehan
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE, USA
- Nebraska Food for Health Center, University of Nebraska, Lincoln, NE, USA
| | - Chenxi Cai
- School of Public Health, Xiamen University, Xiamen, Fujian, China
| | - Karen L. Madsen
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Eytan Wine
- Division of Pediatric Gastroenterology, Departments of Pediatrics and Physiology, University of Alberta, Edmonton, AB, Canada
| | - Guiling Li
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian, China
- Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Xiamen, Fujian, China
| | - Jian Li
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian, China
- Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Xiamen, Fujian, China
| | - Jingwen Liu
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian, China
| | - Zhengxiao Zhang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian, China
- Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Xiamen, Fujian, China
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Jiang T, Liu K, Li J, Zhang Y, Zhang W, Doherty M, Yang Z, Yang T, Yang Y, Weng Q, Luo X, Xie H, Li C, Ai K, Wei J, Lei G, Zeng C. Gut-joint axis in knee synovitis: gut fungal dysbiosis and altered fungi-bacteria correlation network identified in a community-based study. RMD Open 2023; 9:e003529. [PMID: 38114197 DOI: 10.1136/rmdopen-2023-003529] [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: 07/24/2023] [Accepted: 11/24/2023] [Indexed: 12/21/2023] Open
Abstract
OBJECTIVES Knee synovitis is a highly prevalent and potentially curable condition for knee pain; however, its pathogenesis remains unclear. We sought to assess the associations of the gut fungal microbiota and the fungi-bacteria correlation network with knee synovitis. METHODS Participants were derived from a community-based cross-sectional study. We performed an ultrasound examination of both knees. A knee was defined as having synovitis if its synovium was ≥4 mm and/or Power Doppler (PD) signal was within the knee synovium area (PD synovitis). We collected faecal specimens from each participant and assessed gut fungal and bacterial microbiota using internal transcribed spacer 2 and shotgun metagenomic sequencing. We examined the relation of α-diversity, β-diversity, the relative abundance of taxa and the interkingdom correlations to knee synovitis. RESULTS Among 977 participants (mean age: 63.2 years; women: 58.8%), 191 (19.5%) had knee synovitis. β-diversity of the gut fungal microbiota, but not α-diversity, was significantly associated with prevalent knee synovitis. The fungal genus Schizophyllum was inversely correlated with the prevalence and activity (ie, control, synovitis without PD signal and PD synovitis) of knee synovitis. Compared with those without synovitis, the fungi-bacteria correlation network in patients with knee synovitis was smaller (nodes: 93 vs 153; edges: 107 vs 244), and the average number of neighbours was fewer (2.3 vs 3.2). CONCLUSION Alterations of gut fungal microbiota and the fungi-bacteria correlation network are associated with knee synovitis. These novel findings may help understand the mechanisms of the gut-joint axis in knee synovitis and suggest potential targets for future treatment.
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Affiliation(s)
- Ting Jiang
- Department of Orthopaedics, Xiangya Hospital Central South University, Changsha, China
- Department of Ultrasonography, Xiangya Hospital Central South University, Changsha, China
- Academic Rheumatology, University of Nottingham School of Medicine, Nottingham, UK
- Pain Centre Versus Arthritis, Nottingham, UK
| | - Ke Liu
- Department of Orthopaedics, Xiangya Hospital Central South University, Changsha, China
| | - Jiatian Li
- Department of Orthopaedics, Xiangya Hospital Central South University, Changsha, China
| | - Yuqing Zhang
- Division of Rheumatology, Allergy, and Immunology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- The Mongan Institute, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Weiya Zhang
- Academic Rheumatology, University of Nottingham School of Medicine, Nottingham, UK
- Pain Centre Versus Arthritis, Nottingham, UK
| | - Michael Doherty
- Academic Rheumatology, University of Nottingham School of Medicine, Nottingham, UK
- Pain Centre Versus Arthritis, Nottingham, UK
| | - Zidan Yang
- Hunan Key Laboratory of Joint Degeneration and Injury, Xiangya Hospital Central South University, Changsha, China
| | - Tuo Yang
- Academic Rheumatology, University of Nottingham School of Medicine, Nottingham, UK
- Pain Centre Versus Arthritis, Nottingham, UK
- Health Management Center, Xiangya Hospital Central South University, Changsha, China
| | - Yuanheng Yang
- Department of Orthopaedics, Xiangya Hospital Central South University, Changsha, China
- Hunan Key Laboratory of Joint Degeneration and Injury, Xiangya Hospital Central South University, Changsha, China
| | - Qianlin Weng
- Department of Orthopaedics, Xiangya Hospital Central South University, Changsha, China
| | - Xianghang Luo
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital Central South University, Changsha, China
- Key Laboratory of Aging-Related Bone and Joint Diseases Prevention and Treatment, Ministry of Education, Xiangya Hospital Central South University, Changsha, China
| | - Hui Xie
- Department of Orthopaedics, Xiangya Hospital Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital Central South University, Changsha, China
- Key Laboratory of Aging-Related Bone and Joint Diseases Prevention and Treatment, Ministry of Education, Xiangya Hospital Central South University, Changsha, China
| | - Changjun Li
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital Central South University, Changsha, China
- Key Laboratory of Aging-Related Bone and Joint Diseases Prevention and Treatment, Ministry of Education, Xiangya Hospital Central South University, Changsha, China
| | - Kelong Ai
- Key Laboratory of Aging-Related Bone and Joint Diseases Prevention and Treatment, Ministry of Education, Xiangya Hospital Central South University, Changsha, China
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Jie Wei
- Department of Orthopaedics, Xiangya Hospital Central South University, Changsha, China
- Hunan Key Laboratory of Joint Degeneration and Injury, Xiangya Hospital Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital Central South University, Changsha, China
- Key Laboratory of Aging-Related Bone and Joint Diseases Prevention and Treatment, Ministry of Education, Xiangya Hospital Central South University, Changsha, China
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, China
| | - Guanghua Lei
- Department of Orthopaedics, Xiangya Hospital Central South University, Changsha, China
- Hunan Key Laboratory of Joint Degeneration and Injury, Xiangya Hospital Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital Central South University, Changsha, China
- Key Laboratory of Aging-Related Bone and Joint Diseases Prevention and Treatment, Ministry of Education, Xiangya Hospital Central South University, Changsha, China
| | - Chao Zeng
- Department of Orthopaedics, Xiangya Hospital Central South University, Changsha, China
- Hunan Key Laboratory of Joint Degeneration and Injury, Xiangya Hospital Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital Central South University, Changsha, China
- Key Laboratory of Aging-Related Bone and Joint Diseases Prevention and Treatment, Ministry of Education, Xiangya Hospital Central South University, Changsha, China
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, China
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30
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Tang X, Zhang L, Ren S, Zhao Y, Zhang Y. Temporal and geographic distribution of gut microbial enterotypes associated with host thermogenesis characteristics in plateau pikas. Microbiol Spectr 2023; 11:e0002023. [PMID: 37815332 PMCID: PMC10715161 DOI: 10.1128/spectrum.00020-23] [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: 01/03/2023] [Accepted: 08/28/2023] [Indexed: 10/11/2023] Open
Abstract
IMPORTANCE The gut microbiotas of small mammals play an important role in host energy homeostasis. However, it is still unknown whether small mammals with different enterotypes show differences in thermogenesis characteristics. Our study confirmed that plateau pikas with different bacterial enterotypes harbored distinct thermogenesis capabilities and employed various strategies against cold environments. Additionally, we also found that pikas with different fungal enterotypes may display differences in coprophagy.
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Affiliation(s)
- Xianjiang Tang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
- University of Chinese Academy of Sciences, College of Life Sciences, Beijing, China
| | - Liangzhi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Shi'en Ren
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
- University of Chinese Academy of Sciences, College of Life Sciences, Beijing, China
| | - Yaqi Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
- University of Chinese Academy of Sciences, College of Life Sciences, Beijing, China
| | - Yanming Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
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Kreulen IAM, de Jonge WJ, van den Wijngaard RM, van Thiel IAM. Candida spp. in Human Intestinal Health and Disease: More than a Gut Feeling. Mycopathologia 2023; 188:845-862. [PMID: 37294505 PMCID: PMC10687130 DOI: 10.1007/s11046-023-00743-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/09/2023] [Indexed: 06/10/2023]
Abstract
Fungi are an essential part of the normal collection of intestinal microorganisms, even though their collective abundance comprises only 0.1-1% of all fecal microbes. The composition and role of the fungal population is often studied in relation to early-life microbial colonization and development of the (mucosal) immune system. The genus Candida is frequently described as one of the most abundant genera, and altered fungal compositions (including elevated abundance of Candida spp.) have been linked with intestinal diseases such as inflammatory bowel disease and irritable bowel syndrome. These studies are performed using both culture-dependent and genomic (metabarcoding) techniques. In this review, we aimed to summarize existing data on intestinal Candida spp. colonization in relation to intestinal disease and provide a brief overview of the biological and technical challenges in this field, including the recently described role of sub-species strain variation of intestinal Candida albicans. Together, the evidence for a contributing role of Candida spp. in pediatric and adult intestinal disease is quickly expanding, even though technical and biological challenges may limit full understanding of host-microbe interactions.
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Affiliation(s)
- Irini A M Kreulen
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam UMC, Location Academic Medical Center, Meibergdreef 69-71, 1105 BK, Amsterdam, the Netherlands
| | - Wouter J de Jonge
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam UMC, Location Academic Medical Center, Meibergdreef 69-71, 1105 BK, Amsterdam, the Netherlands
- Department of Gastroenterology and Hepatology, Amsterdam UMC, Location Academic Medical Center, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
- Department of General, Visceral, Thoracic and Vascular Surgery, University Hospital Bonn, 53127, Bonn, Germany
| | - René M van den Wijngaard
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam UMC, Location Academic Medical Center, Meibergdreef 69-71, 1105 BK, Amsterdam, the Netherlands
- Department of Gastroenterology and Hepatology, Amsterdam UMC, Location Academic Medical Center, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
| | - Isabelle A M van Thiel
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam UMC, Location Academic Medical Center, Meibergdreef 69-71, 1105 BK, Amsterdam, the Netherlands.
- Royal Netherlands Academy of Arts and Sciences, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands.
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Chen Y, Zhang LY, Fang Y, Li C, Xia DD, Zhang G, Wen Y, Zhang SZ, Hu L, Gu LY, Liu Y, Tian J, Yan YP, Yin XZ, Tao ZH, Zhang BR, Pu JL. Elevated serum anti-Saccharomyces cerevisiae antibody accompanied by gut mycobiota dysbiosis as a biomarker of diagnosis in patients with de novo Parkinson disease. Eur J Neurol 2023; 30:3462-3470. [PMID: 36694359 DOI: 10.1111/ene.15711] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 12/13/2022] [Accepted: 12/29/2022] [Indexed: 01/26/2023]
Abstract
BACKGROUND AND PURPOSE Intestinal inflammation and gut microbiota dysbiosis contribute to Parkinson disease (PD) pathogenesis, and growing evidence suggests associations between inflammatory bowel diseases (IBD) and PD. Considered as markers of chronic gastrointestinal inflammation, elevated serum anti-Saccharomyces cerevisiae antibody (ASCA) levels, against certain gut fungal components, are related to IBD, but their effect on PD is yet to be investigated. METHODS Serum ASCA IgG and IgA levels were measured using an enzyme-linked immunosorbent assay, and the gut mycobiota communities were investigated using ITS2 sequencing and analyzed using the Qiime pipeline. RESULTS The study included 393 subjects (148 healthy controls [HCs], 140 with PD, and 105 with essential tremor [ET]). Both serum ASCA IgG and IgA levels were significantly higher in the PD group than in the ET and HC groups. Combining serum ASCA levels and the occurrence of constipation could discriminate patients with PD from controls (area under the curve [AUC] = 0.81, 95% confidence interval [CI] = 0.76-0.86) and from patients with ET (AUC = 0.85, 95% CI = 0.79-0.89). Furthermore, the composition of the gut fungal community differed between the PD and HC groups. The relative abundances of Saccharomyces cerevisiae, Aspergillus, Candida solani, Aspergillus flavus, ASV601_Fungi, ASV866_Fungi, and ASV755_Fungi were significantly higher in the PD group, and enriched Malassezia restricta was found in the HC group. CONCLUSIONS Our study identified elevated serum ASCA levels and enriched gut Saccharomyces cerevisiae in de novo PD.
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Affiliation(s)
- Ying Chen
- Department of Neurology, Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Li-Ying Zhang
- Natural Medicine Institute of Zhejiang YangShengTang Co., Hangzhou, Zhejiang, China
| | - Yi Fang
- Department of Neurology, Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chuan Li
- Natural Medicine Institute of Zhejiang YangShengTang Co., Hangzhou, Zhejiang, China
| | - Dan-Dan Xia
- Natural Medicine Institute of Zhejiang YangShengTang Co., Hangzhou, Zhejiang, China
| | - Gong Zhang
- Department of Laboratory, Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yi Wen
- Natural Medicine Institute of Zhejiang YangShengTang Co., Hangzhou, Zhejiang, China
| | - Song-Zhao Zhang
- Department of Laboratory, Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Liu Hu
- Natural Medicine Institute of Zhejiang YangShengTang Co., Hangzhou, Zhejiang, China
| | - Lu-Yan Gu
- Department of Neurology, Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yi Liu
- Department of Neurology, Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jun Tian
- Department of Neurology, Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ya-Ping Yan
- Department of Neurology, Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xin-Zhen Yin
- Department of Neurology, Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhi-Hua Tao
- Department of Laboratory, Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Bao-Rong Zhang
- Department of Neurology, Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jia-Li Pu
- Department of Neurology, Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
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Tang X, Zhang L, Ren S, Zhao Y, Liu K, Zhang Y. Stochastic Processes Derive Gut Fungi Community Assembly of Plateau Pikas ( Ochotona curzoniae) along Altitudinal Gradients across Warm and Cold Seasons. J Fungi (Basel) 2023; 9:1032. [PMID: 37888290 PMCID: PMC10607853 DOI: 10.3390/jof9101032] [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: 09/03/2023] [Revised: 10/05/2023] [Accepted: 10/18/2023] [Indexed: 10/28/2023] Open
Abstract
Although fungi occupy only a small proportion of the microbial community in the intestinal tract of mammals, they play important roles in host fat accumulation, nutrition metabolism, metabolic health, and immune development. Here, we investigated the dynamics and assembly of gut fungal communities in plateau pikas inhabiting six altitudinal gradients across warm and cold seasons. We found that the relative abundances of Podospora and Sporormiella significantly decreased with altitudinal gradients in the warm season, whereas the relative abundance of Sarocladium significantly increased. Alpha diversity significantly decreased with increasing altitudinal gradient in the warm and cold seasons. Distance-decay analysis showed that fungal community similarities were significantly and negatively correlated with elevation. The co-occurrence network complexity significantly decreased along the altitudinal gradients as the total number of nodes, number of edges, and degree of nodes significantly decreased. Both the null and neutral model analyses showed that stochastic or neutral processes dominated the gut fungal community assembly in both seasons and that ecological drift was the main ecological process explaining the variation in the gut fungal community across different plateau pikas. Homogeneous selection played a weak role in structuring gut fungal community assembly during the warm season. Collectively, these results expand our understanding of the distribution patterns of gut fungal communities and elucidate the mechanisms that maintain fungal diversity in the gut ecosystems of small mammals.
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Affiliation(s)
- Xianjiang Tang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liangzhi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
| | - Shien Ren
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaqi Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Liu
- Qinghai Provincial Grassland Station, Xining 810008, China
| | - Yanming Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
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Ye L, Hou Y, Hu W, Wang H, Yang R, Zhang Q, Feng Q, Zheng X, Yao G, Hao H. Repressed Blautia-acetate immunological axis underlies breast cancer progression promoted by chronic stress. Nat Commun 2023; 14:6160. [PMID: 37789028 PMCID: PMC10547687 DOI: 10.1038/s41467-023-41817-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 09/20/2023] [Indexed: 10/05/2023] Open
Abstract
Chronic stress is a known risk factor for breast cancer, yet the underlying mechanisms are unclear. This study explores the potential involvement of microbial and metabolic signals in chronic stress-promoted breast cancer progression, revealing that reduced abundances of Blautia and its metabolite acetate may contribute to this process. Treatment with Blautia and acetate increases antitumor responses of CD8+ T cells and reverses stress-promoted breast cancer progression in female mice. Patients with depression exhibit lower abundances of Blautia and acetate, and breast cancer female patients with depression display lower abundances of acetate, decreased numbers of tumor-infiltrating CD8+ T cells, and an increased risk of metastasis. These results suggest that Blautia-derived acetate plays a crucial role in modulating the immune response to breast cancer, and its reduction may contribute to chronic stress-promoted cancer progression. Our findings advance the understanding of microbial and metabolic signals implicated in cancer in patients with depression and may provide therapeutic options for female patients with breast cancer and depression.
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Affiliation(s)
- Ling Ye
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Yuanlong Hou
- State Key Laboratory of Natural Medicines, Jiangsu Province Key Laboratory of Drug Metabolism, China Pharmaceutical University, Nanjing, 210009, China
- Department of Pharmacy, Shenzhen Luohu People's Hospital, Shenzhen, 518000, China
| | - Wanyu Hu
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Hongmei Wang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Ruopeng Yang
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Qihan Zhang
- Breast Center, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Qiaoli Feng
- Breast Center, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Xiao Zheng
- State Key Laboratory of Natural Medicines, Jiangsu Province Key Laboratory of Drug Metabolism, China Pharmaceutical University, Nanjing, 210009, China
| | - Guangyu Yao
- Breast Center, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Haiping Hao
- State Key Laboratory of Natural Medicines, Jiangsu Province Key Laboratory of Drug Metabolism, China Pharmaceutical University, Nanjing, 210009, China.
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Zhu J, Song Y, Xiao Y, Ma L, Hu C, Yang H, Wang X, Lyu W. Metagenomic reconstructions of caecal microbiome in Landes, Roman and Zhedong White geese. Br Poult Sci 2023; 64:565-576. [PMID: 37493577 DOI: 10.1080/00071668.2023.2239172] [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: 01/11/2023] [Revised: 06/10/2023] [Accepted: 06/16/2023] [Indexed: 07/27/2023]
Abstract
1. The caecal microbiota in geese play a crucial role in determining the host's health, disease status and behaviour, as evidenced by extensive epidemiological data. The present investigation conducted 10× metagenomic sequencing of caecal content samples obtained from three distinct goose species, namely Landes geese, Roman geese and Zhedong White geese (n = 5), to explore the contribution of the gut microbiome to carbohydrate metabolism.2. In total, 337GB of Illumina data were generated, which identified 1,048,575 complete genes and construction of 331 metagenomic bins, encompassing 78 species from nine phyla. Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria and Bacteria were identified as the dominant phyla while Prevotella, Bacteroides, Streptococcus, and Subdoligranulum were the most abundant genera in the caecum of geese.3. The genes were allocated to 375 pathways using the Kyoto Encyclopedia of Genes and Genome (KEGG) analysis. The most abundant classes in the caecum of geese were confirmed to be glycoside hydrolases (GHs), glycosyl transferases (GTs), as identified through the carbohydrate-active enzyme (CAZyme) database mapping. Subdoligranulum variabile and Mediterraneibacter glycyrrhizinilyticus were discovered to potentially facilitate carbohydrate digestion in geese.4. Notwithstanding, further investigation and validation are required to establish a connection between these species and CAZymes. Based on binning analysis, Mediterraneibacter glycyrrhizinilyticus and Ruminococcus sp. CAG:177 are potential species in LD geese that contribute to the production of fatty liver.
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Affiliation(s)
- J Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- College of Animal Science, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, China
- Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, China
| | - Y Song
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Y Xiao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - L Ma
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - C Hu
- College of Animal Science, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition (Zhejiang University), Ministry of Education, Hangzhou, China
- Key Laboratory of Animal Nutrition and Feed Science (Eastern of China), Ministry of Agriculture and Rural Affairs, Hangzhou, China
| | - H Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - X Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - W Lyu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Wang R, Halimulati M, Huang X, Ma Y, Li L, Zhang Z. Sulforaphane-driven reprogramming of gut microbiome and metabolome ameliorates the progression of hyperuricemia. J Adv Res 2023; 52:19-28. [PMID: 36371056 PMCID: PMC10555773 DOI: 10.1016/j.jare.2022.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/25/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022] Open
Abstract
INTRODUCTION Currently, revealing how to prevent and control hyperuricemia has become an essential public health issue. Sulforaphane hasawiderangeofapplications in the management of hyperuricemia. OBJECTIVE The study objective was to verify the uric acid-lowering effects and the regulation of the gut-kidney axis mediated by sulforaphane and identify host-microbial co-metabolites in hyperuricemia. METHODS A hyperuricemia model was established by administering feedstuffs with 4% potassium oxonate and 20% yeast. Forty male Sprague-Dawley rats were randomly divided into the normal control, hyperuricemia, allopurinol, and sulforaphane groups. Animals were treated by oral gavage for six consecutive weeks, and then phenotypic parameters, metabolomic profiling, and metagenomicsequencing were performed. RESULTS Sulforaphane could lower uric acid by decreasing urate synthesis and increasing renal urate excretion in hyperuricemic rats (P<0.05). We identified succinic acid and oxoglutaric acid as critical host-gut microbiome co-metabolites. Moreover, sulforaphane improved the diversity of microbial ecosystems and functions, as well as metabolic control of the kidney. Notably, sulforaphane exerted its renoprotective effect through epigenetic modification of Nrf2 and interaction between gut microbiota and epigenetic modification in hyperuricemic rats. CONCLUSION We revealed that sulforaphane could ameliorate the progression of hyperuricemia by reprogramming the gut microbiome and metabolome. Our findings may provide a good means for efficiently preventing and treating hyperuricemia.
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Affiliation(s)
- Ruoyu Wang
- Department of Nutrition and Food Hygiene, School of Public Health, Peking University, Haidian District, Beijing 100191, People's Republic of China
| | - Mairepaiti Halimulati
- Department of Nutrition and Food Hygiene, School of Public Health, Peking University, Haidian District, Beijing 100191, People's Republic of China
| | - Xiaojie Huang
- Department of Nutrition and Food Hygiene, School of Public Health, Peking University, Haidian District, Beijing 100191, People's Republic of China
| | - Yuxin Ma
- Department of Nutrition and Food Hygiene, School of Public Health, Peking University, Haidian District, Beijing 100191, People's Republic of China
| | - Lutong Li
- Department of Nutrition and Food Hygiene, School of Public Health, Peking University, Haidian District, Beijing 100191, People's Republic of China
| | - Zhaofeng Zhang
- Department of Nutrition and Food Hygiene, School of Public Health, Peking University, Haidian District, Beijing 100191, People's Republic of China; Beijing's Key Laboratory of Food Safety Toxicology Research and Evaluation, Beijing 100191, People's Republic of China.
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Zhao X, Hu X, Han J, Yin R, Zhang S, Liu H. Gut mycobiome: A "black box" of gut microbiome-host interactions. WIREs Mech Dis 2023; 15:e1611. [PMID: 37157158 DOI: 10.1002/wsbm.1611] [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: 02/13/2023] [Revised: 04/01/2023] [Accepted: 04/12/2023] [Indexed: 05/10/2023]
Abstract
Fungi, being a necessary component of the gut microbiome, potentially have direct or indirect effects on the health and illness status of the host. The gut mycobiome is an inducer of the host's immunity, maintaining intestinal homeostasis, and protecting against infections, as well as a reservoir of opportunistic microorganisms and a potential cofactor when the host is immunocompromised. In addition, gut fungi interact with a diverse range of microbes in the intestinal niches. In this article, we reviewed the composition of gut mycobiome, their association with host health and illness, and summarized the specific Candida albicans-host interactions, in order to provide insights and directions for the ongoing study of fungi. This article is categorized under: Infectious Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
- Xinyue Zhao
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Xiaomin Hu
- Department of Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Junjie Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ruopeng Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Shuyang Zhang
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Hongwei Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
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38
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Lai S, Yan Y, Pu Y, Lin S, Qiu JG, Jiang BH, Keller MI, Wang M, Bork P, Chen WH, Zheng Y, Zhao XM. Enterotypes of the human gut mycobiome. MICROBIOME 2023; 11:179. [PMID: 37563687 PMCID: PMC10416509 DOI: 10.1186/s40168-023-01586-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 05/31/2023] [Indexed: 08/12/2023]
Abstract
BACKGROUND The fungal component of the human gut microbiome, also known as the mycobiome, plays a vital role in intestinal ecology and human health. However, the overall structure of the gut mycobiome as well as the inter-individual variations in fungal composition remains largely unknown. In this study, we collected a total of 3363 fungal sequencing samples from 16 cohorts across three continents, including 572 newly profiled samples from China. RESULTS We identify and characterize four mycobiome enterotypes using ITS profiling of 3363 samples from 16 cohorts. These enterotypes exhibit stability across populations and geographical locations and significant correlation with bacterial enterotypes. Particularly, we notice that fungal enterotypes have a strong age preference, where the enterotype dominated by Candida (i.e., Can_type enterotype) is enriched in the elderly population and confers an increased risk of multiple diseases associated with a compromised intestinal barrier. In addition, bidirectional mediation analysis reveals that the fungi-contributed aerobic respiration pathway associated with the Can_type enterotype might mediate the association between the compromised intestinal barrier and aging. CONCLUSIONS We show that the human gut mycobiome has stable compositional patterns across individuals and significantly correlates with multiple host factors, such as diseases and host age. Video Abstract.
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Affiliation(s)
- Senying Lai
- Department of Neurology, Zhongshan Hospital and Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Yan Yan
- CAS Key Laboratory of Molecular Virology and Immunology, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Yanni Pu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, China
| | - Shuchun Lin
- The Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Jian-Ge Qiu
- The Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Bing-Hua Jiang
- The Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Marisa Isabell Keller
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Mingyu Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.
- Max Delbrück Centre for Molecular Medicine, Berlin, Germany.
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.
| | - Wei-Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- College of Life Science, Henan Normal University, Xinxiang, Henan, China.
| | - Yan Zheng
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, China.
| | - Xing-Ming Zhao
- Department of Neurology, Zhongshan Hospital and Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China.
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Zhejiang Province, China.
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China.
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Fudan University, Shanghai, China.
- International Human Phenome Institutes (Shanghai), Shanghai, China.
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Medeiros MJ, Seo L, Macias A, Price DK, Yew JY. Bacterial and fungal components of the gut microbiome have distinct, sex-specific roles in Hawaiian Drosophila reproduction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.14.549088. [PMID: 37503295 PMCID: PMC10370118 DOI: 10.1101/2023.07.14.549088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Gut microbiomes provide numerous physiological benefits for host animals. The role of bacterial members of microbiomes in host physiology is well-documented. However, much less is known about the contributions and interactions of fungal members of the microbiome even though fungi are significant components of many microbiomes, including those of humans and insects. Here, we used antibacterial and antifungal drugs to manipulate the gut microbiome of a Hawaiian picture-wing Drosophila species, D. grimshawi, and identified distinct, sex-specific roles for the bacteria and fungi in microbiome community stability and reproduction. Female oogenesis, fecundity and mating drive were significantly diminished when fungal communities were suppressed. By contrast, male fecundity was more strongly affected by bacterial but not fungal populations. For males and females, suppression of both bacteria and fungi severely reduced fecundity and altered fatty acid levels and composition, implicating the importance of interkingdom interactions on reproduction and lipid metabolism. Overall, our results reveal that bacteria and fungi have distinct, sexually-dimorphic effects on host physiology and interkingdom dynamics in the gut help to maintain microbiome community stability and enhance reproduction.
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Affiliation(s)
- Matthew J. Medeiros
- Pacific Biosciences Research Center, University of Hawaiʻi at Mānoa
- Department of Life Sciences, University of Nevada at Las Vegas
| | - Laura Seo
- Department of Life Sciences, University of Nevada at Las Vegas
| | - Aziel Macias
- Department of Life Sciences, University of Nevada at Las Vegas
| | - Donald K. Price
- Department of Life Sciences, University of Nevada at Las Vegas
| | - Joanne Y. Yew
- Pacific Biosciences Research Center, University of Hawaiʻi at Mānoa
- Department of Life Sciences, University of Nevada at Las Vegas
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Wang L, Zhang K, Zeng Y, Luo Y, Peng J, Zhang J, Kuang T, Fan G. Gut mycobiome and metabolic diseases: The known, the unknown, and the future. Pharmacol Res 2023; 193:106807. [PMID: 37244385 DOI: 10.1016/j.phrs.2023.106807] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 05/29/2023]
Abstract
Metabolic diseases, such as type 2 diabetes mellitus (T2DM), non-alcoholic fatty liver disease (NAFLD) and obesity, have become a major public health problem worldwide. In recent years, most research on the role of gut microbes in metabolic diseases has focused on bacteria, whereas fungal microbes have been neglected. This review aims to provide a comprehensive overview of gut fungal alterations in T2DM, obesity, and NAFLD, and to discuss the mechanisms associated with disease development. In addition, several novel strategies targeting gut mycobiome and/or their metabolites to improve T2DM, obesity and NAFLD, including fungal probiotics, antifungal drugs, dietary intervention, and fecal microbiota transplantation, are critically discussed. The accumulated evidence suggests that gut mycobiome plays an important role in the occurrence and development of metabolic diseases. The possible mechanisms by which the gut mycobiome affects metabolic diseases include fungal-induced immune responses, fungal-bacterial interactions, and fungal-derived metabolites. Candida albicans, Aspergillus and Meyerozyma may be potential pathogens of metabolic diseases because they can activate the immune system and/or produce harmful metabolites. Moreover, Saccharomyces boulardii, S. cerevisiae, Alternaria, and Cochliobolus fungi may have the potential to improve metabolic diseases. The information may provide an important reference for the development of new therapeutics for metabolic diseases based on gut mycobiome.
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Affiliation(s)
- Lijie Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy and School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Kun Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy and School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yujiao Zeng
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy and School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yuting Luo
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy and School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jiayan Peng
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy and School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jing Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy and School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Tingting Kuang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy and School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
| | - Gang Fan
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy and School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; Meishan Hospital of Chengdu University of Traditional Chinese Medicine, Meishan, 620010, China.
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Tian Y, Gou W, Ma Y, Shuai M, Liang X, Fu Y, Zheng JS. The Short-Term Variation of Human Gut Mycobiome in Response to Dietary Intervention of Different Macronutrient Distributions. Nutrients 2023; 15:2152. [PMID: 37432284 DOI: 10.3390/nu15092152] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/10/2023] [Accepted: 04/27/2023] [Indexed: 07/12/2023] Open
Abstract
While the human gut is home to a complex and diverse community of microbes, including bacteria and fungi, research on the gut microbiome has largely focused on bacteria, with relatively little attention given to the gut mycobiome. This study aims to investigate how diets with different dietary macronutrient distributions impact the gut mycobiome. We investigated gut mycobiome response to high-carbohydrate, low-fat (HC) and low-carbohydrate high-fat (LC) diet interventions based on a series of 72-day feeding-based n-of-1 clinical trials. A total of 30 participants were enrolled and underwent three sets of HC and LC dietary interventions in a randomized sequence. Each set lasted for 24 days with a 6-day washout period between dietary interventions. We collected and analyzed the fungal composition of 317 stool samples before and after each intervention period. To account for intra-individual variation across the three sets, we averaged the mycobiome data from the repeated sets for analysis. Of the 30 participants, 28 (aged 22-34 years) completed the entire intervention. Our results revealed a significant increase in gut fungal alpha diversity (p < 0.05) and significant changes in fungal composition (beta diversity, p < 0.05) after the HC dietary intervention. Specifically, we observed the enrichment of five fungal genera (Pleurotus, Kazachstania, Auricularia, Paraphaeosphaeria, Ustilaginaceae sp.; FDR < 0.052) and depletion of one fungal genus (Blumeria; FDR = 0.03) after the HC intervention. After the LC dietary intervention, one fungal genus was enriched (Ustilaginaceae sp.; FDR = 0.003), and five fungal genera were depleted (Blumeria, Agaricomycetes spp., Malassezia, Rhizopus, and Penicillium; FDR < 0.1). This study provides novel evidence on how the gut mycobiome structure and composition change in response to the HC and LC dietary interventions and reveals diet-specific changes in the fungal genera.
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Affiliation(s)
- Yunyi Tian
- School of Medicine, Zhejiang University, Hangzhou 310058, China
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310030, China
| | - Wanglong Gou
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310030, China
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310030, China
| | - Yue Ma
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310030, China
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310030, China
| | - Menglei Shuai
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310030, China
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310030, China
| | - Xinxiu Liang
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310030, China
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310030, China
| | - Yuanqing Fu
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310030, China
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310030, China
| | - Ju-Sheng Zheng
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310030, China
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310030, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310030, China
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Yang P, Xu R, Chen F, Chen S, Khan A, Li L, Zhang X, Wang Y, Xu Z, Shen H. Fungal gut microbiota dysbiosis in systemic lupus erythematosus. Front Microbiol 2023; 14:1149311. [PMID: 37089568 PMCID: PMC10115219 DOI: 10.3389/fmicb.2023.1149311] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 03/21/2023] [Indexed: 04/09/2023] Open
Abstract
IntroductionDespite recent developments in our comprehension of how the gut microbiota and systemic lupus erythematosus (SLE) are related. The mycobiome: which is a small but crucial part of the gut microbiota and is involved in hosts’ homeostasis and physiological processes, remained unexplored in SLE.MethodsWe profiled the gut fungal mycobiota based on internal transcribed spacer region 1 (ITS1) sequencing for the gut microbial DNA from the SLE individuals with lupus nephritis (LN) (n = 23), SLE without LN (n = 26) and healthy controls (n = 14) enrolled in Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School.ResultsThe ITS sequencing generated a total of 4.63 million valid tags which were stratified into 4,488 operational taxonomic units (OTUs) and identified about 13 phyla and 262 genera. Patients with SLE were characterized with unique fungal flora feature. The fungal microbiomes of the three groups displayed distinct beta diversity from each other. Compared with HC group, the abundance of fungal dysbiosis was reflected in a higher ratio of opportunistic fungi in SLE or LN group, as well as the loss of Rhizopus and Malassezia. The main principal components of the flora between the SLE and LN group were generally consistent. The relative abundance of Vanrija in the fecal fungal community was higher in LN group, while the relative abundance of Fusarium was higher in SLE group. Moreover, our data revealed superior diagnostic accuracy for SLE with the fungal species (e.g. Candida, Meyerozyma). Correlations between gut fungi and clinical parameters were identified by Spearman’s correlation analysis. Interestingly, Aspergillus in SLE patients was positively correlated with ACR, 24 h proteinuria, proteinuria, anti-dsDNA, ANA, and SLEDAI, while Rhizopus was negatively correlated with lymphocytes and Hb. Finally, we successfully cultured the fungi and identified it as Candida glabrata by microscopic observation and mass spectrometry.DiscussionWe first explored the highly significant gut fungal dysbiosis and ecology in patients with SLE, and demonstrated the applicability of fungal species as SLE diagnostic tools, signifying that the gut fungal mycobiome-host interplay can potentially contribute in disease pathogenesis.
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Affiliation(s)
- Ping Yang
- Department of Clinical Laboratory, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Rui Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Physiology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, School of Life Sciences, NJU Advanced Institute of Life Sciences (NAILS), Nanjing University, Nanjing, China
| | - Fei Chen
- Department of Clinical Laboratory, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Shanshan Chen
- Department of Rheumatology and Immunology, Affiliated Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing, Jiangsu, China
| | - Adeel Khan
- Department of Biotechnology, University of Science and Technology, Bannu, Pakistan
| | - Liang Li
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Physiology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, School of Life Sciences, NJU Advanced Institute of Life Sciences (NAILS), Nanjing University, Nanjing, China
| | - Xiaoshan Zhang
- Department of Clinical Laboratory, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Yanbo Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Physiology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, School of Life Sciences, NJU Advanced Institute of Life Sciences (NAILS), Nanjing University, Nanjing, China
- Yanbo Wang,
| | - Zhipeng Xu
- Department of Pathogen Biology, Jiangsu Province Key Laboratory of Modern Pathogen Biology, Nanjing Medical University, Nanjing, Jiangsu, China
- *Correspondence: Zhipeng Xu,
| | - Han Shen
- Department of Clinical Laboratory, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
- Han Shen,
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Host Factors Associated with Gut Mycobiome Structure. mSystems 2023; 8:e0098622. [PMID: 36786595 PMCID: PMC10134842 DOI: 10.1128/msystems.00986-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
Recent studies revealed a significant role of the gut fungal community in human health. Here, we investigated the content and variation of gut mycobiota among subjects from the European population. We explored the interplay between gut fungi and various host-related sociodemographic, lifestyle, health, and dietary factors. The study included 923 participants. Fecal DNA samples were analyzed by whole-metagenome high-throughput sequencing. Subsequently, fungi taxonomic profiles were determined and accompanied by computational and statistical analyses of the association with 53 host-related factors. Fungal communities were characterized by a high prevalence of Saccharomyces, Candida, and Sporisorium. Ten factors were found to correlate significantly with the overall mycobiota variation. Most were diet related, including the consumption of chips, meat, sodas, sweetening, processed food, and alcohol, followed by age and marital status. Differences in α- and/or β-diversity were also reported for other factors such as body mass index (BMI), job type, autoimmunological diseases, and probiotics. Differential abundance analysis revealed fungal species that exhibited different patterns of changes under specific conditions. The human gut mycobiota is dominated by yeast, including Saccharomyces, Malassezia, and Candida. Although intervolunteer variability was high, several fungal species persisted across most samples, which may be evidence that a core gut mycobiota exists. Moreover, we showed that host-related factors such as diet, age, and marital status influence the variability of gut mycobiota. To our knowledge, this is the first large and comprehensive study of the European cohort in terms of gut mycobiota associations with such an extensive and differentiated host-related set of factors. IMPORTANCE The human gut is inhabited by many organisms, including bacteria and fungi, that may affect human health. However, research on human gut mycobiome is still rare. Moreover, the large European-based cohort study is missing. Here, we analyzed the first large European cohort in terms of gut mycobiota associations with a differentiated host-related set of factors. Our results showed that chips, meat, sodas, sweetening, processed food, beer, alcohol consumption, age, and marital status were associated with the variability of gut mycobiota. Moreover, our analysis revealed changes in abundances at the fungal species level for many investigated factors. Our results can suggest potentially valuable paths for further, narrowly focused research on gut mycobiome and its impact on human health. In the coming era of gut microbiome-based precision medicine, further research into the relationship between different mycobial structures and host-related factors may result in new preventive approaches or therapeutic procedures.
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Research progress in lipid metabolic regulation of bioactive peptides. FOOD PRODUCTION, PROCESSING AND NUTRITION 2023. [DOI: 10.1186/s43014-022-00123-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
AbstractHyperlipidemia poses a serious threat to human health and evaluating the ability of natural active substances to regulate disorders of lipid metabolism is the focus of food functionality research in recent years. Bioactive peptides are distinguished by their broad range of sources, high nutritional content, ease of absorption and use by the body, and ease of determining their sequences. Bioactive peptides have a wide range of potential applications in the area of medicines and food. The regulation of lipid metabolism disorder caused by bioactive peptides from different sources provides a reference for the development and research of bioactive peptides for lipid reduction.
Graphical Abstract
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Fungal-Bacterial Interactions in the Human Gut of Healthy Individuals. J Fungi (Basel) 2023; 9:jof9020139. [PMID: 36836254 PMCID: PMC9965947 DOI: 10.3390/jof9020139] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/07/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023] Open
Abstract
Most studies of the microbiota in the human gut focus on the bacterial part, but increasing information shows that intestinal fungi are also important for maintaining health. This can be either by directly influencing the host or by indirectly influencing the gut bacteria that link to host health. Studies of fungal communities in large cohorts are scarce; therefore, this study aims at obtaining more insight into the mycobiome of healthy individuals and how this mycobiome interacts with the bacterial component of the microbiome. For this purpose, ITS2 and 16S rRNA gene amplicon sequencing was performed on fecal samples from 163 individuals which were available from two separate studies to analyze the fungal and bacterial microbiome, respectively, as well as the cross-kingdom interactions. The results showed a much lower fungal, as compared to bacterial, diversity. Ascomycota and Basidiomycota were the dominant fungal phyla across all the samples, but levels varied enormously between individuals. The ten most abundant fungal genera were Saccharomyces, Candida, Dipodascus, Aureobasidium, Penicillium, Hanseniaspora, Agaricus, Debaryomyces, Aspergillus, and Pichia, and here also extensive inter-individual variation was observed. Correlations were made between bacteria and fungi, and only positive correlations were observed. One of the correlations was between Malassezia restricta and the genus Bacteroides, which have both been previously described as alleviated in IBD. Most of the other correlations found were with fungi that are not known as gut colonizers but originate from food and the environment. To further investigate the importance of the observed correlations found, more research is needed to discriminate between gut colonizers and transient species.
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Abstract
In recent years, it has become clear that gut microbiota plays a major role in the human body, both in health and disease. Because of that, the gut microbiome and its impact on human well-being are getting wider and wider attention. Studies focused on the liver are not an exception. However, the majority of the analyses are concentrated on the bacterial part of the gut microbiota, while the fungi living in the human intestines are often omitted or underappreciated. This review is focused on the gut mycobiome as an important factor that should be taken into consideration regarding liver homeostasis and its perturbations. We have collected the findings in this field and we discuss their importance. We aim to emphasize the fungal compositional changes related to liver diseases and, by that, provide novel insights into the directions of liver research and gut microbiota as a therapeutic target for liver diseases.
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Affiliation(s)
- Natalia Szóstak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Anna Philips
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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Jaswal K, Todd OA, Behnsen J. Neglected gut microbiome: interactions of the non-bacterial gut microbiota with enteric pathogens. Gut Microbes 2023; 15:2226916. [PMID: 37365731 DOI: 10.1080/19490976.2023.2226916] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 06/28/2023] Open
Abstract
A diverse array of commensal microorganisms inhabits the human intestinal tract. The most abundant and most studied members of this microbial community are undoubtedly bacteria. Their important role in gut physiology, defense against pathogens, and immune system education has been well documented over the last decades. However, the gut microbiome is not restricted to bacteria. It encompasses the entire breadth of microbial life: viruses, archaea, fungi, protists, and parasitic worms can also be found in the gut. While less studied than bacteria, their divergent but important roles during health and disease have become increasingly more appreciated. This review focuses on these understudied members of the gut microbiome. We will detail the composition and development of these microbial communities and will specifically highlight their functional interactions with enteric pathogens, such as species of the family Enterobacteriaceae. The interactions can be direct through physical interactions, or indirect through secreted metabolites or modulation of the immune response. We will present general concepts and specific examples of how non-bacterial gut communities modulate bacterial pathogenesis and present an outlook for future gut microbiome research that includes these communities.
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Affiliation(s)
- Kanchan Jaswal
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL, USA
| | - Olivia A Todd
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL, USA
| | - Judith Behnsen
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL, USA
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Darmmikrobiom: Mehr als nur Bakterien. ZEITSCHRIFT FÜR GASTROENTEROLOGIE 2023. [DOI: 10.1055/a-1942-3569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Worsley SF, Davies CS, Mannarelli ME, Komdeur J, Dugdale HL, Richardson DS. Assessing the causes and consequences of gut mycobiome variation in a wild population of the Seychelles warbler. MICROBIOME 2022; 10:242. [PMID: 36575553 PMCID: PMC9795730 DOI: 10.1186/s40168-022-01432-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Considerable research has focussed on the importance of bacterial communities within the vertebrate gut microbiome (GM). However, studies investigating the significance of other microbial kingdoms, such as fungi, are notably lacking, despite their potential to influence host processes. Here, we characterise the fungal GM of individuals living in a natural population of Seychelles warblers (Acrocephalus sechellensis). We evaluate the extent to which fungal GM structure is shaped by environment and host factors, including genome-wide heterozygosity and variation at key immune genes (major histocompatibility complex (MHC) and Toll-like receptor (TLR)). Importantly, we also explore the relationship between fungal GM differences and subsequent host survival. To our knowledge, this is the first time that the genetic drivers and fitness consequences of fungal GM variation have been characterised for a wild vertebrate population. RESULTS Environmental factors, including season and territory quality, explain the largest proportion of variance in the fungal GM. In contrast, neither host age, sex, genome-wide heterozygosity, nor TLR3 genotype was associated with fungal GM differences in Seychelles warblers. However, the presence of four MHC-I alleles and one MHC-II allele was associated with changes in fungal GM alpha diversity. Changes in fungal richness ranged from between 1 and 10 sequencing variants lost or gained; in some cases, this accounted for 20% of the fungal variants carried by an individual. In addition to this, overall MHC-I allelic diversity was associated with small, but potentially important, changes in fungal GM composition. This is evidenced by the fact that fungal GM composition differed between individuals that survived or died within 7 months of being sampled. CONCLUSIONS Our results suggest that environmental factors play a primary role in shaping the fungal GM, but that components of the host immune system-specifically the MHC-may also contribute to the variation in fungal communities across individuals within wild populations. Furthermore, variation in the fungal GM can be associated with differential survival in the wild. Further work is needed to establish the causality of such relationships and, thus, the extent to which components of the GM may impact host evolution. Video Abstract.
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Affiliation(s)
- Sarah F Worsley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK.
| | - Charli S Davies
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Maria-Elena Mannarelli
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK
| | - Jan Komdeur
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
| | - Hannah L Dugdale
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
- Faculty of Biological Sciences, School of Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - David S Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK.
- Nature Seychelles, Roche Caiman, Mahé, Republic of Seychelles.
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Westlake Gut Project: A consortium of microbiome epidemiology for the gut microbiome and health research in China. MEDICINE IN MICROECOLOGY 2022. [DOI: 10.1016/j.medmic.2022.100064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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