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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:e0016924. [PMID: 38767350 DOI: 10.1128/mbio.00169-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [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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2
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Xiao Z, Zhang Y, Zhang W, Zhang A, Wang G, Chen C, Ullah H, Ayaz T, Li S, Zhaxi D, Yan Q, Kang J, Xu X. Characterizations of gut bacteriome, mycobiome, and virome of healthy individuals living in sea-level and high-altitude areas. Int Microbiol 2024:10.1007/s10123-024-00531-9. [PMID: 38758414 DOI: 10.1007/s10123-024-00531-9] [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: 12/27/2023] [Revised: 04/05/2024] [Accepted: 05/09/2024] [Indexed: 05/18/2024]
Abstract
BACKGROUND The contribution of gut microbiota to human high-altitude adaptation remains inadequately understood. METHODS Here a comparative analysis of gut microbiota was conducted between healthy individuals living at sea level and high altitude using deep whole-metagenome shotgun sequencing, to investigate the adaptive mechanisms of gut microbiota in plateau inhabitants. RESULTS The results showed the gut bacteriomes in high-altitude individuals exhibited greater within-sample diversity and significant alterations in both bacterial compositional and functional profiles when compared to those of sea-level individuals, indicating the potential selection of unique bacteria associated with high-altitude environments. The strain-level investigation revealed enrichment of Collinsella aerofaciens and Akkermansia muciniphila in high-altitude populations. The characteristics of gut virome and gut mycobiome were also investigated. Compared to sea-level subjects, high-altitude subjects exhibited a greater diversity in their gut virome, with an increased number of viral operational taxonomic units (vOTUs) and unique annotated genes. Finally, correlation analyses revealed 819 significant correlations between 42 bacterial species and 375 vOTUs, while no significant correlations were observed between bacteria and fungi or between fungi and viruses. CONCLUSION The findings have significantly contributed to an enhanced comprehension of the mechanisms underlying the high-altitude geographic adaptation of the human gut microbiota.
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Affiliation(s)
- Zhen Xiao
- Institute of High-Altitude Medicine, People's Hospital of Nagqu Affiliated to Dalian Medical University, Nagqu, 852099, China
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Dalian Medical University, Dalian, 116011, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan, 430010, China
| | - Wei Zhang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Aiqin Zhang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Guangyang Wang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Changming Chen
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, 550003, China
| | - Hayan Ullah
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Taj Ayaz
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Shenghui Li
- Puensum Genetech Institute, Wuhan, 430010, China
| | - Duoji Zhaxi
- Institute of High-Altitude Medicine, People's Hospital of Nagqu Affiliated to Dalian Medical University, Nagqu, 852099, China
| | - Qiulong Yan
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China.
| | - Jian Kang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China.
| | - Xiaoguang Xu
- Institute of High-Altitude Medicine, People's Hospital of Nagqu Affiliated to Dalian Medical University, Nagqu, 852099, China.
- Department of Neurosurgery, Second Affiliated Hospital of Dalian Medical University, Dalian, 116023, China.
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3
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Yan Q, Li S, Yan Q, Huo X, Wang C, Wang X, Sun Y, Zhao W, Yu Z, Zhang Y, Guo R, Lv Q, He X, Yao C, Li Z, Chen F, Ji Q, Zhang A, Jin H, Wang G, Feng X, Feng L, Wu F, Ning J, Deng S, An Y, Guo DA, Martin FM, Ma X. A genomic compendium of cultivated human gut fungi characterizes the gut mycobiome and its relevance to common diseases. Cell 2024:S0092-8674(24)00469-0. [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 02/17/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
The gut fungal community represents an essential element of human health, yet its functional and metabolic potential remains insufficiently elucidated, largely due to the limited availability of reference genomes. To address this gap, we presented the cultivated gut fungi (CGF) catalog, encompassing 760 fungal genomes derived from the feces of healthy individuals. This catalog comprises 206 species spanning 48 families, including 69 species previously unidentified. We explored the functional and metabolic attributes of the CGF species and utilized this catalog to construct a phylogenetic representation of the gut mycobiome by analyzing over 11,000 fecal metagenomes from Chinese and non-Chinese populations. Moreover, we identified significant common disease-related variations in gut mycobiome composition and corroborated the associations between fungal signatures and inflammatory bowel disease (IBD) through animal experimentation. These resources and findings substantially enrich our understanding of the biological diversity and disease relevance of the human gut mycobiome.
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Affiliation(s)
- Qiulong Yan
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China; Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China; College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Shenghui Li
- Puensum Genetech Institute, Wuhan 430076, China; Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100091, China
| | - Qingsong Yan
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Xiaokui Huo
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Chao Wang
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China; Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China; First Affiliated Hospital, Dalian Medical University, Dalian 116044, China.
| | - Xifan Wang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100091, China; Department of Obstetrics and Gynecology, Columbia University, New York, NY 10027, USA
| | - Yan Sun
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Wenyu Zhao
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Zhenlong Yu
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan 430076, China
| | - Ruochun Guo
- Puensum Genetech Institute, Wuhan 430076, China
| | - Qingbo Lv
- Puensum Genetech Institute, Wuhan 430076, China
| | - Xin He
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China; Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China
| | - Changliang Yao
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China
| | | | - Fang Chen
- College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Qianru Ji
- Puensum Genetech Institute, Wuhan 430076, China
| | - Aiqin Zhang
- Puensum Genetech Institute, Wuhan 430076, China
| | - Hao Jin
- Puensum Genetech Institute, Wuhan 430076, China
| | - Guangyang Wang
- College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Xiaoying Feng
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Lei Feng
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Fan Wu
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Jing Ning
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Sa Deng
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Yue An
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - De-An Guo
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China.
| | - Francis M Martin
- Université de Lorraine, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux 54280, France; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100091, China.
| | - Xiaochi Ma
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China; Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China.
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4
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Chi R, Li M, Zhang M, Zhang N, Zhang G, Cui L, Ma G. Exploring the Association between Anxiety, Depression, and Gut Microbiota during Pregnancy: Findings from a Pregnancy Cohort Study in Shijiazhuang, Hebei Province, China. Nutrients 2024; 16:1460. [PMID: 38794698 PMCID: PMC11123899 DOI: 10.3390/nu16101460] [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: 03/31/2024] [Revised: 05/05/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Negative emotions and gut microbiota during pregnancy both bear significant public health implications. However, the relationship between them has not been fully elucidated. This study, utilizing data from a pregnancy cohort, employed metagenomic sequencing to elucidate the relationship between anxiety, depression, and gut microbiota's diversity, composition, species, and functional pathways. Data from 87 subjects, spanning 225 time points across early, mid, and late pregnancy, were analyzed. The results revealed that anxiety and depression significantly corresponded to lower alpha diversity (including the Shannon entropy and the Simpson index). Anxiety and depression scores, along with categorical distinctions of anxiety/non-anxiety and depression/non-depression, were found to account for 0.723%, 0.731%, 0.651%, and 0.810% of the variance in gut-microbiota composition (p = 0.001), respectively. Increased anxiety was significantly positively associated with the abundance of Oscillibacter sp. KLE 1745, Oscillibacter sp. PEA192, Oscillibacter sp. KLE 1728, Oscillospiraceae bacterium VE202 24, and Treponema socranskii. A similar association was significantly noted for Oscillibacter sp. KLE 1745 with elevated depression scores. While EC.3.5.3.1: arginase appeared to be higher in the anxious group than in the non-anxious group, vitamin B12-related enzymes appeared to be lower in the depression group than in the non-depression group. The changes were found to be not statistically significant after post-multiple comparison adjustment.
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Affiliation(s)
- Ruixin Chi
- Department of Nutrition and Food Hygiene, School of Public Health, Peking University, 38 Xue Yuan Road, Haidian District, Beijing 100191, China; (R.C.); (N.Z.)
| | - Muxia Li
- Department of Scientific Research, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing 100045, China;
| | - Man Zhang
- School of Nursing, Peking University, 38 Xue Yuan Road, Haidian District, Beijing 100191, China;
| | - Na Zhang
- Department of Nutrition and Food Hygiene, School of Public Health, Peking University, 38 Xue Yuan Road, Haidian District, Beijing 100191, China; (R.C.); (N.Z.)
| | - Guohua Zhang
- The Third Department of Obstetrics, Shijiazhuang Obstetrics and Gynecology Hospital, Shijiazhuang 050011, China;
| | - Lijun Cui
- The Seventh Department of Obstetrics, Shijiazhuang Obstetrics and Gynecology Hospital, Shijiazhuang 050011, China;
| | - Guansheng Ma
- Department of Nutrition and Food Hygiene, School of Public Health, Peking University, 38 Xue Yuan Road, Haidian District, Beijing 100191, China; (R.C.); (N.Z.)
- Laboratory of Toxicological Research and Risk Assessment for Food Safety, Peking University, 38 Xue Yuan Road, Haidian District, Beijing 100191, China
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5
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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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6
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Kong FS, Huang P, Chen JH, Ma Y. The Novel Insight of Gut Microbiota from Mouse Model to Clinical Patients and the Role of NF-κB Pathway in Polycystic Ovary Syndrome. Reprod Sci 2024:10.1007/s43032-024-01562-3. [PMID: 38653859 DOI: 10.1007/s43032-024-01562-3] [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: 12/21/2023] [Accepted: 04/12/2024] [Indexed: 04/25/2024]
Abstract
Polycystic Ovary Syndrome (PCOS) is a metabolic disorder characterized by hyperandrogenism and related symptoms in women of reproductive age. Emerging evidence suggests that chronic low-grade inflammation plays a significant role in the development of PCOS. The gut microbiota, a complex bacterial ecosystem, has been extensively studied for various diseases, including PCOS, while the underlying mechanisms are not fully understood. This review comprehensively summarizes the changes in gut microbiota and metabolites observed in PCOS and their potential association with the condition. Additionally, we discuss the role of abnormal nuclear factor κB signaling in the pathogenesis of PCOS. These findings offer valuable insights into the mechanisms of PCOS and may pave the way for the development of control and therapeutic strategies for this condition in clinical practice. By bridging the gap between mouse models and clinical patients, this review contributes to a better understanding of the interplay between gut microbiota and inflammation in PCOS, thus paving new ways for future investigations and interventions.
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Affiliation(s)
- Fan-Sheng Kong
- Department of Pediatrics, Affiliated Hospital of Jiangnan University, Wuxi, 214122, Jiangsu, China
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Panwang Huang
- Department of Pediatrics, Affiliated Hospital of Jiangnan University, Wuxi, 214122, Jiangsu, China
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Jian-Huan Chen
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China.
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China.
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China.
| | - Yaping Ma
- Department of Pediatrics, Affiliated Hospital of Jiangnan University, Wuxi, 214122, Jiangsu, China.
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China.
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7
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Yadav A, Yadav R, Sharma V, Dutta U. A comprehensive guide to assess gut mycobiome and its role in pathogenesis and treatment of inflammatory bowel disease. Indian J Gastroenterol 2024; 43:112-128. [PMID: 38409485 DOI: 10.1007/s12664-023-01510-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/20/2023] [Indexed: 02/28/2024]
Abstract
Inflammatory bowel disease (IBD) is an immune mediated chronic inflammatory disorder of gastrointestinal tract, which has underlying multifactorial pathogenic determinants such as environmental factors, susceptibility genes, gut microbial dysbiosis and a dysregulated immune response. Human gut is a frequent inhabitant of complex microbial ecosystem encompassing bacteria, viruses, parasites, fungi and other microorganisms that have an undisputable role in maintaining balanced homeostasis. All of these microbes interact with immune system and affect human gut physiology either directly or indirectly with interaction of each other. Intestinal fungi represent a smaller but crucial component of the human gut microbiome. Besides interaction with bacteriome and virome, it helps in balancing homoeostasis between pathophysiological and physiological processes, which is often dysregulated in patients with IBD. Understanding of gut mycobiome and its clinical implications are still in in its infancy as opposed to bacterial component of gut microbiome, which is more often focused. Modulation of gut mycobiome represents a novel and promising strategy in the management of patients with IBD. Emerging mycobiome-based therapies such as diet interventions, fecal microbiota transplantation (FMT), probiotics (both fungal and bacterial strains) and antifungals exhibit substantial effects in calibrating the gut mycobiome and restoring dysbalanced immune homeostasis by restoring the core gut mycobiome. In this review, we summarized compositional and functional diversity of the gut mycobiome in healthy individuals and patients with IBD, gut mycobiome dysbiosis in patients with IBD, host immune-fungal interactions and therapeutic role of modulation of intestinal fungi in patients with IBD.
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Affiliation(s)
- Amit Yadav
- Department of Gastroenterology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160 012, India
| | - Renu Yadav
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, 110 029, India
| | - Vishal Sharma
- Department of Gastroenterology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160 012, India
| | - Usha Dutta
- Department of Gastroenterology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160 012, India.
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8
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Nenciarini S, Renzi S, di Paola M, Meriggi N, Cavalieri D. Ascomycetes yeasts: The hidden part of human microbiome. WIREs Mech Dis 2024:e1641. [PMID: 38228159 DOI: 10.1002/wsbm.1641] [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: 05/17/2023] [Revised: 12/17/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024]
Abstract
The fungal component of the microbiota, the mycobiota, has been neglected for a long time due to its poor richness compared to bacteria. Limitations in fungal detection and taxonomic identification arise from using metagenomic approaches, often borrowed from bacteriome analyses. However, the relatively recent discoveries of the ability of fungi to modulate the host immune response and their involvement in human diseases have made mycobiota a fundamental component of the microbial communities inhabiting the human host, deserving some consideration in host-microbe interaction studies and in metagenomics. Here, we reviewed recent data on the identification of yeasts of the Ascomycota phylum across human body districts, focusing on the most representative genera, that is, Saccharomyces and Candida. Then, we explored the key factors involved in shaping the human mycobiota across the lifespan, ranging from host genetics to environment, diet, and lifestyle habits. Finally, we discussed the strengths and weaknesses of culture-dependent and independent methods for mycobiota characterization. Overall, there is still room for some improvements, especially regarding fungal-specific methodological approaches and bioinformatics challenges, which are still critical steps in mycobiota analysis, and to advance our knowledge on the role of the gut mycobiota in human health and disease. This article is categorized under: Immune System Diseases > Genetics/Genomics/Epigenetics Immune System Diseases > Environmental Factors Infectious Diseases > Environmental Factors.
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Affiliation(s)
| | - Sonia Renzi
- Department of Biology, University of Florence, Florence, Italy
| | - Monica di Paola
- Department of Biology, University of Florence, Florence, Italy
| | - Niccolò Meriggi
- Department of Biology, University of Florence, Florence, Italy
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9
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Beurel E. Stress in the microbiome-immune crosstalk. Gut Microbes 2024; 16:2327409. [PMID: 38488630 PMCID: PMC10950285 DOI: 10.1080/19490976.2024.2327409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/04/2024] [Indexed: 03/19/2024] Open
Abstract
The gut microbiota exerts a mutualistic interaction with the host in a fragile ecosystem and the host intestinal, neural, and immune cells. Perturbations of the gastrointestinal track composition after stress have profound consequences on the central nervous system and the immune system. Reciprocally, brain signals after stress affect the gut microbiota highlighting the bidirectional communication between the brain and the gut. Here, we focus on the potential role of inflammation in mediating stress-induced gut-brain changes and discuss the impact of several immune cells and inflammatory molecules of the gut-brain dialogue after stress. Understanding the impact of microbial changes on the immune system after stress might provide new avenues for therapy.
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Affiliation(s)
- Eléonore Beurel
- Department of Psychiatry and Behavioral Sciences, Miller School of Medicine, University of Miami, Miami, FL, USA
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, USA
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10
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Tang LT, Feng L, Cao HY, Shi R, Luo BB, Zhang YB, Liu YM, Zhang J, Li SY. Comparative study of type 2 diabetes mellitus-associated gut microbiota between the Dai and Han populations. World J Diabetes 2023; 14:1766-1783. [PMID: 38222790 PMCID: PMC10784794 DOI: 10.4239/wjd.v14.i12.1766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 10/24/2023] [Accepted: 11/17/2023] [Indexed: 12/14/2023] Open
Abstract
BACKGROUND The global prevalence of type 2 diabetes mellitus (T2DM) is increasing. T2DM is associated with alterations of the gut microbiota, which can be affected by age, illness, and genetics. Previous studies revealed that there are discriminating microbiota compositions between the Dai and the Han populations. However, the specific gut microbiota differences between the two populations have not been elucidated. AIM To compare the gut microbiota differences in subjects with and without T2DM in the Dai and Han populations. METHODS A total of 35 subjects of the Han population (including 15 healthy children, 8 adult healthy controls, and 12 adult T2DM patients) and 32 subjects of the Dai population (including 10 healthy children, 10 adult healthy controls, and 12 adult T2DM patients) were enrolled in this study. Fasting venous blood samples were collected from all the subjects for biochemical analysis. Fecal samples were collected from all the subjects for DNA extraction and 16S rRNA sequencing, which was followed by analyses of the gut microbiota composition. RESULTS No significant difference in alpha diversity was observed between healthy children and adults. The diversity of gut microbiota was decreased in T2DM patients compared to the healthy adults in both the Dai and Han populations. There was a significant difference in gut microbiota between healthy children and healthy adults in the Han population with an increased abundance of Bacteroidetes and decreased Firmicutes in children. However, this difference was less in the Dai population. Significant increases in Bacteroidetes in the Han population and Proteobacteria in the Dai population and decreases in Firmicutes in both the Han and Dai population were observed in T2DM patients compared to healthy adults. Linear discriminant analysis Effect Size analysis also showed that the gut microbiota was different between the Han and Dai populations in heathy children, adults, and T2DM patients. Four bacteria were consistently increased and two consistently decreased in the Han population compared to the Dai population. CONCLUSION Differences in gut microbiota were found between the Han and Dai populations. A significant increase in Bacteroidetes was related to the occurrence of T2DM in the Han population, while a significant increase in Proteobacteria was related to the occurrence of T2DM in the Dai population.
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Affiliation(s)
- Ling-Tong Tang
- Department of Clinical Laboratory, Yan’an Hospital Affiliated to Kunming Medical University, Kunming 650051, Yunnan Province, China
| | - Lei Feng
- Department of Clinical Laboratory, Yan’an Hospital Affiliated to Kunming Medical University, Kunming 650051, Yunnan Province, China
| | - Hui-Ying Cao
- Department of Clinical Laboratory, Yan’an Hospital Affiliated to Kunming Medical University, Kunming 650051, Yunnan Province, China
| | - Rui Shi
- Department of Clinical Laboratory, Sixth Affiliated Hospital of Kunming Medical University, Kunming 650051, Yunnan Province, China
| | - Bei-Bei Luo
- Department of Clinical Laboratory, Sixth Affiliated Hospital of Kunming Medical University, Kunming 650051, Yunnan Province, China
| | - Yan-Bi Zhang
- Department of Clinical Laboratory, Sixth Affiliated Hospital of Kunming Medical University, Kunming 650051, Yunnan Province, China
| | - Yan-Mei Liu
- Department of Clinical Laboratory, Yan’an Hospital Affiliated to Kunming Medical University, Kunming 650051, Yunnan Province, China
| | - Jian Zhang
- Department of Clinical Laboratory, Yan’an Hospital Affiliated to Kunming Medical University, Kunming 650051, Yunnan Province, China
| | - Shuang-Yue Li
- Department of Clinical Laboratory, Yan’an Hospital Affiliated to Kunming Medical University, Kunming 650051, Yunnan Province, China
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11
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Xie Z, Canalda-Baltrons A, d'Enfert C, Manichanh C. Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients. MICROBIOME 2023; 11:275. [PMID: 38098063 PMCID: PMC10720197 DOI: 10.1186/s40168-023-01693-w] [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: 02/28/2023] [Accepted: 10/08/2023] [Indexed: 12/18/2023]
Abstract
BACKGROUND The accuracy of internal-transcribed-spacer (ITS) and shotgun metagenomics has not been robustly evaluated, and the effect of diet on the composition and function of the bacterial and fungal gut microbiome in a longitudinal setting has been poorly investigated. Here we compared two approaches to study the fungal community (ITS and shotgun metagenomics), proposed an enrichment protocol to perform a reliable mycobiome analysis using a comprehensive in-house fungal database, and correlated dietary data with both bacterial and fungal communities. RESULTS We found that shotgun DNA sequencing after a new enrichment protocol combined with the most comprehensive and novel fungal databases provided a cost-effective approach to perform gut mycobiome profiling at the species level and to integrate bacterial and fungal community analyses in fecal samples. The mycobiome was significantly more variable than the bacterial community at the compositional and functional levels. Notably, we showed that microbial diversity, composition, and functions were associated with habitual diet composition instead of driven by global dietary changes. Our study indicates a potential competitive inter-kingdom interaction between bacteria and fungi for food foraging. CONCLUSION Together, our present work proposes an efficient workflow to study the human gut microbiome integrating robustly fungal, bacterial, and dietary data. These findings will further advance our knowledge of the interaction between gut bacteria and fungi and pave the way for future investigations in human mycobiome. Video Abstract.
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Affiliation(s)
- Zixuan Xie
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Departament de Medicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Aleix Canalda-Baltrons
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Christophe d'Enfert
- Institut Pasteur, Université Paris Cité, INRAE USC2019, Unité Biologie et Pathogénicité Fongiques, Paris, France
| | - Chaysavanh Manichanh
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.
- Departament de Medicina, Universitat Autònoma de Barcelona, Barcelona, Spain.
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12
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Eichelberger KR, Paul S, Peters BM, Cassat JE. Candida-bacterial cross-kingdom interactions. Trends Microbiol 2023; 31:1287-1299. [PMID: 37640601 PMCID: PMC10843858 DOI: 10.1016/j.tim.2023.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/14/2023] [Accepted: 08/02/2023] [Indexed: 08/31/2023]
Abstract
While the fungus Candida albicans is a common colonizer of healthy humans, it is also responsible for mucosal infections and severe invasive disease. Understanding the mechanisms that allow C. albicans to exist as both a benign commensal and as an invasive pathogen have been the focus of numerous studies, and recent findings indicate an important role for cross-kingdom interactions on C. albicans biology. This review highlights how C. albicans-bacteria interactions influence healthy polymicrobial community structure, host immune responses, microbial pathogenesis, and how dysbiosis may lead to C. albicans infection. Finally, we discuss how cross-kingdom interactions represent an opportunity to identify new antivirulence compounds that target fungal infections.
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Affiliation(s)
- Kara R Eichelberger
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Saikat Paul
- Department of Clinical Pharmacy and Translational Science, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Brian M Peters
- Department of Clinical Pharmacy and Translational Science, University of Tennessee Health Science Center, Memphis, TN, USA; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - James E Cassat
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA; Vanderbilt Institute for Infection, Immunology, and Inflammation (VI4), Vanderbilt University Medical Center, Nashville, TN, USA
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13
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Yu Y, Wang W, Zhang F. The Next Generation Fecal Microbiota Transplantation: To Transplant Bacteria or Virome. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301097. [PMID: 37914662 PMCID: PMC10724401 DOI: 10.1002/advs.202301097] [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: 02/17/2023] [Revised: 09/02/2023] [Indexed: 11/03/2023]
Abstract
Fecal microbiota transplantation (FMT) has emerged as a promising therapeutic approach for dysbiosis-related diseases. However, the clinical practice of crude fecal transplants presents limitations in terms of acceptability and reproductivity. Consequently, two alternative solutions to FMT are developed: transplanting bacteria communities or virome. Advanced methods for transplanting bacteria mainly include washed microbiota transplantation and bacteria spores treatment. Transplanting the virome is also explored, with the development of fecal virome transplantation, which involves filtering the virome from feces. These approaches provide more palatable options for patients and healthcare providers while minimizing research heterogeneity. In general, the evolution of the next generation of FMT in global trends is fecal microbiota components transplantation which mainly focuses on transplanting bacteria or virome.
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Affiliation(s)
- You Yu
- Department of Microbiota Medicine & Medical Center for Digestive DiseasesThe Second Affiliated Hospital of Nanjing Medical UniversityNanjing210011China
- Key Lab of Holistic Integrative EnterologyNanjing Medical UniversityNanjing210011China
| | - Weihong Wang
- Department of Microbiota Medicine & Medical Center for Digestive DiseasesThe Second Affiliated Hospital of Nanjing Medical UniversityNanjing210011China
- Key Lab of Holistic Integrative EnterologyNanjing Medical UniversityNanjing210011China
| | - Faming Zhang
- Department of Microbiota Medicine & Medical Center for Digestive DiseasesThe Second Affiliated Hospital of Nanjing Medical UniversityNanjing210011China
- Key Lab of Holistic Integrative EnterologyNanjing Medical UniversityNanjing210011China
- Department of Microbiota MedicineSir Run Run HospitalNanjing Medical UniversityNanjing211166China
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14
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Liu NN, Yi CX, Wei LQ, Zhou JA, Jiang T, Hu CC, Wang L, Wang YY, Zou Y, Zhao YK, Zhang LL, Nie YT, Zhu YJ, Yi XY, Zeng LB, Li JQ, Huang XT, Ji HB, Kozlakidis Z, Zhong L, Heeschen C, Zheng XQ, Chen C, Zhang P, Wang H. The intratumor mycobiome promotes lung cancer progression via myeloid-derived suppressor cells. Cancer Cell 2023; 41:1927-1944.e9. [PMID: 37738973 DOI: 10.1016/j.ccell.2023.08.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 06/08/2023] [Accepted: 08/28/2023] [Indexed: 09/24/2023]
Abstract
Although polymorphic microbiomes have emerged as hallmarks of cancer, far less is known about the role of the intratumor mycobiome as living microorganisms in cancer progression. Here, using fungi-enriched DNA extraction and deep shotgun metagenomic sequencing, we have identified enriched tumor-resident Aspergillus sydowii in patients with lung adenocarcinoma (LUAD). By three different syngeneic lung cancer mice models, we find that A. sydowii promotes lung tumor progression via IL-1β-mediated expansion and activation of MDSCs, resulting in suppressed activity of cytotoxic T lymphocyte cells and accumulation of PD-1+ CD8+ T cells. This is mediated by IL-1β secretion via β-glucan/Dectin-1/CARD9 pathway. Analysis of human samples confirms that enriched A. sydowii is associated with immunosuppression and poor patient outcome. Our findings suggest that intratumor mycobiome, albeit at low biomass, promotes lung cancer progression and could be targeted at the strain level to improve patients with LUAD outcome.
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Affiliation(s)
- 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 200025, China.
| | - Cheng-Xiang Yi
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China; Central Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Lu-Qi Wei
- 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 200025, China
| | - Jin-An Zhou
- 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 200025, China
| | - Tong Jiang
- Shanghai Institute of Immunity and Infection, Chinese Academy of Science, (Past Name: Institut Pasteur of Shanghai, Chinese Academy of Sciences), Shanghai 200031, China; Laboratory Services and Biobanking, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Cong-Cong Hu
- Department of Mathematics, Shanghai Normal University, Shanghai 200234, China
| | - Lu Wang
- Department of Mathematics, Shanghai Normal University, Shanghai 200234, China
| | - Yuan-Yuan Wang
- Shanghai Institute of Immunity and Infection, Chinese Academy of Science, (Past Name: Institut Pasteur of Shanghai, Chinese Academy of Sciences), Shanghai 200031, China
| | - Yun Zou
- Shanghai Institute of Immunity and Infection, Chinese Academy of Science, (Past Name: Institut Pasteur of Shanghai, Chinese Academy of Sciences), Shanghai 200031, China
| | - Yi-Kai Zhao
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Le-Le Zhang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China; Central Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Ya-Ting Nie
- Department of Mathematics, Shanghai Normal University, Shanghai 200234, China
| | - Yi-Jing Zhu
- Department of Mathematics, Shanghai Normal University, Shanghai 200234, China
| | - Xin-Yao Yi
- Department of Mathematics, Shanghai Normal University, Shanghai 200234, China
| | - Ling-Bing Zeng
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanchang University, Nanchang 330052, China
| | - Jing-Quan Li
- 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 200025, China
| | - Xiao-Tian Huang
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang 330052, China
| | - Hong-Bin Ji
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zisis Kozlakidis
- Laboratory Services and Biobanking, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Lin Zhong
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Christopher Heeschen
- 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 200025, China
| | - Xiao-Qi 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 200025, China
| | - Changbin Chen
- Shanghai Institute of Immunity and Infection, Chinese Academy of Science, (Past Name: Institut Pasteur of Shanghai, Chinese Academy of Sciences), Shanghai 200031, China; Nanjing Advanced Academy of Life and Health, Nanjing 211135, China.
| | - Peng Zhang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, 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 200025, China.
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15
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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. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542255. [PMID: 37398234 PMCID: PMC10312434 DOI: 10.1101/2023.05.25.542255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
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) associates with compositional shifts in the gut bacterial microbiome and fungal mycobiome, but whether T2D and/or pharmaceutical treatments underpin the community change is unresolved. To differentiate these effects, we curated a gut mycobiome cohort to-date spanning 1,000 human samples across 5 countries and a murine experimental model. We use Bayesian multinomial logistic normal models to show that metformin and T2D both associate with shifts in the relative abundance of distinct gut fungi. T2D associates 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 oral pharmaceuticals 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.
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Affiliation(s)
- Emily Van Syoc
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802, USA
- One Health Microbiome Center, The Pennsylvania State University, University Park, PA 16802, USA
| | - Michelle Pistner Nixon
- College of Information Sciences and Technology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Justin D. Silverman
- One Health Microbiome Center, The Pennsylvania State University, University Park, PA 16802, USA
- College of Information Sciences and Technology, The Pennsylvania State University, University Park, PA 16802, USA
- Departments of Statistics and Medicine, The Pennsylvania State University, University Park, PA 16802, USA
| | - Yuhong Luo
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Frank J. Gonzalez
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, 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, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Connie J. Rogers
- Department of Nutritional Sciences, University of Georgia, Athens, GA 30602, USA
| | - Erika Ganda
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802, USA
- One Health Microbiome Center, The Pennsylvania State University, University Park, PA 16802, USA
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16
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Liu Q, Zhang W, Pei Y, Tao H, Ma J, Li R, Zhang F, Wang L, Shen L, Liu Y, Jia X, Hu Y. Gut mycobiome as a potential non-invasive tool in early detection of lung adenocarcinoma: a cross-sectional study. BMC Med 2023; 21:409. [PMID: 37904139 PMCID: PMC10617124 DOI: 10.1186/s12916-023-03095-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/26/2023] [Indexed: 11/01/2023] Open
Abstract
BACKGROUND The gut mycobiome of patients with lung adenocarcinoma (LUAD) remains unexplored. This study aimed to characterize the gut mycobiome in patients with LUAD and evaluate the potential of gut fungi as non-invasive biomarkers for early diagnosis. METHODS In total, 299 fecal samples from Beijing, Suzhou, and Hainan were collected prospectively. Using internal transcribed spacer 2 sequencing, we profiled the gut mycobiome. Five supervised machine learning algorithms were trained on fungal signatures to build an optimized prediction model for LUAD in a discovery cohort comprising 105 patients with LUAD and 61 healthy controls (HCs) from Beijing. Validation cohorts from Beijing, Suzhou, and Hainan comprising 44, 17, and 15 patients with LUAD and 26, 19, and 12 HCs, respectively, were used to evaluate efficacy. RESULTS Fungal biodiversity and richness increased in patients with LUAD. At the phylum level, the abundance of Ascomycota decreased, while that of Basidiomycota increased in patients with LUAD. Candida and Saccharomyces were the dominant genera, with a reduction in Candida and an increase in Saccharomyces, Aspergillus, and Apiotrichum in patients with LUAD. Nineteen operational taxonomic unit markers were selected, and excellent performance in predicting LUAD was achieved (area under the curve (AUC) = 0.9350) using a random forest model with outcomes superior to those of four other algorithms. The AUCs of the Beijing, Suzhou, and Hainan validation cohorts were 0.9538, 0.9628, and 0.8833, respectively. CONCLUSIONS For the first time, the gut fungal profiles of patients with LUAD were shown to represent potential non-invasive biomarkers for early-stage diagnosis.
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Affiliation(s)
- Qingyan Liu
- Graduate School, Chinese People's Liberation Army Medical School, Beijing, China
- Department of Oncology, Fifth Medical Center of the Chinese People's Liberation Army General Hospital, 28 Fuxing Road, Haidian Distrist, Beijing, 100000, China
| | - Weidong Zhang
- Graduate School, Chinese People's Liberation Army Medical School, Beijing, China
- Department of Thoracic Surgery, First Medical Center of the Chinese People's Liberation Army General Hospital, 28 Fuxing Road, Haidian District, Beijing, 100000, China
| | - Yanbin Pei
- Graduate School, Chinese People's Liberation Army Medical School, Beijing, China
| | - Haitao Tao
- Department of Oncology, Fifth Medical Center of the Chinese People's Liberation Army General Hospital, 28 Fuxing Road, Haidian Distrist, Beijing, 100000, China
| | - Junxun Ma
- Department of Oncology, Fifth Medical Center of the Chinese People's Liberation Army General Hospital, 28 Fuxing Road, Haidian Distrist, Beijing, 100000, China
| | - Rong Li
- Department of Health Medicine, Second Medical Center of the Chinese People's Liberation Army General Hospital, Beijing, China
| | - Fan Zhang
- Department of Oncology, Fifth Medical Center of the Chinese People's Liberation Army General Hospital, 28 Fuxing Road, Haidian Distrist, Beijing, 100000, China
| | - Lijie Wang
- Department of Oncology, Fifth Medical Center of the Chinese People's Liberation Army General Hospital, 28 Fuxing Road, Haidian Distrist, Beijing, 100000, China
| | - Leilei Shen
- Department of Thoracic Surgery, Hainan Medical Center of the Chinese People's Liberation Army General Hospital, Hainan, China
| | - Yang Liu
- Department of Thoracic Surgery, First Medical Center of the Chinese People's Liberation Army General Hospital, 28 Fuxing Road, Haidian District, Beijing, 100000, China.
| | - Xiaodong Jia
- Department of Oncology, Fifth Medical Center of the Chinese People's Liberation Army General Hospital, 28 Fuxing Road, Haidian Distrist, Beijing, 100000, China.
| | - Yi Hu
- Department of Oncology, Fifth Medical Center of the Chinese People's Liberation Army General Hospital, 28 Fuxing Road, Haidian Distrist, Beijing, 100000, China.
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17
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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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18
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Li J, Wei C, Zhou T, Mo C, Wang G, He F, Wang P, Qin L, Peng F. A display and analysis platform for gut microbiomes of minority people and phenotypic data in China. Sci Rep 2023; 13:14247. [PMID: 37648696 PMCID: PMC10469205 DOI: 10.1038/s41598-023-36754-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 06/09/2023] [Indexed: 09/01/2023] Open
Abstract
The minority people panmicrobial community database (MPPCD website: http://mppmcdb.cloudna.cn/ ) is the first microbe-disease association database of Chinese ethnic minorities. To research the relationships between intestinal microbes and diseases/health in the ethnic minorities, we collected the microbes of the Han people for comparison. Based on the data, such as age, among the different ethnic groups of the different regions of Sichuan Province, MPPCD not only provided the gut microbial composition but also presented the relative abundance value at the phylum, class, order, family and genus levels in different groups. In addition, differential analysis was performed in different microbes in the two different groups, which contributed to exploring the difference in intestinal microbe structures between the two groups. Meanwhile, a series of related factors, including age, sex, body mass index, ethnicity, physical condition, and living altitude, were included in the MPPCD, with special focus on living altitude. To date, this is the first intestinal microbe database to introduce altitude features. In conclusion, we hope that MPPCD will serve as a fundamental research support for the relationship between human gut microbes and host health and disease, especially in ethnic minorities.
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Affiliation(s)
- Jun Li
- Department of Gastroenterology, The First Affiliated Hospital of Chengdu Medical College, 278# Bao Guang Road, Xindu District, Chengdu, 610000, Sichuan, People's Republic of China.
| | - Chunxue Wei
- Department of Gastroenterology, The First Affiliated Hospital of Chengdu Medical College, 278# Bao Guang Road, Xindu District, Chengdu, 610000, Sichuan, People's Republic of China
| | - Ting Zhou
- Department of Gastroenterology, The Sixth People's Hospital of Chengdu, Chengdu, Sichuan, China
| | - Chunfen Mo
- Department of Immunology, School of Basic Medical Sciences, Chengdu Medical College, Chengdu, Sichuan, China
| | - Guanjun Wang
- Department of Gastroenterology, The First Affiliated Hospital of Chengdu Medical College, 278# Bao Guang Road, Xindu District, Chengdu, 610000, Sichuan, People's Republic of China
| | - Feng He
- Department of Gastroenterology, The First Affiliated Hospital of Chengdu Medical College, 278# Bao Guang Road, Xindu District, Chengdu, 610000, Sichuan, People's Republic of China
| | - Pengyu Wang
- College of Pharmacy, Chengdu Medical College, Chengdu, Sichuan, China
| | - Ling Qin
- Department of Gastroenterology, The First Affiliated Hospital of Chengdu Medical College, 278# Bao Guang Road, Xindu District, Chengdu, 610000, Sichuan, People's Republic of China
| | - Fujun Peng
- Institute of Basic Medicine, Weifang Medical University, 7166# Baotong West Road, Weifang, 261053, Shandong, People's Republic of China.
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Perlin CM, Longo L, Keingeski MB, Picon RV, Álvares-da-Silva MR. Gut mycobiota changes in liver diseases: A systematic review. Med Mycol 2023; 61:myad071. [PMID: 37463798 DOI: 10.1093/mmy/myad071] [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: 02/08/2023] [Revised: 06/27/2023] [Accepted: 07/16/2023] [Indexed: 07/20/2023] Open
Abstract
Intestinal fungi play an important role in the health-disease process. We observed that in liver diseases, fungal infections lead to high mortality. In this review, we were able to gather and evaluate the available scientific evidence on intestinal mycobiota and liver diseases. We searched PubMed and Embase, using a combination of several entry terms. Only studies in adults ≥ 18 years old with liver disease and published after 2010 were included. We observed that individuals with liver disease have an altered intestinal mycobioma, which accompanies the progression of these diseases. In cirrhotic patients, there are a high number of Candida sp. strains, especially Candida albicans. In early chronic liver disease, there is an increase in alpha diversity at the expense of Candida sp. and conversely, in advanced liver disease, there is a negative correlation between alpha diversity and model for end-stage liver disease score. On the other hand, patients with non-alcoholic fatty liver disease demonstrate greater diversity compared to controls. Our study concluded that the evidence on the subject is sparse, with few studies and a lack of standardization of outcome measures and reporting, and it was not possible to perform a meta-analysis capable of synthesizing relevant parameters of the human mycobiotic profile. However, certain fungal genera such as Candida play an important role in the context of liver disease and that adults with liver disease have a distinct gut mycobiotic profile from healthy controls.
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Affiliation(s)
- Cássio Marques Perlin
- Graduate Program in Gastroenterology and Hepatology, Universidade Federal do Rio Grande do Sul, Porto Alegre, 90035-002, Brazil
- Experimental Laboratory of Hepatology and Gastroenterology, Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, 90035-903, Brazil
| | - Larisse Longo
- Graduate Program in Gastroenterology and Hepatology, Universidade Federal do Rio Grande do Sul, Porto Alegre, 90035-002, Brazil
- Experimental Laboratory of Hepatology and Gastroenterology, Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, 90035-903, Brazil
| | - Melina Belén Keingeski
- Graduate Program in Gastroenterology and Hepatology, Universidade Federal do Rio Grande do Sul, Porto Alegre, 90035-002, Brazil
- Experimental Laboratory of Hepatology and Gastroenterology, Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, 90035-903, Brazil
| | - Rafael V Picon
- Graduate Program in Gastroenterology and Hepatology, Universidade Federal do Rio Grande do Sul, Porto Alegre, 90035-002, Brazil
- School of Medicine, Department of Internal Medicine, Universidade Federal do Rio Grande do Sul; Division of Gastroenterology, Hospital de Clínicas de Porto Alegre, Porto Alegre, 90035-903, Brazil
| | - Mário Reis Álvares-da-Silva
- Graduate Program in Gastroenterology and Hepatology, Universidade Federal do Rio Grande do Sul, Porto Alegre, 90035-002, Brazil
- Experimental Laboratory of Hepatology and Gastroenterology, Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, 90035-903, Brazil
- School of Medicine, Department of Internal Medicine, Universidade Federal do Rio Grande do Sul; Division of Gastroenterology, Hospital de Clínicas de Porto Alegre, Porto Alegre, 90035-903, Brazil
- CNPq researcher
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20
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Vonaesch P, Billy V, Mann AE, Morien E, Habib A, Collard JM, Dédé M, Kapel N, Sansonetti PJ, Parfrey LW. The eukaryome of African children is influenced by geographic location, gut biogeography, and nutritional status. MICROLIFE 2023; 4:uqad033. [PMID: 37680753 PMCID: PMC10481997 DOI: 10.1093/femsml/uqad033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 07/17/2023] [Indexed: 09/09/2023]
Abstract
Eukaryotes have historically been studied as parasites, but recent evidence suggests they may be indicators of a healthy gut ecosystem. Here, we describe the eukaryome along the gastrointestinal tract of children aged 2-5 years and test for associations with clinical factors such as anaemia, intestinal inflammation, chronic undernutrition, and age. Children were enrolled from December 2016 to May 2018 in Bangui, Central African Republic and Antananarivo, Madagascar. We analyzed a total of 1104 samples representing 212 gastric, 187 duodenal, and 705 fecal samples using a metabarcoding approach targeting the full ITS2 region for fungi, and the V4 hypervariable region of the 18S rRNA gene for the overall eukaryome. Roughly, half of all fecal samples showed microeukaryotic reads. We find high intersubject variability, only a handful of taxa that are likely residents of the gastrointestinal tract, and frequent co-occurrence of eukaryotes within an individual. We also find that the eukaryome differs between the stomach, duodenum, and feces and is strongly influenced by country of origin. Our data show trends towards higher levels of Fusarium equiseti, a mycotoxin producing fungus, and lower levels of the protist Blastocystis in stunted children compared to nonstunted controls. Overall, the eukaryome is poorly correlated with clinical variables. Our study is of one of the largest cohorts analyzing the human intestinal eukaryome to date and the first to compare the eukaryome across different compartments of the gastrointestinal tract. Our results highlight the importance of studying populations across the world to uncover common features of the eukaryome in health.
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Affiliation(s)
- Pascale Vonaesch
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Vincent Billy
- Departments of Botany and Zoology, and Biodiversity Research Centre, University of British Columbia, 3200-6270 University Boulevard, V6T1Z4 Vancouver, Canada
| | - Allison E Mann
- Departments of Botany and Zoology, and Biodiversity Research Centre, University of British Columbia, 3200-6270 University Boulevard, V6T1Z4 Vancouver, Canada
| | - Evan Morien
- Departments of Botany and Zoology, and Biodiversity Research Centre, University of British Columbia, 3200-6270 University Boulevard, V6T1Z4 Vancouver, Canada
| | - Azimdine Habib
- Unité de Bactériologie Expérimentale, Institut Pasteur de Madagascar, BP1274 Ambatofotsikely Avaradoha 101 Antananarivo, Madagascar
| | - Jean-Marc Collard
- Unité de Bactériologie Expérimentale, Institut Pasteur de Madagascar, BP1274 Ambatofotsikely Avaradoha 101 Antananarivo, Madagascar
| | - Michel Dédé
- Laboratoire d’Analyse médicale, Institut Pasteur de Bangui, Avenue De Independence Bangui, 923 Central African Republic
| | - Nathalie Kapel
- Laboratoire de Coprologie Fonctionnelle, Assistance Publique- Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, 47-83 Bd de l’Hôpital, 75013 Paris, France
| | - Philippe J Sansonetti
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Laura Wegener Parfrey
- Departments of Botany and Zoology, and Biodiversity Research Centre, University of British Columbia, 3200-6270 University Boulevard, V6T1Z4 Vancouver, Canada
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21
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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: 2] [Impact Index Per Article: 2.0] [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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22
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Abstract
The microbiome may impact cancer development, progression and treatment responsiveness, but its fungal components remain insufficiently studied in this context. In this review, we highlight accumulating evidence suggesting a possible involvement of commensal and pathogenic fungi in modulation of cancer-related processes. We discuss the mechanisms by which fungi can influence tumour biology, locally by activity exerted within the tumour microenvironment, or remotely through secretion of bioactive metabolites, modulation of host immunity and communications with neighbouring bacterial commensals. We examine prospects of utilising fungi-related molecular signatures in cancer diagnosis, patient stratification and assessment of treatment responsiveness, while highlighting challenges and limitations faced in performing such research. In all, we demonstrate that fungi likely constitute important members of mucosal and tumour-residing microbiomes. Exploration of fungal inter-kingdom interactions with the bacterial microbiome and the host and decoding of their causal impacts on tumour biology may enable their harnessing into cancer diagnosis and treatment.
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Affiliation(s)
- Aurelia Saftien
- Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Jens Puschhof
- Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Eran Elinav
- Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
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23
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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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24
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Kelly JR, Clarke G, Harkin A, Corr SC, Galvin S, Pradeep V, Cryan JF, O'Keane V, Dinan TG. Seeking the Psilocybiome: Psychedelics meet the microbiota-gut-brain axis. Int J Clin Health Psychol 2023; 23:100349. [PMID: 36605409 PMCID: PMC9791138 DOI: 10.1016/j.ijchp.2022.100349] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/16/2022] [Indexed: 12/15/2022] Open
Abstract
Moving towards a systems psychiatry paradigm embraces the inherent complex interactions across all levels from micro to macro and necessitates an integrated approach to treatment. Cortical 5-HT2A receptors are key primary targets for the effects of serotonergic psychedelics. However, the therapeutic mechanisms underlying psychedelic therapy are complex and traverse molecular, cellular, and network levels, under the influence of biofeedback signals from the periphery and the environment. At the interface between the individual and the environment, the gut microbiome, via the gut-brain axis, plays an important role in the unconscious parallel processing systems regulating host neurophysiology. While psychedelic and microbial signalling systems operate over different timescales, the microbiota-gut-brain (MGB) axis, as a convergence hub between multiple biofeedback systems may play a role in the preparatory phase, the acute administration phase, and the integration phase of psychedelic therapy. In keeping with an interconnected systems-based approach, this review will discuss the gut microbiome and mycobiome and pathways of the MGB axis, and then explore the potential interaction between psychedelic therapy and the MGB axis and how this might influence mechanism of action and treatment response. Finally, we will discuss the possible implications for a precision medicine-based psychedelic therapy paradigm.
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Affiliation(s)
- John R. Kelly
- Department of Psychiatry, Trinity College, Dublin, Ireland
- Tallaght University Hospital, Dublin, Ireland
| | - Gerard Clarke
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Sinead C. Corr
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Microbiology, Trinity College Dublin, Ireland
| | - Stephen Galvin
- Department of Psychiatry, Trinity College, Dublin, Ireland
| | - Vishnu Pradeep
- Department of Psychiatry, Trinity College, Dublin, Ireland
- Tallaght University Hospital, Dublin, Ireland
| | - John F. Cryan
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Veronica O'Keane
- Department of Psychiatry, Trinity College, Dublin, Ireland
- Tallaght University Hospital, Dublin, Ireland
- Trinity College Institute of Neuroscience, Ireland
| | - Timothy G. Dinan
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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25
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Li M, Zhang G, Cui L, Zhang L, Zhou Q, Mu C, Chi R, Zhang N, Ma G. Dynamic changes in gut microbiota during pregnancy among Chinese women and influencing factors: A prospective cohort study. Front Microbiol 2023; 14:1114228. [PMID: 37065129 PMCID: PMC10096036 DOI: 10.3389/fmicb.2023.1114228] [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: 12/19/2022] [Accepted: 03/09/2023] [Indexed: 03/31/2023] Open
Abstract
Gut microbiota (GM) dynamics during pregnancy vary among different populations and are affected by many factors, such as living environments and diet. This study aims to observe and evaluate the changes in the structure and function of the GM from the first to the third trimester of pregnancy in Chinese women, and to explore the main factors affecting the changes in intestinal microecology. Fifty-five Chinese pregnant women were recruited for this study and their fecal samples were collected during the first (P1), second (P2), and third trimesters (P3) of pregnancy. We exploited metagenomic sequencing to compare the composition and function of the GM in different pregnancy periods. Bioinformatic analysis revealed that there were differences in the composition of the GM among P1, P2, and P3, as indicated by the increase in α-diversity and β-diversity of the GM and the differences in the relative abundances of distinct bacterial phyla. Gestational diabetes mellitus (GDM) was the main factor (P < 0.05) that affected the changes in GM at various stages of pregnancy. There were also disparities in the structure of the GM between the GDM group and non-GDM group in the P1, P2, and P3. The GDM group exhibited increased abundances in Ruminococcus_gnavus, Akkermansia_muciniphila, Alistipes_shahii, Blautia_obeum, and Roseburia_intestinalis; while, the abundances of Bacteroides coprocola, Bacteroides plebeius, Erysipelatoclostridium ramosum, and Prevotella copri were increased in the non-GDM group. Three of the four species enriched in the non-GDM group manifestied significantly negative correlations with the insulin-signaling pathway and lipopolysaccharide biosynthesis (r ≤ −0.3, adjusted P < 0.05). In the GDM group, Bacteroides vulgatus and Ruminococcus gnavus were significantly and positively correlated with insulin signaling pathway and lipopolysaccharide biosynthesis (r ≤ −0.3, adjusted P < 0.05) among the species enriched from early pregnancy. Virtually all of the species enriched in P2 and P3 were positively correlated with steroid hormone biosynthesis. These results suggest a potential role for the GM in the development of GDM, enabling the potential prevention of GDM by targeting the GM.
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Affiliation(s)
- Muxia Li
- Department of Nutrition and Food Hygiene, School of Public Health, Peking University, Beijing, China
| | - Guohua Zhang
- The Third Department of Obstetrics, Shijiazhuang Obstetrics and Gynecology Hospital, Shijiazhuang, China
| | - Lijun Cui
- The Seventh Department of Obstetrics, Shijiazhuang Obstetrics and Gynecology Hospital, Shijiazhuang, China
| | - Lin Zhang
- Department of Pediatrics, The Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Qian Zhou
- Department of Computer Science, City University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Chenxue Mu
- The Third Department of Obstetrics, Shijiazhuang Obstetrics and Gynecology Hospital, Shijiazhuang, China
| | - Ruixin Chi
- Department of Nutrition and Food Hygiene, School of Public Health, Peking University, Beijing, China
| | - Na Zhang
- Department of Nutrition and Food Hygiene, School of Public Health, Peking University, Beijing, China
- Laboratory of Toxicological Research and Risk Assessment for Food Safety, Peking University, Beijing, China
| | - Guansheng Ma
- Department of Nutrition and Food Hygiene, School of Public Health, Peking University, Beijing, China
- Laboratory of Toxicological Research and Risk Assessment for Food Safety, Peking University, Beijing, China
- *Correspondence: Guansheng Ma,
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26
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Sun Y, Zhang X, Jin C, Yue K, Sheng D, Zhang T, Dou X, Liu J, Jing H, Zhang L, Yue J. Prospective, longitudinal analysis of the gut microbiome in patients with locally advanced rectal cancer predicts response to neoadjuvant concurrent chemoradiotherapy. J Transl Med 2023; 21:221. [PMID: 36967379 PMCID: PMC10041716 DOI: 10.1186/s12967-023-04054-1] [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: 12/04/2022] [Accepted: 03/10/2023] [Indexed: 03/28/2023] Open
Abstract
BACKGROUND Neoadjuvant concurrent chemoradiotherapy (nCCRT) is a standard treatment for locally advanced rectal cancer (LARC). The gut microbiome may be reshaped by radiotherapy through its effects on microbial composition, mucosal immunity, and the systemic immune system. We sought to clarify dynamic, longitudinal changes in the gut microbiome and blood immunomodulators throughout nCCRT and to explore the relationship of such changes with outcomes after nCCRT. METHODS A total of 39 patients with LARC were recruited for this study. Fecal samples and peripheral blood samples were collected from all 39 patients before nCCRT, during nCCRT (at week 3), and after nCCRT (at week 5). The gut microbiota and the microbial community structure were analyzed by 16S rRNA sequencing of the V3-V4 region. Levels of blood immunomodulatory proteins were measured with a Millipore HCKPMAG-11 K kit and Luminex 200 platform (Luminex, USA). RESULTS Cross-sectional and longitudinal analyses revealed that the gut microbiome profile and enterotype exhibited characteristic variations that could distinguish patients with good response (AJCC TRG classification 0-1) vs poor response (TRG 2-3) to nCCRT. Sparse partial least squares regression and canonical correspondence analyses showed multivariate associations between specific microbial taxa, host immunomodulatory proteins, immune cells, and outcomes after nCCRT. An integrated model consisting of baseline Clostridium sensu stricto 1 levels, fold changes in Intestinimonas, blood levels of the herpesvirus entry mediator (HVEM/CD270), and lymphocyte counts could predict good vs poor outcome after nCCRT [area under the receiver-operating characteristics curve (AUC)= 0.821; area under the precision-recall curve [AUPR] = 0.911]. CONCLUSIONS Our results showed that longitudinal variations in specific gut taxa, associated host immune cells, and immunomodulatory proteins before and during nCCRT could be useful for early predictions of the efficacy of nCCRT, which could guide the choice of individualized treatment for patients with LARC.
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Affiliation(s)
- Yi Sun
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
- The Comprehensive Cancer Centre of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Xiang Zhang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Chuandi Jin
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- Microbiome-X, National Institute of Health Data Science of China & Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Kaile Yue
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- Microbiome-X, National Institute of Health Data Science of China & Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Dashuang Sheng
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- Microbiome-X, National Institute of Health Data Science of China & Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Tao Zhang
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xue Dou
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Jing Liu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Hongbiao Jing
- Department of Pathology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Lei Zhang
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China.
- Microbiome-X, National Institute of Health Data Science of China & Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan, China.
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
| | - Jinbo Yue
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China.
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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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Zhang Z, Zhang L, Zhang G, Zhao Z, Wang H, Ju F. Deduplication Improves Cost-Efficiency and Yields of De Novo Assembly and Binning of Shotgun Metagenomes in Microbiome Research. Microbiol Spectr 2023; 11:e0428222. [PMID: 36744896 PMCID: PMC10101064 DOI: 10.1128/spectrum.04282-22] [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: 11/03/2022] [Accepted: 01/18/2023] [Indexed: 02/07/2023] Open
Abstract
In the last decade, metagenomics has greatly revolutionized the study of microbial communities. However, the presence of artificial duplicate reads raised mainly from the preparation of metagenomic DNA sequencing libraries and their impacts on metagenomic assembly and binning have never been brought to attention. Here, we explicitly investigated the effects of duplicate reads on metagenomic assemblies and binning based on analyses of five groups of representative metagenomes with distinct microbiome complexities. Our results showed that deduplication considerably increased the binning yields (by 3.5% to 80%) for most of the metagenomic data sets examined thanks to the improved contig length and coverage profiling of metagenome-assembled contigs, whereas it slightly decreased the binning yields of metagenomes with low complexity (e.g., human gut metagenomes). Specifically, 411 versus 397, 331 versus 317, 104 versus 88, and 9 versus 5 metagenome-assembled genomes (MAGs) were recovered from MEGAHIT assemblies of bioreactor sludge, surface water, lake sediment, and forest soil metagenomes, respectively. Noticeably, deduplication significantly reduced the computational costs of the metagenomic assembly, including the elapsed time (9.0% to 29.9%) and the maximum memory requirement (4.3% to 37.1%). Collectively, we recommend the removal of duplicate reads in metagenomes with high complexity before assembly and binning analyses, for example, the forest soil metagenomes examined in this study. IMPORTANCE Duplicated reads in shotgun metagenomes are usually considered technical artifacts. Their presence in metagenomes would theoretically not only introduce bias into the quantitative analysis but also result in mistakes in the coverage profile, leading to adverse effects on or even failures in metagenomic assembly and binning, as the widely used metagenome assemblers and binners all need coverage information for graph partitioning and assembly binning, respectively. However, this issue was seldom noticed, and its impacts on downstream essential bioinformatic procedures (e.g., assembly and binning) remained unclear. In this study, we comprehensively evaluated for the first time the implications of duplicate reads for the de novo assembly and binning of real metagenomic data sets by comparing the assembly qualities, binning yields, and requirements for computational resources with and without the removal of duplicate reads. It was revealed that deduplication considerably increased the binning yields of metagenomes with high complexity and significantly reduced the computational costs, including the elapsed time and the maximum memory requirement, for most of the metagenomes studied. These results provide empirical references for more cost-efficient metagenomic analyses in microbiome research.
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Affiliation(s)
- Zhiguo Zhang
- College of Environmental and Resources Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Lu Zhang
- Research Center for Industries of the Future, Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Guoqing Zhang
- Research Center for Industries of the Future, Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Ze Zhao
- Research Center for Industries of the Future, Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Hui Wang
- Research Center for Industries of the Future, Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Feng Ju
- Research Center for Industries of the Future, Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China
- Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
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Niu C, Tu Y, Jin Q, Chen Z, Yuan K, Wang M, Zhang P, Luo J, Li H, Yang Y, Liu X, Mao M, Dong T, Tan W, Hu X, Pan Y, Hou L, Ma R, Huang Z. Mapping the human oral and gut fungal microbiota in patients with metabolic dysfunction-associated fatty liver disease. Front Cell Infect Microbiol 2023; 13:1157368. [PMID: 37180439 PMCID: PMC10170973 DOI: 10.3389/fcimb.2023.1157368] [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: 02/02/2023] [Accepted: 03/24/2023] [Indexed: 05/16/2023] Open
Abstract
Metabolic dysfunction-associated fatty liver disease (MAFLD) is a phenotype of liver diseases associated with metabolic syndrome. The pathogenesis MAFLD remains unclear. The liver maintains is located near the intestine and is physiologically interdependent with the intestine via metabolic exchange and microbial transmission, underpinning the recently proposed "oral-gut-liver axis" concept. However, little is known about the roles of commensal fungi in the disease development. This study aimed to characterize the alterations of oral and gut mycobiota and their roles in MAFLD. Twenty-one MAFLD participants and 20 healthy controls were enrolled. Metagenomics analyses of saliva, supragingival plaques, and feces revealed significant alterations in the gut fungal composition of MAFLD patients. Although no statistical difference was evident in the oral mycobiome diversity within MAFLD and healthy group, significantly decreased diversities were observed in fecal samples of MAFLD patients. The relative abundance of one salivary species, five supragingival species, and seven fecal species was significantly altered in MAFLD patients. Twenty-two salivary, 23 supragingival, and 22 fecal species were associated with clinical parameters. Concerning the different functions of fungal species, pathways involved in metabolic pathways, biosynthesis of secondary metabolites, microbial metabolism in diverse environments, and carbon metabolism were abundant both in the oral and gut mycobiomes. Moreover, different fungal contributions in core functions were observed between MAFLD patients and the healthy controls, especially in the supragingival plaque and fecal samples. Finally, correlation analysis between oral/gut mycobiome and clinical parameters identified correlations of certain fungal species in both oral and gut niches. Particularly, Mucor ambiguus, which was abundant both in saliva and feces, was positively correlated with body mass index, total cholesterol, low-density lipoprotein, alanine aminotransferase, and aspartate aminotransferase, providing evidence of a possible "oral-gut-liver" axis. The findings illustrate the potential correlation between core mycobiome and the development of MAFLD and could propose potential therapeutic strategies.
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Affiliation(s)
- Chenguang Niu
- Department of Endodontics, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- National Center for Stomatology, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Ye Tu
- Department of Endodontics, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- National Center for Stomatology, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Qiaoqiao Jin
- Department of Endodontics, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- National Center for Stomatology, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Zhanyi Chen
- Department of Endodontics, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- National Center for Stomatology, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Keyong Yuan
- Department of Endodontics, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- National Center for Stomatology, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Min Wang
- Institute of Stomatology, School and Hospital of Stomatology, Wenzhou Medical University, Wenzhou, China
- Department of Endodontics, School and Hospital of Stomatology, Wenzhou Medical University, Wenzhou, China
| | - Pengfei Zhang
- Department of Endodontics, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- National Center for Stomatology, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Junyuan Luo
- Department of Endodontics, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- National Center for Stomatology, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Hao Li
- Department of Endodontics, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- National Center for Stomatology, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Yueyi Yang
- Department of Endodontics, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- National Center for Stomatology, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Xiaoyu Liu
- Department of Endodontics, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- National Center for Stomatology, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Mengying Mao
- Department of Endodontics, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- National Center for Stomatology, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Ting Dong
- Department of Endodontics, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- National Center for Stomatology, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Wenduo Tan
- Department of Endodontics, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- National Center for Stomatology, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Xuchen Hu
- Department of Endodontics, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- National Center for Stomatology, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Yihuai Pan
- Institute of Stomatology, School and Hospital of Stomatology, Wenzhou Medical University, Wenzhou, China
- Department of Endodontics, School and Hospital of Stomatology, Wenzhou Medical University, Wenzhou, China
| | - Lili Hou
- Department of Nursing, Shanghai Ninth People’s Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Rui Ma
- Department of Endodontics, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- National Center for Stomatology, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
- *Correspondence: Zhengwei Huang, ; Rui Ma,
| | - Zhengwei Huang
- Department of Endodontics, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- National Center for Stomatology, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
- *Correspondence: Zhengwei Huang, ; Rui Ma,
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30
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Huang Z, Li Y, Park H, Ho M, Bhardwaj K, Sugimura N, Lee HW, Meng H, Ebert MP, Chao K, Burgermeister E, Bhatt AP, Shetty SA, Li K, Wen W, Zuo T. Unveiling and harnessing the human gut microbiome in the rising burden of non-communicable diseases during urbanization. Gut Microbes 2023; 15:2237645. [PMID: 37498052 PMCID: PMC10376922 DOI: 10.1080/19490976.2023.2237645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 07/28/2023] Open
Abstract
The world is witnessing a global increase in the urban population, particularly in developing Asian and African countries. Concomitantly, the global burden of non-communicable diseases (NCDs) is rising, markedly associated with the changing landscape of lifestyle and environment during urbanization. Accumulating studies have revealed the role of the gut microbiome in regulating the immune and metabolic homeostasis of the host, which potentially bridges external factors to the host (patho-)physiology. In this review, we discuss the rising incidences of NCDs during urbanization and their links to the compositional and functional dysbiosis of the gut microbiome. In particular, we elucidate the effects of urbanization-associated factors (hygiene/pollution, urbanized diet, lifestyles, the use of antibiotics, and early life exposure) on the gut microbiome underlying the pathogenesis of NCDs. We also discuss the potential and feasibility of microbiome-inspired and microbiome-targeted approaches as novel avenues to counteract NCDs, including fecal microbiota transplantation, diet modulation, probiotics, postbiotics, synbiotics, celobiotics, and precision antibiotics.
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Affiliation(s)
- Ziyu Huang
- Key Laboratory of Human Microbiome and Chronic Diseases, Sun Yat-Sen University, Ministry of Education, Guangzhou, China
- Guangdong Institute of Gastroenterology, the Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
- Biomedical Innovation Centre, the Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
- The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yue Li
- Key Laboratory of Human Microbiome and Chronic Diseases, Sun Yat-Sen University, Ministry of Education, Guangzhou, China
- Guangdong Institute of Gastroenterology, the Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
- Biomedical Innovation Centre, the Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
- The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Heekuk Park
- Department of Medicine, Division of Infectious Diseases, Columbia University Irving Medical Centre, New York, NY, USA
| | - Martin Ho
- Department of Engineering, University of Cambridge, Cambridge, UK
| | - Kanchan Bhardwaj
- Department of Biotechnology, Faculty of Engineering and Technology, Manav Rachna International Institute of Research and Studies, Haryana, India
| | - Naoki Sugimura
- Gastrointestinal Centre and Institute of Minimally-Invasive Endoscopic Care (iMEC), Sano Hospital, Kobe, Japan
| | - Hye Won Lee
- Institute of Gastroenterology and Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Huicui Meng
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, China
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Guangzhou, China
- Guangdong Province Engineering Laboratory for Nutrition Translation, Guangzhou, China
| | - Matthias P. Ebert
- Department of Medicine II, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- DKFZ-Hector Cancer Institute, Mannheim, Germany
- Mannheim Cancer Centre (MCC), University Medical Centre Mannheim, Mannheim, Germany
| | - Kang Chao
- The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
- Department of Gastroenterology, the Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Elke Burgermeister
- Department of Medicine II, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Aadra P. Bhatt
- Department of Medicine, Centre for Gastrointestinal Biology and Disease, and the Lineberger Comprehensive Cancer Centre, University of North Carolina, Chapel Hill, NC, USA
| | - Sudarshan A. Shetty
- Department of Medical Microbiology and Infection Prevention, University Medical Centre Groningen, Groningen, The Netherlands
| | - Kai Li
- Key Laboratory of Human Microbiome and Chronic Diseases, Sun Yat-Sen University, Ministry of Education, Guangzhou, China
- Guangdong Institute of Gastroenterology, the Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
- The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Weiping Wen
- Key Laboratory of Human Microbiome and Chronic Diseases, Sun Yat-Sen University, Ministry of Education, Guangzhou, China
- Biomedical Innovation Centre, the Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
- The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Tao Zuo
- Key Laboratory of Human Microbiome and Chronic Diseases, Sun Yat-Sen University, Ministry of Education, Guangzhou, China
- Guangdong Institute of Gastroenterology, the Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
- Biomedical Innovation Centre, the Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
- The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
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31
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Zaongo SD, Ouyang J, Isnard S, Zhou X, Harypursat V, Cui H, Routy JP, Chen Y. Candida albicans can foster gut dysbiosis and systemic inflammation during HIV infection. Gut Microbes 2023; 15:2167171. [PMID: 36722096 PMCID: PMC9897780 DOI: 10.1080/19490976.2023.2167171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Candida albicans (C. albicans) is a ubiquitous fungal commensal component of the human microbiota, and under certain circumstances, such as during an immunocompromised state, it may initiate different types of infection. Moreover, C. albicans continuously and reciprocally interacts with the host immune system as well as with other elements of the gut microbiota, thus contributing significantly to both gut homeostasis and host immunity. People living with HIV (PLWH), including those receiving antiretroviral therapy, are characterized by a depletion of CD4 + T-cells and dysbiosis in their gut. C. albicans colonization is frequent in PLWH, causing both a high prevalence and high morbidity. Gut barrier damage and elevated levels of microbial translocation are also fairly common in this population. Herein, we take a closer look at the reciprocity among C. albicans, gut microbiota, HIV, and the host immune system, thus throwing some light on this complex interplay.
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Affiliation(s)
- Silvere D Zaongo
- Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China,Clinical Research Center, Chongqing Public Health Medical Center, Chongqing, China
| | - Jing Ouyang
- Clinical Research Center, Chongqing Public Health Medical Center, Chongqing, China
| | - Stéphane Isnard
- Infectious Diseases and Immunity in Global Health Program, Research Institute, McGill University Health Centre, Montréal, QC, Canada,Chronic Viral Illness Service, McGill University Health Centre, Montréal, QC, Canada,Canadian HIV Trials Network, Canadian Institutes for Health Research, Vancouver, British Columbia, Canada
| | - Xin Zhou
- Clinical Research Center, Chongqing Public Health Medical Center, Chongqing, China,Cancer Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Vijay Harypursat
- Clinical Research Center, Chongqing Public Health Medical Center, Chongqing, China
| | - Hongjuan Cui
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Jean-Pierre Routy
- Infectious Diseases and Immunity in Global Health Program, Research Institute, McGill University Health Centre, Montréal, QC, Canada,Chronic Viral Illness Service, McGill University Health Centre, Montréal, QC, Canada,Division of Hematology, McGill University Health Centre, Montréal, QC, Canada
| | - Yaokai Chen
- Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China,Clinical Research Center, Chongqing Public Health Medical Center, Chongqing, China,CONTACT Yaokai Chen Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
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32
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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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33
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Zhang F, Aschenbrenner D, Yoo JY, Zuo T. The gut mycobiome in health, disease, and clinical applications in association with the gut bacterial microbiome assembly. THE LANCET. MICROBE 2022; 3:e969-e983. [PMID: 36182668 DOI: 10.1016/s2666-5247(22)00203-8] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 07/04/2022] [Accepted: 07/11/2022] [Indexed: 02/06/2023]
Abstract
The gut mycobiome (fungi) is a small but crucial component of the gut microbiome in humans. Intestinal fungi regulate host homoeostasis, pathophysiological and physiological processes, and the assembly of the co-residing gut bacterial microbiome. Over the past decade, accumulating studies have characterised the gut mycobiome in health and several pathological conditions. We review the compositional and functional diversity of the gut mycobiome in healthy populations from birth to adulthood. We describe factors influencing the gut mycobiome and the roles of intestinal fungi-especially Candida and Saccharomyces spp-in diseases and therapies with a particular focus on their synergism with the gut bacterial microbiome and host immunity. Finally, we discuss the underappreciated effects of gut fungi in clinical implications, and highlight future microbiome-based therapies that harness the tripartite relationship among the gut mycobiome, bacterial microbiome, and host immunity, aiming to restore a core gut mycobiome and microbiome and to improve clinical efficacy.
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Affiliation(s)
- Fen Zhang
- Department of Food Science and Engineering, Institute of Food Safety and Nutrition, College of Science and Engineering, Jinan University, Guangzhou, China
| | - Dominik Aschenbrenner
- Autoimmunity, Transplantation and Inflammation, Novartis Institutes for BioMedical Research, Novartis Pharma, Basel, Switzerland
| | - Ji Youn Yoo
- College of Nursing, University of Tennessee, Knoxville, TN, USA
| | - Tao Zuo
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yatsen University, Sun Yat-sen University, Guangzhou, China; Laboratory Animals Centre, Zhongshan School of Medicine, Sun Yatsen University, Guangzhou, China.
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34
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Tremblay J, Schreiber L, Greer CW. High-resolution shotgun metagenomics: the more data, the better? Brief Bioinform 2022; 23:6780270. [PMID: 36352504 DOI: 10.1093/bib/bbac443] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 09/01/2022] [Accepted: 09/13/2022] [Indexed: 11/11/2022] Open
Abstract
In shotgun metagenomics (SM), the state-of-the-art bioinformatic workflows are referred to as high-resolution shotgun metagenomics (HRSM) and require intensive computing and disk storage resources. While the increase in data output of the latest iteration of high-throughput DNA sequencing systems can allow for unprecedented sequencing depth at a minimal cost, adjustments in HRSM workflows will be needed to properly process these ever-increasing sequence datasets. One potential adaptation is to generate so-called shallow SM datasets that contain fewer sequencing data per sample as compared with the more classic high coverage sequencing. While shallow sequencing is a promising avenue for SM data analysis, detailed benchmarks using real-data are lacking. In this case study, we took four public SM datasets, one massive and the others moderate in size and subsampled each dataset at various levels to mimic shallow sequencing datasets of various sequencing depths. Our results suggest that shallow SM sequencing is a viable avenue to obtain sound results regarding microbial community structures and that high-depth sequencing does not bring additional elements for ecological interpretation. More specifically, results obtained by subsampling as little as 0.5 M sequencing clusters per sample were similar to the results obtained with the largest subsampled dataset for human gut and agricultural soil datasets. For an Antarctic dataset, which contained only a few samples, 4 M sequencing clusters per sample was found to generate comparable results to the full dataset. One area where ultra-deep sequencing and maximizing the usage of all data was undeniably beneficial was in the generation of metagenome-assembled genomes.
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Affiliation(s)
- Julien Tremblay
- Energy Mining and Environment Research Centre, National Research Council Canada, Montreal, QC, Canada H4P-2R2
| | - Lars Schreiber
- Energy Mining and Environment Research Centre, National Research Council Canada, Montreal, QC, Canada H4P-2R2
| | - Charles W Greer
- Energy Mining and Environment Research Centre, National Research Council Canada, Montreal, QC, Canada H4P-2R2
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Syromyatnikov M, Nesterova E, Gladkikh M, Smirnova Y, Gryaznova M, Popov V. Characteristics of the Gut Bacterial Composition in People of Different Nationalities and Religions. Microorganisms 2022; 10:microorganisms10091866. [PMID: 36144468 PMCID: PMC9501501 DOI: 10.3390/microorganisms10091866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 11/25/2022] Open
Abstract
High-throughput sequencing has made it possible to extensively study the human gut microbiota. The links between the human gut microbiome and ethnicity, religion, and race remain rather poorly understood. In this review, data on the relationship between gut microbiota composition and the nationality of people and their religion were generalized. The unique gut microbiome of a healthy European (including Slavic nationality) is characterized by the dominance of the phyla Firmicutes, Bacteroidota, Actinobacteria, Proteobacteria, Fusobacteria, and Verrucomicrobia. Among the African population, the typical members of the microbiota are Bacteroides and Prevotella. The gut microbiome of Asians is very diverse and rich in members of the genera Prevotella, Bacteroides Lactobacillus, Faecalibacterium, Ruminococcus, Subdoligranulum, Coprococcus, Collinsella, Megasphaera, Bifidobacterium, and Phascolarctobacterium. Among Buddhists and Muslims, the Prevotella enterotype is characteristic of the gut microbiome, while other representatives of religions, including Christians, have the Bacteroides enterotype. Most likely, the gut microbiota of people of different nationalities and religions are influenced by food preferences. The review also considers the influences of pathologies such as obesity, Crohn’s disease, cancer, diabetes, etc., on the bacterial composition of the guts of people of different nationalities.
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Affiliation(s)
- Mikhail Syromyatnikov
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
- Correspondence:
| | - Ekaterina Nesterova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
| | - Maria Gladkikh
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
| | - Yuliya Smirnova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
| | - Mariya Gryaznova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
| | - Vasily Popov
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
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Zhao L, Wang H, Gao Y, Hao B, Li X, Wen R, Chen K, Fan L, Liu L. Characteristics of oral microbiota in plateau and plain youth‐positive correlations between blood lipid level, metabolism and specific microflora in the plateau group. Front Cell Infect Microbiol 2022; 12:952579. [PMID: 36034699 PMCID: PMC9400057 DOI: 10.3389/fcimb.2022.952579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/18/2022] [Indexed: 11/15/2022] Open
Abstract
Objectives To analyze the characteristics of oral microbiota in plateau and plain youth and the possible function of the microbiome. Materials and methods A total of 120 healthy young males (80 on the plateau, 40 on the plain) completed this cross-sectional study. Oral microflora samples were collected from all participants. The bacterial 16S rDNA was amplified using PCR and sequenced using Illumina MiSeq high-throughput sequencing. The data were analyzed to determine the microbial distribution and community structure of the oral microflora from the two groups. Metastats was used to test differences in relative species abundance between the groups. The correlation between the abundance of specific bacteria and blood indicators was also analyzed. Results As demonstrated by alpha and beta diversity, the plateau group had lower microbial richness and a less even distribution of oral microbiota than the plain group. All predominant phyla and genera were qualitatively similar between the two groups, but their relative abundances differed. The relative abundance of bacteria in the phylum Firmicutes was significantly higher in the plateau group than in the plain group. At the genus level, Streptococcus spp. and Gemella spp. were also more abundant in the plateau group. The functional prediction indicated vigorous microbial metabolism in the oral bacterial community. We also found that the relative abundance of Streptococcus spp., the dominant genus, was positively correlated with triglyceride levels in the plateau group. Conclusions With increasing altitude, the diversity of oral microbiota and the relative proportion of predominant bacteria were altered. The distribution and related function of Streptococcus spp. were prominent in plateau samples. This comprehensive study of the relationship between oral microecology and elevation provides a point of reference for studying the human body’s adaptability or inadaptability to high altitude.
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Affiliation(s)
- LiBo Zhao
- Cardiology Department of the Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Huanhuan Wang
- College of Nursing, Peking University, Beijing, China
| | - Yinghui Gao
- Sleep Center, Peking University International Hospital, Beijing, China
| | - Benchuan Hao
- Cardiology Department of the Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Xueyan Li
- College of Basic Medicine, Gansu University of Traditional Chinese Medicine, Lanzhou, China
| | - Ruoqing Wen
- College of Integrated Traditional Chinese and Western Medicine, Gansu University of Traditional Chinese Medicine, Lanzhou, China
| | - Kaibing Chen
- Sleep Center, The Affiliated Hospital of Gansu University of Traditional Chinese Medicine, Lanzhou, China
- *Correspondence: Lin Liu, ; Li Fan, ; Kaibing Chen,
| | - Li Fan
- Cardiology Department of the Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese People's Liberation Army General Hospital, Beijing, China
- *Correspondence: Lin Liu, ; Li Fan, ; Kaibing Chen,
| | - Lin Liu
- Department of Pulmonary and Critical Care Medicine of the Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese People's Liberation Army General Hospital, Beijing, China
- *Correspondence: Lin Liu, ; Li Fan, ; Kaibing Chen,
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Xie Z, Manichanh C. FunOMIC: Pipeline with built-in fungal taxonomic and functional databases for human mycobiome profiling. Comput Struct Biotechnol J 2022; 20:3685-3694. [PMID: 35891785 PMCID: PMC9293737 DOI: 10.1016/j.csbj.2022.07.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 11/30/2022] Open
Abstract
While analysis of the bacterial microbiome has become routine, that of the fungal microbiome is still hampered by the lack of robust databases and bioinformatic pipelines. Here, we present FunOMIC, a pipeline with built-in taxonomic (1.6 million marker genes) and functional (3.4 million non-redundant fungal proteins) databases for the identification of fungi. Applied to more than 2,600 human metagenomic samples, the tool revealed fungal species associated with geography, body sites, and diseases. Correlation network analysis provided new insights into inter-kingdom interactions. With this pipeline and two of the most comprehensive fungal databases, we foresee a fast-growing resource for mycobiome studies.
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Key Words
- CD, Crohn’s disease
- ESRD, End-stage renal disease
- FDR, False discovery rate
- Fungal databases
- GS, Gallstones
- HC, Healthy control
- HTS, High throughput sequencing
- ITS, internal transcribed spacer
- Inter-kingdom interactions
- Mycobiome
- NA, Not applicable
- PLWH, People live with HIV
- PSO, Psoriasis
- SCFA, Short chain fatty acid
- SCZ, Schizophrenia
- Shotgun metagenomics
- T1D, Type 1 diabetes
- T2D, Type 2 diabetes
- TB, Tuberculosis
- Taxonomy and functions
- UC, Ulcerative colitis
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Affiliation(s)
- Zixuan Xie
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain.,Departament de Medicina, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
| | - Chaysavanh Manichanh
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain.,Departament de Medicina, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
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Wang S, Huang G, Wang JX, Tian L, Zuo XL, Li YQ, Yu YB. Altered Gut Microbiota in Patients With Peutz–Jeghers Syndrome. Front Microbiol 2022; 13:881508. [PMID: 35910641 PMCID: PMC9326469 DOI: 10.3389/fmicb.2022.881508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 06/06/2022] [Indexed: 11/14/2022] Open
Abstract
Background Peutz–Jeghers syndrome (PJS) is a rare genetic disorder characterized by the development of pigmented spots and gastrointestinal polyps and increased susceptibility to cancers. It remains unknown whether gut microbiota dysbiosis is linked to PJS. Aim This study aimed to assess the structure and composition of the gut microbiota, including both bacteria and fungi, in patients with PJS and investigate the relationship between gut microbiota dysbiosis and PJS pathogenesis. Methods The bacterial and fungal composition of the fecal microbiota was analyzed in 23 patients with PJS (cases), 17 first-degree asymptomatic relatives (ARs), and 24 healthy controls (HCs) using 16S (MiSeq) and ITS2 (pyrosequencing) sequencing for bacteria and fungi, respectively. Differential analyses of the intestinal flora were performed from the phylum to species level. Results Alpha-diversity distributions of bacteria and fungi indicated that the abundance of both taxa differed between PJS cases and controls. However, while the diversity and composition of fecal bacteria in PJS cases were significantly different from those in ARs and HCs, fungal flora was more stable. High-throughput sequencing confirmed the special characteristics and biodiversity of the fecal bacterial and fungal microflora in patients with PJS. They had lower bacterial biodiversity than controls, with a higher frequency of the Proteobacteria phylum, Enterobacteriaceae family, and Escherichia-Shigella genus, and a lower frequency of the Firmicutes phylum and the Lachnospiraceae and Ruminococcaceae families. Of fungi, Candida was significantly higher in PJS cases than in controls. Conclusion The findings reported here confirm gut microbiota dysbiosis in patients with PJS. This is the first report on the bacterial and fungal microbiota profile of subjects with PJS, which may be meaningful to provide a structural basis for further research on intestinal microecology in PJS.
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Affiliation(s)
- Sui Wang
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
| | - Gang Huang
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
| | - Jue-Xin Wang
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
| | - Lin Tian
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
| | - Xiu-Li Zuo
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
| | - Yan-Qing Li
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
| | - Yan-Bo Yu
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, China
- *Correspondence: Yan-Bo Yu
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Li M, Shao D, Zhou J, Gu J, Qin J, Li X, Hao C, Wei W. Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China. Microbiol Spectr 2022; 10:e0064521. [PMID: 35467373 PMCID: PMC9241895 DOI: 10.1128/spectrum.00645-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 03/29/2022] [Indexed: 11/21/2022] Open
Abstract
The objective of this study was to describe and compare the dynamic microbiota characteristics in the gastrointestinal (GI) tract in Chinese participants via high-throughput sequencing techniques. The study collected saliva, esophageal swab, cardia biopsy, noncardia biopsy, gastric juice, and fecal specimens from 40 participants who underwent upper GI tract cancer screening in Linzhou (Henan, China) in August 2019. The V4 region of 16S rRNA genes was amplified and sequenced using the Illumina MiniSeq platform. The observed amplicon sequence variants (ASVs) gradually decreased from saliva to esophageal swab, cardia biopsy, noncardia biopsy, and gastric juice specimens and then increased from gastric juice to fecal specimens (P < 0.05). Each GI site had its own microbial characteristics that overlapped those of adjacent sites. Characteristic genera for each site were as follows: Neisseria and Prevotella in saliva, Streptococcus and Haemophilus in the esophagus, Helicobacter in the noncardia, Pseudomonas in gastric juice, Faecalibacterium, Roseburia, and Blautia in feces, and Weissella in the cardia. Helicobacter pylori-positive participants had decreased observed ASVs (cardia, P < 0.01; noncardia, P < 0.001) and Shannon index values (cardia, P < 0.001; noncardia, P < 0.001) compared with H. pylori-negative participants both in cardia and noncardia specimens. H. pylori infection played a more important role in the microbial composition of noncardia than of cardia specimens. In gastric juice, the gastric pH and H. pylori infection had similar additive effects on the microbial diversity and composition. These results show that each GI site has its own microbial characteristics that overlap those of adjacent sites and that differences and commonalities between and within microbial compositions coexist, providing essential foundations for the continuing exploration of disease-associated microbiota. IMPORTANCE Upper gastrointestinal (UGI) tract cancer is one of the most common cancers worldwide, while limited attention has been paid to the UGI microbiota. Microbial biomarkers, such as Fusobacteria nucleatum and Helicobacter pylori, bring new ideas for early detection of UGI tract cancer, which may be a highly feasible method to reduce its disease burden. This study revealed that each gastrointestinal site had its own microbial characteristics that overlapped those of adjacent sites. There were significant differences between the microbial compositions of the UGI sites and feces. Helicobacter pylori played a more significant role in the microbial composition of the noncardia stomach than in that of the cardia. Gastric pH and Helicobacter pylori had similar additive effects on the microbial diversity of gastric juice. These findings played a key role in delineating the microbiology spectrum of the gastrointestinal tract and provided baseline information for future microbial exploration covering etiology, primary screening, treatment, outcome, and health care products.
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Affiliation(s)
- Minjuan Li
- National Central Cancer Registry, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Dantong Shao
- National Central Cancer Registry, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiachen Zhou
- Department of Epidemiology and Biostatistics, School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an, China
| | - Jianhua Gu
- National Central Cancer Registry, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | - Xinqing Li
- National Central Cancer Registry, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Changqing Hao
- Department of Endoscopy, Cancer Institute/Hospital of Linzhou, Linzhou, China
| | - Wenqiang Wei
- National Central Cancer Registry, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Prevotella species in the human gut is primarily comprised of Prevotella copri, Prevotella stercorea and related lineages. Sci Rep 2022; 12:9055. [PMID: 35641510 PMCID: PMC9156738 DOI: 10.1038/s41598-022-12721-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 04/15/2022] [Indexed: 11/25/2022] Open
Abstract
Prevotella species in the human gut microbiome are primarily comprised of Prevotella copri, and its diversity and function were recently investigated in detail. Much less is known about other Prevotella species in the human gut. Here, we examined the composition of Prevotella species in human guts by mapping publicly available gut metagenomes to a dereplicated set of metagenome-assembled genomes (MAGs) representing Prevotella lineages found in human guts. In most human cohorts, P. copri is the most relatively abundant species (e.g. up to 14.3% relative abundance in Tangshan, China). However, more than half of the metagenome reads in several cohorts mapped to Prevotella MAGs representing P. stercorea and several other species sister to P. stercorea and P. copri. Analyses of genes encoded in these genomes indicated that P. stercorea and related lineages lacked many hemicellulose degrading enzymes and were thus less likely to metabolise hemicelluloses compared with P. copri and copri-related lineages. Instead, P. stercorea genomes possess several carbohydrate esterases that may be involved in releasing ester modifications from carbohydrates to facilitate their degradation. These findings reveal unexplored Prevotella diversity in the human gut and indicate possible niche partitions among these related species.
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de Dios Caballero J, Cantón R, Ponce-Alonso M, García-Clemente MM, Gómez G. de la Pedrosa E, López-Campos JL, Máiz L, del Campo R, Martínez-García MÁ. The Human Mycobiome in Chronic Respiratory Diseases: Current Situation and Future Perspectives. Microorganisms 2022; 10:microorganisms10040810. [PMID: 35456861 PMCID: PMC9029612 DOI: 10.3390/microorganisms10040810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/04/2022] [Accepted: 04/09/2022] [Indexed: 12/15/2022] Open
Abstract
Microbes play an important role in the pathogenesis of chronic lung diseases, such as chronic obstructive pulmonary disease, cystic fibrosis, non-cystic fibrosis bronchiectasis, and asthma. While the role of bacterial pathogens has been extensively studied, the contribution of fungal species to the pathogenesis of chronic lung diseases is much less understood. The recent introduction of next-generation sequencing techniques has revealed the existence of complex microbial lung communities in healthy individuals and patients with chronic respiratory disorders, with fungi being an important part of these communities’ structure (mycobiome). There is growing evidence that the components of the lung mycobiome influence the clinical course of chronic respiratory diseases, not only by direct pathogenesis but also by interacting with bacterial species and with the host’s physiology. In this article, we review the current knowledge on the role of fungi in chronic respiratory diseases, which was obtained by conventional culture and next-generation sequencing, highlighting the limitations of both techniques and exploring future research areas.
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Affiliation(s)
- Juan de Dios Caballero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Rafael Cantón
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-91-336-88-32 or +34-336-83-30
| | - Manuel Ponce-Alonso
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Marta María García-Clemente
- Department of Pneumology, Central Asturias University Hospital, 33011 Oviedo, Spain;
- Principality Asturias Health Research Institute (ISPA), 33011 Oviedo, Spain
| | - Elia Gómez G. de la Pedrosa
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - José Luis López-Campos
- Medical-Surgical Unit for Respiratory Diseases (CIBERES), Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, University of Seville, 41013 Sevilla, Spain;
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain; (L.M.); (M.Á.M.-G.)
| | - Luis Máiz
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain; (L.M.); (M.Á.M.-G.)
- Department of Pneumology, Ramón y Cajal University Hospital, 28034 Madrid, Spain
| | - Rosa del Campo
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Miguel Ángel Martínez-García
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain; (L.M.); (M.Á.M.-G.)
- Department of Pneumology, La Fe University and Polytechnic Hospital, 46026 Valencia, Spain
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Zhufeng Y, Xu J, Miao M, Wang Y, Li Y, Huang B, Guo Y, Tian J, Sun X, Li J, Lu D, Li Z, Li Y, He J. Modification of Intestinal Microbiota Dysbiosis by Low-Dose Interleukin-2 in Dermatomyositis: A Post Hoc Analysis From a Clinical Trial Study. Front Cell Infect Microbiol 2022; 12:757099. [PMID: 35360108 PMCID: PMC8964112 DOI: 10.3389/fcimb.2022.757099] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
The microbiota has been observed altered in autoimmune diseases, including idiopathic inflammatory myopathies (IIMs), and associated with different treatments. Low-dose IL-2 treatment emerges as a new option for active IIMs. This study aims to explore the role of low-dose IL-2 in regulating intestinal dysbiosis involved in the IIMs. In this study, 13 patients with active IIMs were enrolled and received 1 ×106 IU of IL-2 subcutaneously every other day for 12 weeks plus standard care. The clinical response and immune response were assessed. Stool samples were obtained to explore the structural and functional alterations of the fecal microbiota targeting the V3–V4 region of the 16S rRNA gene and analyze their associations with clinical and immunological characteristics. Our study demonstrated that diversity of microbiota decreased remarkably in patients with IIMs, compared to healthy controls. The inflammatory-related bacteria, such as Prevotellaceae increased, while some butyrate-producing bacteria, such as Pseudobutyrivibrio, Lachnospiraceae, Roseburia, and Blautia, decreased significantly. The alteration associated with disease activities in patients with IIMs. After low-dose IL-2 treatment, 92.31% (12/13) of patients achieved IMACS DOI at week 12. Proportion of Treg cells significantly increased at week 12 compared with that in baseline (15.9% [7.73, 19.4%] vs. 9.89% [6.02, 11.8%], P = 0.015). Interestingly, certain butyrate-producing bacteria increase significantly after IL-2 treatment, like Lachnospiraceae, Pseudobutyrivibrio, etc., and are associated with a rise in L-Asparagine and L-Leucine. The effects of low-dose IL-2 on gut microbiota were more apparent in NOD mice. Together, the data presented demonstrated that low-dose IL-2 was effective in active IIMs and highlighted the potential for modifying the intestinal microbiomes of dysbiosis to treat IIMs.
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Affiliation(s)
- Yunzhi Zhufeng
- Department of Rheumatology and Immunology, Peking University People’s Hospital, Beijing, China
| | - Jun Xu
- Department of Gastroenterology, Peking University People’s Hospital, Beijing, China
- Clinical Center of Immune-Mediated Digestive Diseases, Peking University People’s Hospital, Beijing, China
| | - Miao Miao
- Department of Rheumatology and Immunology, Peking University People’s Hospital, Beijing, China
| | - Yifan Wang
- Department of Rheumatology and Immunology, Peking University People’s Hospital, Beijing, China
| | - Yimin Li
- Department of Rheumatology and Immunology, Peking University People’s Hospital, Beijing, China
| | - Bo Huang
- Department of Rheumatology and Immunology, Peking University People’s Hospital, Beijing, China
| | - Yixue Guo
- Department of Rheumatology and Immunology, Peking University People’s Hospital, Beijing, China
| | - Jiayi Tian
- Department of Rheumatology and Immunology, Peking University People’s Hospital, Beijing, China
| | - Xiaolin Sun
- Department of Rheumatology and Immunology, Peking University People’s Hospital, Beijing, China
| | - Jing Li
- Department of Rheumatology and Immunology, Peking University People’s Hospital, Beijing, China
| | - Dan Lu
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Zhanguo Li
- Department of Rheumatology and Immunology, Peking University People’s Hospital, Beijing, China
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yuhui Li
- Department of Rheumatology and Immunology, Peking University People’s Hospital, Beijing, China
- *Correspondence: Yuhui Li, ; Jing He,
| | - Jing He
- Department of Rheumatology and Immunology, Peking University People’s Hospital, Beijing, China
- *Correspondence: Yuhui Li, ; Jing He,
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Underhill DM, Braun J. Fungal microbiome in inflammatory bowel disease: a critical assessment. J Clin Invest 2022; 132:155786. [PMID: 35229726 PMCID: PMC8884899 DOI: 10.1172/jci155786] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The gut microbiome is at the center of inflammatory bowel disease (IBD) pathogenesis and disease activity. While this has mainly been studied in the context of the bacterial microbiome, recent advances have provided tools for the study of host genetics and metagenomics of host-fungal interaction. Through these tools, strong evidence has emerged linking certain fungal taxa, such as Candida and Malassezia, with cellular and molecular pathways of IBD disease biology. Mouse models and human fecal microbial transplant also suggest that some disease-participatory bacteria and fungi may act not via the host directly, but via their fungal-bacterial ecologic interactions. We hope that these insights, and the study design and multi-omics strategies used to develop them, will facilitate the inclusion of the fungal community in basic and translational IBD research.
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Affiliation(s)
- David M Underhill
- F. Widjaja Inflammatory Bowel and Immunobiology Research Institute.,Division of Gastroenterology, Department of Medicine, and.,Research Division of Immunology, Department of Biomedical Sciences; Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Jonathan Braun
- F. Widjaja Inflammatory Bowel and Immunobiology Research Institute.,Division of Gastroenterology, Department of Medicine, and.,Research Division of Immunology, Department of Biomedical Sciences; Cedars-Sinai Medical Center, Los Angeles, California, USA
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44
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Reynoso-García J, Narganes-Storde Y, Santiago-Rodriguez TM, Toranzos GA. Mycobiome-Host Coevolution? The Mycobiome of Ancestral Human Populations Seems to Be Different and Less Diverse Than Those of Extant Native and Urban-Industrialized Populations. Microorganisms 2022; 10:microorganisms10020459. [PMID: 35208912 PMCID: PMC8877467 DOI: 10.3390/microorganisms10020459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/24/2021] [Accepted: 12/07/2021] [Indexed: 02/06/2023] Open
Abstract
Few data exist on the human gut mycobiome in relation to lifestyle, ethnicity, and dietary habits. To understand the effect of these factors on the structure of the human gut mycobiome, we analyzed sequences belonging to two extinct pre-Columbian cultures inhabiting Puerto Rico (the Huecoid and Saladoid) and compared them to coprolite samples found in Mexico and Ötzi, the Iceman’s large intestine. Stool mycobiome samples from extant populations in Peru and urban cultures from the United States were also included. The ancient Puerto Rican cultures exhibited a lower fungal diversity in comparison to the extant populations. Dissimilarity distances showed that the Huecoid gut mycobiome resembled that from ancient Mexico. Fungal genera including Aspergillus spp., Penicillium spp., Rasamsonia spp., Byssochlamys spp., Talaromyces spp., Blastomyces spp., Monascus spp., and Penicilliopsis spp. were differentially abundant in the ancient and extant populations. Despite cultural differences, certain fungal taxa were present in all samples. These results suggest that culture and diet may impact the gut mycobiome and emphasize that modern lifestyles could be associated with the alteration of gut mycobiome diversity. The present study presents data on ancient and extant human gut mycobiomes in terms of lifestyle, ethnicity, and diet in the Americas.
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Affiliation(s)
- Jelissa Reynoso-García
- Environmental Microbiology Laboratory, Biology Department, University of Puerto Rico, San Juan 00931, Puerto Rico;
- Correspondence:
| | - Yvonne Narganes-Storde
- Center for Archaeological Research, Río Piedras Campus, University of Puerto Rico, San Juan 00931, Puerto Rico;
| | | | - Gary A. Toranzos
- Environmental Microbiology Laboratory, Biology Department, University of Puerto Rico, San Juan 00931, Puerto Rico;
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45
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Yu D, Xie L, Chen W, Qin J, Zhang J, Lei M, Wang Y, Tang H, Xue S, Liang X, Miao Z, Xiao C, Shang M, Lu J, Di H, Fu Y. Dynamics of the Gut Bacteria and Fungi Accompanying Low-Carbohydrate Diet-Induced Weight Loss in Overweight and Obese Adults. Front Nutr 2022; 9:846378. [PMID: 35223965 PMCID: PMC8873986 DOI: 10.3389/fnut.2022.846378] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 01/14/2022] [Indexed: 12/31/2022] Open
Abstract
Background Low-carbohydrate (e.g., Atkins) dietary pattern is one of the most effective diets for weight loss, but little is known about the characteristics of the gut microbiota accompanying low-carbohydrate diets-induced weight loss. This study aims to profile dynamics of gut bacteria and fungi accompanying modified Atkins diets-induced weight loss among overweight and obese adults. Methods Overweight and obese adults were screened to follow a modified Atkins diet plan (30% of energy from protein, 40% from carbohydrate and 30% from fat). We longitudinally profiled dynamics of gut bacteria and fungi based on 16S rRNA and ITS rRNA gene sequencing data, respectively. Results A total of 65 participants followed the modified Atkins diets for 20–231 days, with 61 and 27 participants achieving a weight loss of at least 5 and 10%, respectively. Most of the participants who achieved 10% weight loss also experienced improvements on metabolic health. The diversity of gut bacteria and fungi increased after a weight loss of 5% and kept stable thereafter. Bacteria genera including Lachnoclostridium and Ruminococcus 2 from Firmicutes phylum were depleted, while Parabacteroides and Bacteroides from Bacteroidetes phylum were enriched after weight loss. The inter-kingdom analysis found an intensive covariation between gut fungi and bacteria, involving more than half of the weight loss-associated bacteria. Conclusions This study confirmed the modulation of bacterial and fungal composition during weight loss with the low-carbohydrate diets and showed previously unknown links between intestinal bacteria and fungi accompanying the weight loss.
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Affiliation(s)
- Dan Yu
- Department of Nutrition, The Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Libin Xie
- School of Chemical Engineering, Shijiazhuang University, Shijiazhuang, China
| | - Wei Chen
- Department of Orthopedic Surgery, Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Jin Qin
- The Biobank, Third Hospital of Hebei Medical University, Shijiazhuang, China
- Hebei Orthopedic Clinical Research Center, Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Jingjing Zhang
- Clinical Biochemistry Lab, Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Min Lei
- Department of Nutrition, The Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yue Wang
- Department of Nutrition, The Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Hongge Tang
- Department of Nutrition, The Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Sujuan Xue
- Department of Nutrition, The Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Xinxiu Liang
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Zelei Miao
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Congmei Xiao
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Meishuang Shang
- The Biobank, Third Hospital of Hebei Medical University, Shijiazhuang, China
- Hebei Orthopedic Clinical Research Center, Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Jie Lu
- Clinical Biochemistry Lab, Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Hailing Di
- Department of Nutrition, The Third Hospital of Hebei Medical University, Shijiazhuang, China
- *Correspondence: Hailing Di
| | - Yuanqing Fu
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
- Yuanqing Fu
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46
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Abstract
The fungus Candida albicans is a ubiquitous member of the human gut microbiota. Hundreds or thousands of bacterial taxa reside together with this fungus in the intestine, creating a milieu with myriad opportunities for inter-kingdom interactions. Indeed, recent studies examining the broader composition - that is, monitoring not only bacteria but also the often neglected fungal component - of the gut microbiota hint that there are significant interdependencies between fungi and bacteria. Gut bacteria closely associate with C. albicans cells in the colon, break down and feed on complex sugars decorating the fungal cell wall, and shape the intestinal microhabitats occupied by the fungus. Peptidoglycan subunits released by bacteria upon antibiotic treatment can promote C. albicans dissemination from the intestine, seeding bloodstream infections that often become life-threatening. Elucidating the principles that govern the fungus-bacteria interplay may open the door to novel approaches to prevent C. albicans infections originating in the gut.
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Affiliation(s)
- J. Christian Pérez
- Department of Microbiology and Molecular Genetics, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, USA,CONTACT J.Christian Pérez Department of Microbiology and Molecular Genetics, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, USA
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47
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Phuna ZX, Madhavan P. A CLOSER LOOK AT THE MYCOBIOME IN ALZHEIMER'S DISEASE: FUNGAL SPECIES, PATHOGENESIS AND TRANSMISSION. Eur J Neurosci 2022; 55:1291-1321. [DOI: 10.1111/ejn.15599] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Zhi Xin Phuna
- School of Medicine, Faculty of Health & Medical Sciences, Taylor’s University Malaysia Subang Jaya Selangor
| | - Priya Madhavan
- School of Medicine, Faculty of Health & Medical Sciences, Taylor’s University Malaysia Subang Jaya Selangor
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48
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Tian Y, Wu Q, Li H, Wu Q, Xie Y, Li L, Chen H. Distinct Symptoms and Underlying Comorbidities with Latitude and Longitude in COVID-19: A Systematic Review and Meta-Analysis. Can Respir J 2022; 2022:6163735. [PMID: 35096211 PMCID: PMC8793347 DOI: 10.1155/2022/6163735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 12/31/2021] [Indexed: 02/05/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is straining global health resources, and the prevalence of severe disease appears to vary across countries. In accordance with PRISMA guidelines, we performed a systematic review and meta-analysis of clinical features and underlying medical conditions of COVID-19. Eighty-seven studies, involving 1,434,931 COVID-19 patients from the Americas, Asia, Europe, and Oceania, were included. Geographically, the rate of severity was highest in Asia (95% confidence interval (CI) 0.23‒0.30). The rates of comorbidities of COVID-19 patients in the Americas were significantly higher than those in Asia. Most Asian patients had fever (95%CI 0.70‒0.81), and most Oceanian patients had cough (95%CI 0.68‒0.70) as their prevalent symptom. Dyspnea was common in the Americas (95%CI 0.33‒0.64), Europe (95%CI 0.29‒0.64), and high latitude regions (95%CI 0.53‒0.82). European patients exhibited significantly high rates of loss of smell and taste (95%CI 0.60-0.97). In low-latitude regions, cancer (95%CI 14.50‒4.89) had the strongest correlation with illness severity. Comorbid diseases and clinical manifestations of severe COVID-19 patients vary substantially between latitudes and longitudes. Region-specific care should be considered to treat and improve the prognosis of COVID-19 patients.
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Affiliation(s)
- Yong Tian
- 1Department of Rehabilitation Medicine, Haihe Hospital, Tianjin University, Tianjin, China
| | - Qian Wu
- 2Department of Respiratory Medicine, Haihe Hospital, Tianjin University, Tianjin, China
| | - Hongwei Li
- 2Department of Respiratory Medicine, Haihe Hospital, Tianjin University, Tianjin, China
| | - Qi Wu
- 2Department of Respiratory Medicine, Haihe Hospital, Tianjin University, Tianjin, China
| | - Yi Xie
- 3Department of Prevention, Haihe Clinical School, Tianjin Medical University, Tianjin, China
| | - Li Li
- 2Department of Respiratory Medicine, Haihe Hospital, Tianjin University, Tianjin, China
- 4Key Research Laboratory for Infectious Disease Prevention for State Administration of Traditional Chinese Medicine, Tianjin Institute of Respiratory Diseases, Tianjin, China
| | - Huaiyong Chen
- 4Key Research Laboratory for Infectious Disease Prevention for State Administration of Traditional Chinese Medicine, Tianjin Institute of Respiratory Diseases, Tianjin, China
- 5Department of Basic Medicine, Haihe Hospital, Tianjin University, Tianjin, China
- 6Department of Basic Medicine, Haihe Clinical School, Tianjin Medical University, Tianjin, China
- 7Tianjin Key Laboratory of Lung Regenerative Medicine, Tianjin, China
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49
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Xiao W, Gao D, Chen HD, Qiao Y, Ma ZS, Duan L. Diversity Scaling Analysis of Chinese Gut Microbiomes Across Ethnicities and Lifestyles. Front Microbiol 2021; 12:736393. [PMID: 34956110 PMCID: PMC8692740 DOI: 10.3389/fmicb.2021.736393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/21/2021] [Indexed: 12/28/2022] Open
Abstract
Diversity scaling (changes) of human gut microbiome is important because it measures the inter-individual heterogeneity of diversity and other important parameters of population-level diversity. Understanding the heterogeneity of microbial diversity can be used as a reference for the personalized medicine of microbiome-associated diseases. Similar to diversity per se, diversity scaling may also be influenced by host factors, especially lifestyles and ethnicities. Nevertheless, this important topic regarding Chinese populations has not been addressed, to our best knowledge. Here, we fill the gap by applying a recent extension to the classic species–area relationship (SAR), i.e., diversity–area relationship (DAR), to reanalyze a large dataset of Chinese gut microbiomes covering the seven biggest Chinese ethnic groups (covering > 95% Chinese) living rural and urban lifestyles. Four DAR profiles were constructed to investigate the diversity scaling, diversity overlap, potential maximal diversity, and the ratio of local to global diversity of Chinese gut microbiomes. We discovered the following: (i) The diversity scaling parameters (z) at various taxon levels are little affected by either ethnicity or lifestyles, as exhibited by less than 0.5% differences in pairwise comparisons. (ii) The maximal accrual diversity (potential diversity) exhibited difference in only about 5% of pairwise comparisons, and all of the differences occurred in ethnicity comparisons (i.e., lifestyles had no effects). (iii) Ethnicity seems to have stronger effects than lifestyles across all taxon levels, and this may reflect the reality that China has been experiencing rapid urbanization in the last few decades, while the ethnic-related genetic background may change relatively little during the same period.
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Affiliation(s)
- Wanmeng Xiao
- Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, China
| | - Depei Gao
- Radiology Department, The 3rd-Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Hongju Daisy Chen
- Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, China
| | - Yuting Qiao
- Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, China
| | - Zhanshan Sam Ma
- Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Lincan Duan
- The 2nd Thoracic Surgery Department, The 3rd-Affiliated Hospital of Kunming Medical University, Kunming, China
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50
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Shankar J. Food Habit Associated Mycobiota Composition and Their Impact on Human Health. Front Nutr 2021; 8:773577. [PMID: 34881282 PMCID: PMC8645600 DOI: 10.3389/fnut.2021.773577] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/19/2021] [Indexed: 12/17/2022] Open
Abstract
Mycobiota is not only associated with healthy homeostasis in the human gut but also helps to adapt to the environment. Food habits, alcohol consumption, intake of probiotics, and contaminated food with a mycotoxin, often lead to the alteration in the mycobiota composition. Impaired immunity of the host may affect fungal symbiosis leading to mycosis. The human gut adapts to the commensalism fungi belonging to the phylum Ascomycota and Basidiomycota. Diet habits such as plant-or animal-based, phytoestrogens enriched plant products, fat-rich diets also influence the colonization of certain fungal species in the mammalian gut. Food habits or mycotoxin-contaminated food or fungal peptides have an impact on bacterial-fungal interaction and human health. The mycobiota population such as Fusarium, Humicola, Aspergillus, and Candida are altered due to alcohol intake in alcoholic liver disease. The role of associated gut mycobiota due to irregular bowel habits or lifestyle change has been observed in inflammatory bowel disease. In this review, it has been observed that Saccharomyces, Aspergillus, Fusarium, Cladosporium, Candida, and Malassezia were the common genus in the human mycobiota. Therefore, this study focused on how diet habits and alcohol intake, among others., influence mycobiota composition that may affect the human immune system or overall health.
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Affiliation(s)
- Jata Shankar
- Genomics Laboratory, Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, India
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