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Ren Y, Ciwang R, Mehmood K, Li K. Effects of forages on the microbiota of crossed sheep on cold Plateau. Anim Biotechnol 2024; 35:2362639. [PMID: 38856695 DOI: 10.1080/10495398.2024.2362639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Diet is an important component to influence microbiota, there are less data available about the microbiome of Suffolk cross with Tibetan (SCT) animals with different fodders. The current study was conducted for comparing the fungi microbiota in SCT sheep fed with different forages. Sequencing of ileum samples from sheep groups of AH (alfalfa and oat grass), BH (mixture of grass and concentrated feeds), CH (concentrated feed I), DH (concentrated feed II) and EH (concentrated feed III) achieved 3,171,271 raw and 2,719,649 filtered sequences. Concentrated feeds changed fungi microbiota in SCT sheep with three phyla and 47 genera significantly different among the groups. Genera include positive genus of Scytalidium and negative fungi of Sarocladium, Kazachstania, Gibberella, Scytalidium, Candida, Wickerhamomyces. The findings of our study will contribute to efficient feeding of SCT sheep at cold plateau areas.
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Affiliation(s)
- Yue Ren
- Institute of Livestock Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, PR China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lhasa, PR China
| | - Renzeng Ciwang
- Institute of Livestock Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, PR China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lhasa, PR China
| | - Khalid Mehmood
- Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Kun Li
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, PR China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, PR China
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Jensen O, Trujillo E, Hanson L, Ost KS. Controlling Candida: immune regulation of commensal fungi in the gut. Infect Immun 2024; 92:e0051623. [PMID: 38647290 PMCID: PMC11385159 DOI: 10.1128/iai.00516-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024] Open
Abstract
The intestinal microbiome harbors fungi that pose a significant risk to human health as opportunistic pathogens and drivers of inflammation. Inflammatory and autoimmune diseases are associated with dysbiotic fungal communities and the expansion of potentially pathogenic fungi. The gut is also the main reservoir for disseminated fungal infections. Immune interactions are critical for preventing commensal fungi from becoming pathogenic. Significant strides have been made in defining innate and adaptive immune pathways that regulate intestinal fungi, and these discoveries have coincided with advancements in our understanding of the fungal molecular pathways and effectors involved in both commensal colonization and pathogenesis within the gut. In this review, we will discuss immune interactions important for regulating commensal fungi, with a focus on how specific cell types and effectors interact with fungi to limit their colonization or pathogenic potential. This will include how innate and adaptive immune pathways target fungi and orchestrate antifungal immune responses, in addition to how secreted immune effectors, such as mucus and antimicrobial peptides, regulate fungal colonization and inhibit pathogenic potential. These immune interactions will be framed around our current understanding of the fungal effectors and pathways regulating colonization and pathogenesis within this niche. Finally, we highlight important unexplored mechanisms by which the immune system regulates commensal fungi in the gut.
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Affiliation(s)
- Owen Jensen
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Emma Trujillo
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Luke Hanson
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kyla S Ost
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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3
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Crouch AL, Monsey L, Rambeau M, Ramos C, Yracheta JM, Anderson MZ. Metagenomic discovery of microbial eukaryotes in stool microbiomes. mBio 2024:e0206324. [PMID: 39207108 DOI: 10.1128/mbio.02063-24] [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: 07/15/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024] Open
Abstract
Host-associated microbiota form complex microbial communities that are increasingly associated with host behavior and disease. While these microbes include bacterial, archaeal, viral, and eukaryotic constituents, most studies have focused on bacteria due to their dominance in the human host and available tools for investigation. Accumulating evidence suggests microbial eukaryotes in the microbiome play pivotal roles in host health, but our understandings of these interactions are limited to a few readily identifiable taxa because of technical limitations in unbiased eukaryote exploration. Here, we combined cell sorting, optimized eukaryotic cell lysis, and shotgun sequencing to accelerate metagenomic discovery and analysis of host-associated microbial eukaryotes. Using synthetic communities with a 1% microbial eukaryote representation, the eukaryote-optimized cell lysis and DNA recovery method alone yielded a 38-fold increase in eukaryotic DNA. Automated sorting of eukaryotic cells from stool samples of healthy adults increased the number of microbial eukaryote reads in metagenomic pools by up to 28-fold compared to commercial kits. Read frequencies for identified fungi increased by 10,000× on average compared to the Human Microbiome Project and allowed for the identification of novel taxa, de novo assembly of contigs from previously unknown microbial eukaryotes, and gene prediction from recovered genomic segments. These advances pave the way for the unbiased inclusion of microbial eukaryotes in deciphering determinants of health and disease in the host-associated microbiome.IMPORTANCEMicrobial eukaryotes are common constituents of the human gut where they can contribute to local ecology and host health, but they are often overlooked in microbiome studies. The lack of attention is due to current technical limitations that are heavily biased or poorly recovered DNA from microbial eukaryotes. We developed a method to increase the representation of these eukaryotes in metagenomic sequencing of microbiome samples that allows to improve their detection compared to prior methods and allows for the identification of new species. Application of the technique to gut microbiome samples improved detection of fungi, protists, and helminths. New eukaryotic taxa and their encoded genes could be identified by sequencing a small number of samples. This approach can improve the inclusion of eukaryotes into microbiome research.
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Affiliation(s)
- Audra L Crouch
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Laine Monsey
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Molly Rambeau
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Cameron Ramos
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | | | - Matthew Z Anderson
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
- Center for Genomic Science Innovation, University of Wisconsin - Madison, Madison, Wisconsin, USA
- Laboratory of Genetics, University of Wisconsin - Madison, Madison, Wisconsin, USA
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4
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Catalán-Serra I, Thorsvik S, Beisvag V, Bruland T, Underhill D, Sandvik AK, Granlund AVB. Fungal Microbiota Composition in Inflammatory Bowel Disease Patients: Characterization in Different Phenotypes and Correlation With Clinical Activity and Disease Course. Inflamm Bowel Dis 2024; 30:1164-1177. [PMID: 38103028 PMCID: PMC11219482 DOI: 10.1093/ibd/izad289] [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: 02/23/2023] [Indexed: 12/17/2023]
Abstract
BACKGROUND There is growing evidence of the role of the mycobiome in inflammatory bowel disease (IBD). Variations within phenotypes and activity and with prognosis have been poorly studied. METHODS A total of 111 individuals were prospectively enrolled: 89 IBD patients (52 ulcerative colitis and 37 Crohn's disease [CD]) and 22 healthy individuals. Disease characteristics were collected and a fecal calprotectin >100 μg/mg was considered indicative of activity. A subset of patients was followed for 6 ± 2 years. Disease course was designated as either complicated or uncomplicated based on the need of intensified medication and/or surgery. ITS sequencing was performed targeting the ITS1 region. RESULTS We found lower Ascomycota/Basidiomycota ratio in IBD. Patients showed a marked increase in Candida dublinensis and Ca albicans and were depleted of Aspergillus rubrobrunneus and Penicillium brevicompactum (P ≤ .001) Saccharomyces was predominant in total colitis and Penicillium in proctitis. Several Penicillium species were depleted in total colitis vs proctitis. Ileal CD patients were enriched in Debaromyces hansenii and depleted of Ca tropicalis (P ≤ .001). Ca albicans was overrepresented in inflammatory (B1) vs fibrostenosing (B2) CD. Ca dublinensis was more abundant in active patients and correlated positively with fecal calprotectin and neutrophil gelatinase-associated lipocalin, while S pastorianus correlated inversely with activity. Ca sake was associated with complicated disease and increased abundance of Cryptococcus carnescens with the need for surgery in CD. CONCLUSIONS This study shows important differences in the mycobiome in IBD and within phenotypes. Selected fungal species were associated with complicated disease and the need of surgery in CD. This work adds to our understanding of the role of fungi in IBD, with potential clinical implications.
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Affiliation(s)
- Ignacio Catalán-Serra
- Centre of Molecular Inflammation Research, NTNU-Norwegian University of Science and Technology, Trondheim, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Gastroenterology, Department of Medicine, Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
| | - Silje Thorsvik
- Centre of Molecular Inflammation Research, NTNU-Norwegian University of Science and Technology, Trondheim, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Vidar Beisvag
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Torunn Bruland
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Gastroenterology and Hepatology, Clinic of Medicine, St. Olav’s University Hospital, Trondheim, Norway
| | - David Underhill
- Centre of Molecular Inflammation Research, NTNU-Norwegian University of Science and Technology, Trondheim, Norway
- Research Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Arne Kristian Sandvik
- Centre of Molecular Inflammation Research, NTNU-Norwegian University of Science and Technology, Trondheim, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Gastroenterology and Hepatology, Clinic of Medicine, St. Olav’s University Hospital, Trondheim, Norway
| | - Atle van Beelen Granlund
- Centre of Molecular Inflammation Research, NTNU-Norwegian University of Science and Technology, Trondheim, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Gastroenterology and Hepatology, Clinic of Medicine, St. Olav’s University Hospital, Trondheim, Norway
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5
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Yan Q, Li S, Yan Q, Huo X, Wang C, Wang X, Sun Y, Zhao W, Yu Z, Zhang Y, Guo R, Lv Q, He X, Yao C, Li Z, Chen F, Ji Q, Zhang A, Jin H, Wang G, Feng X, Feng L, Wu F, Ning J, Deng S, An Y, Guo DA, Martin FM, Ma X. A genomic compendium of cultivated human gut fungi characterizes the gut mycobiome and its relevance to common diseases. Cell 2024; 187:2969-2989.e24. [PMID: 38776919 DOI: 10.1016/j.cell.2024.04.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 02/17/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
The gut fungal community represents an essential element of human health, yet its functional and metabolic potential remains insufficiently elucidated, largely due to the limited availability of reference genomes. To address this gap, we presented the cultivated gut fungi (CGF) catalog, encompassing 760 fungal genomes derived from the feces of healthy individuals. This catalog comprises 206 species spanning 48 families, including 69 species previously unidentified. We explored the functional and metabolic attributes of the CGF species and utilized this catalog to construct a phylogenetic representation of the gut mycobiome by analyzing over 11,000 fecal metagenomes from Chinese and non-Chinese populations. Moreover, we identified significant common disease-related variations in gut mycobiome composition and corroborated the associations between fungal signatures and inflammatory bowel disease (IBD) through animal experimentation. These resources and findings substantially enrich our understanding of the biological diversity and disease relevance of the human gut mycobiome.
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Affiliation(s)
- Qiulong Yan
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China; Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China; College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Shenghui Li
- Puensum Genetech Institute, Wuhan 430076, China; Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100091, China
| | - Qingsong Yan
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Xiaokui Huo
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Chao Wang
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China; Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China; First Affiliated Hospital, Dalian Medical University, Dalian 116044, China.
| | - Xifan Wang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100091, China; Department of Obstetrics and Gynecology, Columbia University, New York, NY 10027, USA
| | - Yan Sun
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Wenyu Zhao
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Zhenlong Yu
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan 430076, China
| | - Ruochun Guo
- Puensum Genetech Institute, Wuhan 430076, China
| | - Qingbo Lv
- Puensum Genetech Institute, Wuhan 430076, China
| | - Xin He
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China; Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China
| | - Changliang Yao
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China
| | | | - Fang Chen
- College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Qianru Ji
- Puensum Genetech Institute, Wuhan 430076, China
| | - Aiqin Zhang
- Puensum Genetech Institute, Wuhan 430076, China
| | - Hao Jin
- Puensum Genetech Institute, Wuhan 430076, China
| | - Guangyang Wang
- College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Xiaoying Feng
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Lei Feng
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Fan Wu
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Jing Ning
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Sa Deng
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Yue An
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - De-An Guo
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China.
| | - Francis M Martin
- Université de Lorraine, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux 54280, France; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100091, China.
| | - Xiaochi Ma
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China; Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China.
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6
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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; 16:e1641. [PMID: 38228159 DOI: 10.1002/wsbm.1641] [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: 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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Wu D, Guan YX, Li CH, Zheng Q, Yin ZJ, Wang H, Liu NN. "Nutrient-fungi-host" tripartite interaction in cancer progression. IMETA 2024; 3:e170. [PMID: 38882486 PMCID: PMC11170973 DOI: 10.1002/imt2.170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 06/18/2024]
Abstract
The human microbiome exhibits a profound connection with the cancer development, progression, and therapeutic response, with particular emphasis on its components of the mycobiome, which are still in the early stages of research. In this review, we comprehensively summarize cancer-related symbiotic and pathogenic fungal genera. The intricate mechanisms through which fungi impact cancer as an integral member of both gut and tissue-resident microbiomes are further discussed. In addition, we shed light on the pivotal physiological roles of various nutrients, including cholesterol, carbohydrates, proteins and minerals, in facilitating the growth, reproduction, and invasive pathogenesis of the fungi. While our exploration of the interplay between nutrients and cancer, mediated by the mycobiome, is ongoing, the current findings have yet to yield conclusive results. Thus, delving into the relationship between nutrients and fungal pathogenesis in cancer development and progression would provide valuable insights into anticancer therapy and foster precision nutrition and individualized treatments that target fungi from bench to bedside.
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Affiliation(s)
- Di Wu
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Yun-Xuan Guan
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Chen-Hao Li
- Institute of Computing Technology Chinese Academy of Sciences Beijing China
| | - Quan Zheng
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Zuo-Jing Yin
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Hui Wang
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Ning-Ning Liu
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health Shanghai Jiao Tong University School of Medicine Shanghai China
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8
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Cisek AA, Szymańska E, Aleksandrzak-Piekarczyk T, Cukrowska B. The Role of Methanogenic Archaea in Inflammatory Bowel Disease-A Review. J Pers Med 2024; 14:196. [PMID: 38392629 PMCID: PMC10890621 DOI: 10.3390/jpm14020196] [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: 12/31/2023] [Revised: 01/28/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024] Open
Abstract
Methanogenic archaea are a part of the commensal gut microbiota responsible for hydrogen sink and the efficient production of short-chain fatty acids. Dysbiosis of methanogens is suspected to play a role in pathogenesis of variety of diseases, including inflammatory bowel disease (IBD). Unlike bacteria, the diversity of archaea seems to be higher in IBD patients compared to healthy subjects, whereas the prevalence and abundance of gut methanogens declines in IBD, especially in ulcerative colitis. To date, studies focusing on methanogens in pediatric IBD are very limited; nevertheless, the preliminary results provide some evidence that methanogens may be influenced by the chronic inflammatory process in IBD. In this review, we demonstrated the development and diversity of the methanogenic community in IBD, both in adults and children.
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Affiliation(s)
- Agata Anna Cisek
- Department of Pathomorphology, The Children's Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland
| | - Edyta Szymańska
- Department of Gastroenterology, Hepatology, Nutritional Disorders and Pediatrics, The Children's Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland
| | | | - Bożena Cukrowska
- Department of Pathomorphology, The Children's Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland
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9
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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: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 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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10
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Wetzel S, Müller A, Kohnert E, Mehrbarzin N, Huber R, Häcker G, Kreutz C, Lederer AK, Badr MT. Longitudinal dynamics of gut bacteriome and mycobiome interactions pre- and post-visceral surgery in Crohn's disease. Front Cell Infect Microbiol 2024; 13:1275405. [PMID: 38287975 PMCID: PMC10822897 DOI: 10.3389/fcimb.2023.1275405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/12/2023] [Indexed: 01/31/2024] Open
Abstract
Introduction Alterations of the gut microbiome are involved in the pathogenesis of Crohn's disease (CD). The role of fungi in this context is unclear. This study aimed to determine postoperative changes in the bacterial and fungal gut communities of CD patients undergoing intestinal resection, and to evaluate interactions between the bacteriome and mycobiome and their impact on the patients' outcome. Methods We report a subgroup analysis of a prospective cohort study, focusing on 10 CD patients whose fecal samples were collected for bacterial 16S rRNA and fungal ITS2 genes next-generation sequencing the day before surgery and on the 5th or 6th postoperative day. Results No significant differences in bacterial and fungal diversity were observed between preoperative and postoperative stool samples. By in-depth analysis, significant postoperative abundance changes of bacteria and fungi and 17 interkingdom correlations were detected. Network analysis identified 13 microbial clusters in the perioperative gut communities, revealing symbiotic and competitive interactions. Relevant factors were gender, age, BMI, lifestyle habits (smoking, alcohol consumption) and surgical technique. Postoperative abundance changes and identified clusters were associated with clinical outcomes (length of hospital stay, complications) and levels of inflammatory markers. Conclusions Our findings highlight the importance of dissecting the interactions of gut bacterial and fungal communities in CD patients and their potential influence on postoperative and disease outcomes.
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Affiliation(s)
- Simon Wetzel
- Institute of Medical Microbiology and Hygiene, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Alexander Müller
- Center for Complementary Medicine, Department of Medicine II, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Eva Kohnert
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Negin Mehrbarzin
- Institute of Medical Microbiology and Hygiene, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Roman Huber
- Center for Complementary Medicine, Department of Medicine II, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Georg Häcker
- Institute of Medical Microbiology and Hygiene, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Centre for Biological Signaling Studies (BIOSS), University of Freiburg, Freiburg, Germany
| | - Clemens Kreutz
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Ann-Kathrin Lederer
- Center for Complementary Medicine, Department of Medicine II, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of General, Visceral and Transplant Surgery, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Mohamed Tarek Badr
- Institute of Medical Microbiology and Hygiene, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Aufdecken gemeinsamer Prinzipien immunvermittelter Erkrankungen: von der Grundlagenwissenschaft zu neuen Therapien (IMM-PACT)-Program, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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11
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Cisek AA, Szymańska E, Wierzbicka-Rucińska A, Aleksandrzak-Piekarczyk T, Cukrowska B. Methanogenic Archaea in the Pediatric Inflammatory Bowel Disease in Relation to Disease Type and Activity. Int J Mol Sci 2024; 25:673. [PMID: 38203843 PMCID: PMC10779203 DOI: 10.3390/ijms25010673] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/25/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
The inflammatory bowel disease (IBD) is associated with gut microbiota dysbiosis; however, studies on methanogens-especially those focused on children-are extremely limited. The aim of this study was to determine the abundance of total methanogenic archaea and their three subgroups: Methanobrevibacter (Mb.) smithii, Methanosphaera (Ms.) stadtmanae, and Methanomassiliicoccales, in the feces of children with both active and inactive Crohn's disease (CD) and ulcerative colitis (UC). The results of a quantitative real-time PCR were cross-referenced with the disease type (CD vs. UC) and activity assessed with the use of Pediatric Crohn's Disease Activity Index (PCDAI) and Pediatric Ulcerative Colitis Activity Index (PUCAI) indices, and fecal calprotectin (FCP) concentration, and compared with controls. There was a significant decrease in the number of total methanogens in CD and UC compared to controls. The prevalence of total methanogens was also lower in UC compared to controls. Furthermore, patients from the inactive UC group were colonized by a lower number of Mb. smithii, and demonstrated the most pronounced positive correlation between the number of Ms. stadtmanae and the FCP concentration. Our results demonstrate that gut methanogens are related to the type and activity of pediatric IBD.
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Affiliation(s)
- Agata Anna Cisek
- Department of Pathomorphology, The Children’s Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland;
| | - Edyta Szymańska
- Department of Gastroenterology, Hepatology, Nutritional Disorders and Pediatrics, The Children’s Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland;
| | - Aldona Wierzbicka-Rucińska
- Department of Biochemistry, Radioimmunology and Experimental Medicine, The Children’s Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland;
| | | | - Bożena Cukrowska
- Department of Pathomorphology, The Children’s Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland;
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12
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Legaki E, Koutouratsas T, Theocharopoulos C, Lagkada V, Gazouli M. Polymorphisms in CLEC5A and CLEC7A genes modify risk for inflammatory bowel disease. Ann Gastroenterol 2024; 37:64-70. [PMID: 38223252 PMCID: PMC10785015 DOI: 10.20524/aog.2024.0843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 11/13/2023] [Indexed: 01/16/2024] Open
Abstract
Background Inflammatory bowel disease (IBD) seems to arise from an interplay between genetic and environmental factors. CLEC5A and CLEC7A genes code for 2 members of the C-type lectin receptor superfamily, which participate in the immune response against various pathogens, mediating inflammatory signaling. CLEC5A polymorphisms have been linked to the risk of Crohn's disease (CD), whereas CLEC7A has been implicated in fungal dysbiosis, chemically induced colitis in mice and undertreated ulcerative colitis (UC) in humans. This study aimed to explore how specific CLEC5A and CLEC7A polymorphisms contribute to the development of CD and UC. Methods One hundred twelve CD patients, 94 UC patients and 164 sex- and age- matched healthy individuals were genotyped for the single nucleotide polymorphisms rs2078178 and rs16910631 of the CLEC7A gene, and rs1285933 of the CLEC5A gene. Results The CLEC7A rs2078178 AA genotype was more frequent in UC patients compared to healthy individuals, The CLEC7A rs16910631 CT genotype was significantly associated with UC risk compared to healthy individuals, while there was no statistical correlation with CD. The CLEC5A rs1285933 GA genotype was found to be protective against UC and CD, and the AA genotype against CD. Carriers of the rs1285933 A allele appeared to have reduced susceptibility to CD, implying that the presence of the A allele could be protective against CD development. Conclusions This is the first study to correlate the CLEC5A rs1285933 polymorphism with the risk for UC. The rs2078178 AA genotype and the CLEC7A rs16910631 CT could be promising biomarkers for UC susceptibility.
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Affiliation(s)
- Evangelia Legaki
- Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Greece (Evangelia Legaki, Tilemachos Koutouratsas, Charalampos Theocharopoulos, Vivian Lagkada, Maria Gazouli)
| | - Tilemachos Koutouratsas
- Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Greece (Evangelia Legaki, Tilemachos Koutouratsas, Charalampos Theocharopoulos, Vivian Lagkada, Maria Gazouli)
| | - Charalampos Theocharopoulos
- Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Greece (Evangelia Legaki, Tilemachos Koutouratsas, Charalampos Theocharopoulos, Vivian Lagkada, Maria Gazouli)
| | - Vivian Lagkada
- Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Greece (Evangelia Legaki, Tilemachos Koutouratsas, Charalampos Theocharopoulos, Vivian Lagkada, Maria Gazouli)
| | - Maria Gazouli
- Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Greece (Evangelia Legaki, Tilemachos Koutouratsas, Charalampos Theocharopoulos, Vivian Lagkada, Maria Gazouli)
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13
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Pandey H, Jain D, Tang DWT, Wong SH, Lal D. Gut microbiota in pathophysiology, diagnosis, and therapeutics of inflammatory bowel disease. Intest Res 2024; 22:15-43. [PMID: 37935653 PMCID: PMC10850697 DOI: 10.5217/ir.2023.00080] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/23/2023] [Accepted: 08/27/2023] [Indexed: 11/09/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a multifactorial disease, which is thought to be an interplay between genetic, environment, microbiota, and immune-mediated factors. Dysbiosis in the gut microbial composition, caused by antibiotics and diet, is closely related to the initiation and progression of IBD. Differences in gut microbiota composition between IBD patients and healthy individuals have been found, with reduced biodiversity of commensal microbes and colonization of opportunistic microbes in IBD patients. Gut microbiota can, therefore, potentially be used for diagnosing and prognosticating IBD, and predicting its treatment response. Currently, there are no curative therapies for IBD. Microbiota-based interventions, including probiotics, prebiotics, synbiotics, and fecal microbiota transplantation, have been recognized as promising therapeutic strategies. Clinical studies and studies done in animal models have provided sufficient evidence that microbiota-based interventions may improve inflammation, the remission rate, and microscopic aspects of IBD. Further studies are required to better understand the mechanisms of action of such interventions. This will help in enhancing their effectiveness and developing personalized therapies. The present review summarizes the relationship between gut microbiota and IBD immunopathogenesis. It also discusses the use of gut microbiota as a noninvasive biomarker and potential therapeutic option.
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Affiliation(s)
| | | | - Daryl W. T. Tang
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Sunny H. Wong
- Centre for Microbiome Medicine, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Devi Lal
- Department of Zoology, Ramjas College, University of Delhi, Delhi, India
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14
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Zheng R, Xiang X, Shi Y, Qiu A, Luo X, Xie J, Russell R, Zhang D. Chronic jet lag alters gut microbiome and mycobiome and promotes the progression of MAFLD in HFHFD-fed mice. Front Microbiol 2023; 14:1295869. [PMID: 38130943 PMCID: PMC10733492 DOI: 10.3389/fmicb.2023.1295869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023] Open
Abstract
Metabolic dysfunction-associated fatty liver disease (MAFLD) is the most common chronic liver disease worldwide. Circadian disruptors, such as chronic jet lag (CJ), may be new risk factors for MAFLD development. However, the roles of CJ on MAFLD are insufficiently understood, with mechanisms remaining elusive. Studies suggest a link between gut microbiome dysbiosis and MAFLD, but most of the studies are mainly focused on gut bacteria, ignoring other components of gut microbes, such as gut fungi (mycobiome), and few studies have addressed the rhythm of the gut fungi. This study explored the effects of CJ on MAFLD and its related microbiotic and mycobiotic mechanisms in mice fed a high fat and high fructose diet (HFHFD). Forty-eight C57BL6J male mice were divided into four groups: mice on a normal diet exposed to a normal circadian cycle (ND-NC), mice on a normal diet subjected to CJ (ND-CJ), mice on a HFHFD exposed to a normal circadian cycle (HFHFD-NC), and mice on a HFHFD subjected to CJ (HFHFD-CJ). After 16 weeks, the composition and rhythm of microbiota and mycobiome in colon contents were compared among groups. The results showed that CJ exacerbated hepatic steatohepatitis in the HFHFD-fed mice. Compared with HFHFD-NC mice, HFHFD-CJ mice had increases in Aspergillus, Blumeria and lower abundances of Akkermansia, Lactococcus, Prevotella, Clostridium, Bifidobacterium, Wickerhamomyces, and Saccharomycopsis genera. The fungi-bacterial interaction network became more complex after HFHFD and/or CJ interventions. The study revealed that CJ altered the composition and structure of the gut bacteria and fungi, disrupted the rhythmic oscillation of the gut microbiota and mycobiome, affected interactions among the gut microbiome, and promoted the progression of MAFLD in HFHFD mice.
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Affiliation(s)
- Ruoyi Zheng
- Department of Endocrinology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, Changsha, China
| | - Xingwei Xiang
- Department of Endocrinology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ying Shi
- Department of Endocrinology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Anqi Qiu
- Department of Endocrinology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xin Luo
- Department of Endocrinology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Junyan Xie
- Department of Endocrinology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ryan Russell
- Department of Health and Human Performance, College of Health Professions, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Dongmei Zhang
- Department of Endocrinology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Engineering Research Center for Obesity and its Metabolic Complications, Xiangya Hospital, Central South University, Changsha, China
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15
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Han G, Vaishnava S. Microbial underdogs: exploring the significance of low-abundance commensals in host-microbe interactions. Exp Mol Med 2023; 55:2498-2507. [PMID: 38036729 PMCID: PMC10767002 DOI: 10.1038/s12276-023-01120-y] [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: 06/29/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 12/02/2023] Open
Abstract
Our understanding of host-microbe interactions has broadened through numerous studies over the past decades. However, most investigations primarily focus on the dominant members within ecosystems while neglecting low-abundance microorganisms. Moreover, laboratory animals usually do not have microorganisms beyond bacteria. The phenotypes observed in laboratory animals, including the immune system, have displayed notable discrepancies when compared to real-world observations due to the diverse microbial community in natural environments. Interestingly, recent studies have unveiled the beneficial roles played by low-abundance microorganisms. Despite their rarity, these keystone taxa play a pivotal role in shaping the microbial composition and fulfilling specific functions in the host. Consequently, understanding low-abundance microorganisms has become imperative to unravel true commensalism. In this review, we provide a comprehensive overview of important findings on how low-abundance commensal microorganisms, including low-abundance bacteria, fungi, archaea, and protozoa, interact with the host and contribute to host phenotypes, with emphasis on the immune system. Indeed, low-abundance microorganisms play vital roles in the development of the host's immune system, influence disease status, and play a key role in shaping microbial communities in specific niches. Understanding the roles of low-abundance microbes is important and will lead to a better understanding of the true host-microbe relationships.
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Affiliation(s)
- Geongoo Han
- Molecular Microbiology and Immunology, Brown University, Providence, RI, USA.
| | - Shipra Vaishnava
- Molecular Microbiology and Immunology, Brown University, Providence, RI, USA.
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16
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Kreulen IAM, de Jonge WJ, van den Wijngaard RM, van Thiel IAM. Candida spp. in Human Intestinal Health and Disease: More than a Gut Feeling. Mycopathologia 2023; 188:845-862. [PMID: 37294505 PMCID: PMC10687130 DOI: 10.1007/s11046-023-00743-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/09/2023] [Indexed: 06/10/2023]
Abstract
Fungi are an essential part of the normal collection of intestinal microorganisms, even though their collective abundance comprises only 0.1-1% of all fecal microbes. The composition and role of the fungal population is often studied in relation to early-life microbial colonization and development of the (mucosal) immune system. The genus Candida is frequently described as one of the most abundant genera, and altered fungal compositions (including elevated abundance of Candida spp.) have been linked with intestinal diseases such as inflammatory bowel disease and irritable bowel syndrome. These studies are performed using both culture-dependent and genomic (metabarcoding) techniques. In this review, we aimed to summarize existing data on intestinal Candida spp. colonization in relation to intestinal disease and provide a brief overview of the biological and technical challenges in this field, including the recently described role of sub-species strain variation of intestinal Candida albicans. Together, the evidence for a contributing role of Candida spp. in pediatric and adult intestinal disease is quickly expanding, even though technical and biological challenges may limit full understanding of host-microbe interactions.
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Affiliation(s)
- Irini A M Kreulen
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam UMC, Location Academic Medical Center, Meibergdreef 69-71, 1105 BK, Amsterdam, the Netherlands
| | - Wouter J de Jonge
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam UMC, Location Academic Medical Center, Meibergdreef 69-71, 1105 BK, Amsterdam, the Netherlands
- Department of Gastroenterology and Hepatology, Amsterdam UMC, Location Academic Medical Center, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
- Department of General, Visceral, Thoracic and Vascular Surgery, University Hospital Bonn, 53127, Bonn, Germany
| | - René M van den Wijngaard
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam UMC, Location Academic Medical Center, Meibergdreef 69-71, 1105 BK, Amsterdam, the Netherlands
- Department of Gastroenterology and Hepatology, Amsterdam UMC, Location Academic Medical Center, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
| | - Isabelle A M van Thiel
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam UMC, Location Academic Medical Center, Meibergdreef 69-71, 1105 BK, Amsterdam, the Netherlands.
- Royal Netherlands Academy of Arts and Sciences, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands.
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17
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Krawczyk A, Gosiewski T, Zapała B, Kowalska-Duplaga K, Salamon D. Alterations in intestinal Archaea composition in pediatric patients with Crohn's disease based on next-generation sequencing - a pilot study. Gut Microbes 2023; 15:2276806. [PMID: 37955638 PMCID: PMC10653639 DOI: 10.1080/19490976.2023.2276806] [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: 04/06/2023] [Accepted: 10/25/2023] [Indexed: 11/14/2023] Open
Abstract
Intestinal dysbiosis can lead to the induction of systemic immune-mediated inflammatory diseases, such as Crohn's disease Although archaea are part of the commensal microbiota, they are still one of the least studied microorganisms. The aim of our study was the standardization of the optimal conditions and primers for sequencing of the gut archaeome using Next Generation Sequencing, and evaluation of the differences between the composition of archaea in patients and healthy volunteers, as well as analysis of the changes that occur in the archaeome of patients depending on disease activity. Newly diagnosed patients were characterized by similar archeal profiles at every taxonomic level as in healthy individuals (the dominance of Methanobacteria at the class level, and Methanobrevibacter at the genus level). In turn, in patients previously diagnosed with Crohn's disease (both in active and remission phase), an increased prevalence of Thermoplasmata, Thermoprotei, Halobacteria (at the class level), and Halococcus, Methanospaera or Picrophilus (at the genus level) were observed. Furthermore, we have found a significant correlation between the patient's parameters and the individual class or species of Archaea. Our study confirms changes in archaeal composition in pediatric patients with Crohn's disease, however, only in long-standing disease. At the beginning of the disease, the archeal profile is similar to that of healthy people. However, in the chronic form of the disease, significant differences in the composition of archaeome begin to appear. It seems that some archaea may be a good indicator of the chronicity and activity of Crohn's disease.
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Affiliation(s)
- A. Krawczyk
- Department of Molecular Medical Microbiology, Division of Microbiology, Jagiellonian University Medical College, Krakow, Poland
| | - T. Gosiewski
- Department of Molecular Medical Microbiology, Division of Microbiology, Jagiellonian University Medical College, Krakow, Poland
| | - B. Zapała
- Department of Pharmaceutical Microbiology, Jagiellonian University Medical College, Krakow, Poland
- Jagiellonian University Hospital in Krakow, Krakow, Poland
| | - K. Kowalska-Duplaga
- Department of Pediatrics, Gastroenterology and Nutrition,Jagiellonian University Medical College, Krakow, Poland
| | - D. Salamon
- Department of Molecular Medical Microbiology, Division of Microbiology, Jagiellonian University Medical College, Krakow, Poland
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18
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Yoon H, Park S, Jun YK, Choi Y, Shin CM, Park YS, Kim N, Lee DH. Evaluation of Bacterial and Fungal Biomarkers for Differentiation and Prognosis of Patients with Inflammatory Bowel Disease. Microorganisms 2023; 11:2882. [PMID: 38138026 PMCID: PMC10745905 DOI: 10.3390/microorganisms11122882] [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: 11/02/2023] [Revised: 11/20/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
This study aimed to evaluate bacterial and fungal biomarkers to differentiate patients with inflammatory bowel disease (IBD), predict the IBD prognosis, and determine the relationship of these biomarkers with IBD pathogenesis. The composition and function of bacteria and fungi in stool from 100 IBD patients and 97 controls were profiled using next-generation sequencing. We evaluated the cumulative risk of relapse according to bacterial and fungal enterotypes. The microbiome and mycobiome alpha diversity in IBD patients were significantly lower and higher than in the controls, respectively; the micro/mycobiome beta diversity differed significantly between IBD patients and the controls. Ruminococcus gnavus, Cyberlindnera jadinii, and Candida tropicalis increased in IBD patients. Combining functional and species analyses revealed that lower sugar import and higher modified polysaccharide production were associated with IBD pathogenesis. Tricarboxylic acid cycling consuming acetyl CoA was higher in IBD patients than the controls, leading to lower short-chain fatty acid (SCFA) fermentation. Bacterial and fungal enterotypes were not associated with IBD relapse. We found differences in bacterial and fungal species between IBD patients and controls. A working model for the role of gut bacteria in IBD pathogenesis is proposed, wherein bacterial species increase modified N-glycan production and decrease SCFA fermentation.
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Affiliation(s)
- Hyuk Yoon
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Republic of Korea; (Y.K.J.); (Y.C.); (C.M.S.); (Y.S.P.); (N.K.); (D.H.L.)
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Sunghyouk Park
- Department of Manufacturing Pharmacy, Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Yu Kyung Jun
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Republic of Korea; (Y.K.J.); (Y.C.); (C.M.S.); (Y.S.P.); (N.K.); (D.H.L.)
| | - Yonghoon Choi
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Republic of Korea; (Y.K.J.); (Y.C.); (C.M.S.); (Y.S.P.); (N.K.); (D.H.L.)
| | - Cheol Min Shin
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Republic of Korea; (Y.K.J.); (Y.C.); (C.M.S.); (Y.S.P.); (N.K.); (D.H.L.)
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Young Soo Park
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Republic of Korea; (Y.K.J.); (Y.C.); (C.M.S.); (Y.S.P.); (N.K.); (D.H.L.)
| | - Nayoung Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Republic of Korea; (Y.K.J.); (Y.C.); (C.M.S.); (Y.S.P.); (N.K.); (D.H.L.)
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Dong Ho Lee
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Republic of Korea; (Y.K.J.); (Y.C.); (C.M.S.); (Y.S.P.); (N.K.); (D.H.L.)
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
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19
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Carlson SL, Mathew L, Savage M, Kok K, Lindsay JO, Munro CA, McCarthy NE. Mucosal Immunity to Gut Fungi in Health and Inflammatory Bowel Disease. J Fungi (Basel) 2023; 9:1105. [PMID: 37998910 PMCID: PMC10672531 DOI: 10.3390/jof9111105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/25/2023] Open
Abstract
The gut microbiome is a diverse microbial community composed of bacteria, viruses, and fungi that plays a major role in human health and disease. Dysregulation of these gut organisms in a genetically susceptible host is fundamental to the pathogenesis of inflammatory bowel disease (IBD). While bacterial dysbiosis has been a predominant focus of research for many years, there is growing recognition that fungal interactions with the host immune system are an important driver of gut inflammation. Candida albicans is likely the most studied fungus in the context of IBD, being a near universal gut commensal in humans and also a major barrier-invasive pathogen. There is emerging evidence that intra-strain variation in C. albicans virulence factors exerts a critical influence on IBD pathophysiology. In this review, we describe the immunological impacts of variations in C. lbicans colonisation, morphology, genetics, and proteomics in IBD, as well as the clinical and therapeutic implications.
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Affiliation(s)
- Sean L. Carlson
- Centre for Immunobiology, The Blizard Institute, Queen Mary University of London, London E1 2AT, UK
- Gastroenterology Department, Royal London Hospital, Barts Health NHS Trust, London E1 1BB, UK
| | - Liya Mathew
- Centre for Immunobiology, The Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Michael Savage
- Centre for Immunobiology, The Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Klaartje Kok
- Centre for Immunobiology, The Blizard Institute, Queen Mary University of London, London E1 2AT, UK
- Gastroenterology Department, Royal London Hospital, Barts Health NHS Trust, London E1 1BB, UK
| | - James O. Lindsay
- Centre for Immunobiology, The Blizard Institute, Queen Mary University of London, London E1 2AT, UK
- Gastroenterology Department, Royal London Hospital, Barts Health NHS Trust, London E1 1BB, UK
| | - Carol A. Munro
- Aberdeen Fungal Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB24 3FX, UK
| | - Neil E. McCarthy
- Centre for Immunobiology, The Blizard Institute, Queen Mary University of London, London E1 2AT, UK
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20
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Thavamani A, Sankararaman S, Al-Shakhshir H, Retuerto M, Velayuthan S, Sferra TJ, Ghannoum M. Impact of Erythromycin as a Prokinetic on the Gut Microbiome in Children with Feeding Intolerance-A Pilot Study. Antibiotics (Basel) 2023; 12:1606. [PMID: 37998808 PMCID: PMC10668753 DOI: 10.3390/antibiotics12111606] [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: 09/24/2023] [Revised: 10/27/2023] [Accepted: 11/01/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND Studies have demonstrated that the gut microbiome changes upon exposure to systemic antibiotics. There is a paucity of literature regarding impact on the gut microbiome by long-term usage of erythromycin ethyl succinate (EES) when utilized as a prokinetic. METHODS Stool samples from pediatric patients with feeding intolerance who received EES (N = 8) as a prokinetic were analyzed for both bacteriome and mycobiome. Age-matched children with similar clinical characteristics but without EES therapy were included as controls (N = 20). RESULTS In both groups, Proteobacteria, Firmicutes, and Bacteroidetes were the most abundant bacterial phyla. Ascomycota was the most abundant fungal phyla, followed by Basidiomycota. There were no significant differences in richness between the groups for both bacterial and fungal microbiome. Alpha diversity (at genus and species levels) and beta diversity (at the genus level) were not significantly different between the groups for both bacterial and fungal microbiome. At the species level, there was a significant difference between the groups for fungal microbiota, with a p-value of 0.029. We also noted that many fungal microorganisms had significantly higher p-values in the EES group than controls at both genera and species levels. CONCLUSIONS In this observational case-control study, the prokinetic use of EES was associated with changes in beta diversity between the groups for mycobiome at the species level. Many fungal microorganisms were significantly higher in the EES group when compared to the controls. Confirmation of these results in larger trials will provide further evidence regarding the impact of EES on gut microbiota when utilized as a prokinetic agent.
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Affiliation(s)
- Aravind Thavamani
- Division of Pediatric Gastroenterology, Hepatology & Nutrition, Department of Pediatrics, UH Rainbow Babies and Children’s Hospital, Cleveland, OH 44106, USA; (A.T.); (S.V.); (T.J.S.)
- Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Senthilkumar Sankararaman
- Division of Pediatric Gastroenterology, Hepatology & Nutrition, Department of Pediatrics, UH Rainbow Babies and Children’s Hospital, Cleveland, OH 44106, USA; (A.T.); (S.V.); (T.J.S.)
- Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Hilmi Al-Shakhshir
- Department of Radiology and Imaging Sciences, Emory School of Medicine, Atlanta, GA 30307, USA;
- Department of Radiology and Imaging Sciences Atlanta VA Medical Center, Decatur, GA 30033, USA
| | - Mauricio Retuerto
- Center for Medical Mycology, Department of Dermatology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; (M.R.); (M.G.)
| | - Sujithra Velayuthan
- Division of Pediatric Gastroenterology, Hepatology & Nutrition, Department of Pediatrics, UH Rainbow Babies and Children’s Hospital, Cleveland, OH 44106, USA; (A.T.); (S.V.); (T.J.S.)
- Division of Pediatric Neurogastroenterology and Motility, Department of Pediatrics, Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Thomas J. Sferra
- Division of Pediatric Gastroenterology, Hepatology & Nutrition, Department of Pediatrics, UH Rainbow Babies and Children’s Hospital, Cleveland, OH 44106, USA; (A.T.); (S.V.); (T.J.S.)
- Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Mahmoud Ghannoum
- Center for Medical Mycology, Department of Dermatology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; (M.R.); (M.G.)
- Department of Dermatology, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
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21
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Wan T, Wang Y, He K, Zhu S. Microbial sensing in the intestine. Protein Cell 2023; 14:824-860. [PMID: 37191444 PMCID: PMC10636641 DOI: 10.1093/procel/pwad028] [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: 03/21/2023] [Accepted: 05/04/2023] [Indexed: 05/17/2023] Open
Abstract
The gut microbiota plays a key role in host health and disease, particularly through their interactions with the immune system. Intestinal homeostasis is dependent on the symbiotic relationships between the host and the diverse gut microbiota, which is influenced by the highly co-evolved immune-microbiota interactions. The first step of the interaction between the host and the gut microbiota is the sensing of the gut microbes by the host immune system. In this review, we describe the cells of the host immune system and the proteins that sense the components and metabolites of the gut microbes. We further highlight the essential roles of pattern recognition receptors (PRRs), the G protein-coupled receptors (GPCRs), aryl hydrocarbon receptor (AHR) and the nuclear receptors expressed in the intestinal epithelial cells (IECs) and the intestine-resident immune cells. We also discuss the mechanisms by which the disruption of microbial sensing because of genetic or environmental factors causes human diseases such as the inflammatory bowel disease (IBD).
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Affiliation(s)
- Tingting Wan
- Division of Life Sciences and Medicine, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Institute of Immunology, School of Basic Medical Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Yalong Wang
- Division of Life Sciences and Medicine, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Institute of Immunology, School of Basic Medical Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Kaixin He
- Division of Life Sciences and Medicine, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Institute of Immunology, School of Basic Medical Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Shu Zhu
- Division of Life Sciences and Medicine, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Institute of Immunology, School of Basic Medical Sciences, University of Science and Technology of China, Hefei 230027, China
- Department of Digestive Disease, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei 230001, China
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei 230601, China
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22
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Yang J, Yang H, Li Y. The triple interactions between gut microbiota, mycobiota and host immunity. Crit Rev Food Sci Nutr 2023; 63:11604-11624. [PMID: 35776086 DOI: 10.1080/10408398.2022.2094888] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The gut microbiome is mainly composed of microbiota and mycobiota, both of which play important roles in the development of the host immune system, metabolic regulation, and maintenance of intestinal homeostasis. With the increasing awareness of the pathogenic essence of infectious, immunodeficiency, and tumor-related diseases, the interactions between gut bacteria, fungi, and host immunity have been shown to directly influence the disease process or final therapeutic outcome, and collaborative and antagonistic relationships are commonly found between bacteria and fungi. Interventions represented by probiotics, prebiotics, engineered probiotics, fecal microbiota transplantation (FMT), and drugs can effectively modulate the triple interactions. In particular, traditional probiotics represented by Bifidobacterium and Lactobacillus and next-generation probiotics represented by Akkermansia muciniphila and Faecalibacterium prausnitzii showed a high enrichment trend in the gut of patients with a high response to inflammation remission and tumor immunotherapy, which predicts the potential medicinal value of these beneficial microbial formulations. However, there are bottlenecks in all these interventions that need to be broken. Meanwhile, further unraveling the underlying mechanisms of the "triple interactions" model can guide precise interventions and ultimately improve the efficiency of interventions on the host gut microbiome and immune modulation, thus directly or indirectly improving anti-inflammatory and tumor immunotherapy effects.
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Affiliation(s)
- Jingpeng Yang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Hong Yang
- State Key Laboratory of Microbial Metabolism, and School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yanan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
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23
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Ost KS, Round JL. Commensal fungi in intestinal health and disease. Nat Rev Gastroenterol Hepatol 2023; 20:723-734. [PMID: 37479823 DOI: 10.1038/s41575-023-00816-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/28/2023] [Indexed: 07/23/2023]
Abstract
The microbiota is known to influence several facets of mammalian development, digestion and disease. Most studies of the microbiota have focused on the bacterial component, but the importance of commensal fungi in health and disease is becoming increasingly clear. Although fungi account for a smaller proportion of the microbiota than bacteria by number, they are much larger and therefore account for a substantial proportion of the biomass. Moreover, as fungi are eukaryotes, their metabolic pathways are complex and unique. In this Review, we discuss the evidence for involvement of specific members of the mycobiota in intestinal diseases, including inflammatory bowel disease, colorectal cancer and pancreatic cancer. We also highlight the importance of fungal interactions with intestinal bacteria and with the immune system. Although most studies of commensal fungi have focused on their role in disease, we also consider the beneficial effects of fungal colonies in the gut. The evidence highlights potential opportunities to target fungi and their interactions for therapeutic purposes.
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Affiliation(s)
- Kyla S Ost
- Department of Immunology and Microbiology, University of Colorado Anschutz School of Medicine, Aurora, CO, USA.
| | - June L Round
- Department of Pathology, School of Medicine, University of Utah, Salt Lake City, UT, USA.
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
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24
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Hsia K, Zhao N, Chung M, Algarrahi K, Montaser Kouhsari L, Fu M, Chen H, Singh S, Michaud DS, Jangi S. Alterations in the Fungal Microbiome in Ulcerative Colitis. Inflamm Bowel Dis 2023; 29:1613-1621. [PMID: 37221272 PMCID: PMC10547232 DOI: 10.1093/ibd/izad082] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND Although gut fungi have been implicated in the immunopathogenesis of inflammatory bowel disease, the fungal microbiome has not been deeply explored across endohistologic activity and treatment exposure in ulcerative colitis. METHODS We analyzed data from the SPARC IBD (Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease) registry. We evaluated the fungal composition of fecal samples from 98 patients with ulcerative colitis across endoscopic activity (n = 43), endohistologic activity (n = 41), and biologic exposure (n = 82). Across all subgroups, we assessed fungal diversity and differential abundance of taxonomic groups. RESULTS We identified 500 unique fungal amplicon sequence variants across the cohort of 82 patients, dominated by phylum Ascomycota. Compared with endoscopic remission, patients with endoscopic activity had increased Saccharomyces (log2 fold change = 4.54; adjusted P < 5 × 10-5) and increased Candida (log2 fold change = 2.56; adjusted P < .03). After adjusting for age, sex, and biologic exposure among patients with endoscopic activity, Saccharomyces (log2 fold change = 7.76; adjusted P < 1 × 10-15) and Candida (log2 fold change = 7.28; adjusted P< 1 × 10-8) remained enriched during endoscopic activity compared with quiescence. CONCLUSIONS Endoscopic inflammation in ulcerative colitis is associated with an expansion of Saccharomyces and Candida compared with remission. The role of these fungal taxa as potential biomarkers and targets for personalized approaches to therapeutics in ulcerative colitis should be evaluated.
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Affiliation(s)
- Katie Hsia
- Department of Medicine, Tufts Medical Center, Boston, MA, USA
| | - Naisi Zhao
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA, USA
| | - Mei Chung
- Friedman School of Nutrition and Science Policy, Tufts University, Boston, MA, USA
| | - Khalid Algarrahi
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, MA, USA
| | | | - May Fu
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, MA, USA
| | - Hannah Chen
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, MA, USA
| | - Siddharth Singh
- Division of Gastroenterology, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Dominique S Michaud
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA, USA
| | - Sushrut Jangi
- Division of Gastroenterology, Department of Medicine, Tufts Medical Center, Boston, MA, USA
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25
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Fan Y, Wu L, Zhai B. The mycobiome: interactions with host and implications in diseases. Curr Opin Microbiol 2023; 75:102361. [PMID: 37527562 DOI: 10.1016/j.mib.2023.102361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 08/03/2023]
Abstract
Over the past decade, our understanding of the composition and function of the human mucosal surface-associated fungal community (i.e. the mycobiome) has rapidly expanded. Fungi colonize at various sites of the mucosal surface at birth and play important roles in the development and homeostasis of immune system throughout adulthood. Here, we review the recent research progresses in the human mycobiome at different body sites, including the gastrointestinal (GI) tract, the respiratory tract, the urogenital tract, the oral cavity, the skin surface, and the tumor tissues. Researchers have made extensive effort in characterizing the interactions between mycobiome and immune system, especially in the GI tract. We discuss the mycobiome dysbiosis and its implications to the progression of diseases such as inflammatory bowel diseases, alcoholic liver diseases, systemic infections, cancers, and so on, indicating the potential of mycobiome-targeting intervention strategy for life-threatening diseases.
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Affiliation(s)
- Yani Fan
- Clinical laboratory, Shenzhen Bao'an Women's and Children's Hospital, Shenzhen, Guangdong Province, China; Maternal-Fetal Medicine Institute, Shenzhen Bao'an Women's and Children's Hospital, Shenzhen, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Lijuan Wu
- Clinical laboratory, Shenzhen Bao'an Women's and Children's Hospital, Shenzhen, Guangdong Province, China; Maternal-Fetal Medicine Institute, Shenzhen Bao'an Women's and Children's Hospital, Shenzhen, China.
| | - Bing Zhai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
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26
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Zhou X, He Y, Chen J, Xiong X, Yin J, Liang J, Peng C, Huang C, Guan G, Yin Y. Colonic phosphocholine is correlated with Candida tropicalis and promotes diarrhea and pathogen clearance. NPJ Biofilms Microbiomes 2023; 9:62. [PMID: 37666845 PMCID: PMC10477305 DOI: 10.1038/s41522-023-00433-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/24/2023] [Indexed: 09/06/2023] Open
Abstract
Diarrhea is characterized by alterations in the gut microbiota, metabolites, and host response to these changes. Studies have focused on the role of commensal bacteria in diarrhea; however, the effect of fungi on its pathogenesis remains unexplored. Here, using post-weaned piglets with or without diarrhea, we found an unexpected decrease in the abundance of Candida tropicalis in diarrheal piglets. We also observed increased accumulation of reactive oxygen species (ROS) and the formation of neutrophil extracellular traps (NETs) in the colonic tissues of diarrheal piglets. Using dectin-1-knockout mice, we found that the over-accumulation of ROS killed C. tropicalis by promoting NET formation, which was dependent on dectin-1. The decreased abundance of C. tropicalis resulted in reduced phosphocholine consumption. Then, colonic phosphocholine accumulation drives water efflux by increasing cAMP levels by activating adenylyl cyclase, which promotes the clearance of pathogenic bacteria. Collectively, we demonstrated that phosphocholine is correlated with colonic C. tropicalis and promotes diarrhea and pathogen clearance. Our results suggest that mycobiota colonizing the colon might be involved in maintaining intestinal metabolic homeostasis through the consumption of certain metabolites.
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Affiliation(s)
- Xihong Zhou
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, the Chinese Academy of Sciences, Changsha, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
- School of Stomatology, Changsha Medical University, Changsha, China
| | - Yiwen He
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, the Chinese Academy of Sciences, Changsha, China
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Jingqing Chen
- Laboratory Animal Center of the Academy of Military Medical Sciences, Beijing, China
| | - Xia Xiong
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, the Chinese Academy of Sciences, Changsha, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
- School of Stomatology, Changsha Medical University, Changsha, China.
| | - Jie Yin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China.
| | - Jing Liang
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, the Chinese Academy of Sciences, Changsha, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Can Peng
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, the Chinese Academy of Sciences, Changsha, China
| | - Chunxia Huang
- School of Stomatology, Changsha Medical University, Changsha, China
| | - Guiping Guan
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha, China
| | - Yulong Yin
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, the Chinese Academy of Sciences, Changsha, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China.
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27
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Zhao X, Hu X, Han J, Yin R, Zhang S, Liu H. Gut mycobiome: A "black box" of gut microbiome-host interactions. WIREs Mech Dis 2023; 15:e1611. [PMID: 37157158 DOI: 10.1002/wsbm.1611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/01/2023] [Accepted: 04/12/2023] [Indexed: 05/10/2023]
Abstract
Fungi, being a necessary component of the gut microbiome, potentially have direct or indirect effects on the health and illness status of the host. The gut mycobiome is an inducer of the host's immunity, maintaining intestinal homeostasis, and protecting against infections, as well as a reservoir of opportunistic microorganisms and a potential cofactor when the host is immunocompromised. In addition, gut fungi interact with a diverse range of microbes in the intestinal niches. In this article, we reviewed the composition of gut mycobiome, their association with host health and illness, and summarized the specific Candida albicans-host interactions, in order to provide insights and directions for the ongoing study of fungi. This article is categorized under: Infectious Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
- Xinyue Zhao
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Xiaomin Hu
- Department of Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Junjie Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ruopeng Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Shuyang Zhang
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Hongwei Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
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28
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Marsaux B, Moens F, Marzorati M, Van de Wiele T. The Intricate Connection between Bacterial α-Diversity and Fungal Engraftment in the Human Gut of Healthy and Impaired Individuals as Studied Using the In Vitro SHIME ® Model. J Fungi (Basel) 2023; 9:877. [PMID: 37754985 PMCID: PMC10532570 DOI: 10.3390/jof9090877] [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: 07/18/2023] [Revised: 08/17/2023] [Accepted: 08/19/2023] [Indexed: 09/28/2023] Open
Abstract
From the estimated 2.2 to 3.8 million fungal species existing on Earth, only a minor fraction actively colonizes the human gastrointestinal tract. In fact, these fungi only represent 0.1% of the gastrointestinal biosphere. Despite their low abundance, fungi play dual roles in human health-both beneficial and detrimental. Fungal infections are often associated with bacterial dysbiosis following antibiotic use, yet our understanding of gut fungi-bacteria interactions remains limited. Here, we used the SHIME® gut model to explore the colonization of human fecal-derived fungi across gastrointestinal compartments. We accounted for the high inter-individual microbial diversity by using fecal samples from healthy adults, healthy babies, and Crohn's disease patients. Using quantitative Polymerase Chain Reaction and targeted next-generation sequencing, we demonstrated that SHIME®-colonized mycobiomes change upon loss of transient colonizers. In addition, SHIME® reactors from Crohn's disease patients contained comparable bacterial levels as healthy adults but higher fungal concentrations, indicating unpredictable correlations between fungal levels and total bacterial counts. Our findings rather link higher bacterial α-diversity to limited fungal growth, tied to colonization resistance. Hence, while healthy individuals had fewer fungi engrafting the colonic reactors, low α-diversity in impaired (Crohn's disease patients) or immature (babies) microbiota was associated with greater fungal abundance. To validate, antibiotic-treated healthy colonic microbiomes demonstrated increased fungal colonization susceptibility, and bacterial taxa that were negatively correlated with fungal expansion were identified. In summary, fungal colonization varied individually and transiently, and bacterial resistance to fungal overgrowth was more related with specific bacterial genera than total bacterial load. This study sheds light on fungal-bacterial dynamics in the human gut.
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Affiliation(s)
- Benoît Marsaux
- ProDigest B.V., Technologiepark-Zwijnaarde 82, 9052 Ghent, Belgium; (F.M.); (M.M.); (T.V.d.W.)
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Frédéric Moens
- ProDigest B.V., Technologiepark-Zwijnaarde 82, 9052 Ghent, Belgium; (F.M.); (M.M.); (T.V.d.W.)
| | - Massimo Marzorati
- ProDigest B.V., Technologiepark-Zwijnaarde 82, 9052 Ghent, Belgium; (F.M.); (M.M.); (T.V.d.W.)
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Tom Van de Wiele
- ProDigest B.V., Technologiepark-Zwijnaarde 82, 9052 Ghent, Belgium; (F.M.); (M.M.); (T.V.d.W.)
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
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29
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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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30
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Kathrani A, Theelen B, Bond R. Isolation of Malassezia yeasts from dogs with gastrointestinal disease undergoing duodenal endoscopy. J Small Anim Pract 2023. [PMID: 37681754 DOI: 10.1111/jsap.13649] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/03/2023] [Accepted: 06/08/2023] [Indexed: 09/09/2023]
Abstract
OBJECTIVES To culture Malassezia and other fungi from the duodenum of dogs with gastrointestinal signs undergoing routine endoscopic examination. MATERIALS AND METHODS Quantitative microbial culture was performed on duodenal juice aspirated from dogs with suspected enteropathy during routine upper gastrointestinal endoscopy; samples were cultured on Sabouraud's dextrose agar (30, 32 and 37°C) and modified Dixon agar (32°C) for 14 days. Isolates were identified phenotypically and by matrix-assisted laser desorption ionisation-time of flight, and internal transcribed spacer sequencing. Yeast presence was also evaluated by cytological and histopathological examination of smears and biopsy specimens. RESULTS Forty-five dogs were recruited with chronic inflammatory enteropathy (n=38), granulomatous colitis (n=2), gastric adenocarcinoma (n=2), duodenal small cell lymphoma (n=1) and idiopathic severe gastrointestinal haemorrhage (n=2). Fungi were cultured from 14 dogs: Malassezia pachydermatis was isolated from eight [chronic inflammatory enteropathy (n=7) (along with Candida albicans n=1); granulomatous colitis (n=1)] and Malassezia sympodialis from another (gastric adenocarcinoma). Five dogs with chronic inflammatory enteropathy yielded other yeasts (C. albicans, Candida glabrata, Kazachstania slooffiae, Kazachstania telluris, Pichia kudriavzevii [syn. C. krusei]). Yeasts were never observed in histopathological specimens. Fluorescent microscopical examination of cytological specimens showed yeast in only one case, from which K. slooffiae was subsequently isolated. CLINICAL SIGNIFICANCE Based on a literature search, this is the first report of isolation of M. pachydermatis, M. sympodialis, K. slooffiae and K. telluris from the canine duodenum. Further studies are needed to determine whether these are resident or transient fungi in the canine duodenum and whether their presence has a pathogenic effect on the host.
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Affiliation(s)
- A Kathrani
- Clinical Science and Services, Royal Veterinary College, North Mymms, Hatfield, AL9 7TA, UK
| | - B Theelen
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - R Bond
- Clinical Science and Services, Royal Veterinary College, North Mymms, Hatfield, AL9 7TA, UK
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Balderramo DC, Romagnoli PA, Granlund AVB, Catalan-Serra I. Fecal Fungal Microbiota (Mycobiome) Study as a Potential Tool for Precision Medicine in Inflammatory Bowel Disease. Gut Liver 2023; 17:505-515. [PMID: 37305948 PMCID: PMC10352062 DOI: 10.5009/gnl220537] [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: 12/21/2022] [Revised: 02/06/2023] [Accepted: 02/15/2023] [Indexed: 06/13/2023] Open
Abstract
There is growing evidence of the role of fungal microbiota in the pathogenesis of inflammatory bowel disease (IBD). Fungi can exert direct pro-inflammatory effects or modify the bacterial composition via interkingdom interactions. Although several studies have demonstrated alterations in the fecal fungal microbiota composition in IBD, there is a wide variation in the mycobiome in different populations, with no definite pattern that can define the mycobiome in IBD having yet been identified. Recent work has suggested that characterizing the fecal fungal composition may influence therapeutic decisions and help to predict outcomes in a subset of IBD patients. In this study, we review the current literature on the emerging role of the fecal mycobiome as a potential tool for precision medicine in IBD.
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Affiliation(s)
- Domingo C. Balderramo
- Department of Gastroenterology, Private Hospital Medical Center of Cordoba S.A., Cordoba, Argentina
| | - Pablo Alberto Romagnoli
- Universitarian Institute for Biomedical Sciences of Cordoba (IUCBC), Translational Medicine Research Center "Severo R. Amuchastegui" (CIMETSA). G.V. Medical Research Institute "Mercedes and Martin Ferreyra" (INIMEC-CONICET-UNC), Cordoba, Argentina
| | - Atle van Beelen Granlund
- Department of Gastroenterology and Hepatology, Clinic of Medicine, St. Olav’s University Hospital, Trondheim, Norway
- Department of Clinical and Molecular Medicine (IKOM), NTNU-Norwegian University of Science and Technology, Trondheim, Norway
- Centre of Molecular Inflammation Research, NTNU-Norwegian University of Science and Technology, Trondheim, Norway
| | - Ignacio Catalan-Serra
- Department of Clinical and Molecular Medicine (IKOM), NTNU-Norwegian University of Science and Technology, Trondheim, Norway
- Centre of Molecular Inflammation Research, NTNU-Norwegian University of Science and Technology, Trondheim, Norway
- Department of Medicine, Gastroenterology, Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
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Cozzi G, Scagnellato L, Lorenzin M, Savarino E, Zingone F, Ometto F, Favero M, Doria A, Vavricka SR, Ramonda R. Spondyloarthritis with inflammatory bowel disease: the latest on biologic and targeted therapies. Nat Rev Rheumatol 2023:10.1038/s41584-023-00984-8. [PMID: 37386288 DOI: 10.1038/s41584-023-00984-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2023] [Indexed: 07/01/2023]
Abstract
Spondyloarthritis (SpA) encompasses a heterogeneous group of chronic inflammatory diseases that can affect both axial and peripheral joints, tendons and entheses. Among the extra-articular manifestations, inflammatory bowel disease (IBD) is associated with considerable morbidity and effects on quality of life. In everyday clinical practice, treatment of these conditions requires a close collaboration between gastroenterologists and rheumatologists to enable early detection of joint and intestinal manifestations during follow-up and to choose the most effective therapeutic regimen, implementing precision medicine for each patient's subtype of SpA and IBD. The biggest issue in this field is the dearth of drugs that are approved for both diseases, as only TNF inhibitors are currently approved for the treatment of full-spectrum SpA-IBD. Janus tyrosine kinase inhibitors are among the most promising drugs for the treatment of peripheral and axial SpA, as well as for intestinal manifestations. Other therapies such as inhibitors of IL-23 and IL-17, phosphodiesterase 4 inhibitor, α4β7 integrin blockers and faecal microbiota transplantation seem to only be able to control some disease domains, or require further studies. Given the growing interest in the development of novel drugs to treat both conditions, it is important to understand the current state of the art and the unmet needs in the management of SpA-IBD.
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Affiliation(s)
- Giacomo Cozzi
- Rheumatology Unit, Department of Medicine-DIMED, Padova University Hospital, Padova, Italy
| | - Laura Scagnellato
- Rheumatology Unit, Department of Medicine-DIMED, Padova University Hospital, Padova, Italy
| | - Mariagrazia Lorenzin
- Rheumatology Unit, Department of Medicine-DIMED, Padova University Hospital, Padova, Italy
| | - Edoardo Savarino
- Gastroenterology Unit, Department of Surgery, Oncology and Gastroenterology, University Hospital of Padova, Padova, Italy
| | - Fabiana Zingone
- Gastroenterology Unit, Department of Surgery, Oncology and Gastroenterology, University Hospital of Padova, Padova, Italy
| | - Francesca Ometto
- Rheumatology Unit, Department of Medicine-DIMED, Padova University Hospital, Padova, Italy
| | - Marta Favero
- Rheumatology Unit, Department of Medicine-DIMED, Padova University Hospital, Padova, Italy
| | - Andrea Doria
- Rheumatology Unit, Department of Medicine-DIMED, Padova University Hospital, Padova, Italy
| | - Stephan R Vavricka
- Department of Gastroenterology and Hepatology, University Hospital Zürich and Center for Gastroenterology and Hepatology, Zürich, Switzerland
| | - Roberta Ramonda
- Rheumatology Unit, Department of Medicine-DIMED, Padova University Hospital, Padova, Italy.
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Sun M, Ju J, Xu H, Wang Y. Intestinal fungi and antifungal secretory immunoglobulin A in Crohn's disease. Front Immunol 2023; 14:1177504. [PMID: 37359518 PMCID: PMC10285161 DOI: 10.3389/fimmu.2023.1177504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/30/2023] [Indexed: 06/28/2023] Open
Abstract
The human gastrointestinal tract harbors trillions of commensal microorganisms. Emerging evidence points to a possible link between intestinal fungal dysbiosis and antifungal mucosal immunity in inflammatory bowel disease, especially in Crohn's disease (CD). As a protective factor for the gut mucosa, secretory immunoglobulin A (SIgA) prevents bacteria from invading the intestinal epithelium and maintains a healthy microbiota community. In recent years, the roles of antifungal SIgA antibodies in mucosal immunity, including the regulation of intestinal immunity binding to hyphae-associated virulence factors, are becoming increasingly recognized. Here we review the current knowledge on intestinal fungal dysbiosis and antifungal mucosal immunity in healthy individuals and in patients with CD, discuss the factors governing antifungal SIgA responses in the intestinal mucosa in the latter group, and highlight potential antifungal vaccines targeting SIgA to prevent CD.
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Halper-Stromberg A, Dalal SR. The Role of the Microbiome in the Etiology of Inflammatory Bowel Diseases. Clin Colon Rectal Surg 2023; 36:120-126. [PMID: 36844713 PMCID: PMC9946717 DOI: 10.1055/s-0042-1760680] [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] [Indexed: 01/27/2023]
Abstract
Inflammatory bowel diseases (IBDs) result from dysregulated immune responses to environmental and microbial triggers in genetically susceptible hosts. Many clinical observations and animal studies support the role of the microbiome in the pathogenesis of IBD. Restoration of the fecal stream leads to postoperative Crohn's recurrence, while diversion can treat active inflammation. Antibiotics can be effective in prevention of postoperative Crohn's recurrence and in pouch inflammation. Several gene mutations associated with Crohn's risk lead to functional changes in microbial sensing and handling. However, the evidence linking the microbiome to the IBD is largely correlative, given the difficulty in studying the microbiome before disease occurs. Attempts to modify the microbial triggers of inflammation have had modest success to date. Exclusive enteral nutrition can treat Crohn's inflammation though no whole food diet to date has been shown to treat inflammation. Manipulation of the microbiome through fecal microbiota transplant and probiotics have had limited success. Further focus on early changes in the microbiome and functional consequences of microbial changes through the study of metabolomics are needed to help advance the field.
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Affiliation(s)
- Ariel Halper-Stromberg
- University of Chicago Medicine Inflammatory Bowel Disease Center, Dept of Medicine, Chicago, Illinois
| | - Sushila R. Dalal
- University of Chicago Medicine Inflammatory Bowel Disease Center, Dept of Medicine, Chicago, Illinois
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Wang H, Wu H, Li KD, Wang YY, Huang RG, Du YJ, Jin X, Zhang QR, Li XB, Li BZ. Intestinal fungi and systemic autoimmune diseases. Autoimmun Rev 2023; 22:103234. [PMID: 36423833 DOI: 10.1016/j.autrev.2022.103234] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022]
Abstract
Nearly 20 years of studies have shown that fungi and the human immune system (non-specific immunity and specific immunity) and bacterial--fungal interactions maintain a balance that can't lead to diseases. Fungi--microorganism that lives in human intestine--may play an important role in human health and disease. Population studies and animal models in some diseases have found the changes in the diversity and composition of fungi. The dysregulation of the fungi can disrupt the normal "running" of the immune system and bacteria, which triggers the development of inflammatory diseases. The latest studies of fungi in inflammatory bowel disease, systemic lupus erythematosus, ankylosing spondylitis and type 1 diabetes mellitus were summarized. This review considers how the healthy host protect against the potential harm of intestinal fungi through the immune system and how fungal dysregulation alters host immunity.
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Affiliation(s)
- Hua Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Hong Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Kai-Di Li
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Yi-Yu Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Rong-Gui Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Yu-Jie Du
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Xue Jin
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Qian-Ru Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China; Department of Cardiovascular Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Xian-Bao Li
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Bao-Zhu Li
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China.
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Chen Q, Fan Y, Zhang B, Yan C, Chen Z, Wang L, Hu Y, Huang Q, Su J, Ren J, Xu H. Specific fungi associated with response to capsulized fecal microbiota transplantation in patients with active ulcerative colitis. Front Cell Infect Microbiol 2023; 12:1086885. [PMID: 36683707 PMCID: PMC9849685 DOI: 10.3389/fcimb.2022.1086885] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/08/2022] [Indexed: 01/06/2023] Open
Abstract
Objective Fecal microbiota transplantation (FMT) is a novel microbial treatment for patients with ulcerative colitis (UC). In this study, we performed a clinical trial of capsulized FMT in UC patients to determine the association between the gut fungal community and capsulized FMT outcomes. Design This study recruited patients with active UC (N = 22) and healthy individuals (donor, N = 9) according to the criteria. The patients received capsulized FMT three times a week. Patient stool samples were collected before (week 0) and after FMT follow-up visits at weeks 1, 4, and 12. Fungal communities were analysed using shotgun metagenomic sequencing. Results According to metagenomic analysis, fungal community evenness index was greater in samples collected from patients, and the overall fungal community was clustered among the samples collected from donors. The dominant fungi in fecal samples collected from donors and patients were Ascomycota and Basidiomycota. However, capsulized FMT ameliorated microbial fungal diversity and altered fungal composition, based on metagenomic analysis of fecal samples collected before and during follow-up visits after capsulized FMT. Fungal diversity decreased in samples collected from patients who achieved remission after capsulized FMT, similar to samples collected from donors. Patients achieving remission after capsulized FMT had specific enrichment of Kazachstania naganishii, Pyricularia grisea, Lachancea thermotolerans, and Schizosaccharomyces pombe compared with patients who did not achieve remission. In addition, the relative abundance of P. grisea was higher in remission fecal samples during the follow-up visit. Meanwhile, decreased levels of pathobionts, such as Candida and Debaryomyces hansenii, were associated with remission in patients receiving capsulized FMT. Conclusion In the metagenomic analysis of fecal samples from donors and patients with UC receiving capsulized FMT, shifts in gut fungal diversity and composition were associated with capsulized FMT and validated in patients with active UC. We also identified the specific fungi associated with the induction of remission. ClinicalTrails.gov (NCT03426683).
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Affiliation(s)
- Qiongyun Chen
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China,Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
| | - Yanyun Fan
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Bangzhou Zhang
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China,Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
| | - Changsheng Yan
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China,Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
| | - Zhangran Chen
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China,Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
| | - Lin Wang
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Yiqun Hu
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Qingwen Huang
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Jingling Su
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Jianlin Ren
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China,Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China,Xiamen Key Laboratory of Intestinal Microbiome and Human Health, Zhongshan Hospital of Xiamen University, Xiamen, China,Department of Digestive Disease, School of Medicine, Xiamen University, Xiamen, China,*Correspondence: Jianlin Ren, ; Hongzhi Xu,
| | - Hongzhi Xu
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China,Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China,Xiamen Key Laboratory of Intestinal Microbiome and Human Health, Zhongshan Hospital of Xiamen University, Xiamen, China,Department of Digestive Disease, School of Medicine, Xiamen University, Xiamen, China,*Correspondence: Jianlin Ren, ; Hongzhi Xu,
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37
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Yu S, Ge X, Xu H, Tan B, Tian B, Shi Y, Dai Y, Li Y, Hu S, Qian J. Gut microbiome and mycobiome in inflammatory bowel disease patients with Clostridioides difficile infection. Front Cell Infect Microbiol 2023; 13:1129043. [PMID: 36814443 PMCID: PMC9940757 DOI: 10.3389/fcimb.2023.1129043] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 01/24/2023] [Indexed: 02/08/2023] Open
Abstract
Background Clostridium difficile infection (CDI) is common in patients with inflammatory bowel disease (IBD) and has been reported as a risk factor for poor outcome. However, gut microbiome and mycobiome of IBD patients with CDI have been barely investigated. This study aimed to assess the gut microbiome and mycobiome in IBD patients with CDI. Methods We collected fecal samples from patients with active IBD and concomitant CDI (IBD-CDI group, n=25), patients with active IBD and no CDI (IBD-only group, n=51), and healthy subjects (HC, n=40). Patients' characteristics including demographic data, disease severity, and medication history were collected. Metagenomic sequencing, taxonomic and functional analysis were carried out in the samples. Results We found that the bacterial alpha diversity of the IBD-CDI group was decreased. The bacterial and fungal beta diversity variations between IBD patients and HC were significant, regardless of CDI status. But the IBD-CDI group did not significantly cluster separately from the IBD-only group. Several bacterial taxa, including Enterococcus faecium, Ruminococcus gnavus, and Clostridium innocuum were overrepresented in the IBD-CDI group. Furthermore, IBD patients with CDI were distinguished by several fungal taxa, including overrepresentation of Saccharomyces cerevisiae. We also identified functional differences in IBD patients with CDI include enrichment of peptidoglycan biosynthesis. The network analysis indicated specific interactions between microbial markers in IBD-CDI patients. Conclusion IBD patients with CDI had pronounced microbial dysbiosis. Gut micro-ecological changes in IBD patients with CDI might provide insight into the pathological process and potential strategies for diagnosis and treatment in this subset of patients.
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Affiliation(s)
- Si Yu
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiaomeng Ge
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hui Xu
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bei Tan
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bowen Tian
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yujie Shi
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yimin Dai
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yue Li
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- *Correspondence: Yue Li, ; Songnian Hu,
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Yue Li, ; Songnian Hu,
| | - Jiaming Qian
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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Association between ustekinumab therapy and changes in specific anti-microbial response, serum biomarkers, and microbiota composition in patients with IBD: A pilot study. PLoS One 2022; 17:e0277576. [PMID: 36584073 PMCID: PMC9803183 DOI: 10.1371/journal.pone.0277576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/29/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Ustekinumab, is a new therapy for patients with IBD, especially for patients suffering from Crohn's disease (CD) who did not respond to anti-TNF treatment. To shed light on the longitudinal effect of ustekinumab on the immune system, we investigated the effect on skin and gut microbiota composition, specific immune response to commensals, and various serum biomarkers. METHODOLOGY/PRINCIPAL FINDINGS We recruited 11 patients with IBD who were monitored over 40 weeks of ustekinumab therapy and 39 healthy controls (HC). We found differences in the concentrations of serum levels of osteoprotegerin, TGF-β1, IL-33, and serum IgM antibodies against Lactobacillus plantarum between patients with IBD and HC. The levels of these biomarkers did not change in response to ustekinumab treatment or with disease improvement during the 40 weeks of observation. Additionally, we identified differences in stool abundance of uncultured Subdoligranulum, Faecalibacterium, and Bacteroides between patients with IBD and HC. CONCLUSION/SIGNIFICANCE In this preliminary study, we provide a unique overview of the longitudinal monitoring of fecal and skin microbial profiles as well as various serum biomarkers and humoral and cellular response to gut commensals in a small cohort of patients with IBD on ustekinumab therapy.
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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: 115] [Impact Index Per Article: 57.5] [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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40
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Feng Y, Hang L, Zhou Y, Jiang FR, Yuan JY. Gut microbiota plays a role in irritable bowel syndrome by regulating 5-HT metabolism. Shijie Huaren Xiaohua Zazhi 2022; 30:941-949. [DOI: 10.11569/wcjd.v30.i21.941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Irritable bowel syndrome (IBS) is a common chronic functional gastrointestinal disorder. Brain-gut-microbiota axis dysfunction is an important pathogenic factor for IBS, in which neurotransmitters and gut microbes play key roles. The gastrointestinal tract contains large amounts of serotonin (5-hydroxytryptamine, 5-HT), a neurotransmitter that has been strongly linked to IBS-related symptoms. More than 90% of serotonin is synthesized in the gut by enterochromaffin cells (ECs), and certain intestinal flora can affect the occurrence and development of IBS by regulating 5-HT and its metabolism. In this review, we will discuss the role of gut microbiota in IBS by regulating 5-HT.
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Affiliation(s)
- Ya Feng
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Lu Hang
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Yan Zhou
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Feng-Ru Jiang
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Jian-Ye Yuan
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
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Huo X, Li D, Wu F, Li S, Qiao Y, Wang C, Wang Y, Zhou C, Sun L, Luan Z, Yan Q, Wang J, Zhang Y, Zhao T, An Y, Zhang B, Tian X, Yu Z, Ma X. Cultivated human intestinal fungus Candida metapsilosis M2006B attenuates colitis by secreting acyclic sesquiterpenoids as FXR agonists. Gut 2022; 71:2205-2217. [PMID: 35173042 DOI: 10.1136/gutjnl-2021-325413] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 01/25/2022] [Indexed: 12/15/2022]
Abstract
OBJECTIVE Dysbiosis of the intestinal fungal community has been observed in inflammatory bowel disease (IBD); however, its potential role in IBD development and prevention remains unclear. Here, we explored the biological effects and molecular mechanisms of intestinal fungi isolated from human faeces on colitis in mice. DESIGN Intestinal fungal strains with differential abundance in IBD were cultivated in human faeces and their effects on various mouse models of experimental colitis were evaluated. In addition, the bioactive metabolites secreted by the target fungus were accurately identified and their pharmacological effects and potential molecular targets were investigated in vitro and in vivo. RESULTS The abundance of Candida spp was significantly higher in patients with IBD. After large-scale human intestinal fungal cultivation and functional analysis, Candida metapsilosis M2006B significantly attenuated various models of experimental colitis in wild-type, antibiotic-treated, germ-free, and IL10-/- mice by activating farnesoid X receptor (FXR). Among the seven acyclic sesquiterpenoids (F1-F7) identified as major secondary metabolites of M2006B, F4 and F5 attenuated colitis in mice by acting as novel FXR agonists. The therapeutic effects of M2006B and its metabolites on colitis via specific FXR activation were confirmed in Fxr -/- mice. CONCLUSION This study revealed that C. metapsilosis M2006B significantly attenuated colitis in mice and identified two acyclic sesquiterpenoids (F4 and F5) as major active metabolites of M2006B. Notably, these metabolites were able to effectively treat experimental colitis by selectively activating FXR. Together, this study demonstrates that M2006B could be a beneficial intestinal fungus for treating and preventing IBD.
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Affiliation(s)
- Xiaokui Huo
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Pharmacy, Dalian Medical University, Dalian, China.,Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Dawei Li
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Pharmacy, Dalian Medical University, Dalian, China.,First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Fan Wu
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Pharmacy, Dalian Medical University, Dalian, China.,Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Shenghui Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Yanling Qiao
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Pharmacy, Dalian Medical University, Dalian, China.,Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Chao Wang
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Pharmacy, Dalian Medical University, Dalian, China
| | - Yan Wang
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Pharmacy, Dalian Medical University, Dalian, China
| | | | - Liqun Sun
- Dalian University Affiliated Xinhua Hospital, Dalian, China
| | - Zhilin Luan
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Pharmacy, Dalian Medical University, Dalian, China
| | - Qiulong Yan
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Pharmacy, Dalian Medical University, Dalian, China
| | - Jiayue Wang
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Pharmacy, Dalian Medical University, Dalian, China.,Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Yu Zhang
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Pharmacy, Dalian Medical University, Dalian, China.,Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Ting Zhao
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Pharmacy, Dalian Medical University, Dalian, China.,Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Yue An
- Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Baojing Zhang
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Pharmacy, Dalian Medical University, Dalian, China
| | - Xiangge Tian
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Pharmacy, Dalian Medical University, Dalian, China.,Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Zhenlong Yu
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Pharmacy, Dalian Medical University, Dalian, China
| | - Xiaochi Ma
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Pharmacy, Dalian Medical University, Dalian, China .,Second Affiliated Hospital of Dalian Medical University, Dalian, China
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42
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Dohlman AB, Klug J, Mesko M, Gao IH, Lipkin SM, Shen X, Iliev ID. A pan-cancer mycobiome analysis reveals fungal involvement in gastrointestinal and lung tumors. Cell 2022; 185:3807-3822.e12. [PMID: 36179671 PMCID: PMC9564002 DOI: 10.1016/j.cell.2022.09.015] [Citation(s) in RCA: 131] [Impact Index Per Article: 65.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/30/2022] [Accepted: 09/02/2022] [Indexed: 01/26/2023]
Abstract
Fungal microorganisms (mycobiota) comprise a small but immunoreactive component of the human microbiome, yet little is known about their role in human cancers. Pan-cancer analysis of multiple body sites revealed tumor-associated mycobiomes at up to 1 fungal cell per 104 tumor cells. In lung cancer, Blastomyces was associated with tumor tissues. In stomach cancers, high rates of Candida were linked to the expression of pro-inflammatory immune pathways, while in colon cancers Candida was predictive of metastatic disease and attenuated cellular adhesions. Across multiple GI sites, several Candida species were enriched in tumor samples and tumor-associated Candida DNA was predictive of decreased survival. The presence of Candida in human GI tumors was confirmed by external ITS sequencing of tumor samples and by culture-dependent analysis in an independent cohort. These data implicate the mycobiota in the pathogenesis of GI cancers and suggest that tumor-associated fungal DNA may serve as diagnostic or prognostic biomarkers.
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Affiliation(s)
- Anders B Dohlman
- Department of Biomedical Engineering, Center for Genomics and Computational Biology, Duke Microbiome Center, Duke University, Durham, NC 27708, USA.
| | - Jared Klug
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Marissa Mesko
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Iris H Gao
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Steven M Lipkin
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Xiling Shen
- Department of Biomedical Engineering, Center for Genomics and Computational Biology, Duke Microbiome Center, Duke University, Durham, NC 27708, USA; Terasaki Institute, Los Angeles, CA 90024, USA
| | - Iliyan D Iliev
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.
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43
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Boix-Amorós A, Monaco H, Sambataro E, Clemente JC. Novel technologies to characterize and engineer the microbiome in inflammatory bowel disease. Gut Microbes 2022; 14:2107866. [PMID: 36104776 PMCID: PMC9481095 DOI: 10.1080/19490976.2022.2107866] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We present an overview of recent experimental and computational advances in technology used to characterize the microbiome, with a focus on how these developments improve our understanding of inflammatory bowel disease (IBD). Specifically, we present studies that make use of flow cytometry and metabolomics assays to provide a functional characterization of microbial communities. We also describe computational methods for strain-level resolution, temporal series, mycobiome and virome data, co-occurrence networks, and compositional data analysis. In addition, we review novel techniques to therapeutically manipulate the microbiome in IBD. We discuss the benefits and drawbacks of these technologies to increase awareness of specific biases, and to facilitate a more rigorous interpretation of results and their potential clinical application. Finally, we present future lines of research to better characterize the relation between microbial communities and IBD pathogenesis and progression.
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Affiliation(s)
- Alba Boix-Amorós
- Department of Genetics and Genomic Sciences, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai. New York, NY, USA
| | - Hilary Monaco
- Department of Genetics and Genomic Sciences, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai. New York, NY, USA
| | - Elisa Sambataro
- Department of Biological Sciences, CUNY Hunter College, New York, NY, USA
| | - Jose C. Clemente
- Department of Genetics and Genomic Sciences, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai. New York, NY, USA,CONTACT Jose C. Clemente Department of Genetics and Genomic Sciences, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai. New York, NY10029USA
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44
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Yang Y, Cao S, Xu W, Zang C, Zhang F, Xie Y, Wu C. Dual modulation of gut bacteria and fungi manifests the gut-based anti-hyperlipidemic effect of Coptidis Rhizoma. Biomed Pharmacother 2022; 153:113542. [DOI: 10.1016/j.biopha.2022.113542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/07/2022] [Accepted: 08/10/2022] [Indexed: 11/02/2022] Open
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45
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Crnčević N, Hukić M, Deumić S, Selimagić A, Dozić A, Gavrankapetanović I, Klepo D, Avdić M. Gastrointestinal Tract Microbiome Effect and Role in Disease Development. Diseases 2022; 10:diseases10030045. [PMID: 35892739 PMCID: PMC9326677 DOI: 10.3390/diseases10030045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/17/2022] [Accepted: 07/05/2022] [Indexed: 02/01/2023] Open
Abstract
In recent years, it has been shown that gastrointestinal microflora has a substantial impact on the development of a large number of chronic diseases. The imbalance in the number or type of microbes in the gastrointestinal tract can lead to diseases and conditions, including autism spectrum disorder, celiac disease, Crohn’s disease, diabetes, and small bowel cancers. This can occur as a result of genetics, alcohol, tobacco, chemotherapeutics, cytostatics, as well as antibiotic overuse. Due to this, essential taxa can be lost, and the host’s metabolism can be severely affected. A less known condition called small intestine bacterial overgrowth (SIBO) can be seen in patients who suffer from hypochlorhydria and small intestine cancers. It is characterized as a state in which the bacterial population in the small intestine exceeds 105–106 organisms/mL. The latest examination methods such as double-balloon enteroscopy and wireless capsule endoscopy have the potential to increase the accuracy and precision of diagnosis and provide better patient care. This review paper aims to summarize the effect of the gastrointestinal environment on chronic disease severity and the development of cancers.
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Affiliation(s)
- Neira Crnčević
- Department of Genetics and Bioengineering, International Burch University, Francuske revolucije bb, Ilidža, 71210 Sarajevo, Bosnia and Herzegovina; (S.D.); (D.K.); (M.A.)
- Correspondence: ; Tel.: +387-61-034-487
| | - Mirsada Hukić
- Academy of Sciences and Arts of Bosnia and Herzegovina, Center for Disease Control and Geohealth Studies, Bistrik 7, 71000 Sarajevo, Bosnia and Herzegovina;
- Institute for Biomedical Diagnostics and Research Nalaz, Čekaluša 69, 71000 Sarajevo, Bosnia and Herzegovina
| | - Sara Deumić
- Department of Genetics and Bioengineering, International Burch University, Francuske revolucije bb, Ilidža, 71210 Sarajevo, Bosnia and Herzegovina; (S.D.); (D.K.); (M.A.)
| | - Amir Selimagić
- Department of Gastroenterohepatology, General Hospital “Prim. dr. Abdulah Nakas”, 71000 Sarajevo, Bosnia and Herzegovina;
| | - Ada Dozić
- Department of Internal Medicine, General Hospital “Prim. dr. Abdulah Nakas”, 71000 Sarajevo, Bosnia and Herzegovina;
| | - Ismet Gavrankapetanović
- University Clinical Center Sarajevo, Clinic of Orthopedics and Traumatology, Bolnička 25, 71000 Sarajevo, Bosnia and Herzegovina;
| | - Dženana Klepo
- Department of Genetics and Bioengineering, International Burch University, Francuske revolucije bb, Ilidža, 71210 Sarajevo, Bosnia and Herzegovina; (S.D.); (D.K.); (M.A.)
| | - Monia Avdić
- Department of Genetics and Bioengineering, International Burch University, Francuske revolucije bb, Ilidža, 71210 Sarajevo, Bosnia and Herzegovina; (S.D.); (D.K.); (M.A.)
- Academy of Sciences and Arts of Bosnia and Herzegovina, Center for Disease Control and Geohealth Studies, Bistrik 7, 71000 Sarajevo, Bosnia and Herzegovina;
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46
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Gubatan J, Boye TL, Temby M, Sojwal RS, Holman DR, Sinha SR, Rogalla SR, Nielsen OH. Gut Microbiome in Inflammatory Bowel Disease: Role in Pathogenesis, Dietary Modulation, and Colitis-Associated Colon Cancer. Microorganisms 2022; 10:1371. [PMID: 35889090 PMCID: PMC9316834 DOI: 10.3390/microorganisms10071371] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/03/2022] [Accepted: 07/05/2022] [Indexed: 12/11/2022] Open
Abstract
The gut microbiome has increasingly been recognized as a critical and central factor in inflammatory bowel disease (IBD). Here, we review specific microorganisms that have been suggested to play a role in the pathogenesis of IBD and the current state of fecal microbial transplants as a therapeutic strategy in IBD. We discuss specific nutritional and dietary interventions in IBD and their effects on gut microbiota composition. Finally, we examine the role and mechanisms of the gut microbiome in mediating colitis-associated colon cancer.
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Affiliation(s)
- John Gubatan
- Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.T.); (R.S.S.); (D.R.H.); (S.R.S.); (S.R.R.)
| | - Theresa Louise Boye
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, DK-2730 Copenhagen, Denmark; (T.L.B.); or (O.H.N.)
| | - Michelle Temby
- Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.T.); (R.S.S.); (D.R.H.); (S.R.S.); (S.R.R.)
| | - Raoul S. Sojwal
- Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.T.); (R.S.S.); (D.R.H.); (S.R.S.); (S.R.R.)
| | - Derek R. Holman
- Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.T.); (R.S.S.); (D.R.H.); (S.R.S.); (S.R.R.)
| | - Sidhartha R. Sinha
- Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.T.); (R.S.S.); (D.R.H.); (S.R.S.); (S.R.R.)
| | - Stephan R. Rogalla
- Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.T.); (R.S.S.); (D.R.H.); (S.R.S.); (S.R.R.)
| | - Ole Haagen Nielsen
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, DK-2730 Copenhagen, Denmark; (T.L.B.); or (O.H.N.)
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47
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Li Q, Zhou S, Wang Y, Cong J. Changes of intestinal microbiota and microbiota-based treatments in IBD. Arch Microbiol 2022; 204:442. [PMID: 35776212 DOI: 10.1007/s00203-022-03069-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/13/2022] [Indexed: 12/15/2022]
Abstract
Inflammatory bowel disease (IBD) has gained increasing attention from researchers in terms of its pathophysiology as a global disease with a growing incidence. Although the exact etiology of IBD is still unknown currently, various studies have made us realize that it is related to the dysbiosis of intestinal microbiota and the link between the two may not just be a simple causal relationship, but also a dynamic and complicated one. The intestinal microbiota has been confirmed to be closely related to the occurrence, development, and treatment of IBD. Therefore, this review focuses on the changes in the structure, function, and metabolites of intestinal bacteria, fungi, and viruses in influencing IBD, as well as various approaches to IBD treatment by changing disordered intestinal microbiota. Ultimately, more clinical studies will be needed to focus on the efficacy of intestinal microbiota-based treatments in IBD, because of the existence of both advantages and disadvantages.
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Affiliation(s)
- Qianyu Li
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, People's Republic of China
| | - Siyu Zhou
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, People's Republic of China
| | - Yanna Wang
- Department of Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Jing Cong
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, People's Republic of China.
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48
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Mycobiota composition and changes across pregnancy in patients with gestational diabetes mellitus (GDM). Sci Rep 2022; 12:9192. [PMID: 35654937 PMCID: PMC9163055 DOI: 10.1038/s41598-022-13438-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/12/2022] [Indexed: 01/09/2023] Open
Abstract
The gut mycobiota has never been studied either during pregnancy or in patients with gestational diabetes (GDM). This study aimed to analyze the fecal mycobiota of GDM patients during the second (T2) and third (T3) trimester of pregnancy and to compare it with the mycobiota of pregnant normoglycemic women (controls). Forty-one GDM patients and 121 normoglycemic women were studied. GDM mycobiota was composed almost exclusively by the Ascomycota phylum; Basidiomicota accounted for 43% of the relative frequency of the controls. Kluyveromyces (p < 0.001), Metschnikowia (p < 0.001), and Pichia (p < 0.001) showed a significantly higher frequency in GDM patients, while Saccharomyces (p = 0.019), were more prevalent in controls. From T2 to T3, a reduction in fungal alpha diversity was found in GDM patients, with an increase of the relative frequency of Candida, and the reduction of some pro-inflammatory taxa. Many associations between fungi and foods and nutrients were detected. Finally, several fungi and bacteria showed competition or co-occurrence. Patients with GDM showed a predominance of fungal taxa with potential inflammatory effects when compared to normoglycemic pregnant women, with a marked shift in their mycobiota during pregnancy, and complex bacteria-fungi interactions.
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49
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Metwaly A, Reitmeier S, Haller D. Microbiome risk profiles as biomarkers for inflammatory and metabolic disorders. Nat Rev Gastroenterol Hepatol 2022; 19:383-397. [PMID: 35190727 DOI: 10.1038/s41575-022-00581-2] [Citation(s) in RCA: 88] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/10/2022] [Indexed: 12/12/2022]
Abstract
The intestine harbours a complex array of microorganisms collectively known as the gut microbiota. The past two decades have witnessed increasing interest in studying the gut microbiota in health and disease, largely driven by rapid innovation in high-throughput multi-omics technologies. As a result, microbial dysbiosis has been linked to many human pathologies, including type 2 diabetes mellitus and inflammatory bowel disease. Integrated analyses of multi-omics data, including metagenomics and metabolomics along with measurements of host response and cataloguing of bacterial isolates, have identified many bacteria and bacterial products that are correlated with disease. Nevertheless, insight into the mechanisms through which microbes affect intestinal health requires going beyond correlation to causation. Current understanding of the contribution of the gut microbiota to disease causality remains limited, largely owing to the heterogeneity of microbial community structures, interindividual differences in disease evolution and incomplete understanding of the mechanisms that integrate microbiota-derived signals into host signalling pathways. In this Review, we provide a broad insight into the microbiome signatures linked to inflammatory and metabolic disorders, discuss outstanding challenges in this field and propose applications of multi-omics technologies that could lead to an improved mechanistic understanding of microorganism-host interactions.
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Affiliation(s)
- Amira Metwaly
- Chair of Nutrition and Immunology, Technical University of Munich, Freising, Germany
| | - Sandra Reitmeier
- ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Dirk Haller
- Chair of Nutrition and Immunology, Technical University of Munich, Freising, Germany. .,ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany.
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50
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Li M, Zhang R, Li J, Li J. The Role of C-Type Lectin Receptor Signaling in the Intestinal Microbiota-Inflammation-Cancer Axis. Front Immunol 2022; 13:894445. [PMID: 35619716 PMCID: PMC9127077 DOI: 10.3389/fimmu.2022.894445] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/04/2022] [Indexed: 12/13/2022] Open
Abstract
As a subset of pattern recognition receptors (PRRs), C-type lectin-like receptors (CLRs) are mainly expressed by myeloid cells as both transmembrane and soluble forms. CLRs recognize not only pathogen associated molecular patterns (PAMPs), but also damage-associated molecular patterns (DAMPs) to promote innate immune responses and affect adaptive immune responses. Upon engagement by PAMPs or DAMPs, CLR signaling initiates various biological activities in vivo, such as cytokine secretion and immune cell recruitment. Recently, several CLRs have been implicated as contributory to the pathogenesis of intestinal inflammation, which represents a prominent risk factor for colorectal cancer (CRC). CLRs function as an interface among microbiota, intestinal epithelial barrier and immune system, so we firstly discussed the relationship between dysbiosis caused by microbiota alteration and inflammatory bowel disease (IBD), then focused on the role of CLRs signaling in pathogenesis of IBD (including Mincle, Dectin-3, Dectin-1, DCIR, DC-SIGN, LOX-1 and their downstream CARD9). Given that CLRs mediate intricate inflammatory signals and inflammation plays a significant role in tumorigenesis, we finally highlight the specific effects of CLRs on CRC, especially colitis-associated cancer (CAC), hoping to open new horizons on pathogenesis and therapeutics of IBD and CAC.
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Affiliation(s)
- Muhan Li
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Key Laboratory of Gut Microbiota Translational Medicine Research, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Runfeng Zhang
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Key Laboratory of Gut Microbiota Translational Medicine Research, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ji Li
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Key Laboratory of Gut Microbiota Translational Medicine Research, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jingnan Li
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Key Laboratory of Gut Microbiota Translational Medicine Research, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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