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Angebault C, Botterel F. Metagenomics Applied to the Respiratory Mycobiome in Cystic Fibrosis. Mycopathologia 2024; 189:82. [PMID: 39264513 PMCID: PMC11392981 DOI: 10.1007/s11046-024-00887-6] [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: 05/10/2024] [Accepted: 08/21/2024] [Indexed: 09/13/2024]
Abstract
Cystic fibrosis (CF) is a genetic disorder characterized by chronic microbial colonization and inflammation of the respiratory tract (RT), leading to pulmonary exacerbation (PEx) and lung damage. Although the lung bacterial microbiota has been extensively studied, the mycobiome remains understudied. However, its importance as a contributor to CF pathophysiology has been highlighted. The objective of this review is to provide an overview of the current state of knowledge regarding the mycobiome, as described through NGS-based studies, in patients with CF (pwCF).Several studies have demonstrated that the mycobiome in CF lungs is a dynamic entity, exhibiting a lower diversity and abundance than the bacterial microbiome. Nevertheless, the progression of lung damage is associated with a decrease in fungal and bacterial diversity. The core mycobiome of the RT in pwCFs is mainly composed of yeasts (Candida spp., Malassezia spp.) and molds with lower abundance. Some fungi (Aspergillus, Scedosporium/Pseudallescheria) have been demonstrated to play a role in PEx, while the involvement of others (Candida, Pneumocystis) remains uncertain. The "climax attack" ecological model has been proposed to explain the complexity and interplay of microbial populations in the RT, leading to PEx and lung damage. NGS-based studies also enable the detection of intra- and interkingdom correlations between fungi and bacteria. Further studies are required to ascertain the biological and pathophysiological relevance of these correlations. Finally, with the recent advent of CFTR modulators, our understanding of the pulmonary microbiome and mycobiome in pwCFs is about to change.
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Affiliation(s)
- Cécile Angebault
- Unité de Parasitologie-Mycologie, Département de Prévention, Diagnostic et Traitement des Infections, Hôpitaux Universitaires Henri Mondor, Assistance Publique des Hôpitaux de Paris (APHP), Créteil, France.
- Dynamyc UR 7380, USC Anses, Ecole Nationale Vétérinaire d'Alfort (ENVA), Faculté de Santé, Univ. Paris-Est Créteil (UPEC), Créteil, France.
| | - Françoise Botterel
- Unité de Parasitologie-Mycologie, Département de Prévention, Diagnostic et Traitement des Infections, Hôpitaux Universitaires Henri Mondor, Assistance Publique des Hôpitaux de Paris (APHP), Créteil, France
- Dynamyc UR 7380, USC Anses, Ecole Nationale Vétérinaire d'Alfort (ENVA), Faculté de Santé, Univ. Paris-Est Créteil (UPEC), Créteil, France
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2
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Wei G. Insights into gut fungi in pigs: A comprehensive review. J Anim Physiol Anim Nutr (Berl) 2024. [PMID: 39154229 DOI: 10.1111/jpn.14036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 06/17/2024] [Accepted: 08/04/2024] [Indexed: 08/19/2024]
Abstract
Fungi in the gut microbiota of mammals play a crucial role in host physiological regulation, including intestinal homeostasis and host immune regulation. However, our understanding of gut fungi in mammals remains limited, especially in economically valuable animals, such as pigs. Therefore, this review first describes the classification and characterisation of fungi, provides insights into the methods used to study gut fungi, and summarises the recent progress on pig gut fungi. Additionally, it discusses the challenges in the study of pig gut fungi and highlights potential perspectives. The aim of this review is to serve as a valuable reference for advancing our knowledge of gut fungi in animals.
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Affiliation(s)
- Guanyue Wei
- National Key Laboratory of Pig Genetic Improvement and Germplasm Innovation, Jiangxi Agricultural University, Nanchang, China
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3
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Yan Q, Li S, Yan Q, Huo X, Wang C, Wang X, Sun Y, Zhao W, Yu Z, Zhang Y, Guo R, Lv Q, He X, Yao C, Li Z, Chen F, Ji Q, Zhang A, Jin H, Wang G, Feng X, Feng L, Wu F, Ning J, Deng S, An Y, Guo DA, Martin FM, Ma X. A genomic compendium of cultivated human gut fungi characterizes the gut mycobiome and its relevance to common diseases. Cell 2024; 187:2969-2989.e24. [PMID: 38776919 DOI: 10.1016/j.cell.2024.04.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 02/17/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
The gut fungal community represents an essential element of human health, yet its functional and metabolic potential remains insufficiently elucidated, largely due to the limited availability of reference genomes. To address this gap, we presented the cultivated gut fungi (CGF) catalog, encompassing 760 fungal genomes derived from the feces of healthy individuals. This catalog comprises 206 species spanning 48 families, including 69 species previously unidentified. We explored the functional and metabolic attributes of the CGF species and utilized this catalog to construct a phylogenetic representation of the gut mycobiome by analyzing over 11,000 fecal metagenomes from Chinese and non-Chinese populations. Moreover, we identified significant common disease-related variations in gut mycobiome composition and corroborated the associations between fungal signatures and inflammatory bowel disease (IBD) through animal experimentation. These resources and findings substantially enrich our understanding of the biological diversity and disease relevance of the human gut mycobiome.
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Affiliation(s)
- Qiulong Yan
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China; Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China; College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Shenghui Li
- Puensum Genetech Institute, Wuhan 430076, China; Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100091, China
| | - Qingsong Yan
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Xiaokui Huo
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Chao Wang
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China; Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China; First Affiliated Hospital, Dalian Medical University, Dalian 116044, China.
| | - Xifan Wang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100091, China; Department of Obstetrics and Gynecology, Columbia University, New York, NY 10027, USA
| | - Yan Sun
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Wenyu Zhao
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Zhenlong Yu
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan 430076, China
| | - Ruochun Guo
- Puensum Genetech Institute, Wuhan 430076, China
| | - Qingbo Lv
- Puensum Genetech Institute, Wuhan 430076, China
| | - Xin He
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China; Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China
| | - Changliang Yao
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China
| | | | - Fang Chen
- College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Qianru Ji
- Puensum Genetech Institute, Wuhan 430076, China
| | - Aiqin Zhang
- Puensum Genetech Institute, Wuhan 430076, China
| | - Hao Jin
- Puensum Genetech Institute, Wuhan 430076, China
| | - Guangyang Wang
- College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Xiaoying Feng
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Lei Feng
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Fan Wu
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Jing Ning
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Sa Deng
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Yue An
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - De-An Guo
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China.
| | - Francis M Martin
- Université de Lorraine, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux 54280, France; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100091, China.
| | - Xiaochi Ma
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China; Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China.
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Trecarten S, Fongang B, Liss M. Current Trends and Challenges of Microbiome Research in Prostate Cancer. Curr Oncol Rep 2024; 26:477-487. [PMID: 38573440 DOI: 10.1007/s11912-024-01520-x] [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] [Accepted: 03/18/2024] [Indexed: 04/05/2024]
Abstract
PURPOSE OF REVIEW The role of the gut microbiome in prostate cancer is an emerging area of research interest. However, no single causative organism has yet been identified. The goal of this paper is to examine the role of the microbiome in prostate cancer and summarize the challenges relating to methodology in specimen collection, sequencing technology, and interpretation of results. RECENT FINDINGS Significant heterogeneity still exists in methodology for stool sampling/storage, preservative options, DNA extraction, and sequencing database selection/in silico processing. Debate persists over primer choice in amplicon sequencing as well as optimal methods for data normalization. Statistical methods for longitudinal microbiome analysis continue to undergo refinement. While standardization of methodology may help yield more consistent results for organism identification in prostate cancer, this is a difficult task due to considerable procedural variation at each step in the process. Further reproducibility and methodology research is required.
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Affiliation(s)
- Shaun Trecarten
- Department of Urology, UT Health San Antonio, 7703 Floyd Curl Dr, San Antonio, TX, 78229, USA
| | - Bernard Fongang
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX, USA
- Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, TX, USA
- Department of Population Health Sciences, UT Health San Antonio, San Antonio, TX, USA
| | - Michael Liss
- Department of Urology, UT Health San Antonio, 7703 Floyd Curl Dr, San Antonio, TX, 78229, USA.
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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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Guo J, Shi W, Li X, Yang B, Qin C, Su L. Comparative Analysis of Gut Microbiomes in Laboratory Chinchillas, Ferrets, and Marmots: Implications for Pathogen Infection Research. Microorganisms 2024; 12:646. [PMID: 38674591 PMCID: PMC11051751 DOI: 10.3390/microorganisms12040646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/17/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
Gut microbes play a vital role in the health and disease of animals, especially in relation to pathogen infections. Chinchillas, ferrets, and marmots are commonly used as important laboratory animals for infectious disease research. Here, we studied the bacterial and fungal microbiota and discovered that chinchillas had higher alpha diversity and a higher abundance of bacteria compared to marmots and ferrets by using the metabarcoding of 16S rRNA genes and ITS2, coupled with co-occurrence network analysis. The dominant microbes varied significantly among the three animal species, particularly in the gut mycobiota. In the ferrets, the feces were dominated by yeast such as Rhodotorula and Kurtzmaniella, while in the chinchillas, we found Teunomyces and Penicillium dominating, and Acaulium, Piromyces, and Kernia in the marmots. Nevertheless, the dominant bacterial genera shared some similarities, such as Clostridium and Pseudomonas across the three animal species. However, there were significant differences observed, such as Vagococcus and Ignatzschineria in the ferrets, Acinetobacter and Bacteroides in the chinchillas, and Bacteroides and Cellvibrio in the marmots. Additionally, our differential analysis revealed significant differences in classification levels among the three different animal species, as well as variations in feeding habitats that resulted in distinct contributions from the host microbiome. Therefore, our data are valuable for monitoring and evaluating the impacts of the microbiome, as well as considering potential applications.
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Affiliation(s)
| | | | | | | | | | - Lei Su
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, International Center for Technology and Innovation of Animal Model, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Comparative Medicine Center, Peking Union Medical College (PUMC), Beijing 100021, China; (J.G.); (W.S.); (X.L.); (B.Y.); (C.Q.)
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7
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Yadav A, Yadav R, Sharma V, Dutta U. A comprehensive guide to assess gut mycobiome and its role in pathogenesis and treatment of inflammatory bowel disease. Indian J Gastroenterol 2024; 43:112-128. [PMID: 38409485 DOI: 10.1007/s12664-023-01510-0] [Citation(s) in RCA: 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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8
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Buttar J, Kon E, Lee A, Kaur G, Lunken G. Effect of diet on the gut mycobiome and potential implications in inflammatory bowel disease. Gut Microbes 2024; 16:2399360. [PMID: 39287010 PMCID: PMC11409510 DOI: 10.1080/19490976.2024.2399360] [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: 09/07/2023] [Revised: 07/31/2024] [Accepted: 08/28/2024] [Indexed: 09/19/2024] Open
Abstract
The gut microbiome is a complex, unique entity implicated in the prevention, pathogenesis, and progression of common gastrointestinal diseases. While largely dominated by bacterial populations, advanced sequencing techniques have identified co-inhabiting fungal communities, collectively referred to as the mycobiome. Early studies identified that gut inflammation is associated with altered microbial composition, known as gut dysbiosis. Altered microbial profiles are implicated in various pathological diseases, such as inflammatory bowel disease (IBD), though their role as a cause or consequence of systemic inflammation remains the subject of ongoing research. Diet plays a crucial role in the prevention and management of various diseases and is considered to be an essential regulator of systemic inflammation. This review compiles current literature on the impact of dietary modulation on the mycobiome, showing that dietary changes can alter the fungal architecture of the gut. Further research is required to understand the impact of diet on gut fungi, including the metabolic pathways and enzymes involved in fungal fermentation. Additionally, investigating whether dietary modulation of the gut mycobiome could be utilized as a therapy in IBD is essential.
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Affiliation(s)
- J Buttar
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - E Kon
- Department of Pediatrics, University of British Columbia, Vancouver, Canada
- BC Children's Hospital Research Institute, Vancouver, Canada
| | - A Lee
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, Canada
| | - G Kaur
- Department of Pediatrics, University of British Columbia, Vancouver, Canada
| | - G Lunken
- Department of Medicine, University of British Columbia, Vancouver, Canada
- Department of Pediatrics, University of British Columbia, Vancouver, Canada
- BC Children's Hospital Research Institute, Vancouver, Canada
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Rintarhat P, Cho YJ, Koh H, Park S, Lee EJ, Lim H, Noh J, Lee DW, Jung WH. Assessment of DNA extraction methods for human gut mycobiome analysis. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231129. [PMID: 38204788 PMCID: PMC10776226 DOI: 10.1098/rsos.231129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 12/11/2023] [Indexed: 01/12/2024]
Abstract
The gut mycobiome plays an important role in the health and disease of the human gut, but its exact function is still under investigation. While there is a wealth of information available on the bacterial community of the human gut microbiome, research on the fungal community is still relatively limited. In particular, technical methodologies for mycobiome analysis, especially the DNA extraction method for human faecal samples, varied in different studies. In the current study, two commercial kits commonly used in DNA extraction, the QIAamp® Fast DNA Stool Mini Kit and DNeasy PowerSoil Pro Kit, and one manual method, the International Human Microbiome Standards Protocol Q, were compared. Furthermore, the effectiveness of two different bead-beating machines, the Mini-Beadbeater-16 and FastPrep-24TM 5G, was compared in parallel. A mock fungal community with a known composition of fungal strains was also generated and included to compare different DNA extraction methods. Our results suggested that the method using the DNeasy PowerSoil Pro Kit and Mini-Beadbeater-16 provides the best results to extract DNA from human faecal samples. Based on our data, we propose a standard operating procedure for DNA extraction from human faecal samples for mycobiome analysis.
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Affiliation(s)
- Piyapat Rintarhat
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Korea
| | - Yong-Joon Cho
- Department of Molecular Bioscience, Kangwon National University, Chuncheon 24341, Korea
| | - Hong Koh
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Sowon Park
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Eun Joo Lee
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Hyeji Lim
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Jihye Noh
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Dong-Woo Lee
- Department of Biotechnology, Yonsei University, Seoul, Korea
| | - Won Hee Jung
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Korea
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Lu J, Zhang X, Zhang X, Wang L, Zhao R, Liu XY, Liu X, Zhuang W, Chen L, Cai L, Wang J. Nanopore sequencing of full rRNA operon improves resolution in mycobiome analysis and reveals high diversity in both human gut and environments. Mol Ecol 2023; 32:6330-6344. [PMID: 35593386 DOI: 10.1111/mec.16534] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 04/24/2022] [Accepted: 05/12/2022] [Indexed: 10/18/2022]
Abstract
High-throughput sequencing has substantially improved our understanding of fungal diversity. However, the short read (<500 bp) length of current second-generation sequencing approaches provides limited taxonomic and phylogenetic resolution for species discrimination. Longer sequences containing more information are highly desired to provide greater taxonomic resolution. Here, we amplified full-length rRNA operons (~5.5 kb) and established a corresponding fungal rRNA operon database for ONT sequences (FRODO), which contains ONT sequences representing eight phyla, 41 classes, 109 orders, 256 families, 524 genera and 1116 species. We also benchmarked the optimal method for sequence classification and determined that the RDP classifier based on our FRODO database was capable of improving the classification of ONT reads, with an average of 98%-99% reads correctly classified at the genus or species level. We investigated the applicability of our approach in three representative mycobiomes, namely, the soil, marine and human gut mycobiomes, and found that the gut contains the largest number of unknown species (over 90%), followed by the marine (42%) and soil (33.8%) mycobiomes. We also observed a distinct difference in the composition of the marine and soil mycobiomes, with the highest richness and diversity detected in soils. Overall, our study provides a systematic approach for mycobiome studies and revealed that the previous methods might have underestimated the diversity of mycobiome species. Future application of this method will lead to a better understanding of the taxonomic and functional diversity of fungi in environmental and health-related mycobiomes.
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Affiliation(s)
- Jingjing Lu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xudong Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xuan Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Linqi Wang
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ruilin Zhao
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiao Yong Liu
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Xinzhan Liu
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wenying Zhuang
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Liang Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Lei Cai
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jun Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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11
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Renzi S, Nenciarini S, Bacci G, Cavalieri D. Yeast metagenomics: analytical challenges in the analysis of the eukaryotic microbiome. MICROBIOME RESEARCH REPORTS 2023; 3:2. [PMID: 38455081 PMCID: PMC10917621 DOI: 10.20517/mrr.2023.27] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 10/09/2023] [Accepted: 10/17/2023] [Indexed: 03/09/2024]
Abstract
Even if their impact is often underestimated, yeasts and yeast-like fungi represent the most prevalent eukaryotic members of microbial communities on Earth. They play numerous roles in natural ecosystems and in association with their hosts. They are involved in the food industry and pharmaceutical production, but they can also cause diseases in other organisms, making the understanding of their biology mandatory. The ongoing loss of biodiversity due to overexploitation of environmental resources is a growing concern in many countries. Therefore, it becomes crucial to understand the ecology and evolutionary history of these organisms to systematically classify them. To achieve this, it is essential that our knowledge of the mycobiota reaches a level similar to that of the bacterial communities. To overcome the existing challenges in the study of fungal communities, the first step should be the establishment of standardized techniques for the correct identification of species, even from complex matrices, both in wet lab practices and in bioinformatic tools.
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Affiliation(s)
| | | | | | - Duccio Cavalieri
- Correspondence to: Prof. Duccio Cavalieri, Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino 50019, Italy. E-mail:
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Arfken AM, Frey JF, Carrillo NI, Dike NI, Onyeachonamm O, Rivera DN, Davies CP, Summers KL. Porcine fungal mock community analyses: Implications for mycobiome investigations. Front Cell Infect Microbiol 2023; 13:928353. [PMID: 36844394 PMCID: PMC9945231 DOI: 10.3389/fcimb.2023.928353] [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: 04/25/2022] [Accepted: 01/16/2023] [Indexed: 02/11/2023] Open
Abstract
Introduction The gut microbiome is an integral partner in host health and plays a role in immune development, altered nutrition, and pathogen prevention. The mycobiome (fungal microbiome) is considered part of the rare biosphere but is still a critical component in health. Next generation sequencing has improved our understanding of fungi in the gut, but methodological challenges remain. Biases are introduced during DNA isolation, primer design and choice, polymerase selection, sequencing platform selection, and data analyses, as fungal reference databases are often incomplete or contain erroneous sequences. Methods Here, we compared the accuracy of taxonomic identifications and abundances from mycobiome analyses which vary among three commonly selected target gene regions (18S, ITS1, or ITS2) and the reference database (UNITE - ITS1, ITS2 and SILVA - 18S). We analyze multiple communities including individual fungal isolates, a mixed mock community created from five common fungal isolates found in weanling piglet feces, a purchased commercial fungal mock community, and piglet fecal samples. In addition, we calculated gene copy numbers for the 18S, ITS1, and ITS2 regions of each of the five isolates from the piglet fecal mock community to determine whether copy number affects abundance estimates. Finally, we determined the abundance of taxa from several iterations of our in-house fecal community to assess the effects of community composition on taxon abundance. Results Overall, no marker-database combination consistently outperformed the others. Internal transcribed space markers were slightly superior to 18S in the identification of species in tested communities, but Lichtheimia corymbifera, a common member of piglet gut communities, was not amplified by ITS1 and ITS2 primers. Thus, ITS based abundance estimates of taxa in piglet mock communities were skewed while 18S marker profiles were more accurate. Kazachstania slooffiae displayed the most stable copy numbers (83-85) while L. corymbifera displayed significant variability (90-144) across gene regions. Discussion This study underscores the importance of preliminary studies to assess primer combinations and database choice for the mycobiome sample of interest and raises questions regarding the validity of fungal abundance estimates.
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Affiliation(s)
- Ann M. Arfken
- Oak Ridge Institute for Science and Education, Center for Disease Control, Atlanta, GA, United States
| | - Juli Foster Frey
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Nora Isabel Carrillo
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Nneka Ijeoma Dike
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Ogechukwu Onyeachonamm
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Daniela Nieves Rivera
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Cary Pirone Davies
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Katie Lynn Summers
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
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13
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Maas E, Penders J, Venema K. Modelling the Gut Fungal-Community in TIM-2 with a Microbiota from Healthy Individuals. J Fungi (Basel) 2023; 9:jof9010104. [PMID: 36675926 PMCID: PMC9866872 DOI: 10.3390/jof9010104] [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: 12/03/2022] [Revised: 01/07/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
Most research on the human microbiome focuses on the bacterial component, and this has led to a lack of information about the fungal component (mycobiota) and how this can influence human health, e.g., by modulation through the diet. The validated, dynamic computer-controlled model of the colon (TIM-2) is an in vitro model to study the microbiome and how this is influenced by interventions such as diet. In this study, it was used to the study the gut fungal-community. This was done in combination with next-generation sequencing of the ITS2 region for fungi and 16S rRNA for bacteria. Different dietary interventions (control diet (SIEM), high-carbohydrate, high-protein, glucose as a carbon source) were performed, to see if diet could shape the mycobiome. The mycobiome was investigated after the adaptation period, and throughout the intervention period which lasted 72 h, and samples were taken every 24 h. The fungal community showed low diversity and a greater variability when compared to bacteria. The mycobiome was affected most in the first hours of the adaptation period. Taxonomic classification showed that at the phylum-level Ascomycota and Basidiomycota dominated, while Agaricus, Aspergillus, Candida, Penicillum, Malassezia, Saccharomyces, Aureobasidium, Mycosphaerella, Mucor and Clavispora were the most abundant genera. During the intervention period, it was shown that the change of diet could influence the diversity. Clustering of samples for different time points was analyzed using Bray−Curtis dissimilarities. Samples of t0 clustered together, and samples of all other time points clustered together. The Bray−Curtis-dissimilarity analysis also showed that for the different dietary interventions, samples treated with glucose clustered together and were different from the other groups (p < 0.05, PERMANOVA). Taxonomic classification showed that the genera Alternaria, Thanatephorus, Candida and Dekkera differentially changed for the various diet groups (p < 0.05, Kruskal−Wallis). These results show that the mycobiota could be modelled in TIM-2; however, the low diversity and high variability make studying fungal, as compared to bacterial, communities, much more challenging. Future research should focus on the optimization of the stability of the fungal community to increase the strength of the results.
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Affiliation(s)
- Evy Maas
- Centre for Healthy Eating & Food Innovation, Maastricht University—Campus Venlo, Villa Floraweg 1, 5928 SZ Venlo, The Netherlands
- Euregional Microbiome Center, P. Debyelaan 25, 6229 HX Maastricht, The Netherlands
| | - John Penders
- Euregional Microbiome Center, P. Debyelaan 25, 6229 HX Maastricht, The Netherlands
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM) and Care and Public Health Research Institute (Caphri), Maastricht University, P. Debyelaan 25, 6229 HX Maastricht, The Netherlands
| | - Koen Venema
- Centre for Healthy Eating & Food Innovation, Maastricht University—Campus Venlo, Villa Floraweg 1, 5928 SZ Venlo, The Netherlands
- Euregional Microbiome Center, P. Debyelaan 25, 6229 HX Maastricht, The Netherlands
- Correspondence: ; Tel.: +31-622435111
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14
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James SA, Parker A, Purse C, Telatin A, Baker D, Holmes S, Durham J, Funnell SGP, Carding SR. The Cynomolgus Macaque Intestinal Mycobiome Is Dominated by the Kazachstania Genus and K. pintolopesii Species. J Fungi (Basel) 2022; 8:1054. [PMID: 36294619 PMCID: PMC9605169 DOI: 10.3390/jof8101054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/02/2022] [Accepted: 09/30/2022] [Indexed: 08/10/2023] Open
Abstract
The cynomolgus macaque, Macaca fascicularis, is a non-human primate (NHP) widely used in biomedical research as its genetics, immunology and physiology are similar to those of humans. They may also be a useful model of the intestinal microbiome as their prokaryome resembles that of humans. However, beyond the prokaryome relatively little is known about other constituents of the macaque intestinal microbiome including the mycobiome. Here, we conducted a region-by-region taxonomic survey of the cynomolgus intestinal mycobiota, from duodenum to distal colon, of sixteen captive animals of differing age (from young to old). Using a high-throughput ITS1 amplicon sequencing-based approach, the cynomolgus gut mycobiome was dominated by fungi from the Ascomycota phylum. The budding yeast genus Kazachstania was most abundant, with the thermotolerant species K. pintolopesii highly prevalent, and the predominant species in both the small and large intestines. This is in marked contrast to humans, in which the intestinal mycobiota is characterised by other fungal genera including Candida and Saccharomyces, and Candida albicans. This study provides a comprehensive insight into the fungal communities present within the captive cynomolgus gut, and for the first time identifies K. pintolopesii as a candidate primate gut commensal.
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Affiliation(s)
- Steve A. James
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Aimee Parker
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Catherine Purse
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Andrea Telatin
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - David Baker
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Sandy Holmes
- UK Health Security Agency, Porton Down, Salisbury SP4 0JG, UK
| | - James Durham
- UK Health Security Agency, Porton Down, Salisbury SP4 0JG, UK
| | - Simon G. P. Funnell
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
- UK Health Security Agency, Porton Down, Salisbury SP4 0JG, UK
| | - Simon R. Carding
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
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15
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Parker A, James SA, Purse C, Brion A, Goldson A, Telatin A, Baker D, Carding SR. Absence of Bacteria Permits Fungal Gut-To-Brain Translocation and Invasion in Germfree Mice but Ageing Alone Does Not Drive Pathobiont Expansion in Conventionally Raised Mice. Front Aging Neurosci 2022; 14:828429. [PMID: 35923548 PMCID: PMC9339909 DOI: 10.3389/fnagi.2022.828429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Age-associated changes in the structure of the intestinal microbiome and in its interaction with the brain via the gut-brain axis are increasingly being implicated in neurological and neurodegenerative diseases. Intestinal microbial dysbiosis and translocation of microbes and microbial products including fungal species into the brain have been implicated in the development of dementias such as Alzheimer's disease. Using germ-free mice, we investigated if the fungal gut commensal, Candida albicans, an opportunistic pathogen in humans, can traverse the gastrointestinal barrier and disseminate to brain tissue and whether ageing impacts on the gut mycobiome as a pre-disposing factor in fungal brain infection. C. albicans was detected in different regions of the brain of colonised germ-free mice in both yeast and hyphal cell forms, often in close association with activated (Iba-1+) microglial cells. Using high-throughput ITS1 amplicon sequencing to characterise the faecal gut fungal composition of aged and young SPF mice, we identified several putative gut commensal fungal species with pathobiont potential although their abundance was not significantly different between young and aged mice. Collectively, these results suggest that although some fungal species can travel from the gut to brain where they can induce an inflammatory response, ageing alone is not correlated with significant changes in gut mycobiota composition which could predispose to these events. These results are consistent with a scenario in which significant disruptions to the gut microbiota or intestinal barrier, beyond those which occur with natural ageing, are required to allow fungal escape and brain infection.
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Affiliation(s)
- Aimée Parker
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich, United Kingdom
| | - Steve A. James
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich, United Kingdom
| | - Catherine Purse
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich, United Kingdom
| | - Arlaine Brion
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich, United Kingdom
| | - Andrew Goldson
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich, United Kingdom
| | - Andrea Telatin
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich, United Kingdom
| | - David Baker
- Gut Microbes and Health Research Programme, Quadram Institute, Norwich, United Kingdom
| | - Simon R. Carding
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
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16
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Sharon I, Quijada NM, Pasolli E, Fabbrini M, Vitali F, Agamennone V, Dötsch A, Selberherr E, Grau JH, Meixner M, Liere K, Ercolini D, de Filippo C, Caderni G, Brigidi P, Turroni S. The Core Human Microbiome: Does It Exist and How Can We Find It? A Critical Review of the Concept. Nutrients 2022; 14:nu14142872. [PMID: 35889831 PMCID: PMC9323970 DOI: 10.3390/nu14142872] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 11/16/2022] Open
Abstract
The core microbiome, which refers to a set of consistent microbial features across populations, is of major interest in microbiome research and has been addressed by numerous studies. Understanding the core microbiome can help identify elements that lead to dysbiosis, and lead to treatments for microbiome-related health states. However, defining the core microbiome is a complex task at several levels. In this review, we consider the current state of core human microbiome research. We consider the knowledge that has been gained, the factors limiting our ability to achieve a reliable description of the core human microbiome, and the fields most likely to improve that ability. DNA sequencing technologies and the methods for analyzing metagenomics and amplicon data will most likely facilitate higher accuracy and resolution in describing the microbiome. However, more effort should be invested in characterizing the microbiome’s interactions with its human host, including the immune system and nutrition. Other components of this holobiontic system should also be emphasized, such as fungi, protists, lower eukaryotes, viruses, and phages. Most importantly, a collaborative effort of experts in microbiology, nutrition, immunology, medicine, systems biology, bioinformatics, and machine learning is probably required to identify the traits of the core human microbiome.
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Affiliation(s)
- Itai Sharon
- Migal-Galilee Research Institute, P.O. Box 831, Kiryat Shmona 11016, Israel
- Faculty of Sciences and Technology, Tel-Hai Academic College, Upper Galilee 1220800, Israel
- Correspondence:
| | - Narciso Martín Quijada
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, A-1210 Vienna, Austria; (N.M.Q.); (E.S.)
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, A-3430 Tulln an der Donau, Austria
| | - Edoardo Pasolli
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, 80055 Portici, Italy; (E.P.); (D.E.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80055 Portici, Italy
| | - Marco Fabbrini
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy; (M.F.); (S.T.)
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy;
| | - Francesco Vitali
- Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Via Moruzzi 1, 56124 Pisa, Italy; (F.V.); (C.d.F.)
| | - Valeria Agamennone
- Microbiology and Systems Biology, Netherlands Organization for Applied Scientific Research (TNO), Utrechtseweg 48, 3704 HE Zeist, The Netherlands;
| | - Andreas Dötsch
- Department of Physiology and Biochemistry of Nutrition, Max Rubner-Institut (MRI)-Federal Research Institute of Nutrition and Food, 76131 Karlsruhe, Germany;
| | - Evelyne Selberherr
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, A-1210 Vienna, Austria; (N.M.Q.); (E.S.)
| | - José Horacio Grau
- Amedes Genetics, Amedes Medizinische Dienstleistungen GmbH, 10117 Berlin, Germany; (J.H.G.); (M.M.); (K.L.)
- Center for Species Survival, Smithsonian Conservation Biology Institute, Washington, DC 20008, USA
| | - Martin Meixner
- Amedes Genetics, Amedes Medizinische Dienstleistungen GmbH, 10117 Berlin, Germany; (J.H.G.); (M.M.); (K.L.)
| | - Karsten Liere
- Amedes Genetics, Amedes Medizinische Dienstleistungen GmbH, 10117 Berlin, Germany; (J.H.G.); (M.M.); (K.L.)
| | - Danilo Ercolini
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, 80055 Portici, Italy; (E.P.); (D.E.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80055 Portici, Italy
| | - Carlotta de Filippo
- Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Via Moruzzi 1, 56124 Pisa, Italy; (F.V.); (C.d.F.)
| | - Giovanna Caderni
- NEUROFARBA Department, Pharmacology and Toxicology Section, University of Florence, Viale Pieraccini 6, 50139 Florence, Italy;
| | - Patrizia Brigidi
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy;
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy; (M.F.); (S.T.)
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17
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Gamal A, Elshaer M, Alabdely M, Kadry A, McCormick TS, Ghannoum M. The Mycobiome: Cancer Pathogenesis, Diagnosis, and Therapy. Cancers (Basel) 2022; 14:2875. [PMID: 35740541 PMCID: PMC9221014 DOI: 10.3390/cancers14122875] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 02/01/2023] Open
Abstract
Cancer is among the leading causes of death globally. Despite advances in cancer research, a full understanding of the exact cause has not been established. Recent data have shown that the microbiome has an important relationship with cancer on various levels, including cancer pathogenesis, diagnosis and prognosis, and treatment. Since most studies have focused only on the role of bacteria in this process, in this article we review the role of fungi-another important group of the microbiome, the totality of which is referred to as the "mycobiome"-in the development of cancer and how it can impact responses to anticancer medications. Furthermore, we provide recent evidence that shows how the different microbial communities interact and affect each other at gastrointestinal and non-gastrointestinal sites, including the skin, thereby emphasizing the importance of investigating the microbiome beyond bacteria.
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Affiliation(s)
- Ahmed Gamal
- Department of Dermatology, Case Western Reserve University, Cleveland, OH 44106, USA; (A.G.); (M.E.); (A.K.); (T.S.M.)
| | - Mohammed Elshaer
- Department of Dermatology, Case Western Reserve University, Cleveland, OH 44106, USA; (A.G.); (M.E.); (A.K.); (T.S.M.)
- Department of Clinical Pathology, Faculty of Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Mayyadah Alabdely
- Department of Internal Medicine, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA;
| | - Ahmed Kadry
- Department of Dermatology, Case Western Reserve University, Cleveland, OH 44106, USA; (A.G.); (M.E.); (A.K.); (T.S.M.)
- Department of Dermatology and Venereology, Al-Azhar University, Cairo 11651, Egypt
| | - Thomas S. McCormick
- Department of Dermatology, Case Western Reserve University, Cleveland, OH 44106, USA; (A.G.); (M.E.); (A.K.); (T.S.M.)
| | - Mahmoud Ghannoum
- Department of Dermatology, Case Western Reserve University, Cleveland, OH 44106, USA; (A.G.); (M.E.); (A.K.); (T.S.M.)
- Department of Dermatology, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
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18
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Brito Devoto T, Toscanini MA, Hermida Alava K, Etchecopaz AN, Pola SJ, Martorell MM, Ansaldo M, Negrete J, Ruberto L, Mac Cormack W, Cuestas ML. Exploring fungal diversity in Antarctic wildlife: isolation and molecular identification of culturable fungi from penguins and pinnipeds. N Z Vet J 2022; 70:263-272. [DOI: 10.1080/00480169.2022.2087784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- T Brito Devoto
- Universidad de Buenos Aires, CONICET, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Buenos Aires, Argentina
| | - M. A. Toscanini
- Universidad de Buenos Aires, CONICET, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Buenos Aires, Argentina
- Universidad de Buenos Aires, CONICET, Instituto de Nanobiotecnología (NANOBIOTEC), Buenos Aires, Argentina
| | - K Hermida Alava
- Universidad de Buenos Aires, CONICET, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Buenos Aires, Argentina
| | - A. N. Etchecopaz
- Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Cátedra de Enfermedades Infecciosas, Buenos Aires, Argentina
| | - S. J. Pola
- Universidad de Buenos Aires, CONICET, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Buenos Aires, Argentina
| | - M. M. Martorell
- Universidad de Buenos Aires, CONICET, Instituto de Nanobiotecnología (NANOBIOTEC), Buenos Aires, Argentina
- Instituto Antártico Argentino, Buenos Aires, Argentina
| | - M Ansaldo
- Instituto Antártico Argentino, Buenos Aires, Argentina
| | - J Negrete
- Universidad Nacional de La Plata, Facultad de Ciencias Naturales y Museo, Cátedra de Zoología III Vertebrados, Buenos Aires, Argentina
| | - L Ruberto
- Universidad de Buenos Aires, CONICET, Instituto de Nanobiotecnología (NANOBIOTEC), Buenos Aires, Argentina
- Instituto Antártico Argentino, Buenos Aires, Argentina
| | - W Mac Cormack
- Universidad de Buenos Aires, CONICET, Instituto de Nanobiotecnología (NANOBIOTEC), Buenos Aires, Argentina
- Instituto Antártico Argentino, Buenos Aires, Argentina
| | - M. L. Cuestas
- Universidad de Buenos Aires, CONICET, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Buenos Aires, Argentina
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19
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Tiew PY, Thng KX, Chotirmall SH. Clinical Aspergillus Signatures in COPD and Bronchiectasis. J Fungi (Basel) 2022; 8:jof8050480. [PMID: 35628736 PMCID: PMC9146266 DOI: 10.3390/jof8050480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 04/30/2022] [Accepted: 05/03/2022] [Indexed: 12/21/2022] Open
Abstract
Pulmonary mycoses remain a global threat, causing significant morbidity and mortality. Patients with airways disease, including COPD and bronchiectasis, are at increased risks of pulmonary mycoses and its associated complications. Frequent use of antibiotics and corticosteroids coupled with impaired host defenses predispose patients to fungal colonization and airway persistence, which are associated with negative clinical consequences. Notably, Aspergillus species remain the best-studied fungal pathogen and induce a broad spectrum of clinical manifestations in COPD and bronchiectasis ranging from colonization and sensitization to more invasive disease. Next-generation sequencing (NGS) has gained prominence in the field of respiratory infection, and in some cases is beginning to act as a viable alternative to traditional culture. NGS has revolutionized our understanding of airway microbiota and in particular fungi. In this context, it permits the identification of the previously unculturable, fungal composition, and dynamic change within microbial communities of the airway, including potential roles in chronic respiratory disease. Furthermore, inter-kingdom microbial interactions, including fungi, in conjunction with host immunity have recently been shown to have important clinical roles in COPD and bronchiectasis. In this review, we provide an overview of clinical Aspergillus signatures in COPD and bronchiectasis and cover the current advances in the understanding of the mycobiome in these disease states. The challenges and limitations of NGS will be addressed.
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Affiliation(s)
- Pei Yee Tiew
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore 168753, Singapore;
- Duke-NUS Medical School, Singapore 169857, Singapore
| | - Kai Xian Thng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore;
| | - Sanjay H. Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore;
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore 308433, Singapore
- Correspondence:
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20
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de Dios Caballero J, Cantón R, Ponce-Alonso M, García-Clemente MM, Gómez G. de la Pedrosa E, López-Campos JL, Máiz L, del Campo R, Martínez-García MÁ. The Human Mycobiome in Chronic Respiratory Diseases: Current Situation and Future Perspectives. Microorganisms 2022; 10:810. [PMID: 35456861 PMCID: PMC9029612 DOI: 10.3390/microorganisms10040810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/04/2022] [Accepted: 04/09/2022] [Indexed: 12/15/2022] Open
Abstract
Microbes play an important role in the pathogenesis of chronic lung diseases, such as chronic obstructive pulmonary disease, cystic fibrosis, non-cystic fibrosis bronchiectasis, and asthma. While the role of bacterial pathogens has been extensively studied, the contribution of fungal species to the pathogenesis of chronic lung diseases is much less understood. The recent introduction of next-generation sequencing techniques has revealed the existence of complex microbial lung communities in healthy individuals and patients with chronic respiratory disorders, with fungi being an important part of these communities' structure (mycobiome). There is growing evidence that the components of the lung mycobiome influence the clinical course of chronic respiratory diseases, not only by direct pathogenesis but also by interacting with bacterial species and with the host's physiology. In this article, we review the current knowledge on the role of fungi in chronic respiratory diseases, which was obtained by conventional culture and next-generation sequencing, highlighting the limitations of both techniques and exploring future research areas.
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Affiliation(s)
- Juan de Dios Caballero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Rafael Cantón
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Manuel Ponce-Alonso
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Marta María García-Clemente
- Department of Pneumology, Central Asturias University Hospital, 33011 Oviedo, Spain;
- Principality Asturias Health Research Institute (ISPA), 33011 Oviedo, Spain
| | - Elia Gómez G. de la Pedrosa
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - José Luis López-Campos
- Medical-Surgical Unit for Respiratory Diseases (CIBERES), Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, University of Seville, 41013 Sevilla, Spain;
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain; (L.M.); (M.Á.M.-G.)
| | - Luis Máiz
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain; (L.M.); (M.Á.M.-G.)
- Department of Pneumology, Ramón y Cajal University Hospital, 28034 Madrid, Spain
| | - Rosa del Campo
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Miguel Ángel Martínez-García
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain; (L.M.); (M.Á.M.-G.)
- Department of Pneumology, La Fe University and Polytechnic Hospital, 46026 Valencia, Spain
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21
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Reynoso-García J, Narganes-Storde Y, Santiago-Rodriguez TM, Toranzos GA. Mycobiome-Host Coevolution? The Mycobiome of Ancestral Human Populations Seems to Be Different and Less Diverse Than Those of Extant Native and Urban-Industrialized Populations. Microorganisms 2022; 10:microorganisms10020459. [PMID: 35208912 PMCID: PMC8877467 DOI: 10.3390/microorganisms10020459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/24/2021] [Accepted: 12/07/2021] [Indexed: 02/06/2023] Open
Abstract
Few data exist on the human gut mycobiome in relation to lifestyle, ethnicity, and dietary habits. To understand the effect of these factors on the structure of the human gut mycobiome, we analyzed sequences belonging to two extinct pre-Columbian cultures inhabiting Puerto Rico (the Huecoid and Saladoid) and compared them to coprolite samples found in Mexico and Ötzi, the Iceman’s large intestine. Stool mycobiome samples from extant populations in Peru and urban cultures from the United States were also included. The ancient Puerto Rican cultures exhibited a lower fungal diversity in comparison to the extant populations. Dissimilarity distances showed that the Huecoid gut mycobiome resembled that from ancient Mexico. Fungal genera including Aspergillus spp., Penicillium spp., Rasamsonia spp., Byssochlamys spp., Talaromyces spp., Blastomyces spp., Monascus spp., and Penicilliopsis spp. were differentially abundant in the ancient and extant populations. Despite cultural differences, certain fungal taxa were present in all samples. These results suggest that culture and diet may impact the gut mycobiome and emphasize that modern lifestyles could be associated with the alteration of gut mycobiome diversity. The present study presents data on ancient and extant human gut mycobiomes in terms of lifestyle, ethnicity, and diet in the Americas.
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Affiliation(s)
- Jelissa Reynoso-García
- Environmental Microbiology Laboratory, Biology Department, University of Puerto Rico, San Juan 00931, Puerto Rico;
- Correspondence:
| | - Yvonne Narganes-Storde
- Center for Archaeological Research, Río Piedras Campus, University of Puerto Rico, San Juan 00931, Puerto Rico;
| | | | - Gary A. Toranzos
- Environmental Microbiology Laboratory, Biology Department, University of Puerto Rico, San Juan 00931, Puerto Rico;
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22
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One Giant Leap from Mouse to Man: The Microbiota-Gut-Brain Axis in Mood Disorders and Translational Challenges Moving towards Human Clinical Trials. Nutrients 2022; 14:nu14030568. [PMID: 35276927 PMCID: PMC8840472 DOI: 10.3390/nu14030568] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 12/13/2022] Open
Abstract
The microbiota–gut–brain axis is a bidirectional communication pathway that enables the gut microbiota to communicate with the brain through direct and indirect signaling pathways to influence brain physiology, function, and even behavior. Research has shown that probiotics can improve several aspects of health by changing the environment within the gut, and several lines of evidence now indicate a beneficial effect of probiotics on mental and brain health. Such evidence has prompted the arrival of a new term to the world of biotics research: psychobiotics, defined as any exogenous influence whose effect on mental health is bacterially mediated. Several taxonomic changes in the gut microbiota have been reported in neurodevelopmental disorders, mood disorders such as anxiety and depression, and neurodegenerative disorders such as Alzheimer’s disease. While clinical evidence supporting the role of the gut microbiota in mental and brain health, and indeed demonstrating the beneficial effects of probiotics is rapidly accumulating, most of the evidence to date has emerged from preclinical studies employing different animal models. The purpose of this review is to focus on the role of probiotics and the microbiota–gut–brain axis in relation to mood disorders and to review the current translational challenges from preclinical to clinical research.
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23
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Analyzing the human gut mycobiome – a short guide for beginners. Comput Struct Biotechnol J 2022; 20:608-614. [PMID: 35116136 PMCID: PMC8790610 DOI: 10.1016/j.csbj.2022.01.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/04/2022] [Accepted: 01/08/2022] [Indexed: 12/30/2022] Open
Abstract
The human body is a dynamic ecosystem consisting of millions of microbes which are often comprised under the term microbiome. Compared to bacteria, which count for the overwhelming majority of the microbiome, the number of human-associated fungi is small and often underestimated. Nonetheless, they can be found in different host niches such as the gut, the oral cavity and the skin. The fungal community has several potential roles in health and disease of the human host. In this review we will focus on intestinal fungi and their interaction with the host as well as bacteria. We also summarize technical challenges and possible biases researchers must be aware of when conducting mycobiome analysis.
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24
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Begum N, Harzandi A, Lee S, Uhlen M, Moyes DL, Shoaie S. Host-mycobiome metabolic interactions in health and disease. Gut Microbes 2022; 14:2121576. [PMID: 36151873 PMCID: PMC9519009 DOI: 10.1080/19490976.2022.2121576] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/31/2022] [Accepted: 08/31/2022] [Indexed: 02/04/2023] Open
Abstract
Fungal communities (mycobiome) have an important role in sustaining the resilience of complex microbial communities and maintenance of homeostasis. The mycobiome remains relatively unexplored compared to the bacteriome despite increasing evidence highlighting their contribution to host-microbiome interactions in health and disease. Despite being a small proportion of the total species, fungi constitute a large proportion of the biomass within the human microbiome and thus serve as a potential target for metabolic reprogramming in pathogenesis and disease mechanism. Metabolites produced by fungi shape host niches, induce immune tolerance and changes in their levels prelude changes associated with metabolic diseases and cancer. Given the complexity of microbial interactions, studying the metabolic interplay of the mycobiome with both host and microbiome is a demanding but crucial task. However, genome-scale modelling and synthetic biology can provide an integrative platform that allows elucidation of the multifaceted interactions between mycobiome, microbiome and host. The inferences gained from understanding mycobiome interplay with other organisms can delineate the key role of the mycobiome in pathophysiology and reveal its role in human disease.
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Affiliation(s)
- Neelu Begum
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London, UK
| | - Azadeh Harzandi
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London, UK
| | - Sunjae Lee
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London, UK
| | - Mathias Uhlen
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
| | - David L. Moyes
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London, UK
| | - Saeed Shoaie
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London, UK
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
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25
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Romo JA, Kumamoto CA. Characterization of the Effects of Candida Gastrointestinal Colonization on Clostridioides difficile Infection in a Murine Model. Methods Mol Biol 2022; 2542:271-285. [PMID: 36008672 DOI: 10.1007/978-1-0716-2549-1_20] [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: 06/15/2023]
Abstract
The role of fungal colonizers of the gastrointestinal tract during disease states is not well understood. Antibiotic treatment renders patients highly susceptible to infection by the bacterial pathogen C. difficile while also leading to blooms in fungal commensals, setting the stage for trans-kingdom interactions. Here, we describe a murine model of Candida gastrointestinal colonization coupled to a C. difficile infection (CDI) model, the measurement of CFU of both organisms, and collection of cecum and colon contents for the purpose of quantifying C. difficile toxin production. Additionally, we describe how to induce and purify C. difficile spores.
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Affiliation(s)
- Jesús A Romo
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Carol A Kumamoto
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA.
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26
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Su L, Zhu H, Sun P, Li X, Yang B, Gao H, Xiang Z, Qin C. Species diversity in Penicillium and Acaulium from herbivore dung in China, and description of Acaulium stercorarius sp. nov. Mycol Prog 2021. [DOI: 10.1007/s11557-021-01747-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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27
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Mohamed N, Litlekalsøy J, Ahmed IA, Martinsen EMH, Furriol J, Javier-Lopez R, Elsheikh M, Gaafar NM, Morgado L, Mundra S, Johannessen AC, Osman TAH, Nginamau ES, Suleiman A, Costea DE. Analysis of Salivary Mycobiome in a Cohort of Oral Squamous Cell Carcinoma Patients From Sudan Identifies Higher Salivary Carriage of Malassezia as an Independent and Favorable Predictor of Overall Survival. Front Cell Infect Microbiol 2021; 11:673465. [PMID: 34712619 PMCID: PMC8547610 DOI: 10.3389/fcimb.2021.673465] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 08/27/2021] [Indexed: 12/20/2022] Open
Abstract
Background Microbial dysbiosis and microbiome-induced inflammation have emerged as important factors in oral squamous cell carcinoma (OSCC) tumorigenesis during the last two decades. However, the “rare biosphere” of the oral microbiome, including fungi, has been sparsely investigated. This study aimed to characterize the salivary mycobiome in a prospective Sudanese cohort of OSCC patients and to explore patterns of diversities associated with overall survival (OS). Materials and Methods Unstimulated saliva samples (n = 72) were collected from patients diagnosed with OSCC (n = 59) and from non-OSCC control volunteers (n = 13). DNA was extracted using a combined enzymatic–mechanical extraction protocol. The salivary mycobiome was assessed using a next-generation sequencing (NGS)-based methodology by amplifying the ITS2 region. The impact of the abundance of different fungal genera on the survival of OSCC patients was analyzed using Kaplan–Meier and Cox regression survival analyses (SPPS). Results Sixteen genera were identified exclusively in the saliva of OSCC patients. Candida, Malassezia, Saccharomyces, Aspergillus, and Cyberlindnera were the most relatively abundant fungal genera in both groups and showed higher abundance in OSCC patients. Kaplan–Meier survival analysis showed higher salivary carriage of the Candida genus significantly associated with poor OS of OSCC patients (Breslow test: p = 0.043). In contrast, the higher salivary carriage of Malassezia showed a significant association with favorable OS in OSCC patients (Breslow test: p = 0.039). The Cox proportional hazards multiple regression model was applied to adjust the salivary carriage of both Candida and Malassezia according to age (p = 0.029) and identified the genus Malassezia as an independent predictor of OS (hazard ratio = 0.383, 95% CI = 0.16–0.93, p = 0.03). Conclusion The fungal compositional patterns in saliva from OSCC patients were different from those of individuals without OSCC. The fungal genus Malassezia was identified as a putative prognostic biomarker and therapeutic target for OSCC.
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Affiliation(s)
- Nazar Mohamed
- Gade Laboratory for Pathology, Department of Clinical Medicine, and Center for Cancer Biomarkers CCBIO, University of Bergen, Bergen, Norway.,Department of Oral and Maxillofacial Surgery/Department of Basic Sciences, University of Khartoum, Khartoum, Sudan
| | - Jorunn Litlekalsøy
- Gade Laboratory for Pathology, Department of Clinical Medicine, and Center for Cancer Biomarkers CCBIO, University of Bergen, Bergen, Norway
| | - Israa Abdulrahman Ahmed
- Gade Laboratory for Pathology, Department of Clinical Medicine, and Center for Cancer Biomarkers CCBIO, University of Bergen, Bergen, Norway.,Department of Operative Dentistry, University of Science & Technology, Omdurman, Sudan
| | | | - Jessica Furriol
- Department of Nephrology, Haukeland University Hospital, Bergen, Norway
| | - Ruben Javier-Lopez
- Department of Biological Sciences, The Faculty of Mathematics and Natural Sciences, University of Bergen, Bergen, Norway
| | - Mariam Elsheikh
- Department of Oral and Maxillofacial Surgery/Department of Basic Sciences, University of Khartoum, Khartoum, Sudan.,Department of Oral & Maxillofacial Surgery, Khartoum Dental Teaching Hospital, Khartoum, Sudan
| | - Nuha Mohamed Gaafar
- Gade Laboratory for Pathology, Department of Clinical Medicine, and Center for Cancer Biomarkers CCBIO, University of Bergen, Bergen, Norway.,Department of Oral and Maxillofacial Surgery/Department of Basic Sciences, University of Khartoum, Khartoum, Sudan
| | - Luis Morgado
- Section for Genetics and Evolutionary Biology (EvoGene), Department of Biosciences, The Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Sunil Mundra
- Section for Genetics and Evolutionary Biology (EvoGene), Department of Biosciences, The Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.,Department of Biology, College of Science, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
| | - Anne Christine Johannessen
- Gade Laboratory for Pathology, Department of Clinical Medicine, and Center for Cancer Biomarkers CCBIO, University of Bergen, Bergen, Norway.,Department of Pathology, Laboratory Clinic, Haukeland University Hospital, Bergen, Norway
| | - Tarig Al-Hadi Osman
- Gade Laboratory for Pathology, Department of Clinical Medicine, and Center for Cancer Biomarkers CCBIO, University of Bergen, Bergen, Norway
| | - Elisabeth Sivy Nginamau
- Gade Laboratory for Pathology, Department of Clinical Medicine, and Center for Cancer Biomarkers CCBIO, University of Bergen, Bergen, Norway.,Department of Pathology, Laboratory Clinic, Haukeland University Hospital, Bergen, Norway
| | - Ahmed Suleiman
- Department of Oral and Maxillofacial Surgery/Department of Basic Sciences, University of Khartoum, Khartoum, Sudan.,Department of Oral & Maxillofacial Surgery, Khartoum Dental Teaching Hospital, Khartoum, Sudan
| | - Daniela Elena Costea
- Gade Laboratory for Pathology, Department of Clinical Medicine, and Center for Cancer Biomarkers CCBIO, University of Bergen, Bergen, Norway.,Department of Pathology, Laboratory Clinic, Haukeland University Hospital, Bergen, Norway
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28
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Lavrinienko A, Scholier T, Bates ST, Miller AN, Watts PC. Defining gut mycobiota for wild animals: a need for caution in assigning authentic resident fungal taxa. Anim Microbiome 2021; 3:75. [PMID: 34711273 PMCID: PMC8554864 DOI: 10.1186/s42523-021-00134-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 09/27/2021] [Indexed: 12/15/2022] Open
Abstract
Animal gut mycobiota, the community of fungi that reside within the gastrointestinal tract, make an important contribution to host health. Accordingly, there is an emerging interest to quantify the gut mycobiota of wild animals. However, many studies of wild animal gut mycobiota do not distinguish between the fungi that likely can reside within animal gastrointestinal tracts from the fungal taxa that are non-residents, such as macrofungi, lichens or plant symbionts/pathogens that can be ingested as part of the host's diet. Confounding the non-resident and resident gut fungi may obscure attempts to identify processes associated with the authentic, resident gut mycobiota per se. To redress this problem, we propose some strategies to filter the taxa identified within an apparent gut mycobiota based on an assessment of host ecology and fungal traits. Consideration of the different sources and roles of fungi present within the gastrointestinal tract should facilitate a more precise understanding of the causes and consequences of variation in wild animal gut mycobiota composition.
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Affiliation(s)
- Anton Lavrinienko
- Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Tiffany Scholier
- Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Scott T Bates
- Department of Biological Sciences, Purdue University Northwest, Westville, IN, 46391, USA
| | - Andrew N Miller
- University of Illinois Urbana-Champaign, Illinois Natural History Survey, 1816 South Oak Street, Champaign, IL, 61820-6970, USA
| | - Phillip C Watts
- Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland.
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29
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Zhang L, Zhan H, Xu W, Yan S, Ng SC. The role of gut mycobiome in health and diseases. Therap Adv Gastroenterol 2021; 14:17562848211047130. [PMID: 34589139 PMCID: PMC8474302 DOI: 10.1177/17562848211047130] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 08/31/2021] [Indexed: 02/04/2023] Open
Abstract
The gut microbiome comprised of microbes from multiple kingdoms, including bacteria, fungi, and viruses. Emerging evidence suggests that the intestinal fungi (the gut "mycobiome") play an important role in host immunity and inflammation. Advances in next generation sequencing methods to study the fungi in fecal samples and mucosa tissues have expanded our understanding of gut fungi in intestinal homeostasis and systemic immunity in health and their contribution to different human diseases. In this review, the current status of gut mycobiome in health, early life, and different diseases including inflammatory bowel disease, colorectal cancer, and metabolic diseases were summarized.
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Affiliation(s)
| | | | - Wenye Xu
- Center for Gut Microbiota Research, Faculty of
Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong,
China,Li Ka Shing Institute of Health Science, The
Chinese University of Hong Kong, Shatin, Hong Kong, China,State Key Laboratory for Digestive disease,
Institute of Digestive Disease, The Chinese University of Hong Kong, Shatin,
Hong Kong, China,Department of Medicine and Therapeutics,
Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong,
China
| | - Shuai Yan
- Center for Gut Microbiota Research, Faculty of
Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong,
China,Li Ka Shing Institute of Health Science, The
Chinese University of Hong Kong, Shatin, Hong Kong, China,State Key Laboratory for Digestive disease,
Institute of Digestive Disease, The Chinese University of Hong Kong, Shatin,
Hong Kong, China,Department of Anaesthesia and Intensive Care
and Peter Hung Pain Research Institute, The Chinese University of Hong Kong,
Shatin, Hong Kong, China
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30
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Naik B, Ahmed SMQ, Laha S, Das SP. Genetic Susceptibility to Fungal Infections and Links to Human Ancestry. Front Genet 2021; 12:709315. [PMID: 34490039 PMCID: PMC8417537 DOI: 10.3389/fgene.2021.709315] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/13/2021] [Indexed: 12/25/2022] Open
Abstract
Over the ages, fungi have associated with different parts of the human body and established symbiotic associations with their host. They are mostly commensal unless there are certain not so well-defined factors that trigger the conversion to a pathogenic state. Some of the factors that induce such transition can be dependent on the fungal species, environment, immunological status of the individual, and most importantly host genetics. In this review, we discuss the different aspects of how host genetics play a role in fungal infection since mutations in several genes make hosts susceptible to such infections. We evaluate how mutations modulate the key recognition between the pathogen associated molecular patterns (PAMP) and the host pattern recognition receptor (PRR) molecules. We discuss the polymorphisms in the genes of the immune system, the way it contributes toward some common fungal infections, and highlight how the immunological status of the host determines fungal recognition and cross-reactivity of some fungal antigens against human proteins that mimic them. We highlight the importance of single nucleotide polymorphisms (SNPs) that are associated with several of the receptor coding genes and discuss how it affects the signaling cascade post-infection, immune evasion, and autoimmune disorders. As part of personalized medicine, we need the application of next-generation techniques as a feasible option to incorporate an individual’s susceptibility toward invasive fungal infections based on predisposing factors. Finally, we discuss the importance of studying genomic ancestry and reveal how genetic differences between the human race are linked to variation in fungal disease susceptibility.
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Affiliation(s)
- Bharati Naik
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Sumayyah M Q Ahmed
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Suparna Laha
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Shankar Prasad Das
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
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31
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Evolution in a Community Context: towards Understanding the Causes and Consequences of Adaptive Evolution in the Human Gut Microbiota over Short Time Scales. mSystems 2021; 6:e0083221. [PMID: 34427532 PMCID: PMC8407120 DOI: 10.1128/msystems.00832-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
How important is adaptive evolution to the unique diversity that we can observe for each individual human gut microbiome? How do gut microbes evolve in response to changes in their environment, and how does evolution in real time impact microbial functionality in the context of host health? My interdisciplinary research uses in vitro microcosm models to test how different abiotic and biotic factors impact microbial evolution in a community context. We complement this approach by tracking focal species as they evolve in real time and in their natural environment of the human gut. Our aim is to provide a better understanding of how the dynamics and outcomes of microbial evolution differ between individual gut environments, and in response to different selection pressures, so that we can move closer to rational gut microbiome treatments that promote host health and prevent and treat human disease.
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32
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Ventin-Holmberg R, Eberl A, Saqib S, Korpela K, Virtanen S, Sipponen T, Salonen A, Saavalainen P, Nissilä E. Bacterial and Fungal Profiles as Markers of Infliximab Drug Response in Inflammatory Bowel Disease. J Crohns Colitis 2021; 15:1019-1031. [PMID: 33300552 DOI: 10.1093/ecco-jcc/jjaa252] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND AIMS Inflammatory bowel diseases [IBDs], Crohn's disease [CD] and ulcerative colitis [UC], are globally increasing chronic gastro-intestinal inflammatory disorders associated with altered gut microbiota. Infliximab [IFX], a tumour necrosis factor [TNF]-alpha blocker, is used to treat IBD patients successfully, though one-third of the patients do not respond to therapy. No reliable biomarkers are available for prediction of IFX response. Our aims were to investigate the faecal bacterial and fungal communities during IFX therapy and find predictors for IFX treatment response in IBD patients. METHODS A total of 72 IBD patients [25 CD and 47 UC] started IFX therapy and were followed for 1 year or until IFX treatment was discontinued. An amplicon sequencing approach, targeting the bacterial 16S rRNA gene and fungal ITS 1 region separately, was used to determine the microbiota profiles in faecal samples collected before IFX therapy and 2, 6, and 12 weeks and 1 year after initiation of therapy. The response to IFX was evaluated by colonoscopy and clinically at 12 weeks after initiation. RESULTS Both faecal bacterial and fungal profiles differed significantly between response groups before start of IFX treatment. Non-responders had lower abundances of short chain fatty acid producers, particularly of the class Clostridia, and higher abundances of pro-inflammatory bacteria and fungi, such as the genus Candida, compared with responders. This was further indicated by bacterial taxa predicting the response in both CD and UC patients [area under the curve >0.8]. CONCLUSIONS Faecal bacterial and fungal microbiota composition could provide a predictive tool to estimate IFX response in IBD patients.
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Affiliation(s)
| | - Anja Eberl
- Department of Gastroenterology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Schahzad Saqib
- Human Microbiome Research Program, University of Helsinki, Helsinki, Finland
| | - Katri Korpela
- Human Microbiome Research Program, University of Helsinki, Helsinki, Finland
| | - Seppo Virtanen
- Obstetrics and Gynaecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Taina Sipponen
- Department of Gastroenterology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Anne Salonen
- Human Microbiome Research Program, University of Helsinki, Helsinki, Finland
| | - Päivi Saavalainen
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Eija Nissilä
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
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33
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Berthelot JM, Darrieutort-Laffite C, Trang C, Maugars Y, Le Goff B. Contribution of mycobiota to the pathogenesis of spondyloarthritis. Joint Bone Spine 2021; 88:105245. [PMID: 34166798 DOI: 10.1016/j.jbspin.2021.105245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/09/2021] [Indexed: 12/18/2022]
Abstract
This review lists current evidences for a contribution of gut mycobiota to the pathogenesis of SpA and related conditions. Gut mycobiota has a small size as compared to bacterial microbiota, but an even greater inter- and intra-individual variability. Although most fungi (brought by food or air) are only transitory present, a core mycobiota of gut resident fungi exists, and interplays with bacteria in a complex manner. A dysbiosis of this gut mycobiota has been observed in Crohn's disease and sclerosing cholangitis, with decreased proportion of Saccharomyces cerevisiae and outgrowth of more pathogenic gut fungi. Fungal-induced lower number of commensal gut bacteria can promote translocation of some bacterial/fungal antigens through mucosae, and live fungi can also cross the epithelial border in Crohn's disease. This dysbiosis also lower the ability of bacteria to metabolize tryptophan into regulatory metabolites, consequently enhancing tryptophan metabolism within human cells, which might contribute to fatigue. Translocation of mycobiotal antigens like curdlan (beta-glucan), which plays a major role in the pathogenesis of SpA in the SGK mice, has been observed in humans. This translocation of fungal antigens in human SpA might account for the anti-Saccharomyces antibodies found in this setting. Contribution of fungal antigens to psoriasis and hidradenitis suppurativa would fit with the preferential homing of fungi in the skin area most involved in those conditions. Fungal antigens also possess autoimmune uveitis-promoting function. As genes associated with SpA (CARD9 and IL23R) strongly regulate the innate immune response against fungi, further studies on fungi contribution to SpA are needed.
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Affiliation(s)
- Jean-Marie Berthelot
- Service de rhumatologie, Hôtel-Dieu, CHU de Nantes, place Alexis-Ricordeau, 44093 Nantes cedex 01, France.
| | | | - Caroline Trang
- Service de gastro-entérologie, Hôtel-Dieu, CHU de Nantes, place Alexis-Ricordeau, 44093 Nantes cedex 01, France
| | - Yves Maugars
- Service de rhumatologie, Hôtel-Dieu, CHU de Nantes, place Alexis-Ricordeau, 44093 Nantes cedex 01, France
| | - Benoît Le Goff
- Service de rhumatologie, Hôtel-Dieu, CHU de Nantes, place Alexis-Ricordeau, 44093 Nantes cedex 01, France
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d'Enfert C, Kaune AK, Alaban LR, Chakraborty S, Cole N, Delavy M, Kosmala D, Marsaux B, Fróis-Martins R, Morelli M, Rosati D, Valentine M, Xie Z, Emritloll Y, Warn PA, Bequet F, Bougnoux ME, Bornes S, Gresnigt MS, Hube B, Jacobsen ID, Legrand M, Leibundgut-Landmann S, Manichanh C, Munro CA, Netea MG, Queiroz K, Roget K, Thomas V, Thoral C, Van den Abbeele P, Walker AW, Brown AJP. The impact of the Fungus-Host-Microbiota interplay upon Candida albicans infections: current knowledge and new perspectives. FEMS Microbiol Rev 2021; 45:fuaa060. [PMID: 33232448 PMCID: PMC8100220 DOI: 10.1093/femsre/fuaa060] [Citation(s) in RCA: 137] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 11/18/2020] [Indexed: 12/11/2022] Open
Abstract
Candida albicans is a major fungal pathogen of humans. It exists as a commensal in the oral cavity, gut or genital tract of most individuals, constrained by the local microbiota, epithelial barriers and immune defences. Their perturbation can lead to fungal outgrowth and the development of mucosal infections such as oropharyngeal or vulvovaginal candidiasis, and patients with compromised immunity are susceptible to life-threatening systemic infections. The importance of the interplay between fungus, host and microbiota in driving the transition from C. albicans commensalism to pathogenicity is widely appreciated. However, the complexity of these interactions, and the significant impact of fungal, host and microbiota variability upon disease severity and outcome, are less well understood. Therefore, we summarise the features of the fungus that promote infection, and how genetic variation between clinical isolates influences pathogenicity. We discuss antifungal immunity, how this differs between mucosae, and how individual variation influences a person's susceptibility to infection. Also, we describe factors that influence the composition of gut, oral and vaginal microbiotas, and how these affect fungal colonisation and antifungal immunity. We argue that a detailed understanding of these variables, which underlie fungal-host-microbiota interactions, will present opportunities for directed antifungal therapies that benefit vulnerable patients.
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Affiliation(s)
- Christophe d'Enfert
- Unité Biologie et Pathogénicité Fongiques, Département de Mycologie, Institut Pasteur, USC 2019 INRA, 25, rue du Docteur Roux, 75015 Paris, France
| | - Ann-Kristin Kaune
- Aberdeen Fungal Group, Institute of Medical Sciences, University of Aberdeen, Ashgrove Road West, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Leovigildo-Rey Alaban
- BIOASTER Microbiology Technology Institute, 40 avenue Tony Garnier, 69007 Lyon, France
- Université de Paris, Sorbonne Paris Cité, 25, rue du Docteur Roux, 75015 Paris, France
| | - Sayoni Chakraborty
- Microbial Immunology Research Group, Emmy Noether Junior Research Group Adaptive Pathogenicity Strategies, and the Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
- Institute of Microbiology, Friedrich Schiller University, Neugasse 25, 07743 Jena, Germany
| | - Nathaniel Cole
- Gut Microbiology Group, Rowett Institute, University of Aberdeen, Ashgrove Road West, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Margot Delavy
- Unité Biologie et Pathogénicité Fongiques, Département de Mycologie, Institut Pasteur, USC 2019 INRA, 25, rue du Docteur Roux, 75015 Paris, France
- Université de Paris, Sorbonne Paris Cité, 25, rue du Docteur Roux, 75015 Paris, France
| | - Daria Kosmala
- Unité Biologie et Pathogénicité Fongiques, Département de Mycologie, Institut Pasteur, USC 2019 INRA, 25, rue du Docteur Roux, 75015 Paris, France
- Université de Paris, Sorbonne Paris Cité, 25, rue du Docteur Roux, 75015 Paris, France
| | - Benoît Marsaux
- ProDigest BV, Technologiepark 94, B-9052 Gent, Belgium
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links, 9000 Ghent, Belgium
| | - Ricardo Fróis-Martins
- Immunology Section, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 266a, Zurich 8057, Switzerland
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, Zürich 8057, Switzerland
| | - Moran Morelli
- Mimetas, Biopartner Building 2, J.H. Oortweg 19, 2333 CH Leiden, The Netherlands
| | - Diletta Rosati
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Marisa Valentine
- Microbial Immunology Research Group, Emmy Noether Junior Research Group Adaptive Pathogenicity Strategies, and the Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Zixuan Xie
- Gut Microbiome Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119–129, 08035 Barcelona, Spain
| | - Yoan Emritloll
- Unité Biologie et Pathogénicité Fongiques, Département de Mycologie, Institut Pasteur, USC 2019 INRA, 25, rue du Docteur Roux, 75015 Paris, France
| | - Peter A Warn
- Magic Bullet Consulting, Biddlecombe House, Ugbrook, Chudleigh Devon, TQ130AD, UK
| | - Frédéric Bequet
- BIOASTER Microbiology Technology Institute, 40 avenue Tony Garnier, 69007 Lyon, France
| | - Marie-Elisabeth Bougnoux
- Unité Biologie et Pathogénicité Fongiques, Département de Mycologie, Institut Pasteur, USC 2019 INRA, 25, rue du Docteur Roux, 75015 Paris, France
| | - Stephanie Bornes
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMRF0545, 20 Côte de Reyne, 15000 Aurillac, France
| | - Mark S Gresnigt
- Microbial Immunology Research Group, Emmy Noether Junior Research Group Adaptive Pathogenicity Strategies, and the Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Bernhard Hube
- Microbial Immunology Research Group, Emmy Noether Junior Research Group Adaptive Pathogenicity Strategies, and the Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Ilse D Jacobsen
- Microbial Immunology Research Group, Emmy Noether Junior Research Group Adaptive Pathogenicity Strategies, and the Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Mélanie Legrand
- Unité Biologie et Pathogénicité Fongiques, Département de Mycologie, Institut Pasteur, USC 2019 INRA, 25, rue du Docteur Roux, 75015 Paris, France
| | - Salomé Leibundgut-Landmann
- Immunology Section, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 266a, Zurich 8057, Switzerland
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, Zürich 8057, Switzerland
| | - Chaysavanh Manichanh
- Gut Microbiome Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119–129, 08035 Barcelona, Spain
| | - Carol A Munro
- Aberdeen Fungal Group, Institute of Medical Sciences, University of Aberdeen, Ashgrove Road West, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Karla Queiroz
- Mimetas, Biopartner Building 2, J.H. Oortweg 19, 2333 CH Leiden, The Netherlands
| | - Karine Roget
- NEXBIOME Therapeutics, 22 allée Alan Turing, 63000 Clermont-Ferrand, France
| | - Vincent Thomas
- BIOASTER Microbiology Technology Institute, 40 avenue Tony Garnier, 69007 Lyon, France
| | - Claudia Thoral
- NEXBIOME Therapeutics, 22 allée Alan Turing, 63000 Clermont-Ferrand, France
| | | | - Alan W Walker
- Gut Microbiology Group, Rowett Institute, University of Aberdeen, Ashgrove Road West, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Alistair J P Brown
- MRC Centre for Medical Mycology, Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
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35
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Wu X, Xia Y, He F, Zhu C, Ren W. Intestinal mycobiota in health and diseases: from a disrupted equilibrium to clinical opportunities. MICROBIOME 2021; 9:60. [PMID: 33715629 PMCID: PMC7958491 DOI: 10.1186/s40168-021-01024-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/04/2021] [Indexed: 05/08/2023]
Abstract
Bacteria, viruses, protozoa, and fungi establish a complex ecosystem in the gut. Like other microbiota, gut mycobiota plays an indispensable role in modulating intestinal physiology. Notably, the most striking characteristics of intestinal fungi are their extraintestinal functions. Here, we provide a comprehensive review of the importance of gut fungi in the regulation of intestinal, pulmonary, hepatic, renal, pancreatic, and brain functions, and we present possible opportunities for the application of gut mycobiota to alleviate/treat human diseases. Video Abstract.
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Affiliation(s)
- Xiaoyan Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China
| | - Yaoyao Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China
| | - Fang He
- College of Animal Science and Technology, Southwest University, Chongqing, 400716 China
| | - Congrui Zhu
- College of Veterinary Medicine, Kansas State University, Manhattan, KS USA
| | - Wenkai Ren
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, 510642 China
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36
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Bandini F, Misci C, Taskin E, Cocconcelli PS, Puglisi E. Biopolymers modulate microbial communities in municipal organic waste digestion. FEMS Microbiol Ecol 2021; 96:5902845. [PMID: 32897356 DOI: 10.1093/femsec/fiaa183] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 09/04/2020] [Indexed: 11/15/2022] Open
Abstract
The development of biopolymers has raised issues about their recalcitrance in the environment. Their disposal is mainly carried out with the organic fraction of municipal solid waste (OFMSW) through thermophilic anaerobic digestion and aerobic composting, bioprocesses aimed at turning organic matter into biogas and compost. However, the effects of biopolymers on OFMSW treatment, on the final compost and on the microbial communities involved are partly unexplored. In this study, the OFMSW treatment was reproduced on a laboratory-scale respecting real plant conditions and testing the impacts of mixing polylactic acid (PLA) and starch-based bioplastic (SBB) separately. The dynamics of bacterial, archaeal and fungal communities during the process was screened by high-throughput sequencing (HTS) of phylogenetic amplicons. Starch-based bioplastic showed a minor and heterogeneous microbial diversity between the anaerobic and aerobic phases. Contrariwise, PLA treatment resulted in wider and more diverse bacterial and fungal communities for the compost and the aerobic biofilm. Since the biodiversity in compost may play a crucial role in its stability and safety, the modulation of environmental microbial communities induced by higher concentrations of PLA in OFMSW treatment can pose relevant issues.
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Affiliation(s)
- Francesca Bandini
- Dipartimento di Scienze e Tecnologie Alimentari per la sostenibilità della filiera agro-alimentare (DISTAS), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, Italy
| | - Chiara Misci
- Dipartimento di Scienze e Tecnologie Alimentari per la sostenibilità della filiera agro-alimentare (DISTAS), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, Italy
| | - Eren Taskin
- Dipartimento di Scienze e Tecnologie Alimentari per la sostenibilità della filiera agro-alimentare (DISTAS), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, Italy
| | - Pier Sandro Cocconcelli
- Dipartimento di Scienze e Tecnologie Alimentari per la sostenibilità della filiera agro-alimentare (DISTAS), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, Italy
| | - Edoardo Puglisi
- Dipartimento di Scienze e Tecnologie Alimentari per la sostenibilità della filiera agro-alimentare (DISTAS), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, Italy
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37
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The fecal mycobiome in patients with Irritable Bowel Syndrome. Sci Rep 2021; 11:124. [PMID: 33420127 PMCID: PMC7794320 DOI: 10.1038/s41598-020-79478-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/25/2020] [Indexed: 02/07/2023] Open
Abstract
Alterations of the gut microbiota have been reported in various gastrointestinal disorders, but knowledge of the mycobiome is limited. We investigated the gut mycobiome of 80 patients with Irritable Bowel Syndrome (IBS) in comparison with 64 control subjects. The fungal-specific internal transcribed spacer 1 (ITS-1) amplicon was sequenced, and mycobiome zero-radius operational taxonomic units (zOTUs) were defined representing known and unknown species and strains. The fungal community was sparse and individual-specific in all (both IBS and control) subjects. Although beta-diversity differed significantly between IBS and controls, no difference was found among clinical subtypes of IBS or in comparison with the mycobiome of subjects with bile acid malabsorption (BAM), a condition which may overlap with IBS with diarrhoea. The mycobiome alterations co-varied significantly with the bacteriome and metabolome but were not linked with dietary habits. As a putative biomarker of IBS, the predictive power of the fecal mycobiome in machine learning models was significantly better than random but insufficient for clinical diagnosis. The mycobiome presents limited therapeutic and diagnostic potential for IBS, despite co-variation with bacterial components which do offer such potential.
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38
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De Musis C, Granata L, Dallio M, Miranda A, Gravina AG, Romano M. Inflammatory Bowel Diseases: The Role of Gut Microbiota. Curr Pharm Des 2021; 26:2951-2961. [PMID: 32310042 DOI: 10.2174/1381612826666200420144128] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/13/2020] [Indexed: 12/12/2022]
Abstract
Inflammatory bowel diseases (IBD) are chronic multifactorial diseases characterized by partially unclear pathogenic mechanisms including changes in intestinal microbiota. Despite the microbiota, alteration is well established in IBD patients, as reported by 16RNA sequencing analysis, an important goal is to define if it is just a consequence of the disease progression or a trigger factor of the disease itself. To date, gut microbiota composition and gut microbiota-related metabolites seem to affect the host healthy state both by modulating metabolic pathways or acting on the expression of different genes through epigenetic effects. Because of this, it has been suggested that intestinal microbiota might represent a promising therapeutic target for IBD patients. The aim of this review is to summarize both the most recent acquisitions in the field of gut microbiota and its involvement in intestinal inflammation together with the available strategies for the modulation of microbiota, such as prebiotics and/or probiotics administration or fecal microbiota transplantation.
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Affiliation(s)
- Cristiana De Musis
- Departments of Precision Medicine and Polyspecialistic Internal Medicine, University of Campania ''Luigi Vanvitelli'' and University Hospital, Naples, Italy
| | - Lucia Granata
- Departments of Precision Medicine and Polyspecialistic Internal Medicine, University of Campania ''Luigi Vanvitelli'' and University Hospital, Naples, Italy
| | - Marcello Dallio
- Departments of Precision Medicine and Polyspecialistic Internal Medicine, University of Campania ''Luigi Vanvitelli'' and University Hospital, Naples, Italy
| | - Agnese Miranda
- Departments of Precision Medicine and Polyspecialistic Internal Medicine, University of Campania ''Luigi Vanvitelli'' and University Hospital, Naples, Italy
| | - Antonietta G Gravina
- Departments of Precision Medicine and Polyspecialistic Internal Medicine, University of Campania ''Luigi Vanvitelli'' and University Hospital, Naples, Italy
| | - Marco Romano
- Departments of Precision Medicine and Polyspecialistic Internal Medicine, University of Campania ''Luigi Vanvitelli'' and University Hospital, Naples, Italy
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Jiang L, Stärkel P, Fan JG, Fouts DE, Bacher P, Schnabl B. The gut mycobiome: a novel player in chronic liver diseases. J Gastroenterol 2021; 56:1-11. [PMID: 33151407 PMCID: PMC7819863 DOI: 10.1007/s00535-020-01740-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 10/15/2020] [Indexed: 02/07/2023]
Abstract
The human gut microbiome (bacteria, fungi, viruses, and archaea) is a complex and diverse ecosystem. It plays an important role in human health, but is involved in several intestinal and extraintestinal diseases. Most research to date has focused on the role of bacteria, while studies focusing on fungi (also referred to as "mycobiome" or "fungome") are still in its infancy. In this review, we focus on the existing literature available about the gut mycobiome with an emphasis on compositional mycobiome changes associated with liver diseases, the impact on pathogenesis of disease, and its potential use as therapeutic targets. We also provide insights into current methodologies of studying mycobiome, and we highlight the interkingdom interactions in the context of disease and how they affect health of the host. Herein, by focusing on the gut mycobiome, this review provides novel insights and directions for liver research.
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Affiliation(s)
- Lu Jiang
- Department of Medicine, University of California San Diego, MC0063, 9500 Gilman Drive, La Jolla, CA 92093 USA ,Department of Medicine, VA San Diego Healthcare System, San Diego, CA USA
| | - Peter Stärkel
- Cliniques Universitaires Saint Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Jian-Gao Fan
- Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - Petra Bacher
- Institute of Immunology, Christian-Albrechts-University of Kiel and UKSH Schleswig-Holstein, Kiel, Germany ,Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Bernd Schnabl
- Department of Medicine, University of California San Diego, MC0063, 9500 Gilman Drive, La Jolla, CA 92093 USA ,Department of Medicine, VA San Diego Healthcare System, San Diego, CA USA
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40
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Aguirre García MM, Mancilla-Galindo J, Paredes-Paredes M, Tiburcio ÁZ, Ávila-Vanzzini N. Mechanisms of infection by SARS-CoV-2, inflammation and potential links with the microbiome. Future Virol 2021. [PMCID: PMC7876557 DOI: 10.2217/fvl-2020-0310] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The pandemic SARS coronavirus 2 utilizes efficient mechanisms to establish infection and evade the immune system. Established infection leads to severe inflammation in susceptible patients, the main hallmark of progression to severe coronavirus disease (COVID-19). Knowledge of the mechanisms of disease has expanded rapidly. As inflammation emerges as the central pathophysiological feature in COVID-19, elucidating how the immune system, lungs and gut communicate and interact with microbial components of the ecological niches that conform the human microbiome will shed light on how inflammation and disease progression are promoted. Studying the microbiome in COVID-19 could allow scientists to identify novel approaches to prevent severe inflammation by targeting components of the human microbiome. Innovation in the aforementioned is needed to combat this pandemic.
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Affiliation(s)
- María Magdalena Aguirre García
- División de Investigación, Facultad de Medicina, Unidad de Investigación UNAM-INC, Instituto Nacional de Cardiología Ignacio Chávez, Juan Badiano No. 1, Col. Sección XVI, Tlalpan C.P. 14080, Ciudad de México, Mexico
| | - Javier Mancilla-Galindo
- División de Investigación, Facultad de Medicina, Unidad de Investigación UNAM-INC, Instituto Nacional de Cardiología Ignacio Chávez, Juan Badiano No. 1, Col. Sección XVI, Tlalpan C.P. 14080, Ciudad de México, Mexico
| | - Mercedes Paredes-Paredes
- División de Investigación, Facultad de Medicina, Unidad de Investigación UNAM-INC, Instituto Nacional de Cardiología Ignacio Chávez, Juan Badiano No. 1, Col. Sección XVI, Tlalpan C.P. 14080, Ciudad de México, Mexico
| | - Álvaro Zamudio Tiburcio
- Departamento de Gastroenterología, Unidad de Trasplante de Microbiota Intestinal, Especialidades Médicas Nápoles, Oficina 12, Pennsylvania No. 209 Esq. Kansas, Col. Nápoles, Benito Juárez C.P 03810, Ciudad de México, Mexico
| | - Nydia Ávila-Vanzzini
- Departamento de Consulta Externa, Instituto Nacional de Cardiología Ignacio Chávez, Juan Badiano No. 1, Col. Sección XVI, Tlalpan C.P. 14080, Ciudad de México, Mexico
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Gil-Rodríguez AM, Garcia-Gutierrez E. Antimicrobial mechanisms and applications of yeasts. ADVANCES IN APPLIED MICROBIOLOGY 2020; 114:37-72. [PMID: 33934852 DOI: 10.1016/bs.aambs.2020.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Yeasts and humans have had a close relationship for millenia. Yeast have been used for food production since the first human societies. Since then, alternative uses have been discovered. Nowadays, antibiotic resistance constitutes a pressing need worldwide. In order to overcome this threat, one of the most important strategies is the search for new antimicrobials in natural sources. Moreover, biopreservation based on natural sources has emerged as an alternative to more common chemical preservatives. Yeasts constitute an underexploited source of antagonistic activity against other microorganisms. Here, we compile a summary of the antagonistic activity of yeast origin against other yeast and other microorganisms, such as bacteria or parasites. We present the mechanisms of action used by yeasts to display these activities. We also provide applications of these antagonistic activities in food industry and agriculture, medicine and veterinary, where yeast promise to play a pivotal role in the near future.
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Moreno-Sabater A, Autaa G, Sterlin D, Jerbi A, Villette R, Holm JB, Parizot C, Selim S, Senghor Y, Ghillani-Dalbin P, Bachmeyer C, Hennequin C, Gorochov G, Larsen M. Systemic anti-commensal response to fungi analyzed by flow cytometry is related to gut mycobiome ecology. MICROBIOME 2020; 8:159. [PMID: 33190643 PMCID: PMC7667786 DOI: 10.1186/s40168-020-00924-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/15/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Interest for the study of gut mycobiota in relation with human health and immune homeostasis has increased in the last years. From this perspective, new tools to study the immune/fungal interface are warranted. Systemic humoral immune responses could reflect the dynamic relationships between gut mycobiota and immunity. Using a novel flow cytometry technology (Fungi-Flow) to determine immunoglobulin (Ig) responses to fungi, we studied the relationships between gut mycobiota and systemic humoral anti-commensal immunity. RESULTS The Fungi-Flow method allows a sensitive and specific measurement of systemic IgG responses against 17 commensal and environmental fungi from the two main divisions; Ascomycota and Basidiomycota. IgG responses exhibited a high inter-individual variability. Anti-commensal IgG responses were contrasted with the relative abundance, alpha-diversity, and intra-genus richness of fungal species in gut mycobiota of twenty healthy donors. Categorization of gut mycobiota composition revealed two differentiated fungal ecosystems. Significant difference of anti-Saccharomyces systemic IgG responses were observed in healthy donors stratified according to the fungal ecosystem colonizing their gut. A positive and significant correlation was observed between the variety of IgG responses against fungal commensals and intestinal alpha-diversity. At the level of intra-genus species richness, intense IgG responses were associated with a low intra-genus richness for known pathobionts, but not commensals. CONCLUSIONS Fungi-Flow allows an easy and reliable measure of personalized humoral responses against commensal fungi. Combining sequencing technology with our novel Fungi-Flow immunological method, we propose that there are at least two defined ecosystems in the human gut mycobiome associated with systemic humoral responses. Fungi-Flow opens new opportunities to improve our knowledge about the impact of mycobiota in humoral anti-commensal immunity and homeostasis. Video Abstract.
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Affiliation(s)
- Alicia Moreno-Sabater
- Sorbonne Université, Inserm U1135, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), 75013 Paris, France
- Service de Parasitologie-Mycologie AP-HP, Hôpital Saint-Antoine, 75012 Paris, France
| | - Gaelle Autaa
- Sorbonne Université, Inserm U1135, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), 75013 Paris, France
| | - Delphine Sterlin
- Sorbonne Université, Inserm U1135, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), 75013 Paris, France
- Service d’immunologie, AP-HP, Hôpital Pitié-Salpêtrière, 75013 Paris, France
- Unit of Antibodies in Therapy and Pathology, Institut Pasteur, UMR1222 Inserm, 75015 Paris, France
| | - Amenie Jerbi
- Service d’immunologie, AP-HP, Hôpital Pitié-Salpêtrière, 75013 Paris, France
| | - Remy Villette
- Sorbonne Université, Inserm U1135, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), 75013 Paris, France
| | - Johanna B. Holm
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD USA
| | - Christophe Parizot
- Service d’immunologie, AP-HP, Hôpital Pitié-Salpêtrière, 75013 Paris, France
| | - Sameh Selim
- College of Agricultural Sciences AGHYLE Res, Unit. Institut Polytechnique UniLaSalle, 60026 Beauvais, France
| | - Yaye Senghor
- Service de Parasitologie-Mycologie AP-HP, Hôpital Saint-Antoine, 75012 Paris, France
| | | | | | - Christophe Hennequin
- Service de Parasitologie-Mycologie AP-HP, Hôpital Saint-Antoine, 75012 Paris, France
- Centre de Recherche Saint-Antoine, CRSA, AP-HP, Sorbonne Université, Inserm, 75012 Paris, France
| | - Guy Gorochov
- Sorbonne Université, Inserm U1135, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), 75013 Paris, France
- Service d’immunologie, AP-HP, Hôpital Pitié-Salpêtrière, 75013 Paris, France
| | - Martin Larsen
- Sorbonne Université, Inserm U1135, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), 75013 Paris, France
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State of the Art in the Culture of the Human Microbiota: New Interests and Strategies. Clin Microbiol Rev 2020; 34:34/1/e00129-19. [PMID: 33115723 DOI: 10.1128/cmr.00129-19] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The last 5 years have seen a turning point in the study of the gut microbiota with a rebirth of culture-dependent approaches to study the gut microbiota. High-throughput methods have been developed to study bacterial diversity with culture conditions aimed at mimicking the gut environment by using rich media such as YCFA (yeast extract, casein hydrolysate, fatty acids) and Gifu anaerobic medium in an anaerobic workstation, as well as media enriched with rumen and blood and coculture, to mimic the symbiosis of the gut microbiota. Other culture conditions target phenotypic and metabolic features of bacterial species to facilitate their isolation. Preexisting technologies such as next-generation sequencing and flow cytometry have also been utilized to develop innovative methods to isolate previously uncultured bacteria or explore viability in samples of interest. These techniques have been applied to isolate CPR (Candidate Phyla Radiation) among other, more classic approaches. Methanogenic archaeal and fungal cultures present different challenges than bacterial cultures. Efforts to improve the available systems to grow archaea have been successful through coculture systems. For fungi that are more easily isolated from the human microbiota, the challenge resides in the identification of the isolates, which has been approached by applying matrix-assisted laser desorption ionization-time of flight mass spectrometry technology to fungi. Bacteriotherapy represents a nonnegligible avenue in the future of medicine to correct dysbiosis and improve health or response to therapy. Although great strides have been achieved in the last 5 years, efforts in bacterial culture need to be sustained to continue deciphering the dark matter of metagenomics, particularly CPR, and extend these methods to archaea and fungi.
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Garcia-Gutierrez E, Narbad A, Rodríguez JM. Autism Spectrum Disorder Associated With Gut Microbiota at Immune, Metabolomic, and Neuroactive Level. Front Neurosci 2020; 14:578666. [PMID: 33117122 PMCID: PMC7578228 DOI: 10.3389/fnins.2020.578666] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/16/2020] [Indexed: 12/21/2022] Open
Abstract
There is increasing evidence suggesting a link between the autism spectrum disorder (ASD) and the gastrointestinal (GI) microbiome. Experimental and clinical studies have shown that patients diagnosed with ASD display alterations of the gut microbiota. These alterations do not only extend to the gut microbiota composition but also to the metabolites they produce, as a result of its connections with diet and the bidirectional interaction with the host. Thus, production of metabolites and neurotransmitters stimulate the immune system and influence the central nervous system (CNS) by stimulation of the vagal nerve, as an example of the gut-brain axis pathway. In this review we compose an overview of the interconnectivity of the different GI-related elements that have been associated with the development and severity of the ASD in patients and animal models. We review potential biomarkers to be used in future studies to unlock further connections and interventions in the treatment of ASD.
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Affiliation(s)
- Enriqueta Garcia-Gutierrez
- Gut Microbes and Health Institute Strategic Program, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Arjan Narbad
- Gut Microbes and Health Institute Strategic Program, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Juan Miguel Rodríguez
- Department of Nutrition and Food Science, Complutense University of Madrid, Madrid, Spain
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Steinert RE, Rehman A, Souto Lima EJ, Agamennone V, Schuren FHJ, Gero D, Schreiner P, Vonlanthen R, Ismaeil A, Tzafos S, Hosa H, Vetter D, Misselwitz B, Bueter M. Roux-en-Y gastric bypass surgery changes fungal and bacterial microbiota in morbidly obese patients-A pilot study. PLoS One 2020; 15:e0236936. [PMID: 32735609 PMCID: PMC7394366 DOI: 10.1371/journal.pone.0236936] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Accepted: 07/16/2020] [Indexed: 02/07/2023] Open
Abstract
The Roux-en-Y gastric bypass (RYGB) remains the most effective treatment for morbidly obese patients to lower body weight and improve glycemic control. There is recent evidence that the mycobiome (fungal microbiome) can aggravate disease severity in a number of diseases including inflammatory bowel disease (IBD), irritable bowel syndrome (IBS) and hepatitis; moreover, a dysbiotic fungal microbiota has been reported in the obese. We characterized fungal and bacterial microbial composition in fecal samples of 16 morbidly obese patients before and three months after RYGB surgery and compared with nine healthy controls. We found that RYGB surgery induced a clear alteration in structure and composition of the gut fungal and bacterial microbiota. Beta diversity analysis revealed significant differences in bacterial microbiota between obese patients before surgery and healthy controls (P < 0.005) and a significant, unidirectional shift in RYGB patients after surgery (P < 0.001 vs. before surgery). In contrast, there was no significant difference in fungal microbiota between groups but individually specific changes after RYGB surgery. Interestingly, RYGB surgery induced a significant reduction in fungal alpha diversity namely Chao1, Sobs, and Shannon diversity index (P<0.05, respectively) which contrasts the trend for uniform changes in bacteria towards increased richness and diversity post-surgery. We did not observe any inter-kingdom relations in RYGB patients but in the healthy control cohort and there were several correlations between fungi and bacteria and clinical parameters (P<0.05, respectively) that warrant further research. Our study identifies changes in intestinal fungal communities in RYGB patients that are distinct to changes in the bacterial microbiota.
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Affiliation(s)
- Robert E. Steinert
- Department of Surgery, University Hospital Zürich, Zürich, Switzerland
- * E-mail:
| | - Ateequr Rehman
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Everton Job Souto Lima
- Microbiology and Systems Biology, The Netherlands Organization for Applied Scientific Research (TNO), Zeist, The Netherlands
| | - Valeria Agamennone
- Microbiology and Systems Biology, The Netherlands Organization for Applied Scientific Research (TNO), Zeist, The Netherlands
| | - Frank H. J. Schuren
- Microbiology and Systems Biology, The Netherlands Organization for Applied Scientific Research (TNO), Zeist, The Netherlands
| | - Daniel Gero
- Department of Surgery, University Hospital Zürich, Zürich, Switzerland
| | - Phillip Schreiner
- Department of Surgery, University Hospital Zürich, Zürich, Switzerland
| | - René Vonlanthen
- Department of Surgery, University Hospital Zürich, Zürich, Switzerland
| | - Aiman Ismaeil
- Department of Surgery, University Hospital Zürich, Zürich, Switzerland
- Department of Surgery, Aswan University, Tingar, Egypt
| | - Stefanos Tzafos
- Department of Surgery, University Hospital Zürich, Zürich, Switzerland
| | - Hanna Hosa
- Department of Surgery, University Hospital Zürich, Zürich, Switzerland
| | - Diana Vetter
- Department of Surgery, University Hospital Zürich, Zürich, Switzerland
| | - Benjamin Misselwitz
- Division of Visceral Surgery and Medicine, Inselspital Bern and Bern University, Bern, Switzerland
| | - Marco Bueter
- Department of Surgery, University Hospital Zürich, Zürich, Switzerland
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Zhang D, Wang Y, Shen S, Hou Y, Chen Y, Wang T. The mycobiota of the human body: a spark can start a prairie fire. Gut Microbes 2020; 11:655-679. [PMID: 32150513 PMCID: PMC7524315 DOI: 10.1080/19490976.2020.1731287] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Mycobiota are inseparable from human health, shaking up the unique position held by bacteria among microorganisms. What is surprising is that this seemingly small species can trigger huge changes in the human body. Dysbiosis and invasion of mycobiota are confirmed to cause disease in different parts of the body. Meanwhile, our body also produces corresponding immune changes upon mycobiota infection. Several recent studies have made a connection between intestinal mycobiota and the human immune system. In this review, we focus on questions related to mycobiota, starting with an introduction of select species, then we summarize the typical diseases caused by mycobiota in different parts of the human body. Moreover, we constructed a framework for the human anti-fungal immune system based on genetics and immunology. Finally, the progression of fungal detection methods is also reviewed.
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Affiliation(s)
- Di Zhang
- The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School of Nanjing University, Nanjing, China
| | - Ying Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School of Nanjing University, Nanjing, China
| | - Sunan Shen
- The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School of Nanjing University, Nanjing, China,Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China
| | - Yayi Hou
- The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School of Nanjing University, Nanjing, China,Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China
| | - Yugen Chen
- Department of Colorectal Surgery, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Tingting Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School of Nanjing University, Nanjing, China,Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China,CONTACT Tingting Wang The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School of Nanjing University, Nanjing210093, China
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Angebault C, Payen M, Woerther PL, Rodriguez C, Botterel F. Combined bacterial and fungal targeted amplicon sequencing of respiratory samples: Does the DNA extraction method matter? PLoS One 2020; 15:e0232215. [PMID: 32343737 PMCID: PMC7188255 DOI: 10.1371/journal.pone.0232215] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 04/09/2020] [Indexed: 12/14/2022] Open
Abstract
Background High-throughput sequencing techniques are used to analyse the diversity of the respiratory microbiota in health and disease. Although extensive data are available regarding bacterial respiratory microbiota, its fungal component remains poorly studied. This is partly due to the technical issues associated with fungal metagenomics analyses. In this study, we compared two DNA extraction protocols and two fungal amplification targets for combined bacterial and fungal targeted amplicon sequencing analyses of the respiratory microbiota. Methods Six sputa, randomly selected from routine samples in Mondor Hospital (Creteil, France) and treated anonymously, were tested after bacterial and fungal routine culture. Two of which were spiked with Aspergillus Fumigati and Aspergillus Nigri (105 conidia/mL). After mechanical lysis, DNA was extracted using automated QIAsymphony® extraction (AQE) or manual PowerSoil® MoBio extraction (MPE). DNA yield and purity were compared. DNA extracted from spiked sputa was subjected to (i) real-time PCR for Aspergillus DNA detection and (ii) combined metagenomic analyses targeting barcoded primers for fungal ITS1 and ITS2, and bacterial V1-V2 and V3-V4 16S regions. Amplicon libraries were prepared using MiSeq Reagent V3 kit on Illumina platform. Data were analysed using PyroMIC© and SHAMAN software, and compared with culture results. Results AQE extraction provided a higher yield of DNA (AQE/MPE DNA ratio = 4.5 [1.3–11]) in a shorter time. The yield of Aspergillus DNA detected by qPCR was similar for spiked sputa regardless of extraction protocol. The extraction moderately impacted the diversity or relative abundances of bacterial communities using targeted amplicon sequencing (2/43 taxa impacted). For fungi, the relative abundances of 4/11 major taxa were impacted and AQE results were closer to culture results. The V1-V2 or V3-V4 and ITS1 or ITS2 targets assessed similarly the diversity of bacterial and fungal major taxa, but ITS2 and V3-V4 detected more minor taxa. Conclusion Our results showed the importance of DNA extraction for combined bacterial and fungal targeted metagenomics of respiratory samples. The extraction protocol can affect DNA yield and the relative abundances of few bacterial but more fungal taxa. For fungal analysis, ITS2 allowed the detection of a greater number of minor taxa compared with ITS1.
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Affiliation(s)
- Cécile Angebault
- Unité de Parasitologie-Mycologie, Département de Prévention, Diagnostic et Traitement des Infections, CHU Henri Mondor, Assistance Publique des Hôpitaux de Paris (APHP), Créteil, France
- EA DYNAMiC 7380, Faculté de Santé, Univ Paris-Est Créteil, Créteil, France
- EA DYNAMiC 7380, Ecole nationale vétérinaire d’Alfort, USC Anses, Maison-Alfort, France
- * E-mail:
| | - Mathilde Payen
- Unité de Parasitologie-Mycologie, Département de Prévention, Diagnostic et Traitement des Infections, CHU Henri Mondor, Assistance Publique des Hôpitaux de Paris (APHP), Créteil, France
| | - Paul-Louis Woerther
- EA DYNAMiC 7380, Faculté de Santé, Univ Paris-Est Créteil, Créteil, France
- Unité de Bactériologie-Hygiène, Département de Prévention, Diagnostic et Traitement des Infections, CHU Henri Mondor, APHP, Créteil, France
| | - Christophe Rodriguez
- Next-Generation Sequencing Platform”Génomiques”, INSERM U955, APHP, IMRB Créteil, Créteil, France
| | - Françoise Botterel
- Unité de Parasitologie-Mycologie, Département de Prévention, Diagnostic et Traitement des Infections, CHU Henri Mondor, Assistance Publique des Hôpitaux de Paris (APHP), Créteil, France
- EA DYNAMiC 7380, Faculté de Santé, Univ Paris-Est Créteil, Créteil, France
- EA DYNAMiC 7380, Ecole nationale vétérinaire d’Alfort, USC Anses, Maison-Alfort, France
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Mogilnicka I, Ufnal M. Gut Mycobiota and Fungal Metabolites in Human Homeostasis. Curr Drug Targets 2020; 20:232-240. [PMID: 30047327 DOI: 10.2174/1389450119666180724125020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 05/13/2018] [Accepted: 07/19/2018] [Indexed: 12/17/2022]
Abstract
BACKGROUND Accumulating evidence suggests that microbiota play an important role in host's homeostasis. Thus far, researchers have mostly focused on the role of bacterial microbiota. However, human gut is a habitat for several fungal species, which produce numerous metabolites. Furthermore, various types of food and beverages are rich in a wide spectrum of fungi and their metabolites. METHODS We searched PUBMED and Google Scholar databases to identify clinical and pre-clinical studies on fungal metabolites, composition of human mycobiota and fungal dysbiosis. RESULTS Fungal metabolites may serve as signaling molecules and exert significant biological effects including trophic, anti-inflammatory or antibacterial actions. Finally, research suggests an association between shifts in gut fungi composition and human health. Changes in mycobiota composition have been found in obesity, hepatitis and inflammatory bowel diseases. CONCLUSION The influence of mycobiota and dietary fungi on homeostasis in mammals suggests a pharmacotherapeutic potential of modulating the mycobiota which may include treatment with probiotics and fecal transplantation. Furthermore, antibacterial action of fungi-derived molecules may be considered as a substitution for currently used antibacterial agents and preservatives in food industry.
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Affiliation(s)
- Izabella Mogilnicka
- Department of Experimental Physiology and Pathophysiology, Laboratory of the Centre for Preclinical Research, Medical University of Warsaw, Warsaw, Poland
| | - Marcin Ufnal
- Department of Experimental Physiology and Pathophysiology, Laboratory of the Centre for Preclinical Research, Medical University of Warsaw, Warsaw, Poland
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Romo JA, Kumamoto CA. On Commensalism of Candida. J Fungi (Basel) 2020; 6:E16. [PMID: 31963458 PMCID: PMC7151168 DOI: 10.3390/jof6010016] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 01/13/2020] [Accepted: 01/15/2020] [Indexed: 01/09/2023] Open
Abstract
Candida species are both opportunistic fungal pathogens and common members of the human mycobiome. Over the years, the main focus of the fungal field has been on understanding the pathogenic potential and disease manifestation of these organisms. Therefore, understanding of their commensal lifestyle, interactions with host epithelial barriers, and initial transition into pathogenesis is less developed. In this review, we will describe the current knowledge on the commensal lifestyle of these fungi, how they are able to adhere to and colonize host epithelial surfaces, compete with other members of the microbiota, and interact with the host immune response, as well as their transition into opportunistic pathogens by invading the gastrointestinal epithelium.
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Affiliation(s)
| | - Carol A. Kumamoto
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02111, USA;
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Nel Van Zyl K, Whitelaw AC, Newton-Foot M. The effect of storage conditions on microbial communities in stool. PLoS One 2020; 15:e0227486. [PMID: 31935223 PMCID: PMC6959592 DOI: 10.1371/journal.pone.0227486] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/19/2019] [Indexed: 12/11/2022] Open
Abstract
Microbiome research has experienced a surge of interest in recent years due to the advances and reduced cost of next-generation sequencing technology. The production of high quality and comparable data is dependent on proper sample collection and storage and should be standardized as far as possible. However, this becomes challenging when samples are collected in the field, especially in resource-limited settings. We investigated the impact of different stool storage methods common to the TB-CHAMP clinical trial on the microbial communities in stool. Ten stool samples were subjected to DNA extraction after 48-hour storage at -80°C, room temperature and in a cooler-box, as well as immediate DNA extraction. Three stool DNA extraction kits were evaluated based on DNA yield and quality. Quantitative PCR was performed to determine the relative abundance of the two major gut phyla Bacteroidetes and Firmicutes, and other representative microbial groups. The bacterial populations in the frozen group closely resembled the immediate extraction group, supporting previous findings that storage at -80°C is equivalent to the gold standard of immediate DNA extraction. More variation was seen in the room temperature and cooler-box groups, which may be due to the growth temperature preferences of certain bacterial populations. However, for most bacterial populations, no significant differences were found between the storage groups. As seen in other microbiome studies, the variation between participant samples was greater than that related to differences in storage. We determined that the risk of introducing bias to microbial community profiling through differences in storage will likely be minimal in our setting.
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Affiliation(s)
- Kristien Nel Van Zyl
- Division of Medical Microbiology, Department of Pathology, Stellenbosch University, South Africa
- * E-mail:
| | - Andrew C. Whitelaw
- Division of Medical Microbiology, Department of Pathology, Stellenbosch University, South Africa
- National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
- African Microbiome Institute, Stellenbosch University, South Africa
| | - Mae Newton-Foot
- Division of Medical Microbiology, Department of Pathology, Stellenbosch University, South Africa
- National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
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