1
|
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.
Collapse
Affiliation(s)
- Guanyue Wei
- National Key Laboratory of Pig Genetic Improvement and Germplasm Innovation, Jiangxi Agricultural University, Nanchang, China
| |
Collapse
|
2
|
Zhan H, Wan Y, Sun Y, Xu Z, Zhang F, Yang K, Zhu W, Cheung CP, Tang W, Ng EK, Wong SK, Yeoh YK, Kl Chan F, Miao Y, Zuo T, Zeng Z, Ng SC. Gut mycobiome alterations in obesity in geographically different regions. Gut Microbes 2024; 16:2367297. [PMID: 38899956 PMCID: PMC11195487 DOI: 10.1080/19490976.2024.2367297] [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: 10/26/2023] [Accepted: 06/07/2024] [Indexed: 06/21/2024] Open
Abstract
The gut fungi play important roles in human health and are involved in energy metabolism. This study aimed to examine gut mycobiome composition in obese subjects in two geographically different regions in China and to identify specific gut fungi associated with obesity. A total of 217 subjects from two regions with different urbanization levels [Hong Kong (HK): obese, n = 59; lean, n = 59; Kunming (KM): obese, n = 50; lean, n = 49. Mean body mass index (BMI) for obesity = 33.7] were recruited. We performed deep shotgun metagenomic sequencing on fecal samples to compare gut mycobiome composition and trophic functions in lean and obese subjects across these two regions. The gut mycobiome of obese subjects in both HK and KM were altered compared to those of lean subjects, characterized by a decrease in the relative abundance of Nakaseomyces, Schizosaccharomyces pombe, Candida dubliniensis and an increase in the abundance of Lanchanceathermotolerans, Saccharomyces paradox, Parastagonospora nodorum and Myceliophthorathermophila. Reduced fungal - bacterial and fungal - fungal correlations as well as increased negative fungal-bacterial correlations were observed in the gut of obese subjects. Furthermore, the anti-obesity effect of fungus S. pombe was further validated using a mouse model. Supplementing high-fat diet-induced obese mice with the fungus for 12 weeks led to a significant reduction in body weight gain (p < 0.001), and an improvement in lipid and glucose metabolism compared to mice without intervention. In conclusion, the gut mycobiome composition and functionalities of obese subjects were altered. These data shed light on the potential of utilizing fungus-based therapeutics for the treatment of obesity. S. pombe may serve as a potential fungal probiotic in the prevention of diet-induced obesity and future human trials are needed.
Collapse
Affiliation(s)
- Hui Zhan
- Microbiota I-Center (MagIC) Limited, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yating Wan
- Microbiota I-Center (MagIC) Limited, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yang Sun
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Yunnan Province Clinical Research Center for Digestive Diseases, Yunnan, China
- Yunnan Geriatric Medical Center, Kunming, Yunnan, China
| | - Zhilu Xu
- Microbiota I-Center (MagIC) Limited, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Fen Zhang
- Microbiota I-Center (MagIC) Limited, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Keli Yang
- Microbiota I-Center (MagIC) Limited, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wenyi Zhu
- Microbiota I-Center (MagIC) Limited, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chun Pan Cheung
- Microbiota I-Center (MagIC) Limited, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Whitney Tang
- Microbiota I-Center (MagIC) Limited, Hong Kong SAR, China
| | - Enders Kw Ng
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Simon Kh Wong
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yun Kit Yeoh
- Microbiota I-Center (MagIC) Limited, Hong Kong SAR, China
| | - Francis Kl Chan
- Microbiota I-Center (MagIC) Limited, Hong Kong SAR, China
- Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yinglei Miao
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Yunnan Province Clinical Research Center for Digestive Diseases, Yunnan, China
| | - Tao Zuo
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zhong Zeng
- Department of Organ Transplantation Center, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Siew C Ng
- Microbiota I-Center (MagIC) Limited, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| |
Collapse
|
3
|
Kreulen IAM, de Jonge WJ, van den Wijngaard RM, van Thiel IAM. Candida spp. in Human Intestinal Health and Disease: More than a Gut Feeling. Mycopathologia 2023; 188:845-862. [PMID: 37294505 PMCID: PMC10687130 DOI: 10.1007/s11046-023-00743-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/09/2023] [Indexed: 06/10/2023]
Abstract
Fungi are an essential part of the normal collection of intestinal microorganisms, even though their collective abundance comprises only 0.1-1% of all fecal microbes. The composition and role of the fungal population is often studied in relation to early-life microbial colonization and development of the (mucosal) immune system. The genus Candida is frequently described as one of the most abundant genera, and altered fungal compositions (including elevated abundance of Candida spp.) have been linked with intestinal diseases such as inflammatory bowel disease and irritable bowel syndrome. These studies are performed using both culture-dependent and genomic (metabarcoding) techniques. In this review, we aimed to summarize existing data on intestinal Candida spp. colonization in relation to intestinal disease and provide a brief overview of the biological and technical challenges in this field, including the recently described role of sub-species strain variation of intestinal Candida albicans. Together, the evidence for a contributing role of Candida spp. in pediatric and adult intestinal disease is quickly expanding, even though technical and biological challenges may limit full understanding of host-microbe interactions.
Collapse
Affiliation(s)
- Irini A M Kreulen
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam UMC, Location Academic Medical Center, Meibergdreef 69-71, 1105 BK, Amsterdam, the Netherlands
| | - Wouter J de Jonge
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam UMC, Location Academic Medical Center, Meibergdreef 69-71, 1105 BK, Amsterdam, the Netherlands
- Department of Gastroenterology and Hepatology, Amsterdam UMC, Location Academic Medical Center, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
- Department of General, Visceral, Thoracic and Vascular Surgery, University Hospital Bonn, 53127, Bonn, Germany
| | - René M van den Wijngaard
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam UMC, Location Academic Medical Center, Meibergdreef 69-71, 1105 BK, Amsterdam, the Netherlands
- Department of Gastroenterology and Hepatology, Amsterdam UMC, Location Academic Medical Center, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
| | - Isabelle A M van Thiel
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam UMC, Location Academic Medical Center, Meibergdreef 69-71, 1105 BK, Amsterdam, the Netherlands.
- Royal Netherlands Academy of Arts and Sciences, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands.
| |
Collapse
|
4
|
Shen K, Din AU, Sinha B, Zhou Y, Qian F, Shen B. Translational informatics for human microbiota: data resources, models and applications. Brief Bioinform 2023; 24:7152256. [PMID: 37141135 DOI: 10.1093/bib/bbad168] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 05/05/2023] Open
Abstract
With the rapid development of human intestinal microbiology and diverse microbiome-related studies and investigations, a large amount of data have been generated and accumulated. Meanwhile, different computational and bioinformatics models have been developed for pattern recognition and knowledge discovery using these data. Given the heterogeneity of these resources and models, we aimed to provide a landscape of the data resources, a comparison of the computational models and a summary of the translational informatics applied to microbiota data. We first review the existing databases, knowledge bases, knowledge graphs and standardizations of microbiome data. Then, the high-throughput sequencing techniques for the microbiome and the informatics tools for their analyses are compared. Finally, translational informatics for the microbiome, including biomarker discovery, personalized treatment and smart healthcare for complex diseases, are discussed.
Collapse
Affiliation(s)
- Ke Shen
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
| | - Ahmad Ud Din
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
| | - Baivab Sinha
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
| | - Yi Zhou
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
| | - Fuliang Qian
- Center for Systems Biology, Suzhou Medical College of Soochow University, Suzhou 215123, China
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Suzhou 215123, China
| | - Bairong Shen
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
| |
Collapse
|
5
|
Boix-Amorós A, Monaco H, Sambataro E, Clemente JC. Novel technologies to characterize and engineer the microbiome in inflammatory bowel disease. Gut Microbes 2022; 14:2107866. [PMID: 36104776 PMCID: PMC9481095 DOI: 10.1080/19490976.2022.2107866] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We present an overview of recent experimental and computational advances in technology used to characterize the microbiome, with a focus on how these developments improve our understanding of inflammatory bowel disease (IBD). Specifically, we present studies that make use of flow cytometry and metabolomics assays to provide a functional characterization of microbial communities. We also describe computational methods for strain-level resolution, temporal series, mycobiome and virome data, co-occurrence networks, and compositional data analysis. In addition, we review novel techniques to therapeutically manipulate the microbiome in IBD. We discuss the benefits and drawbacks of these technologies to increase awareness of specific biases, and to facilitate a more rigorous interpretation of results and their potential clinical application. Finally, we present future lines of research to better characterize the relation between microbial communities and IBD pathogenesis and progression.
Collapse
Affiliation(s)
- Alba Boix-Amorós
- Department of Genetics and Genomic Sciences, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai. New York, NY, USA
| | - Hilary Monaco
- Department of Genetics and Genomic Sciences, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai. New York, NY, USA
| | - Elisa Sambataro
- Department of Biological Sciences, CUNY Hunter College, New York, NY, USA
| | - Jose C. Clemente
- Department of Genetics and Genomic Sciences, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai. New York, NY, USA,CONTACT Jose C. Clemente Department of Genetics and Genomic Sciences, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai. New York, NY10029USA
| |
Collapse
|
6
|
Molecular Markers: An Overview of Data Published for Fungi over the Last Ten Years. J Fungi (Basel) 2022; 8:jof8080803. [PMID: 36012792 PMCID: PMC9410331 DOI: 10.3390/jof8080803] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/21/2022] [Accepted: 07/27/2022] [Indexed: 02/01/2023] Open
Abstract
Fungi are amongst the most abundant and diverse organisms. Despite being widely known for their adverse role in food spoilage or as pathogens for humans, animals, or plants, they also present several beneficial effects. Fungi contribute to human well-being due to their role as decomposers, degrading decay matter into smaller molecules which can be easily used by other ecosystem members. These organisms can produce medicinal compounds or modulate protective immune responses in human intestine. Fungi intervene in diverse food processes or act as a food supply. Due to fungal diversity, the unequivocal identification of these organisms is crucial to increasing their practical applications and decreasing their adverse effects. The process of identification could be achieved through the integral sequencing of fungi genomes. However, this procedure would be time-consuming and rather cost-inefficient. Therefore, several molecular markers have been developed to overcome these limitations. The chronology of DNA-based molecular markers development can be divided into three main steps: (1) prior to the development of the PCR technique (RFLP); (2) after the development of the PCR technique (RAPD, AFLP, ISSR, VNTR, SNP, InDels, and DNA barcoding); (3) after the development of the massive parallel sequencing technique (Metabarcoding and WGS). Therefore, the present review covers an overview of the most recently developed molecular markers used for fungal detection and identification.
Collapse
|
7
|
Xie Z, Manichanh C. FunOMIC: Pipeline with built-in fungal taxonomic and functional databases for human mycobiome profiling. Comput Struct Biotechnol J 2022; 20:3685-3694. [PMID: 35891785 PMCID: PMC9293737 DOI: 10.1016/j.csbj.2022.07.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 11/30/2022] Open
Abstract
While analysis of the bacterial microbiome has become routine, that of the fungal microbiome is still hampered by the lack of robust databases and bioinformatic pipelines. Here, we present FunOMIC, a pipeline with built-in taxonomic (1.6 million marker genes) and functional (3.4 million non-redundant fungal proteins) databases for the identification of fungi. Applied to more than 2,600 human metagenomic samples, the tool revealed fungal species associated with geography, body sites, and diseases. Correlation network analysis provided new insights into inter-kingdom interactions. With this pipeline and two of the most comprehensive fungal databases, we foresee a fast-growing resource for mycobiome studies.
Collapse
Key Words
- CD, Crohn’s disease
- ESRD, End-stage renal disease
- FDR, False discovery rate
- Fungal databases
- GS, Gallstones
- HC, Healthy control
- HTS, High throughput sequencing
- ITS, internal transcribed spacer
- Inter-kingdom interactions
- Mycobiome
- NA, Not applicable
- PLWH, People live with HIV
- PSO, Psoriasis
- SCFA, Short chain fatty acid
- SCZ, Schizophrenia
- Shotgun metagenomics
- T1D, Type 1 diabetes
- T2D, Type 2 diabetes
- TB, Tuberculosis
- Taxonomy and functions
- UC, Ulcerative colitis
Collapse
Affiliation(s)
- Zixuan Xie
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain.,Departament de Medicina, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
| | - Chaysavanh Manichanh
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain.,Departament de Medicina, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
| |
Collapse
|
8
|
Auchtung TA, Stewart CJ, Smith DP, Triplett EW, Agardh D, Hagopian WA, Ziegler AG, Rewers MJ, She JX, Toppari J, Lernmark Å, Akolkar B, Krischer JP, Vehik K, Auchtung JM, Ajami NJ, Petrosino JF. Temporal changes in gastrointestinal fungi and the risk of autoimmunity during early childhood: the TEDDY study. Nat Commun 2022; 13:3151. [PMID: 35672407 PMCID: PMC9174155 DOI: 10.1038/s41467-022-30686-w] [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] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 05/09/2022] [Indexed: 12/11/2022] Open
Abstract
Fungal infections are a major health problem that often begin in the gastrointestinal tract. Gut microbe interactions in early childhood are critical for proper immune responses, yet there is little known about the development of the fungal population from infancy into childhood. Here, as part of the TEDDY (The Environmental Determinants of Diabetes in the Young) study, we examine stool samples of 888 children from 3 to 48 months and find considerable differences between fungi and bacteria. The metagenomic relative abundance of fungi was extremely low but increased while weaning from milk and formula. Overall fungal diversity remained constant over time, in contrast with the increase in bacterial diversity. Fungal profiles had high temporal variation, but there was less variation from month-to-month in an individual than among different children of the same age. Fungal composition varied with geography, diet, and the use of probiotics. Multiple Candida spp. were at higher relative abundance in children than adults, while Malassezia and certain food-associated fungi were lower in children. There were only subtle fungal differences associated with the subset of children that developed islet autoimmunity or type 1 diabetes. Having proper fungal exposures may be crucial for children to establish appropriate responses to fungi and limit the risk of infection: the data here suggests those gastrointestinal exposures are limited and variable.
Collapse
Grants
- U01 DK063821 NIDDK NIH HHS
- UC4 DK063863 NIDDK NIH HHS
- UL1 TR002535 NCATS NIH HHS
- U01 DK063790 NIDDK NIH HHS
- UL1 TR000064 NCATS NIH HHS
- HHSN267200700014C NLM NIH HHS
- U01 DK063836 NIDDK NIH HHS
- U01 DK063829 NIDDK NIH HHS
- U01 DK063865 NIDDK NIH HHS
- UC4 DK095300 NIDDK NIH HHS
- UC4 DK063861 NIDDK NIH HHS
- UC4 DK063829 NIDDK NIH HHS
- UC4 DK063821 NIDDK NIH HHS
- UC4 DK117483 NIDDK NIH HHS
- UC4 DK063836 NIDDK NIH HHS
- UC4 DK112243 NIDDK NIH HHS
- U01 DK124166 NIDDK NIH HHS
- U01 DK063861 NIDDK NIH HHS
- P30 ES030285 NIEHS NIH HHS
- U01 DK128847 NIDDK NIH HHS
- UC4 DK063865 NIDDK NIH HHS
- U01 DK063863 NIDDK NIH HHS
- UC4 DK106955 NIDDK NIH HHS
- UC4 DK100238 NIDDK NIH HHS
- This research was performed on behalf of the TEDDY Study Group, which is funded by U01 DK63829, U01 DK63861, U01 DK63821, U01 DK63865, U01 DK63863, U01 DK63836, U01 DK63790, UC4 DK63829, UC4 DK63861, UC4 DK63821, UC4 DK63865, UC4 DK63863, UC4 DK63836, UC4 DK95300, UC4 DK100238, UC4 DK106955, UC4 DK112243, UC4 DK117483, U01 DK124166, U01 DK128847, and Contract No. HHSN267200700014C from the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institute of Allergy and Infectious Diseases (NIAID), Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institute of Environmental Health Sciences (NIEHS), Centers for Disease Control and Prevention (CDC), and JDRF. This work is supported in part by the NIH/NCATS Clinical and Translational Science Awards to the University of Florida (UL1 TR000064) and the University of Colorado (UL1 TR002535).
Collapse
Affiliation(s)
- Thomas A Auchtung
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA.
| | - Christopher J Stewart
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Daniel P Smith
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Eric W Triplett
- Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Daniel Agardh
- Department of Clinical Sciences, Lund University Clinical Research Center, Skåne University Hospital, Malmö, Sweden
| | | | - Anette G Ziegler
- Institute of Diabetes Research, Helmholtz Zentrum München, Munich, Germany
- Forschergruppe Diabetes, Technische Universität München, Klinikum Rechts der Isar, Munich, Germany
- Forschergruppe Diabetes e.V. at Helmholtz Zentrum München, Munich, Germany
| | - Marian J Rewers
- Barbara Davis Center for Childhood Diabetes, University of Colorado, Aurora, CO, USA
| | - Jin-Xiong She
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA, USA
- Jinfiniti Precision Medicine, Inc, Augusta, GA, USA
| | - Jorma Toppari
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, Turku, Finland
- Department of Pediatrics, Turku University Hospital, Turku, Finland
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University/CRC, Skane University Hospital, Malmö, Sweden
| | - Beena Akolkar
- National Institute of Diabetes & Digestive & Kidney Diseases, Bethesda, MD, USA
| | - Jeffrey P Krischer
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Kendra Vehik
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Jennifer M Auchtung
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Nadim J Ajami
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Program for Innovative Microbiome and Translational Research, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Stengel A, Stanke KM, Quattrone AC, Herr JR. Improving Taxonomic Delimitation of Fungal Species in the Age of Genomics and Phenomics. Front Microbiol 2022; 13:847067. [PMID: 35250961 PMCID: PMC8892103 DOI: 10.3389/fmicb.2022.847067] [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: 01/01/2022] [Accepted: 01/28/2022] [Indexed: 01/04/2023] Open
Abstract
Species concepts have long provided a source of debate among biologists. These lively debates have been important for reaching consensus on how to communicate across scientific disciplines and for advancing innovative strategies to study evolution, population biology, ecology, natural history, and disease epidemiology. Species concepts are also important for evaluating variability and diversity among communities, understanding biogeographical distributions, and identifying causal agents of disease across animal and plant hosts. While there have been many attempts to address the concept of species in the fungi, there are several concepts that have made taxonomic delimitation especially challenging. In this review we discuss these major challenges and describe methodological approaches that show promise for resolving ambiguity in fungal taxonomy by improving discrimination of genetic and functional traits. We highlight the relevance of eco-evolutionary theory used in conjunction with integrative taxonomy approaches to improve the understanding of interactions between environment, ecology, and evolution that give rise to distinct species boundaries. Beyond recent advances in genomic and phenomic methods, bioinformatics tools and modeling approaches enable researchers to test hypothesis and expand our knowledge of fungal biodiversity. Looking to the future, the pairing of integrative taxonomy approaches with multi-locus genomic sequencing and phenomic techniques, such as transcriptomics and proteomics, holds great potential to resolve many unknowns in fungal taxonomic classification.
Collapse
Affiliation(s)
- Ashley Stengel
- Complex Biosystems Interdisciplinary Life Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Kimberly M. Stanke
- Complex Biosystems Interdisciplinary Life Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Amanda C. Quattrone
- Complex Biosystems Interdisciplinary Life Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Joshua R. Herr
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, United States
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, United States
| |
Collapse
|
11
|
Guzzo GL, Andrews JM, Weyrich LS. The Neglected Gut Microbiome: Fungi, Protozoa, and Bacteriophages in Inflammatory Bowel Disease. Inflamm Bowel Dis 2022; 28:1112-1122. [PMID: 35092426 PMCID: PMC9247841 DOI: 10.1093/ibd/izab343] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Indexed: 12/14/2022]
Abstract
The gut microbiome has been implicated in the pathogenesis of inflammatory bowel disease (IBD). Studies suggest that the IBD gut microbiome is less diverse than that of the unaffected population, a phenomenon often referred to as dysbiosis. However, these studies have heavily focused on bacteria, while other intestinal microorganisms-fungi, protozoa, and bacteriophages-have been neglected. Of the nonbacterial microbes that have been studied in relation to IBD, most are thought to be pathogens, although there is evidence that some of these species may instead be harmless commensals. In this review, we discuss the nonbacterial gut microbiome of IBD, highlighting the current biases, limitations, and outstanding questions that can be addressed with high-throughput DNA sequencing methods. Further, we highlight the importance of studying nonbacterial microorganisms alongside bacteria for a comprehensive view of the whole IBD biome and to provide a more precise definition of dysbiosis in patients. With the rise in popularity of microbiome-altering therapies for the treatment of IBD, such as fecal microbiota transplantation, it is important that we address these knowledge gaps to ensure safe and effective treatment of patients.
Collapse
Affiliation(s)
- Gina L Guzzo
- Address correspondence to: Gina L. Guzzo, The University of Adelaide, Adelaide, South Australia, Australia ()
| | - Jane M Andrews
- Inflammatory Bowel Disease Service, Department of Gastroenterology and Hepatology, Royal Adelaide Hospital and School of Medicine, Faculty of Health Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Laura S Weyrich
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia,Department of Anthropology and Huck Institutes of the Life Sciences, Pennsylvania State University, State College, PA, USA
| |
Collapse
|
12
|
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.
Collapse
|
13
|
RESCRIPt: Reproducible sequence taxonomy reference database management. PLoS Comput Biol 2021; 17:e1009581. [PMID: 34748542 PMCID: PMC8601625 DOI: 10.1371/journal.pcbi.1009581] [Citation(s) in RCA: 239] [Impact Index Per Article: 79.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 11/18/2021] [Accepted: 10/21/2021] [Indexed: 12/22/2022] Open
Abstract
Nucleotide sequence and taxonomy reference databases are critical resources for widespread applications including marker-gene and metagenome sequencing for microbiome analysis, diet metabarcoding, and environmental DNA (eDNA) surveys. Reproducibly generating, managing, using, and evaluating nucleotide sequence and taxonomy reference databases creates a significant bottleneck for researchers aiming to generate custom sequence databases. Furthermore, database composition drastically influences results, and lack of standardization limits cross-study comparisons. To address these challenges, we developed RESCRIPt, a Python 3 software package and QIIME 2 plugin for reproducible generation and management of reference sequence taxonomy databases, including dedicated functions that streamline creating databases from popular sources, and functions for evaluating, comparing, and interactively exploring qualitative and quantitative characteristics across reference databases. To highlight the breadth and capabilities of RESCRIPt, we provide several examples for working with popular databases for microbiome profiling (SILVA, Greengenes, NCBI-RefSeq, GTDB), eDNA and diet metabarcoding surveys (BOLD, GenBank), as well as for genome comparison. We show that bigger is not always better, and reference databases with standardized taxonomies and those that focus on type strains have quantitative advantages, though may not be appropriate for all use cases. Most databases appear to benefit from some curation (quality filtering), though sequence clustering appears detrimental to database quality. Finally, we demonstrate the breadth and extensibility of RESCRIPt for reproducible workflows with a comparison of global hepatitis genomes. RESCRIPt provides tools to democratize the process of reference database acquisition and management, enabling researchers to reproducibly and transparently create reference materials for diverse research applications. RESCRIPt is released under a permissive BSD-3 license at https://github.com/bokulich-lab/RESCRIPt. Generating and managing sequence and taxonomy reference data presents a bottleneck to many researchers, whether they are generating custom databases or attempting to format existing, curated reference databases for use with standard sequence analysis tools. Evaluating database quality and choosing the “best” database can be an equally formidable challenge. We developed RESCRIPt to alleviate this bottleneck, supporting reproducible, streamlined generation, curation, and evaluation of reference sequence databases. RESCRIPt uses QIIME 2 artifact file formats, which store all processing steps as data provenance within each file, allowing researchers to retrace the computational steps used to generate any given file. We used RESCRIPt to benchmark several commonly used marker-gene sequence databases for 16S rRNA genes, ITS, and COI sequences, demonstrating both the utility of RESCRIPt to streamline use of these databases, but also to evaluate several qualitative and quantitative characteristics of each database. We show that larger databases are not always best, and curation steps to reduce redundancy and filter out noisy sequences may be beneficial for some applications. We anticipate that RESCRIPt will streamline the use, management, and evaluation/selection of reference database materials for microbiomics, diet metabarcoding, eDNA, and other diverse applications.
Collapse
|
14
|
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.
Collapse
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
| | | |
Collapse
|
15
|
Zhang F, Zuo T, Yeoh YK, Cheng FWT, Liu Q, Tang W, Cheung KCY, Yang K, Cheung CP, Mo CC, Hui M, Chan FKL, Li CK, Chan PKS, Ng SC. Longitudinal dynamics of gut bacteriome, mycobiome and virome after fecal microbiota transplantation in graft-versus-host disease. Nat Commun 2021; 12:65. [PMID: 33397897 PMCID: PMC7782528 DOI: 10.1038/s41467-020-20240-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 10/23/2020] [Indexed: 02/07/2023] Open
Abstract
Fecal microbiota transplant (FMT) has emerged as a potential treatment for severe colitis associated with graft-versus-host disease (GvHD) following hematopoietic stem cell transplant. Bacterial engraftment from FMT donor to recipient has been reported, however the fate of fungi and viruses after FMT remains unclear. Here we report longitudinal dynamics of the gut bacteriome, mycobiome and virome in a teenager with GvHD after receiving four doses of FMT at weekly interval. After serial FMTs, the gut bacteriome, mycobiome and virome of the patient differ from compositions before FMT with variable temporal dynamics. Diversity of the gut bacterial community increases after each FMT. Gut fungal community initially shows expansion of several species followed by a decrease in diversity after multiple FMTs. In contrast, gut virome community varies substantially over time with a stable rise in diversity. The bacterium, Corynebacterium jeikeium, and Torque teno viruses, decrease after FMTs in parallel with an increase in the relative abundance of Caudovirales bacteriophages. Collectively, FMT may simultaneously impact on the various components of the gut microbiome with distinct effects.
Collapse
Affiliation(s)
- Fen Zhang
- Center for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Tao Zuo
- Center for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yun Kit Yeoh
- Center for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Frankie W T Cheng
- Department of Pediatrics, The Chinese University of Hong Kong, Hong Kong, China
| | - Qin Liu
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Whitney Tang
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kitty C Y Cheung
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Keli Yang
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Chun Pan Cheung
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Chow Chung Mo
- Department of Pediatrics, The Chinese University of Hong Kong, Hong Kong, China
| | - Mamie Hui
- Center for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Francis K L Chan
- Center for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Chi-Kong Li
- Department of Pediatrics, The Chinese University of Hong Kong, Hong Kong, China
| | - Paul K S Chan
- Center for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China.
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China.
| | - Siew C Ng
- Center for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China.
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| |
Collapse
|
16
|
Sun Y, Zuo T, Cheung CP, Gu W, Wan Y, Zhang F, Chen N, Zhan H, Yeoh YK, Niu J, Du Y, Zhang F, Wen Y, Yu J, Sung JJY, Chan PKS, Chan FKL, Wang K, Ng SC, Miao Y. Population-Level Configurations of Gut Mycobiome Across 6 Ethnicities in Urban and Rural China. Gastroenterology 2021; 160:272-286.e11. [PMID: 32956679 DOI: 10.1053/j.gastro.2020.09.014] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 09/10/2020] [Accepted: 09/14/2020] [Indexed: 12/31/2022]
Abstract
BACKGROUND & AIMS Beyond bacteria, the human gastrointestinal tract is host to a vast diversity of fungi, collectively known as the gut mycobiome. Little is known of the impact of geography, ethnicity, and urbanization on the gut mycobiome at a large population level. We aim to delineate the variation of human gut mycobiome and its association with host factors, environmental factors, and diets. METHODS Using shotgun metagenomic sequencing, we profiled and compared the fecal mycobiome of 942 healthy individuals across different geographic regions in China (Hong Kong and Yunnan), spanning 6 ethnicities: Han, Zang, Bai, Hani, Dai, and Miao (including both urban and rural residents of each ethnicity). In parallel to fecal sampling, we collected participant metadata (environmental exposure, bowel habits, anthropometrics, and medication), diet, and clinical blood measurement results (a total of 118 variables) and investigated their impact on the gut mycobiome variation in humans. RESULTS The human gut mycobiome was highly variable across populations. Urbanization-related factors had the strongest impact on gut mycobiome variation, followed by geography, dietary habit, and ethnicity. The Hong Kong population (highly urbanized) had a significantly lower fungal richness compared with Yunnan population. Saccharomyces cerevisiae was highly enriched in urban compared with rural populations and showed significant inverse correlations with liver pathology-associated blood parameters, including aspartate transaminase, alanine transaminase, gamma-glutamyltransferase, and direct bilirubin. Candida dubliniensis, which was decreased in urban relative to rural populations, showed correlations with host metabolism-related parameters in blood, including a positive correlation with fasting high-density lipoprotein cholesterol levels and a negative correlation with fasting glucose levels. The fungal-blood parameter correlations were highly geography- and ethnicity-specific. Food choices had differential influences on gut mycobiome and bacterial microbiome, where taxa from the same genus tended to be coregulated by food and thereby cobloom. Ethnicity-specific fungal signatures were associated with distinct habitual foods in each ethnic group. CONCLUSIONS Our data highlight, for the first time to our knowledge, that geography, urbanization, ethnicity, and habitual diet play an important role in shaping the gut mycobiome composition. Gut fungal configurations in combination with population characteristics (such as residing region, ethnicity, diet, lifestyle) influence host metabolism and health.
Collapse
Affiliation(s)
- Yang Sun
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Diseases, Kunming, Yunnan, China
| | - Tao Zuo
- Center for Gut microbiota research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; State Key Laboratory of Digestive Diseases, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Chun Pan Cheung
- Center for Gut microbiota research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; State Key Laboratory of Digestive Diseases, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Wenxi Gu
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Diseases, Kunming, Yunnan, China
| | - Yating Wan
- Center for Gut microbiota research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; State Key Laboratory of Digestive Diseases, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Fen Zhang
- Center for Gut microbiota research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; State Key Laboratory of Digestive Diseases, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Nan Chen
- Center for Gut microbiota research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; State Key Laboratory of Digestive Diseases, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Hui Zhan
- Center for Gut microbiota research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; State Key Laboratory of Digestive Diseases, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Yun Kit Yeoh
- Center for Gut microbiota research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Junkun Niu
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Diseases, Kunming, Yunnan, China
| | - Yan Du
- Department of Clinical Laboratory, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Fengrui Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Diseases, Kunming, Yunnan, China
| | - Yunling Wen
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Diseases, Kunming, Yunnan, China
| | - Jun Yu
- Center for Gut microbiota research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; State Key Laboratory of Digestive Diseases, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Joseph J Y Sung
- State Key Laboratory of Digestive Diseases, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Paul K S Chan
- Center for Gut microbiota research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Francis K L Chan
- Center for Gut microbiota research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; State Key Laboratory of Digestive Diseases, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Kunhua Wang
- National Health Commission Key Laboratory of Drug Addiction Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, Yunnan, China.
| | - Siew C Ng
- Center for Gut microbiota research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; State Key Laboratory of Digestive Diseases, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.
| | - Yinglei Miao
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Diseases, Kunming, Yunnan, China.
| |
Collapse
|
17
|
R Marcelino V, Holmes EC, Sorrell TC. The use of taxon-specific reference databases compromises metagenomic classification. BMC Genomics 2020; 21:184. [PMID: 32106809 PMCID: PMC7045516 DOI: 10.1186/s12864-020-6592-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/19/2020] [Indexed: 11/10/2022] Open
Abstract
A recent article in BMC Genomics describes a new bioinformatics tool, HumanMycobiomeScan, to classify fungal taxa in metagenomic samples. This tool was used to characterize the gut mycobiome of hunter-gatherers and Western populations, resulting in the identification of a range of fungal species in the vast majority of samples. In the HumanMycobiomeScan pipeline, sequence reads are mapped against a reference database containing fungal genome sequences only. We argue that using reference databases comprised of a single taxonomic group leads to an unacceptably high number of false-positives due to: (i) mapping to conserved genetic regions in reference genomes, and (ii) sequence contamination in the assembled reference genomes. To demonstrate this, we replaced the HumanMycobiomeScan's fungal reference database with one containing genome sequences of amphibians and reptiles and re-analysed their case study. The classification pipeline recovered all species present in the reference database, revealing turtles (Geoemydidae), bull frogs (Pyxicephalidae) and snakes (Colubridae) as the most abundant herpetological taxa in the human gut. We also re-analysed their case study using a kingdom-agnostic pipeline. This revealed that while the gut of hunter-gatherers and Western subjects may be colonized by a range of microbial eukaryotes, only three fungal families were retrieved. These results highlight the pitfalls of using taxon-specific reference databases for metagenome classification, even when they are comprised of curated whole genome data. We propose that databases containing all domains of life provide the most suitable option for metagenomic species profiling, especially when targeting microbial eukaryotes.
Collapse
Affiliation(s)
- Vanessa R Marcelino
- Marie Bashir Institute for Infectious Diseases and Biosecurity and Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, 2006, Australia.
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, 2145, Australia.
- School of Life & Environmental Sciences, Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia.
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity and Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, 2006, Australia
- School of Life & Environmental Sciences, Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Tania C Sorrell
- Marie Bashir Institute for Infectious Diseases and Biosecurity and Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, 2006, Australia
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, 2145, Australia
| |
Collapse
|