151
|
Abstract
The microbiome plays a significant role in human health, homeostasis, immune system, and disease pathogenesis. Disrupted communication between the microbiome and host has been extensively studied in gastrointestinal diseases. To a lesser extent, there is emerging research on the skin microbiome and its connection with the gut, referred to as the gut-skin axis and its effects on dermatologic conditions. A basic overview will be provided of the gut and skin microbiome with a focus on the impact of this connection on cutaneous diseases, such as psoriasis, atopic dermatitis, rosacea, acne vulgaris, photoaging, and cutaneous wounds. In addition, we shall discuss nutrition-based approaches mediated through the gut-skin axis and topical treatments that could serve as potential adjunctive management by manipulation of the microbiome. In particular, there is a growing body of research on oral probiotics, prebiotics, and dietary modifications that may help improve symptoms for a variety of dermatologic conditions in select demographic groups.
Collapse
Affiliation(s)
- Shivani Sinha
- Frank H. Netter M.D. School of Medicine at Quinnipiac University, North Haven, Connecticut, USA
| | - Gloria Lin
- Department of Dermatology, University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - Katalin Ferenczi
- Department of Dermatology, University of Connecticut School of Medicine, Farmington, Connecticut, USA.
| |
Collapse
|
152
|
Chen QW, Qiao JY, Liu XH, Zhang C, Zhang XZ. Customized materials-assisted microorganisms in tumor therapeutics. Chem Soc Rev 2021; 50:12576-12615. [PMID: 34605834 DOI: 10.1039/d0cs01571g] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Microorganisms have been extensively applied as active biotherapeutic agents or drug delivery vehicles for antitumor treatment because of their unparalleled bio-functionalities. Taking advantage of the living attributes of microorganisms, a new avenue has been opened in anticancer research. The integration of customized functional materials with living microorganisms has demonstrated unprecedented potential in solving existing questions and even conferring microorganisms with updated antitumor abilities and has also provided an innovative train of thought for enhancing the efficacy of microorganism-based tumor therapy. In this review, we have summarized the emerging development of customized materials-assisted microorganisms (MAMO) (including bacteria, viruses, fungi, microalgae, as well as their components) in tumor therapeutics with an emphasis on the rational utilization of chosen microorganisms and tailored materials, the ingenious design of biohybrid systems, and the efficacious antitumor mechanisms. The future perspectives and challenges in this field are also discussed.
Collapse
Affiliation(s)
- Qi-Wen Chen
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China.
| | - Ji-Yan Qiao
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China.
| | - Xin-Hua Liu
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China.
| | - Cheng Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China.
| | - Xian-Zheng Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China.
| |
Collapse
|
153
|
Fitzgerald RS, Sanderson IR, Claesson MJ. Paediatric Inflammatory Bowel Disease and its Relationship with the Microbiome. MICROBIAL ECOLOGY 2021; 82:833-844. [PMID: 33666710 PMCID: PMC8551107 DOI: 10.1007/s00248-021-01697-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 01/19/2021] [Indexed: 05/07/2023]
Abstract
Paediatric inflammatory bowel disease (IBD) is a chronic inflammatory disorder of the digestive tract, comprising of Crohn's disease (CD), ulcerative colitis (UC), and, where classification is undetermined, inflammatory bowel disease unclassified (IBDU). Paediatric IBD incidence is increasing globally, with prevalence highest in the developed world. Though no specific causative agent has been identified for paediatric IBD, it is believed that a number of factors may contribute to the development of the disease, including genetics and the environment. Another potential component in the development of IBD is the microbiota in the digestive tract, particularly the gut. While the exact role that the microbiome plays in IBD is unclear, many studies acknowledge the complex relationship between the gut bacteria and pathogenesis of IBD. In this review, we look at the increasing number of studies investigating the role the microbiome and other biomes play in paediatric patients with IBD, particularly changes associated with IBD, varying disease states, and therapeutics. The paediatric IBD microbiome is significantly different to that of healthy children, with decreased diversity and differences in bacterial composition (such as a decrease in Firmicutes). Changes in the microbiome relating to various treatments of IBD and disease severity have also been observed in multiple studies. Changes in diversity and composition may also extend to other biomes in paediatric IBD, such as the virome and the mycobiome. Research into biome differences in IBD paediatric patients may help progress our understanding of the aetiology of the disease.
Collapse
Affiliation(s)
- Rachel S Fitzgerald
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Ian R Sanderson
- Centre for Immunobiology, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Marcus J Claesson
- School of Microbiology, University College Cork, Cork, Ireland.
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
| |
Collapse
|
154
|
Abstract
Inflammatory bowel disease (IBD) is a life-threatening and chronic inflammatory disease of gastrointestinal tissue, with complex pathogenesis. Current research on IBD has mainly focused on bacteria; however, the role of fungi in IBD is largely unknown due to the incomplete annotation of fungi in current genomic databases. With the development of molecular techniques, the gut mycobiome has been found to have great diversity. In addition, increasing evidence has shown intestinal mycobiome plays an important role in the physiological and pathological processes of IBD. In this review, we will systemically introduce the recent knowledge about multi-dimensional fungal dysbiosis associated with IBD, the interactions between fungus and bacteria, the role of fungi in inflammation in IBD, and highlight recent advances in the potential therapeutic role of fungus in IBD, which may hold the keys to develop new predictive, therapeutic or prognostic approaches in IBD.
Collapse
Affiliation(s)
- Sui Wang
- Laboratory of Translational Gastroenterology, Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Yu-Rong Zhang
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education (Peking University), Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Yan-Bo Yu
- Department of Gastroenterology, Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| |
Collapse
|
155
|
Silva M, Brunner V, Tschurtschenthaler M. Microbiota and Colorectal Cancer: From Gut to Bedside. Front Pharmacol 2021; 12:760280. [PMID: 34658896 PMCID: PMC8514721 DOI: 10.3389/fphar.2021.760280] [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: 08/17/2021] [Accepted: 09/20/2021] [Indexed: 12/21/2022] Open
Abstract
Colorectal cancer (CRC) is a complex condition with heterogeneous aetiology, caused by a combination of various environmental, genetic, and epigenetic factors. The presence of a homeostatic gut microbiota is critical to maintaining host homeostasis and determines the delicate boundary between health and disease. The gut microbiota has been identified as a key environmental player in the pathogenesis of CRC. Perturbations of the gut microbiota structure (loss of equilibrium and homeostasis) are associated with several intestinal diseases including cancer. Such dysbiosis encompasses the loss of beneficial microorganisms, outgrowth of pathogens and pathobionts and a general loss of local microbiota diversity and richness. Notably, several mechanisms have recently been identified how bacteria induce cellular transformation and promote tumour progression. In particular, the formation of biofilms, the production of toxic metabolites or the secretion of genotoxins that lead to DNA damage in intestinal epithelial cells are newly discovered processes by which the microbiota can initiate tumour formation. The gut microbiota has also been implicated in the metabolism of therapeutic drugs (conventional chemotherapy) as well as in the modulation of radiotherapy responses and targeted immunotherapy. These new findings suggest that the efficacy of a given therapy depends on the composition of the host’s gut microbiota and may therefore vary from patient to patient. In this review we discuss the role of host-microbiota interactions in cancer with a focus on CRC pathogenesis. Additionally, we show how gut bacteria can be exploited in current therapies and how mechanisms directed by microbiota, such as immune cell boost, probiotics and oncolytic bacteria, can be applied in the development of novel therapies.
Collapse
Affiliation(s)
- Miguel Silva
- Institute of Molecular Oncology and Functional Genomics, Center for Translational Cancer Research (TranslaTUM), Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany.,Graduate Program in Areas of Basic and Applied Biology (GABBA)/ICBAS - Institute for the Biomedical Sciences Abel Salazar, Porto University, Porto, Portugal
| | - Valentina Brunner
- Institute for Experimental Cancer Therapy, Center for Translational Cancer Research (TranslaTUM), Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany.,Department of Internal Medicine II, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Markus Tschurtschenthaler
- Institute for Experimental Cancer Therapy, Center for Translational Cancer Research (TranslaTUM), Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany.,Department of Internal Medicine II, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| |
Collapse
|
156
|
Sultan S, El-Mowafy M, Elgaml A, Ahmed TAE, Hassan H, Mottawea W. Metabolic Influences of Gut Microbiota Dysbiosis on Inflammatory Bowel Disease. Front Physiol 2021; 12:715506. [PMID: 34646151 PMCID: PMC8502967 DOI: 10.3389/fphys.2021.715506] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/18/2021] [Indexed: 12/12/2022] Open
Abstract
Inflammatory bowel diseases (IBD) are chronic medical disorders characterized by recurrent gastrointestinal inflammation. While the etiology of IBD is still unknown, the pathogenesis of the disease results from perturbations in both gut microbiota and the host immune system. Gut microbiota dysbiosis in IBD is characterized by depleted diversity, reduced abundance of short chain fatty acids (SCFAs) producers and enriched proinflammatory microbes such as adherent/invasive E. coli and H2S producers. This dysbiosis may contribute to the inflammation through affecting either the immune system or a metabolic pathway. The immune responses to gut microbiota in IBD are extensively discussed. In this review, we highlight the main metabolic pathways that regulate the host-microbiota interaction. We also discuss the reported findings indicating that the microbial dysbiosis during IBD has a potential metabolic impact on colonocytes and this may underlie the disease progression. Moreover, we present the host metabolic defectiveness that adds to the impact of symbiont dysbiosis on the disease progression. This will raise the possibility that gut microbiota dysbiosis associated with IBD results in functional perturbations of host-microbiota interactions, and consequently modulates the disease development. Finally, we shed light on the possible therapeutic approaches of IBD through targeting gut microbiome.
Collapse
Affiliation(s)
- Salma Sultan
- Faculty of Health Sciences, School of Nutrition Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Mohammed El-Mowafy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Abdelaziz Elgaml
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt.,Department of Microbiology and Immunology, Faculty of Pharmacy, Horus University, New Damietta, Egypt
| | - Tamer A E Ahmed
- Faculty of Health Sciences, School of Nutrition Sciences, University of Ottawa, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Hebatoallah Hassan
- Faculty of Health Sciences, School of Nutrition Sciences, University of Ottawa, Ottawa, ON, Canada.,Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | - Walid Mottawea
- Faculty of Health Sciences, School of Nutrition Sciences, University of Ottawa, Ottawa, ON, Canada.,Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| |
Collapse
|
157
|
Chronic Diseases Associated with Malassezia Yeast. J Fungi (Basel) 2021; 7:jof7100855. [PMID: 34682276 PMCID: PMC8540640 DOI: 10.3390/jof7100855] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/04/2021] [Accepted: 10/06/2021] [Indexed: 01/01/2023] Open
Abstract
Malassezia are a lipid-dependent basidiomycetous yeast of the normal skin microbiome, although Malassezia DNA has been recently detected in other body sites and has been associated with certain chronic human diseases. This new perspective raises many questions. Are these yeasts truly present in the investigated body site or were they contaminated by other body sites, adjacent or not? Does this DNA contamination come from living or dead yeast? If these yeasts are alive, do they belong to the resident mycobiota or are they transient colonizers which are not permanently established within these niches? Finally, are these yeasts associated with certain chronic diseases or not? In an attempt to shed light on this knowledge gap, we critically reviewed the 31 published studies focusing on the association of Malassezia spp. with chronic human diseases, including psoriasis, atopic dermatitis (AD), chronic rhinosinusitis (CRS), asthma, cystic fibrosis (CF), HIV infection, inflammatory bowel disease (IBD), colorectal cancer (CRC), and neurodegenerative diseases.
Collapse
|
158
|
Theelen B, Christinaki AC, Dawson TL, Boekhout T, Kouvelis VN. Comparative analysis of Malassezia furfur mitogenomes and the development of a mitochondria-based typing approach. FEMS Yeast Res 2021; 21:6375414. [PMID: 34562093 PMCID: PMC8510979 DOI: 10.1093/femsyr/foab051] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/29/2021] [Indexed: 12/24/2022] Open
Abstract
Malassezia furfur is a yeast species belonging to Malasseziomycetes, Ustilaginomycotina and Basidiomycota that is found on healthy warm-blooded animal skin, but also involved in various skin disorders like seborrheic dermatitis/dandruff and pityriasis versicolor. Moreover, Malassezia are associated with bloodstream infections, Crohn's disease and pancreatic carcinoma. Recent advances in Malassezia genomics and genetics have focused on the nuclear genome. In this work, we present the M. furfur mitochondrial (mt) genetic heterogenicity with full analysis of 14 novel and six available M. furfur mt genomes. The mitogenome analysis reveals a mt gene content typical for fungi, including identification of variable mt regions suitable for intra-species discrimination. Three of them, namely the trnK–atp6 and cox3–nad3 intergenic regions and intron 2 of the cob gene, were selected for primer design to identify strain differences. Malassezia furfur strains belonging to known genetic variable clusters, based on AFLP and nuclear loci, were assessed for their mt variation using PCR amplification and sequencing. The results suggest that these mt regions are excellent molecular markers for the typing of M. furfur strains and may provide added value to nuclear regions when assessing evolutionary relationships at the intraspecies level.
Collapse
Affiliation(s)
- Bart Theelen
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Anastasia C Christinaki
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.,Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15701, Greece
| | - Thomas L Dawson
- Agency for Science, Technology, and Research (A∗STAR), Skin Research Institute of Singapore (SRIS), 11 Mandalay Rd, #17-01, Singapore 308232, Singapore.,Center for Cell Death, Injury and Regeneration, Departments of Drug Discovery and Biomedical Sciences and Biochemistry and Molecular Biology, Medical University of South Carolina, 280 Calhoun St, Charleston, SC, 29425, USA
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Vassili N Kouvelis
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15701, Greece
| |
Collapse
|
159
|
Yang Q, Liu J, Robinson KJ, Whitmore MA, Stewart SN, Zhang G. Perturbations of the ileal mycobiota by necrotic enteritis in broiler chickens. J Anim Sci Biotechnol 2021; 12:107. [PMID: 34625122 PMCID: PMC8501549 DOI: 10.1186/s40104-021-00628-5] [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] [Received: 05/14/2021] [Accepted: 08/05/2021] [Indexed: 02/02/2023] Open
Abstract
Background Intestinal microbiota is critical for maintaining animal health and homeostasis. However, involvement of the fungal community, also known as the mycobiota, in animal health and disease is poorly understood. This study was aimed to examine the association between the intestinal mycobiota and the severity of necrotic enteritis (NE), an economically significant poultry disease. Methods A total of 90 day-of-hatch Cobb broilers were infected with Eimeria maxima on d 10, followed by an oral challenge with C. perfringens on d 14 to induce NE, while another 10 broilers were served as mock-infected controls. On d 17, the lesions in the jejunum were scored, and the ileal digesta were subjected to DNA isolation and real-time PCR quantification of total bacterial and fungi populations. Internal transcribed spacer 2 (ITS2) amplicon sequencing was also performed to profile the ileal mycobiota composition. Changes in the ileal mycobiota in response to NE were investigated. Spearman correlation analysis was further conducted to identify the correlations between relative abundances of individual ileal fungi and the severity of NE. Results While the total bacterial population in the ileum was increased by 2- to 3-fold in NE chickens, the total fungal population was progressively declined in more exacerbated NE, with the most severely infected chickens showing a nearly 50-fold reduction relative to mock-infected controls. Richness of the ileal mycobiota also tended to reduce in chickens with NE (P = 0.06). Compositionally, among 30 most abundant fungal amplicon sequence variants (ASVs), 11 were diminished and 7 were enriched (P < 0.05), while 12 remained largely unchanged in NE-afflicted chickens (P > 0.05). Multiple Wallemia and Aspergillus species were markedly diminished in NE (P < 0.05) and also showed a significant negative correlation with NE severity (P < 0.05). Conclusions Dysbiosis of the ileal mycobiota is induced evidently by NE and the extent of the dysbiosis is positively correlated with disease severity. These findings suggest a possible role of the intestinal mycobiota in NE pathogenesis and highlight the mycobiota as a new potential target for NE mitigation in poultry. Supplementary Information The online version contains supplementary material available at 10.1186/s40104-021-00628-5.
Collapse
Affiliation(s)
- Qing Yang
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Jing Liu
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Kelsy J Robinson
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, USA.,Present address: Poultry Production and Product Safety Research Unit, USDA-Agricultural Research Service, Fayetteville, AR, USA
| | - Melanie A Whitmore
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Sydney N Stewart
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, USA.,Present address: Safety and Security Division, Institute for Public Research, CNA, Arlington, VA, USA
| | - Guolong Zhang
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, USA.
| |
Collapse
|
160
|
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
|
161
|
Mok K, Suratanon N, Roytrakul S, Charoenlappanit S, Patumcharoenpol P, Chatchatee P, Vongsangnak W, Nakphaichit M. ITS2 Sequencing and Targeted Meta-Proteomics of Infant Gut Mycobiome Reveal the Functional Role of Rhodotorula sp. during Atopic Dermatitis Manifestation. J Fungi (Basel) 2021; 7:jof7090748. [PMID: 34575786 PMCID: PMC8471346 DOI: 10.3390/jof7090748] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/04/2021] [Accepted: 09/08/2021] [Indexed: 12/12/2022] Open
Abstract
Association between the gut mycobiome and atopic dermatitis was investigated in 9-12-month-old infants using metagenomics. Two groups of atopic dermatitis infants were classified according to their symptom development as outgrown (recovered) and persisted (still undergoing). The evenness and diversity of the mycobiome in the persisted group were higher than in the healthy and outgrown groups. Dysbiosis of the microbiome in the persisted group was observed by a reduction in the Ascomycota/Basidiomycota ratio. Five fungi were selected as markers from each sample group. In the persisted group, Rhodotorula sp. abundance increased significantly, while Wickerhamomyces sp. and Kodamaea sp. abundance increased in the healthy group, and Acremonium sp. and Rhizopus sp. abundance increased considerably in the outgrown group. Metaproteomic analysis revealed that the persisted group had a high abundance of fungal proteins, particularly those from Rhodotorula sp. Unique proteins such as RAN-binding protein 1 and glycerol kinase from Rhodotorula sp. were hypothesized to be related to atopic dermatitis manifestation in infants.
Collapse
Affiliation(s)
- Kevin Mok
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand;
- Specialized Research Unit: Probiotics and Prebiotics for Health, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand
| | - Narissara Suratanon
- Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok 10330, Thailand; (N.S.); (P.C.)
| | - Sittiruk Roytrakul
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (S.R.); (S.C.)
| | - Sawanya Charoenlappanit
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (S.R.); (S.C.)
| | - Preecha Patumcharoenpol
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
| | - Pantipa Chatchatee
- Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok 10330, Thailand; (N.S.); (P.C.)
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
- Correspondence: (W.V.); (M.N.)
| | - Massalin Nakphaichit
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand;
- Specialized Research Unit: Probiotics and Prebiotics for Health, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand
- Correspondence: (W.V.); (M.N.)
| |
Collapse
|
162
|
Shiao SL, Kershaw KM, Limon JJ, You S, Yoon J, Ko EY, Guarnerio J, Potdar AA, McGovern DPB, Bose S, Dar TB, Noe P, Lee J, Kubota Y, Maymi VI, Davis MJ, Henson RM, Choi RY, Yang W, Tang J, Gargus M, Prince AD, Zumsteg ZS, Underhill DM. Commensal bacteria and fungi differentially regulate tumor responses to radiation therapy. Cancer Cell 2021; 39:1202-1213.e6. [PMID: 34329585 PMCID: PMC8830498 DOI: 10.1016/j.ccell.2021.07.002] [Citation(s) in RCA: 123] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/28/2020] [Accepted: 07/01/2021] [Indexed: 12/20/2022]
Abstract
Studies suggest that the efficacy of cancer chemotherapy and immunotherapy is influenced by intestinal bacteria. However, the influence of the microbiome on radiation therapy is not as well understood, and the microbiome comprises more than bacteria. Here, we find that intestinal fungi regulate antitumor immune responses following radiation in mouse models of breast cancer and melanoma and that fungi and bacteria have opposite influences on these responses. Antibiotic-mediated depletion or gnotobiotic exclusion of fungi enhances responsiveness to radiation, whereas antibiotic-mediated depletion of bacteria reduces responsiveness and is associated with overgrowth of commensal fungi. Further, elevated intratumoral expression of Dectin-1, a primary innate sensor of fungi, is negatively associated with survival in patients with breast cancer and is required for the effects of commensal fungi in mouse models of radiation therapy.
Collapse
Affiliation(s)
- Stephen L Shiao
- Department of Radiation Oncology, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
| | - Kathleen M Kershaw
- Department of Radiation Oncology, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA; F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jose J Limon
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Sungyong You
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Junhee Yoon
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Emily Y Ko
- Department of Radiation Oncology, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Jlenia Guarnerio
- Department of Radiation Oncology, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Alka A Potdar
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Shikha Bose
- Department of Pathology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Tahir B Dar
- Department of Radiation Oncology, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Paul Noe
- Department of Radiation Oncology, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Jung Lee
- Department of Radiation Oncology, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Yuzu Kubota
- Department of Radiation Oncology, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Viviana I Maymi
- Department of Radiation Oncology, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Madison J Davis
- Department of Radiation Oncology, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Regina M Henson
- Department of Radiation Oncology, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Rachel Y Choi
- Department of Radiation Oncology, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Wensha Yang
- Department of Radiation Oncology, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Jie Tang
- Genomics Core, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Matthew Gargus
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Alexander D Prince
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Zachary S Zumsteg
- Department of Radiation Oncology, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - David M Underhill
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| |
Collapse
|
163
|
Association of Fungi and Archaea of the Gut Microbiota with Crohn's Disease in Pediatric Patients-Pilot Study. Pathogens 2021; 10:pathogens10091119. [PMID: 34578152 PMCID: PMC8468012 DOI: 10.3390/pathogens10091119] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/29/2021] [Accepted: 08/29/2021] [Indexed: 01/10/2023] Open
Abstract
The composition of bacteria is often altered in Crohn’s disease (CD), but its connection to the disease is not fully understood. Gut archaea and fungi have recently been suggested to play a role as well. In our study, the presence and number of selected species of fungi and archaea in pediatric patients with CD and healthy controls were evaluated. Stool samples were collected from children with active CD (n = 54), non-active CD (n = 37) and control subjects (n = 33). The prevalence and the number of selected microorganisms were assessed by real-time PCR. The prevalence of Candida tropicalis was significantly increased in active CD compared to non-active CD and the control group (p = 0.011 and p = 0.036, respectively). The number of Malassezia spp. cells was significantly lower in patients with active CD compared to the control group, but in non-active CD, a significant increase was observed (p = 0.005 and p = 0.020, respectively). There were no statistically significant differences in the colonization by archaea. The obtained results indicate possible correlations with the course of the CD; however, further studies of the entire archeobiome and the mycobiome are necessary in order to receive a complete picture.
Collapse
|
164
|
Impact of gut fungal and bacterial communities on the outcome of allogeneic hematopoietic cell transplantation. Mucosal Immunol 2021; 14:1127-1132. [PMID: 34282272 DOI: 10.1038/s41385-021-00429-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/05/2021] [Accepted: 07/04/2021] [Indexed: 02/04/2023]
Abstract
Patients receiving allogeneic hematopoietic cell transplantation (alloHCT) were previously shown to display a bacterial gut dysbiosis; however, limited data are available regarding the role of fungal microbiota in these patients. We evaluated the bacterial and fungal composition of the fecal microbiota at day 0 of alloHCT. Higher bacterial diversity was associated with an improved overall survival (OS) and disease-free survival (DFS). While fungal diversity had no impact on patient outcomes, we observed that high versus low relative abundance of Candida albicans in alloHCT patients at day 0 was associated with a significantly lower OS, DFS and graft-versus-host-free, relapse-free survival (GRFS) (p = 0.0008, p = 0.0064 and p = 0.026, respectively). While these results are limited by low patient numbers and low fungal read counts in some samples, they suggest a potentially important role for C albicans in alloHCT.
Collapse
|
165
|
Hartmann P, Lang S, Zeng S, Duan Y, Zhang X, Wang Y, Bondareva M, Kruglov A, Fouts DE, Stärkel P, Schnabl B. Dynamic Changes of the Fungal Microbiome in Alcohol Use Disorder. Front Physiol 2021; 12:699253. [PMID: 34349667 PMCID: PMC8327211 DOI: 10.3389/fphys.2021.699253] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/24/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Alcohol-associated liver disease (ALD) is an important cause of morbidity and mortality worldwide. The intestinal microbiota is involved in the development and progression of ALD; however, little is known about commensal fungi therein. METHODS We studied the dynamic changes of the intestinal fungal microbiome, or mycobiome, in 66 patients with alcohol use disorder (AUD) and after 2 weeks of alcohol abstinence using internal transcribed spacer 2 (ITS2) amplicon sequencing of fecal samples. RESULTS Patients with AUD had significantly increased abundance of the genera Candida, Debaryomyces, Pichia, Kluyveromyces, and Issatchenkia, and of the species Candida albicans and Candida zeylanoides compared with control subjects. Significantly improved liver health markers caspase-cleaved and intact cytokeratin 18 (CK18-M65) levels and controlled attenuation parameter (CAP) in AUD patients after 2 weeks of alcohol abstinence were associated with significantly lower abundance of the genera Candida, Malassezia, Pichia, Kluyveromyces, Issatchenkia, and the species C. albicans and C. zeylanoides. This was mirrored by significantly higher specific anti-C. albicans immunoglobulin G (IgG) and M (IgM) serum levels in AUD patients in relation to control participants, and significantly decreased anti-C. albicans IgG levels in AUD subjects after 2 weeks of abstinence. The intestinal abundance of the genus Malassezia was significantly higher in AUD subjects with progressive liver disease compared with non-progressive liver disease. CONCLUSION In conclusion, improved liver health in AUD patients after alcohol abstinence was associated with lower intestinal abundances of Candida and Malassezia, and lower serum anti-C. albicans IgG levels. Intestinal fungi might serve as a therapeutic target to improve the outcome of patients in ALD.
Collapse
Affiliation(s)
- Phillipp Hartmann
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States
- Department of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Sonja Lang
- Department of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Suling Zeng
- Department of Medicine, University of California, San Diego, La Jolla, CA, United States
- Department of Medicine, VA San Diego Healthcare System, San Diego, CA, United States
| | - Yi Duan
- Department of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Xinlian Zhang
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health, University of California, San Diego, La Jolla, CA, United States
| | - Yanhan Wang
- Department of Medicine, University of California, San Diego, La Jolla, CA, United States
- Department of Medicine, VA San Diego Healthcare System, San Diego, CA, United States
| | - Marina Bondareva
- Chronic Inflammation Lab, German Rheumatism Research Center, a Leibniz Institute, Berlin, Germany
- Belozerskiy Research Institute for Physical and Chemical Biology and Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Andrey Kruglov
- Chronic Inflammation Lab, German Rheumatism Research Center, a Leibniz Institute, Berlin, Germany
| | - Derrick E. Fouts
- Department of Genomic Medicine, J. Craig Venter Institute, Rockville, MD, United States
| | - Peter Stärkel
- Cliniques Universitaires Saint-Luc, Université catholique de Louvain, Brussels, Belgium
| | - Bernd Schnabl
- Department of Medicine, University of California, San Diego, La Jolla, CA, United States
- Department of Medicine, VA San Diego Healthcare System, San Diego, CA, United States
| |
Collapse
|
166
|
Mantilla MJ, Cabrera Díaz CE, Ariza-Aranguren G, de Cock H, Helms JB, Restrepo S, Jiménez E, Celis Ramírez AM. Back to the Basics: Two Approaches for the Identification and Extraction of Lipid Droplets from Malassezia pachydermatis CBS1879 and Malassezia globosa CBS7966. Curr Protoc 2021; 1:e122. [PMID: 33950584 DOI: 10.1002/cpz1.122] [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] [Indexed: 12/21/2022]
Abstract
Malassezia spp. are lipid-dependent yeasts that have been related to skin mycobiota and dermatological and systemic diseases. Study of lipid droplets (LDs) is relevant to elucidate the unknown role of these organelles in Malassezia and to gain a broader overview of lipid metabolism in Malassezia. Here, we standardized two protocols for the analysis of LDs in M. pachydermatis and M. globosa. The first describes co-staining for confocal laser-scanning fluorescence microscopy, and the second details extraction and purification of LDs. The double stain is achieved with three different neutral lipid fluorophores, namely Nile Red, BODIPY™ 493/503, and HCS LipidTOX™ Deep Red Neutral, in combination with Calcofluor White. For LD extraction, cell wall rupture is conducted using Trichoderma harzianum enzymes and cycles of vortexing with zirconium beads. LD purification is performed in a three-step ultracentrifugation process. These standardizations will contribute to the study of the dynamics, morphology, and composition of LDs in Malassezia. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Lipid droplet fluorescence staining Basic Protocol 2: Lipid droplet extraction and purification Support Protocol: Malassezia spp. culture conditions.
Collapse
Affiliation(s)
- Maria Juliana Mantilla
- Grupo de Investigación Celular y Molecular de Microorganismos Patógenos (CeMoP), Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
| | | | - Gabriela Ariza-Aranguren
- Grupo de Investigación Celular y Molecular de Microorganismos Patógenos (CeMoP), Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
| | - Hans de Cock
- Microbiology, Department of Biology, Faculty of Science, Institute of Biomembranes, Utrecht University, Utrecht, The Netherlands
| | - J Bernd Helms
- Department of Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Silvia Restrepo
- Laboratorio de Micología y Fitopatología (LAMFU), Chemical and Food Engineering Department, Universidad de Los Andes, Bogotá, Colombia
| | - Elizabeth Jiménez
- Applied Biochemistry Research Group (GIBA), Department of Chemistry, Universidad de Los Andes, Bogotá, Colombia
| | - Adriana Marcela Celis Ramírez
- Grupo de Investigación Celular y Molecular de Microorganismos Patógenos (CeMoP), Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
| |
Collapse
|
167
|
Park M, Park S, Jung WH. Skin Commensal Fungus Malassezia and Its Lipases. J Microbiol Biotechnol 2021; 31:637-644. [PMID: 33526754 PMCID: PMC9705927 DOI: 10.4014/jmb.2012.12048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 01/11/2021] [Accepted: 01/25/2021] [Indexed: 12/15/2022]
Abstract
Malassezia is the most abundant genus in the fungal microflora found on human skin, and it is associated with various skin diseases. Among the 18 different species of Malassezia that have been identified to date, M. restricta and M. globosa are the most predominant fungal species found on human skin. Several studies have suggested a possible link between Malassezia and skin disorders. However, our knowledge on the physiology and pathogenesis of Malassezia in human body is still limited. Malassezia is unable to synthesize fatty acids; hence, it uptakes external fatty acids as a nutrient source for survival, a characteristic compensated by the secretion of lipases and degradation of sebum to produce and uptake external fatty acids. Although it has been reported that the activity of secreted lipases may contribute to pathogenesis of Malassezia, majority of the data were indirect evidences; therefore, enzymes' role in the pathogenesis of Malassezia infections is still largely unknown. This review focuses on the recent advances on Malassezia in the context of an emerging interest for lipases and summarizes the existing knowledge on Malassezia, diseases associated with the fungus, and the role of the reported lipases in its physiology and pathogenesis.
Collapse
Affiliation(s)
- Minji Park
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Sungmin Park
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Won Hee Jung
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea,Corresponding author Phone: +82-31-670-3068 Fax: +82-31-675-1381 E-mail:
| |
Collapse
|
168
|
LeibundGut-Landmann S. Tissue-Resident Memory T Cells in Antifungal Immunity. Front Immunol 2021; 12:693055. [PMID: 34113356 PMCID: PMC8185520 DOI: 10.3389/fimmu.2021.693055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/10/2021] [Indexed: 12/26/2022] Open
Abstract
Fungi are an integral part of the mammalian microbiota colonizing most if not all mucosal surfaces and the skin. Maintaining stable colonization on these surfaces is critical for preventing fungal dysbiosis and infection, which in some cases can lead to life threatening consequences. The epithelial barriers are protected by T cells and additional controlling immune mechanisms. Noncirculating memory T cells that reside stably in barrier tissues play an important role for host protection from commensals and recurrent pathogens due to their fast response and local activity, which provides them a strategic advantage. So far, only a few specific examples of tissue resident memory T cells (TRMs) that act against fungi have been reported. This review provides an overview of the characteristics and functional attributes of TRMs that have been established based on human and mouse studies with various microbes. It highlights what is currently known about fungi specific TRMs mediating immunosurveillance, how they have been targeted in preclinical vaccination approaches and how they can promote immunopathology, if not controlled. A better appreciation of the host protective and damaging roles of TRMs might accelerate the development of novel tissue specific preventive strategies against fungal infections and fungi-driven immunopathologies.
Collapse
Affiliation(s)
- Salomé LeibundGut-Landmann
- Section of Immunology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland
- Institute of Experimental Immunology, University of Zürich, Zürich, Switzerland
| |
Collapse
|
169
|
Henke MT, Brown EM, Cassilly CD, Vlamakis H, Xavier RJ, Clardy J. Capsular polysaccharide correlates with immune response to the human gut microbe Ruminococcus gnavus. Proc Natl Acad Sci U S A 2021; 118:e2007595118. [PMID: 33972416 PMCID: PMC8157926 DOI: 10.1073/pnas.2007595118] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Active inflammatory bowel disease (IBD) often coincides with increases of Ruminococcus gnavus, a gut microbe found in nearly everyone. It was not known how, or if, this correlation contributed to disease. We investigated clinical isolates of R. gnavus to identify molecular mechanisms that would link R. gnavus to inflammation. Here, we show that only some isolates of R. gnavus produce a capsular polysaccharide that promotes a tolerogenic immune response, whereas isolates lacking functional capsule biosynthetic genes elicit robust proinflammatory responses in vitro. Germ-free mice colonized with an isolate of R. gnavus lacking a capsule show increased measures of gut inflammation compared to those colonized with an encapsulated isolate in vivo. These observations in the context of our earlier identification of an inflammatory cell-wall polysaccharide reveal how some strains of R. gnavus could drive the inflammatory responses that characterize IBD.
Collapse
Affiliation(s)
- Matthew T Henke
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Eric M Brown
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Chelsi D Cassilly
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Hera Vlamakis
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Ramnik J Xavier
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA 02114
| | - Jon Clardy
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115;
| |
Collapse
|
170
|
Gutierrez MW, Arrieta MC. The intestinal mycobiome as a determinant of host immune and metabolic health. Curr Opin Microbiol 2021; 62:8-13. [PMID: 33993019 DOI: 10.1016/j.mib.2021.04.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 12/27/2022]
Abstract
The inclusion of fungi in recent human and animal microbiome studies has revealed that microbiome features associated with health or disease are not exclusively bacterial. Factors known to impact bacterial microbiome development, such as gestational age at birth, breast feeding status and antibiotics also impact the mycobiome. Strong inter-kingdom interactions take place in the luminal gut, and while the mycobiome exhibits increased inter-individual variability, certain fungi are stable colonizers. Here, we review recent studies showing that the gut mycobiome also plays an important role in disease states related to host immunity and energy metabolism. Some persistent species, such as Candida sp., as well as other less stable colonizers have been shown to play an important role in host-mycobiome immune cross talk. Mechanisms by which gut fungi interact with immune development have begun to be elucidated yet the majority remain elusive. Further investigation into these immune and metabolic mechanisms hold great potential for novel discoveries and will provided a much needed multi-kingdom understanding of the microbiome's influence on host health.
Collapse
Affiliation(s)
- Mackenzie W Gutierrez
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; International Microbiome Center, University of Calgary, AB, Canada
| | - Marie-Claire Arrieta
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; International Microbiome Center, University of Calgary, AB, Canada.
| |
Collapse
|
171
|
Mahmoudi E, Mozhgani SH, Sharifinejad N. The role of mycobiota-genotype association in inflammatory bowel diseases: a narrative review. Gut Pathog 2021; 13:31. [PMID: 33964975 PMCID: PMC8106830 DOI: 10.1186/s13099-021-00426-4] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 04/29/2021] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic inflammatory disease affecting various parts of the gastrointestinal tract. A majority of the current evidence points out the involvement of intestinal dysbiosis in the IBD pathogenesis. Recently, the association of intestinal fungal composition With IBD susceptibility and severity has been reported. These studies suggested gene polymorphisms in the front line of host defense against intestinal microorganisms are considered to play a role in IBD pathogenesis. The studies have also detected increased susceptibility to fungal infections in patients carrying IBD-related mutations. Therefore, a literature search was conducted in related databases to review articles addressing the mycobiota-genotype association in IBD.
Collapse
Affiliation(s)
- Elaheh Mahmoudi
- Division of Mycology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Sayed-Hamidreza Mozhgani
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Niusha Sharifinejad
- Student Research Committee, Alborz University of Medical Sciences, Karaj, Iran. .,Alborz Office of USERN, Universal Scientific Education and Research Network (USERN), Alborz University of Medical Sciences, Karaj, Iran.
| |
Collapse
|
172
|
Sheng K, Zhang G, Sun M, He S, Kong X, Wang J, Zhu F, Zha X, Wang Y. Grape seed proanthocyanidin extract ameliorates dextran sulfate sodium-induced colitis through intestinal barrier improvement, oxidative stress reduction, and inflammatory cytokines and gut microbiota modulation. Food Funct 2021; 11:7817-7829. [PMID: 32808642 DOI: 10.1039/d0fo01418d] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
It is widely believed that grape seed proanthocyanidin extract (GSPE) exerts antioxidant and anti-inflammatory effects. Dietary supplementation with GSPE has been reported to alleviate colitis signs in mice, but the mechanisms involved require further exploration. The present study investigated how the oral administration of GSPE ameliorates colitis signs and reduces colitis-associated inflammation. C57BL/6 mice were treated with GSPE for 21 days. During the final 7 days of treatment, the mice were administered dextran sulfate sodium (DSS) dissolved in drinking water to induce experimental colitis. We found that GSPE treatment improved DSS-induced colitis, which was evidenced by decreases in disease activity index (DAI) scores, pathological scores, and oxidative stress and increases in zonula occludens-1 (ZO-1), occludin, and claudin-1 mRNA levels of colon tissue. Notably, the proinflammatory cytokines TNF-α and IL-1β were significantly downregulated as a result of GSPE treatment in colon tissues. GSPE treatment also reduced NLR family pyrin domain-containing 3 (NLRP3) inflammasome mRNA levels of colon tissue. Furthermore, an analysis of 16S rRNA sequences showed that GSPE rebalanced the DSS-damaged gut microbiota, including reducing Bacteroidetes, Dubosiella, and Veillonella, increasing Verrucomicrobia and Akkermansia, and elevating the Firmicutes to Bacteroidetes ratio. In conclusion, GSPE supplementation alleviates DSS-induced colitis by modulating inflammatory cytokines and oxidation stress, maintaining the intestinal barrier, and improving the microbial community. These results indicate that GSPE might be a new dietary strategy for the treatment of ulcerative colitis.
Collapse
Affiliation(s)
- Kangliang Sheng
- School of Life Sciences, Anhui University, Hefei 230601, Anhui, China. and Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, China and Anhui Key Laboratory of Modern Biomanufacturing, Hefei 230601, Anhui, China
| | - Guanghui Zhang
- School of Life Sciences, Anhui University, Hefei 230601, Anhui, China. and Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, China and Anhui Key Laboratory of Modern Biomanufacturing, Hefei 230601, Anhui, China
| | - Ming Sun
- School of Life Sciences, Anhui University, Hefei 230601, Anhui, China. and Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, China and Anhui Key Laboratory of Modern Biomanufacturing, Hefei 230601, Anhui, China
| | - Shiman He
- School of Life Sciences, Anhui University, Hefei 230601, Anhui, China. and Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, China and Anhui Key Laboratory of Modern Biomanufacturing, Hefei 230601, Anhui, China
| | - Xiaowei Kong
- School of Life Sciences, Anhui University, Hefei 230601, Anhui, China. and Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, China and Anhui Key Laboratory of Modern Biomanufacturing, Hefei 230601, Anhui, China
| | - Jingmin Wang
- School of Life Sciences, Anhui University, Hefei 230601, Anhui, China. and Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, China and Anhui Key Laboratory of Modern Biomanufacturing, Hefei 230601, Anhui, China
| | - Fenfang Zhu
- School of Life Sciences, Anhui University, Hefei 230601, Anhui, China. and Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, China and Anhui Key Laboratory of Modern Biomanufacturing, Hefei 230601, Anhui, China
| | - Xiangdong Zha
- School of Life Sciences, Anhui University, Hefei 230601, Anhui, China. and Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, China and Anhui Key Laboratory of Modern Biomanufacturing, Hefei 230601, Anhui, China
| | - Yongzhong Wang
- School of Life Sciences, Anhui University, Hefei 230601, Anhui, China. and Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, China and Anhui Key Laboratory of Modern Biomanufacturing, Hefei 230601, Anhui, China and Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, Anhui, China
| |
Collapse
|
173
|
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: 126] [Impact Index Per Article: 42.0] [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.
Collapse
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
| |
Collapse
|
174
|
Nelson A, Stewart CJ, Kennedy NA, Lodge JK, Tremelling M, Probert CS, Parkes M, Mansfield JC, Smith DL, Hold GL, Lees CW, Bridge SH, Lamb CA. The Impact of NOD2 Genetic Variants on the Gut Mycobiota in Crohn's Disease Patients in Remission and in Individuals Without Gastrointestinal Inflammation. J Crohns Colitis 2021; 15:800-812. [PMID: 33119074 PMCID: PMC8095387 DOI: 10.1093/ecco-jcc/jjaa220] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS Historical and emerging data implicate fungi in Crohn's disease [CD] pathogenesis. However, a causal link between mycobiota, dysregulated immunity, and any impact of NOD2 variants remains elusive. This study aims to evaluate associations between NOD2 variants and faecal mycobiota in CD patients and non-CD subjects. METHODS Faecal samples were obtained from 34 CD patients [18 NOD2 mutant, 16 NOD2 wild-type] identified from the UK IBD Genetics Consortium. To avoid confounding influence of mucosal inflammation, CD patients were in clinical remission and had a faecal calprotectin <250 μg/g; 47 non-CD subjects were included as comparator groups, including 22 matched household [four NOD2 mutant] and 25 non-household subjects with known NOD2 genotype [14 NOD2 mutant] identified by the NIHR BioResource Cambridge. Faecal mycobiota composition was determined using internal transcribed spacer 1 [ITS1] sequencing and was compared with 16S rRNA gene sequences and volatile organic compounds. RESULTS CD was associated with higher numbers of fungal observed taxonomic units [OTUs] [p = 0.033]. Principal coordinates analysis using Jaccard index [p = 0.018] and weighted Bray-Curtis dissimilarities [p = 0.01] showed Candida spp. clustered closer to CD patients whereas Cryptococcus spp. clustered closer to non-CD. In CD, we found higher relative abundance of Ascomycota [p = 0.001] and lower relative abundance Basidiomycota [p = 0.019] phyla. An inverse relationship was found between bacterial and fungal Shannon diversity in NOD2 wild-type which was independent of CD [r = -0.349; p = 0.029]. CONCLUSIONS This study confirms compositional changes in the gut mycobiota in CD and provides evidence that fungi may play a role in CD pathogenesis. No NOD2 genotype-specific differences were observed in the faecal mycobiota.
Collapse
Affiliation(s)
- Andrew Nelson
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Christopher J Stewart
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Nicholas A Kennedy
- IBD Pharmacogenetics Group, University of Exeter, Exeter, UK
- Department of Gastroenterology, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - John K Lodge
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Mark Tremelling
- Department of Gastroenterology, Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, UK
| | | | - Chris S Probert
- Institute of Translational Medicine, University of Liverpool, Liverpool, UK
- Department of Gastroenterology, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Miles Parkes
- Department of Gastroenterology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - John C Mansfield
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Darren L Smith
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Georgina L Hold
- Gastrointestinal Research Group, University of Aberdeen, Aberdeen, UK
- Microbiome Research Centre, St George and Sutherland Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Charlie W Lees
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Edinburgh IBD Unit, Western General Hospital, Edinburgh, UK
| | - Simon H Bridge
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Christopher A Lamb
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| |
Collapse
|
175
|
Abstract
Malassezia are emerging fungal pathogens causing opportunistic skin and severe systemic infection. Nosocomial outbreaks are associated with azole resistance and understanding of the underlying mechanisms are limited to knowledge from other fungal species. Herein, we identified distinct antifungal susceptibility patterns in 26 Malassezia furfur isolates derived from healthy and diseased individuals. A Y67F CYP51 mutation was identified in five isolates of M. furfur However, this mutation alone was insufficient to induce reduce azole susceptibility in the wild type strain. RNA-seq and differential gene analysis of healthy and disease derived strains exposed to clotrimazole in vitro identified several key metabolic pathways and transporter proteins which are involved in reduce azole susceptibility. The pleiotropic drug transporter PDR10 was the single most highly upregulated transporter gene in multiple strains of M. furfur after azole treatment and increased expression of PDR10 is associated with reduced azole susceptibility in some systemic disease isolates of M. furfur Deletion of PDR10 in a pathogenic M. furfur strain with reduced susceptibility reduced MIC values to the level of that in susceptible isolates. The current dearth of antifungal technologies, globally emerging multi-azole resistance, and broad agriculture and consumer care use of azoles means improved understanding of the mechanisms underlying intrinsic and acquired azole resistance in Malassezia is crucial for development of antibiotic stewardship and antifungal treatment strategies.
Collapse
|
176
|
Lv L, Gu S, Jiang H, Yan R, Chen Y, Chen Y, Luo R, Huang C, Lu H, Zheng B, Zhang H, Xia J, Tang L, Sheng G, Li L. Gut mycobiota alterations in patients with COVID-19 and H1N1 infections and their associations with clinical features. Commun Biol 2021; 4:480. [PMID: 33850296 PMCID: PMC8044104 DOI: 10.1038/s42003-021-02036-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 03/24/2021] [Indexed: 02/06/2023] Open
Abstract
The relationship between gut microbes and COVID-19 or H1N1 infections is not fully understood. Here, we compared the gut mycobiota of 67 COVID-19 patients, 35 H1N1-infected patients and 48 healthy controls (HCs) using internal transcribed spacer (ITS) 3-ITS4 sequencing and analysed their associations with clinical features and the bacterial microbiota. Compared to HCs, the fungal burden was higher. Fungal mycobiota dysbiosis in both COVID-19 and H1N1-infected patients was mainly characterized by the depletion of fungi such as Aspergillus and Penicillium, but several fungi, including Candida glabrata, were enriched in H1N1-infected patients. The gut mycobiota profiles in COVID-19 patients with mild and severe symptoms were similar. Hospitalization had no apparent additional effects. In COVID-19 patients, Mucoromycota was positively correlated with Fusicatenibacter, Aspergillus niger was positively correlated with diarrhoea, and Penicillium citrinum was negatively correlated with C-reactive protein (CRP). In H1N1-infected patients, Aspergillus penicilloides was positively correlated with Lachnospiraceae members, Aspergillus was positively correlated with CRP, and Mucoromycota was negatively correlated with procalcitonin. Therefore, gut mycobiota dysbiosis occurs in both COVID-19 patients and H1N1-infected patients and does not improve until the patients are discharged and no longer require medical attention. Lv et al. associate the gut mycobiota with clinical features and the bacterial microbiota by comparing COVID-19 patients to those infected with H1N1 and healthy controls. They find that gut mycobiota dysbiosis occurs in both COVID-19 patients and those infected with H1N1 and that it does not improve until patients no longer require medical attention, providing insights into a better healthcare guideline.
Collapse
Affiliation(s)
- Longxian Lv
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Silan Gu
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Huiyong Jiang
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Ren Yan
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yanfei Chen
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yunbo Chen
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Rui Luo
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Chenjie Huang
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Haifeng Lu
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Beiwen Zheng
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Hua Zhang
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jiafeng Xia
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Lingling Tang
- Department of Infectious Diseases, Shulan (Hangzhou) Hospital, Affiliated to Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Guoping Sheng
- Department of Infectious Diseases, Shulan (Hangzhou) Hospital, Affiliated to Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Lanjuan Li
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
| |
Collapse
|
177
|
Rios-Navarro A, Gonzalez M, Carazzone C, Celis Ramírez AM. Learning about microbial language: possible interactions mediated by microbial volatile organic compounds (VOCs) and relevance to understanding Malassezia spp. metabolism. Metabolomics 2021; 17:39. [PMID: 33825999 PMCID: PMC8026438 DOI: 10.1007/s11306-021-01786-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 03/13/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND Microorganisms synthesize and release a large diversity of small molecules like volatile compounds, which allow them to relate and interact with their environment. Volatile organic compounds (VOCs) are carbon-based compounds with low molecular weight and generally, high vapor pressure; because of their nature, they spread easily in the environment. Little is known about the role of VOCs in the interaction processes, and less is known about VOCs produced by Malassezia, a genus of yeasts that belongs to the human skin mycobiota. These yeasts have been associated with several dermatological diseases and currently, they are considered as emerging opportunistic yeasts. Research about secondary metabolites of these yeasts is limited. The pathogenic role and the molecular mechanisms involved in the infection processes of this genus are yet to be clarified. VOCs produced by Malassezia yeasts could play an important function in their metabolism; in addition, they might be involved in either beneficial or pathogenic host-interaction processes. Since these yeasts present differences in their nutritional requirements, like lipids to grow, it is possible that these variations of growth requirements also define differences in the volatile organic compounds produced in Malassezia species. AIM OF REVIEW We present a mini review about VOCs produced by microorganisms and Malassezia species, and hypothesize about their role in its metabolism, which would reveal clues about host-pathogen interaction. KEY SCIENTIFIC CONCEPTS OF REVIEW Since living organisms inhabit a similar environment, the interaction processes occur naturally; as a result, a signal and a response from participants of these processes become important in understanding several biological behaviors. The efforts to elucidate how living organisms interact has been studied from several perspectives. An important issue is that VOCs released by the microbiota plays a key role in the setup of relationships between living micro and macro organisms. The challenge is to determine what is the role of these VOCs produced by human microbiota in commensal/pathogenic scenarios, and how these allow understanding the species metabolism. Malassezia is part of the human mycobiota, and it is implicated in commensal and pathogenic processes. It is possible that their VOCs are involved in these behavioral changes, but the knowledge about this remains overlocked. For this reason, VOCs produced by microorganisms and Malassezia spp. and their role in several biological processes are the main topic in this review.
Collapse
Affiliation(s)
- Andrea Rios-Navarro
- grid.7247.60000000419370714Cellular and Molecular of Pathogenic Microorganisms Research Group (CeMoP), Biological Sciences Department, Universidad de Los Andes, Cra 1 No. 18A-12, Bogotá, 111711 Cundinamarca Colombia
| | - Mabel Gonzalez
- grid.7247.60000000419370714Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP), Chemistry Department, Universidad de Los Andes, Cra 1 No. 18A-12, Bogotá, 111711 Cundinamarca Colombia
| | - Chiara Carazzone
- grid.7247.60000000419370714Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP), Chemistry Department, Universidad de Los Andes, Cra 1 No. 18A-12, Bogotá, 111711 Cundinamarca Colombia
| | - Adriana Marcela Celis Ramírez
- grid.7247.60000000419370714Cellular and Molecular of Pathogenic Microorganisms Research Group (CeMoP), Biological Sciences Department, Universidad de Los Andes, Cra 1 No. 18A-12, Bogotá, 111711 Cundinamarca Colombia
| |
Collapse
|
178
|
Axelrad JE, Cadwell KH, Colombel JF, Shah SC. The role of gastrointestinal pathogens in inflammatory bowel disease: a systematic review. Therap Adv Gastroenterol 2021; 14:17562848211004493. [PMID: 33868457 PMCID: PMC8020742 DOI: 10.1177/17562848211004493] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 03/04/2021] [Indexed: 02/04/2023] Open
Abstract
The inflammatory bowel diseases (IBD), comprising Crohn's disease (CD) and ulcerative colitis (UC), are chronic, progressive, inflammatory conditions of the gastrointestinal tract. Imbalance in the gut microbial community, or dysbiosis, and the subsequent immune response, represent the critical relationship between genetic susceptibility, microbes, and environment factors, that result in IBD. Gastrointestinal pathogens - a common cause of dysbiosis - have been implicated as an environmental trigger in new onset IBD, as well as flare of existing IBD. In this article, we systematically review clinical data regarding the association between specific gastrointestinal pathogens and IBD. Numerous bacteria, viruses, fungi, and parasites have been implicated in the pathogenesis of IBD, and exacerbations of existing disease. In this article, we will also specifically discuss the less recognized microbes that have an inverse association with IBD, including certain bacterial pathogens, such as Helicobacter pylori, and parasites, such as Trichuris species. Future prospective and experimental studies are required to establish causality and clarify potential mechanisms of enteric pathogens in modifying the risk and course of IBD.
Collapse
Affiliation(s)
| | - Ken H. Cadwell
- Division of Gastroenterology, Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA,Kimmel Center for Biology and Medicine at the Skirball Institute, NYU Grossman School of Medicine, New York, NY, USA,Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Jean-Frederic Colombel
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shailja C. Shah
- Section of Gastroenterology, Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN,San Diego Health System, La Jolla, CA, USA,Division of Gastroenterology, University of California, San Diego, La Jolla, CA, USA
| |
Collapse
|
179
|
Crossing Kingdoms: How the Mycobiota and Fungal-Bacterial Interactions Impact Host Health and Disease. Infect Immun 2021; 89:IAI.00648-20. [PMID: 33526565 PMCID: PMC8090948 DOI: 10.1128/iai.00648-20] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The term “microbiota” invokes images of mucosal surfaces densely populated with bacteria. These surfaces and the luminal compartments they form indeed predominantly harbor bacteria. The term “microbiota” invokes images of mucosal surfaces densely populated with bacteria. These surfaces and the luminal compartments they form indeed predominantly harbor bacteria. However, research from this past decade has started to complete the picture by focusing on important but largely neglected constituents of the microbiota: fungi, viruses, and archaea. The community of commensal fungi, also called the mycobiota, interacts with commensal bacteria and the host. It is thus not surprising that changes in the mycobiota have significant impact on host health and are associated with pathological conditions such as inflammatory bowel disease (IBD). In this review we will give an overview of why the mycobiota is an important research area and different mycobiota research tools. We will specifically focus on distinguishing transient and actively colonizing fungi of the oral and gut mycobiota and their roles in health and disease. In addition to correlative and observational studies, we will discuss mechanistic studies on specific cross-kingdom interactions of fungi, bacteria, and the host.
Collapse
|
180
|
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: 63] [Impact Index Per Article: 21.0] [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.
Collapse
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
| |
Collapse
|
181
|
Lind AL, Pollard KS. Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing. MICROBIOME 2021; 9:58. [PMID: 33658077 PMCID: PMC7931531 DOI: 10.1186/s40168-021-01015-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 02/02/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND Microbial eukaryotes are found alongside bacteria and archaea in natural microbial systems, including host-associated microbiomes. While microbial eukaryotes are critical to these communities, they are challenging to study with shotgun sequencing techniques and are therefore often excluded. RESULTS Here, we present EukDetect, a bioinformatics method to identify eukaryotes in shotgun metagenomic sequencing data. Our approach uses a database of 521,824 universal marker genes from 241 conserved gene families, which we curated from 3713 fungal, protist, non-vertebrate metazoan, and non-streptophyte archaeplastida genomes and transcriptomes. EukDetect has a broad taxonomic coverage of microbial eukaryotes, performs well on low-abundance and closely related species, and is resilient against bacterial contamination in eukaryotic genomes. Using EukDetect, we describe the spatial distribution of eukaryotes along the human gastrointestinal tract, showing that fungi and protists are present in the lumen and mucosa throughout the large intestine. We discover that there is a succession of eukaryotes that colonize the human gut during the first years of life, mirroring patterns of developmental succession observed in gut bacteria. By comparing DNA and RNA sequencing of paired samples from human stool, we find that many eukaryotes continue active transcription after passage through the gut, though some do not, suggesting they are dormant or nonviable. We analyze metagenomic data from the Baltic Sea and find that eukaryotes differ across locations and salinity gradients. Finally, we observe eukaryotes in Arabidopsis leaf samples, many of which are not identifiable from public protein databases. CONCLUSIONS EukDetect provides an automated and reliable way to characterize eukaryotes in shotgun sequencing datasets from diverse microbiomes. We demonstrate that it enables discoveries that would be missed or clouded by false positives with standard shotgun sequence analysis. EukDetect will greatly advance our understanding of how microbial eukaryotes contribute to microbiomes. Video abstract.
Collapse
Affiliation(s)
- Abigail L Lind
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Katherine S Pollard
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.
- Institute for Human Genetics, University of California, San Francisco, CA, USA.
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA.
- Institute for Computational Health Sciences, University of California, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| |
Collapse
|
182
|
Kirchner FR, LeibundGut-Landmann S. Tissue-resident memory Th17 cells maintain stable fungal commensalism in the oral mucosa. Mucosal Immunol 2021; 14:455-467. [PMID: 32719409 PMCID: PMC7946631 DOI: 10.1038/s41385-020-0327-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/06/2020] [Indexed: 02/04/2023]
Abstract
Keeping a stable equilibrium between the host and commensal microbes to which we are constantly exposed, poses a major challenge for the immune system. The host mechanisms that regulate homeostasis of the microbiota to prevent infection and inflammatory disorders are not fully understood. Here, we provide evidence that CD4+ tissue-resident memory T (TRM) cells act as central players in this process. Using a murine model of C. albicans commensalism we show that IL-17 producing CD69+CD103+CD4+ memory T cells persist in the colonized tissue long-term and independently of circulatory supplies. Consistent with the requirement of Th17 cells for limiting fungal growth, IL-17-producing TRM cells in the mucosa were sufficient to maintain prolonged colonization, while circulatory T cells were dispensable. Although TRM cells were first proposed to protect from pathogens causing recurrent acute infections, our results support a central function of TRM cells in the maintenance of commensalism.
Collapse
Affiliation(s)
- Florian R Kirchner
- Section of Immunology, Vetsuisse Faculty, University of Zürich, Winterthurerstrasse 266a, CH-8057, Zürich, Switzerland
- Institute of Experimental Immunology, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Salomé LeibundGut-Landmann
- Section of Immunology, Vetsuisse Faculty, University of Zürich, Winterthurerstrasse 266a, CH-8057, Zürich, Switzerland.
- Institute of Experimental Immunology, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland.
| |
Collapse
|
183
|
Iliev ID, Cadwell K. Effects of Intestinal Fungi and Viruses on Immune Responses and Inflammatory Bowel Diseases. Gastroenterology 2021; 160:1050-1066. [PMID: 33347881 PMCID: PMC7956156 DOI: 10.1053/j.gastro.2020.06.100] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/23/2020] [Accepted: 06/23/2020] [Indexed: 12/26/2022]
Abstract
The intestinal microbiota comprises diverse fungal and viral components, in addition to bacteria. These microbes interact with the immune system and affect human physiology. Advances in metagenomics have associated inflammatory and autoimmune diseases with alterations in fungal and viral species in the gut. Studies of animal models have found that commensal fungi and viruses can activate host-protective immune pathways related to epithelial barrier integrity, but can also induce reactions that contribute to events associated with inflammatory bowel disease. Changes in our environment associated with modernization and the COVID-19 pandemic have exposed humans to new fungi and viruses, with unknown consequences. We review the lessons learned from studies of animal viruses and fungi commonly detected in the human gut and how these might affect health and intestinal disease.
Collapse
Affiliation(s)
- Iliyan D Iliev
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, New York; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, New York.
| | - Ken Cadwell
- Kimmel Center for Biology and Medicine, Skirball Institute, New York University Grossman School of Medicine, New York, New York; Department of Microbiology, New York University Grossman School of Medicine, New York, New York; Division of Gastroenterology and Hepatology, Department of Medicine, New York University Langone Health, New York, New York.
| |
Collapse
|
184
|
Doron I, Leonardi I, Li XV, Fiers WD, Semon A, Bialt-DeCelie M, Migaud M, Gao IH, Lin WY, Kusakabe T, Puel A, Iliev ID. Human gut mycobiota tune immunity via CARD9-dependent induction of anti-fungal IgG antibodies. Cell 2021; 184:1017-1031.e14. [PMID: 33548172 PMCID: PMC7936855 DOI: 10.1016/j.cell.2021.01.016] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 12/04/2020] [Accepted: 01/12/2021] [Indexed: 12/11/2022]
Abstract
Antibodies mediate natural and vaccine-induced immunity against viral and bacterial pathogens, whereas fungi represent a widespread kingdom of pathogenic species for which neither vaccine nor neutralizing antibody therapies are clinically available. Here, using a multi-kingdom antibody profiling (multiKAP) approach, we explore the human antibody repertoires against gut commensal fungi (mycobiota). We identify species preferentially targeted by systemic antibodies in humans, with Candida albicans being the major inducer of antifungal immunoglobulin G (IgG). Fungal colonization of the gut induces germinal center (GC)-dependent B cell expansion in extraintestinal lymphoid tissues and generates systemic antibodies that confer protection against disseminated C. albicans or C. auris infection. Antifungal IgG production depends on the innate immunity regulator CARD9 and CARD9+CX3CR1+ macrophages. In individuals with invasive candidiasis, loss-of-function mutations in CARD9 are associated with impaired antifungal IgG responses. These results reveal an important role of gut commensal fungi in shaping the human antibody repertoire through CARD9-dependent induction of host-protective antifungal IgG.
Collapse
Affiliation(s)
- Itai Doron
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Irina Leonardi
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Xin V Li
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - William D Fiers
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Alexa Semon
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Meghan Bialt-DeCelie
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Mélanie Migaud
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Iris H Gao
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Woan-Yu Lin
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Takato Kusakabe
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Anne Puel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065 USA; University of Paris, Imagine Institute, 75015 Paris, France
| | - Iliyan D Iliev
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.
| |
Collapse
|
185
|
Beheshti-Maal A, Shahrokh S, Ansari S, Mirsamadi ES, Yadegar A, Mirjalali H, Zali MR. Gut mycobiome: The probable determinative role of fungi in IBD patients. Mycoses 2021; 64:468-476. [PMID: 33421192 DOI: 10.1111/myc.13238] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 12/15/2020] [Accepted: 01/04/2021] [Indexed: 12/12/2022]
Abstract
Inflammatory bowel disease (IBD) is a multi-factorial autoimmune disorder that its causative agents are unknown. The gut microbiota comprises of bacteria, viruses, fungi and protozoa that its role in IBD has remained controversially. Bacteria constitute more than 99% of the gut microbiota composition, and the main core of the gut microbiota is composed from Bacteroidetes and Firmicutes. The gut microbiota plays an important role in training, development and haemostasis of the immune responses during the life. Fungi compose a very small portion of gut microbiota, but play determinative roles in homeostasis of the gut bacterial composition and the mucosal immune responses. An interkingdom correlation between bacteria and fungi has been suggested. For example, the presence of Salmonella enterica serovar Typhimurium reduces the viability and colonisation of C albicans. Alterations in the composition and function of the gut microbiota, which is known as dysbiosis, are a usual event in patients who suffer from IBD. Although the main reason for this alteration is not clear, the interaction between gut bacteria and gut fungi seems to be an important subject in IBD patients. This review covers new findings on the interaction between fungi and bacteria and the role of fungi in the pathophysiology of IBD.
Collapse
Affiliation(s)
- Alireza Beheshti-Maal
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shabnam Shahrokh
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Saham Ansari
- Department of Medical Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Elnaz Sadat Mirsamadi
- Department of Microbiology, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamed Mirjalali
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| |
Collapse
|
186
|
Elmaghrawy K, Hussey S, Moran GP. The Oral Microbiome in Pediatric IBD: A Source of Pathobionts or Biomarkers? Front Pediatr 2021; 8:620254. [PMID: 33553076 PMCID: PMC7859511 DOI: 10.3389/fped.2020.620254] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/14/2020] [Indexed: 12/22/2022] Open
Abstract
The oral cavity is continuous with the gastrointestinal tract and in children, oral health may be closely linked with the overall health of the GI tract. In the case of pediatric Crohn's disease (CD), oral manifestations are an important clinical indicator of intestinal disease. Recent studies of the microbiome in IBD suggest that translocation of oral microbes to the gut may be a common feature of the microbial dysbiosis which is a signature of both CD and ulcerative colitis (UC). Murine studies suggest that translocation of oral bacteria and yeasts to the lower GI tract may trigger inflammation in susceptible hosts, providing a mechanistic link to the development of IBD. Conversely, some studies have shown that dysbiosis of the oral microbiome may occur, possibly as a result of inflammatory responses and could represent a useful source of biomarkers of GI health. This review summarizes our current knowledge of the oral microbiome in IBD and presents current hypotheses on the potential role of this community in the pathogenesis of these diseases.
Collapse
Affiliation(s)
- Khalid Elmaghrawy
- School of Dental Science, Trinity College Dublin and Dublin Dental University Hospital, Dublin, Ireland
| | - Séamus Hussey
- Department of Paediatrics, University of Medicine and Health Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
- National Children's Research Centre, Dublin, Ireland
| | - Gary P. Moran
- School of Dental Science, Trinity College Dublin and Dublin Dental University Hospital, Dublin, Ireland
| |
Collapse
|
187
|
Gill T, Rosenbaum JT. Putative Pathobionts in HLA-B27-Associated Spondyloarthropathy. Front Immunol 2021; 11:586494. [PMID: 33537028 PMCID: PMC7848169 DOI: 10.3389/fimmu.2020.586494] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 12/02/2020] [Indexed: 12/11/2022] Open
Abstract
Spondyloarthritis (SpA) is a group of immune mediated inflammatory diseases with a strong association to the major histocompatibility (MHC) class I molecule, HLA-B27. Although the association between HLA-B27 and AS has been known for almost 50 years, the mechanisms underlying disease pathogenesis are elusive. Over the years, three hypotheses have been proposed to explain HLA-B27 and disease association: 1) HLA B27 presents arthritogenic peptides and thus creates a pathological immune response; 2) HLA-B27 misfolding causes endoplasmic reticulum (ER) stress which activates the unfolded protein response (UPR); 3) HLA-B27 dimerizes on the cell surface and acts as a target for natural killer (NK) cells. None of these hypotheses explains SpA pathogenesis completely. Evidence supports the hypothesis that HLA-B27-related diseases have a microbial pathogenesis. In animal models of various SpAs, a germ-free environment abrogates disease development and colonizing these animals with gut commensal microbes can restore disease manifestations. The depth of microbial influence on SpA development has been realized due to our ability to characterize microbial communities in the gut using next-generation sequencing approaches. In this review, we will discuss various putative pathobionts in the pathogenesis of HLA-B27-associated diseases. We pursue whether a single pathobiont or a disruption of microbial community and function is associated with HLA-B27-related diseases. Furthermore, rather than a specific pathobiont, metabolic functions of various disease-associated microbes might be key. While the use of germ-free models of SpA have facilitated understanding the role of microbes in disease development, future studies with animal models that mimic diverse microbial communities instead of mono-colonization are indispensable. We discuss the causal mechanisms underlying disease pathogenesis including the role of these pathobionts on mucin degradation, mucosal adherence, and gut epithelial barrier disruption and inflammation. Finally, we review the various uses of microbes as therapeutic modalities including pre/probiotics, diet, microbial metabolites and fecal microbiota transplant. Unravelling these complex host-microbe interactions will lead to the development of new targets/therapies for alleviation of SpA and other HLA-B27 associated diseases.
Collapse
Affiliation(s)
- Tejpal Gill
- Division of Arthritis and Rheumatic Diseases, Department of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - James T Rosenbaum
- Departments of Ophthalmology, Medicine, and Cell Biology, Oregon Health & Science University, Portland, OR, United States.,Legacy Devers Eye Institute, Portland, OR, United States
| |
Collapse
|
188
|
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.
Collapse
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
| |
Collapse
|
189
|
Molina Ortiz JP, McClure DD, Shanahan ER, Dehghani F, Holmes AJ, Read MN. Enabling rational gut microbiome manipulations by understanding gut ecology through experimentally-evidenced in silico models. Gut Microbes 2021; 13:1965698. [PMID: 34455914 PMCID: PMC8432618 DOI: 10.1080/19490976.2021.1965698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 07/01/2021] [Accepted: 07/27/2021] [Indexed: 02/04/2023] Open
Abstract
The gut microbiome has emerged as a contributing factor in non-communicable disease, rendering it a target of health-promoting interventions. Yet current understanding of the host-microbiome dynamic is insufficient to predict the variation in intervention outcomes across individuals. We explore the mechanisms that underpin the gut bacterial ecosystem and highlight how a more complete understanding of this ecology will enable improved intervention outcomes. This ecology varies within the gut over space and time. Interventions disrupt these processes, with cascading consequences throughout the ecosystem. In vivo studies cannot isolate and probe these processes at the required spatiotemporal resolutions, and in vitro studies lack the representative complexity required. However, we highlight that, together, both approaches can inform in silico models that integrate cellular-level dynamics, can extrapolate to explain bacterial community outcomes, permit experimentation and observation over ecological processes at high spatiotemporal resolution, and can serve as predictive platforms on which to prototype interventions. Thus, it is a concerted integration of these techniques that will enable rational targeted manipulations of the gut ecosystem.
Collapse
Affiliation(s)
- Juan P. Molina Ortiz
- School of Chemical and Biomolecular Engineering, Faculty of Engineering, The University of Sydney, Sydney, Australia
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
| | - Dale D. McClure
- School of Chemical and Biomolecular Engineering, Faculty of Engineering, The University of Sydney, Sydney, Australia
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
| | - Erin R. Shanahan
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - Fariba Dehghani
- School of Chemical and Biomolecular Engineering, Faculty of Engineering, The University of Sydney, Sydney, Australia
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
| | - Andrew J. Holmes
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - Mark N. Read
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- School of Computer Science, Faculty of Engineering, The University of Sydney, Sydney, Australia
| |
Collapse
|
190
|
Lee M, Chang EB. Inflammatory Bowel Diseases (IBD) and the Microbiome-Searching the Crime Scene for Clues. Gastroenterology 2021; 160:524-537. [PMID: 33253681 PMCID: PMC8098834 DOI: 10.1053/j.gastro.2020.09.056] [Citation(s) in RCA: 267] [Impact Index Per Article: 89.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 02/07/2023]
Abstract
Inflammatory bowel diseases (IBD) develop via convergence of environmental, microbial, immunological, and genetic factors. Alterations in the gut microbiota have been associated with development and progression of IBD, but it is not clear which populations of microbes are involved or how they might contribute to IBD. We review the genetic and environmental factors affecting the gut microbiota, the roles of gut microbes and their bioproducts in the development and clinical course of IBD, and strategies by which microbiome-based therapies can be used to prevent, manage, and eventually cure IBD. We discuss research findings that help bridge the gap between the basic sciences and clinical application.
Collapse
Affiliation(s)
| | - Eugene B Chang
- Department of Medicine, University of Chicago, Chicago, Illinois.
| |
Collapse
|
191
|
Ji C, Yang Z, Zhong X, Xia J. The role and mechanism of CARD9 gene polymorphism in diseases. Biomed J 2020; 44:560-566. [PMID: 34690098 PMCID: PMC8640546 DOI: 10.1016/j.bj.2020.12.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/02/2020] [Accepted: 12/22/2020] [Indexed: 01/03/2023] Open
Abstract
CARD9 is a cytosolic adaptor in myeloid cells, has a critical role in inflammatory disorders, and provides a protective function against microbial pathogen, especially fungal infection. Recently, CARD9 polymorphisms are of interest, showing a positive correlation with the elevated risk of fungal infection, inflammatory bowel disease, and other autoimmune diseases. Mechanistically, CARD9 polymorphisms impair the activation of RelB, a subunit of non-canonical NF-κB, which lead to the reduced cytokine and chemokine production by innate immune cells. In addition, CARD9 polymorphisms show a defective neutrophil accumulation in infectious sites. Furthermore, CARD9 polymorphisms could alter the composition of the gut microbiome. In this review, we summarize the latest findings of CARD9 polymorphisms with respect to inflammatory diseases.
Collapse
Affiliation(s)
- Changxue Ji
- Songjiang Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (Preparatory Stage), Shanghai, China
| | - Zhiwen Yang
- Songjiang Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (Preparatory Stage), Shanghai, China
| | | | - Jindong Xia
- Songjiang Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (Preparatory Stage), Shanghai, China.
| |
Collapse
|
192
|
Fungal Dysbiosis Correlates with the Development of Tumor-Induced Cachexia in Mice. J Fungi (Basel) 2020; 6:jof6040364. [PMID: 33322197 PMCID: PMC7770573 DOI: 10.3390/jof6040364] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 12/12/2022] Open
Abstract
Cachexia (CC) is a devastating metabolic syndrome associated with a series of underlying diseases that greatly affects life quality and expectancy among cancer patients. Studies involving mouse models, in which CC was induced through inoculation with tumor cells, originally suggested the existence of a direct correlation between the development of this syndrome and changes in the relative proportions of several bacterial groups present in the digestive tract. However, these analyses have focus solely on the characterization of bacterial dysbiosis, ignoring the possible existence of changes in the relative populations of fungi, during the development of CC. Thus, the present study sought to expand such analyses, by characterizing changes that occur in the gut fungal population (mycobiota) of mice, during the development of cancer-induced cachexia. Our results confirm that cachectic animals, submitted to Lewis lung carcinoma (LLC) transplantation, display significant differences in their gut mycobiota, when compared to healthy controls. Moreover, identification of dysbiotic fungi showed remarkable consistency across successive levels of taxonomic hierarchy. Many of these fungi have also been associated with dysbioses observed in a series of gut inflammatory diseases, such as obesity, colorectal cancer (CRC), myalgic encephalomyelitis (ME) and inflammatory bowel disease (IBD). Nonetheless, the dysbiosis verified in the LLC model of cancer cachexia seems to be unique, presenting features observed in both obesity (reduced proportion of Mucoromycota) and CRC/ME/IBD (increased proportions of Sordariomycetes, Saccharomycetaceae and Malassezia). One species of Mucoromycota (Rhyzopus oryzae) stands out as a promising probiotic candidate in adjuvant therapies, aimed at treating and/or preventing the development of CC.
Collapse
|
193
|
Abstract
Within the last decade, our understanding of the role of the intestinal microbiota in health and disease has rapidly increased due to significant advances in next-generation sequencing technologies. Scientists have discovered more and more gut microbes with supposedly "beneficial" roles for human health and are starting to identify the underlying mechanisms. In this review, we summarize the latest knowledge about the human intestinal microbiota, including the intestinal bacteriome, virome and mycobiome. We discuss the function that recent studies attribute to the intestinal microbiota in preventing or controlling selected diseases and present recent research on biotherapeutic approaches to control these diseases.
Collapse
Affiliation(s)
- Pipat Piewngam
- Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, U.S. National Institutes of Health, 50 South Drive, Bethesda, Maryland 20814, USA
| | - François De Mets
- Department of Biology, Georgetown University, Washington, DC, 20057, USA
| | - Michael Otto
- Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, U.S. National Institutes of Health, 50 South Drive, Bethesda, Maryland 20814, USA
| |
Collapse
|
194
|
Zhu F, Feng D, Ding C, Zhang T, Chen J, Yu Z, Zhao L, Xu Y, Zhu W, Gong J. Fungal Dysbiosis Aggravates Pouchitis in a Rat Model of Ileal Pouch Anal Anastomosis. Inflamm Bowel Dis 2020; 26:1831-1842. [PMID: 32608473 DOI: 10.1093/ibd/izaa111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Although the interaction between gut microbiota and pouchitis after ileal pouch anal anastomosis (IPAA) for ulcerative colitis (UC) has been confirmed, evidence of commensal mycobiota in the etiology of pouchitis is still lacking. This study aimed to investigate the role of fungi in the pathogenesis of pouchitis. METHODS Fecal samples were collected from UC patients with or without pouchitis after IPAA. Experimental pouchitis was induced by 5% dextran sulfate sodium for 7 consecutive days in a rat model of IPAA. Fungal dysbiosis was induced by 0.5% fluconazole (Flu), and commensal fungal recognition through dectin-1 was blocked by 5% laminarin. Fecal fungal composition was analyzed using internal transcribed spacer 2 sequencing. Severity of pouchitis and activation of the CARD9-nuclear factor kappa-B pathway was determined among different groups. RESULTS Patients with pouchitis had a lower alpha (α) diversity in mycobiota composition and a higher abundance of Saccharomyces at the genus level compared with those with a normal pouch. In the rat model of pouchitis, Flu treatment decreased fungal burden but induced fungal dysbiosis, characterized by increased α diversity, a decreased relative abundance of Kazachstania, and increased Polythrincium and Saccharomyces. In addition, Flu treatment worsened dextran sulfate sodium pouchitis, as indicated by increased mortality, weight loss, higher histological score, and CD4+ cell infiltration. Laminarin also increased the severity of pouchitis. In the Flu and laminarin groups, the expression of interferon-γ, tumor necrosis factor-α, CARD9, and phosphorylated nuclear factor kappa-B inhibitor alpha was decreased. CONCLUSIONS Patients with pouchitis had altered fungal composition. Fungal dysbiosis or recognition deficiency by the host may exacerbate experimental pouchitis. Strategies targeting commensal mycobiota may provide therapeutic potential against pouchitis, especially for antibiotic-refractory patients.
Collapse
Affiliation(s)
- Feng Zhu
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China.,Department of General Surgery, Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Dengyu Feng
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Chao Ding
- Department of General Surgery, Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Tenghui Zhang
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | | | - Zeqian Yu
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Lei Zhao
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Yi Xu
- Department of General Surgery, Jinling Hospital, Medical School of Southeast University, Nanjing, China
| | - Weiming Zhu
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Jianfeng Gong
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| |
Collapse
|
195
|
Qiu X, Zhao X, Cui X, Mao X, Tang N, Jiao C, Wang D, Zhang Y, Ye Z, Zhang H. Characterization of fungal and bacterial dysbiosis in young adult Chinese patients with Crohn's disease. Therap Adv Gastroenterol 2020; 13:1756284820971202. [PMID: 33240394 PMCID: PMC7672770 DOI: 10.1177/1756284820971202] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/14/2020] [Indexed: 02/04/2023] Open
Abstract
Intestinal microbiota dysbiosis has been described in inflammatory bowel disease (IBD), but data from China are limited. In this study, we performed molecular analysis of the fecal microbial community from 20 healthy Chinese subjects and 25 patients with Crohn's disease (CD), and evaluated associations with bacterial and fungal compositions. Decreased richness and diversity of bacterial composition was observed in the CD group compared with healthy (H) subjects. Significant structural differences in bacterial (but not fungal) composition among healthy controls and CD patients were found. A reduction in Firmicutes and Actinobacteria abundance, and overrepresentation of Proteobacteria were observed in the CD patients compared with the H group. The Escherichia-Shigella genus was overrepresented in the CD group, whereas Faecalibacterium, Gemmiger, Bifidobacterium, Romboutsia, Ruminococcus, Roseburia, and Fusicatenibacter abundance were decreased in the CD group compared with H subjects. Differences in fungal microbiota between the H and CD groups were observed at the genus rather than at the phylum level. The Candida genus was overrepresented in the CD (active disease) group compared with the H group, whereas no difference between CD (remission) and H groups was observed. Aspergillus, unclassified_Sordariomycetes, and Penicillium genera had greater representation in the H subjects compared with the CD group. Bacterial and fungal intra- and inter-kingdom correlations were observed between the H and CD groups. Therefore, fecal bacterial and fungal microbiome communities differed considerably between H and CD patients, and between Chinese and Western populations. The role of gut microbiota in homeostasis and in gastrointestinal disorders should be investigated further.
Collapse
Affiliation(s)
| | | | - Xiufang Cui
- Department of Gastroenterology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaqiong Mao
- Department of Gastroenterology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Nana Tang
- Department of Gastroenterology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chunhua Jiao
- Department of Gastroenterology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Di Wang
- Department of Gastroenterology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yue Zhang
- Department of Gastroenterology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ziping Ye
- Department of Gastroenterology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hongjie Zhang
- Department of Gastroenterology, First Affiliated Hospital of Nanjing Medical University, Guangzhou Road 300#, Nanjing, 210029, China
| |
Collapse
|
196
|
Fernández-Espejo E. Microorganisms that are related with increased risk for Parkinson's disease. Neurologia 2020; 38:S0213-4853(20)30301-7. [PMID: 33160724 DOI: 10.1016/j.nrl.2020.08.020] [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: 06/03/2020] [Revised: 08/04/2020] [Accepted: 08/26/2020] [Indexed: 11/25/2022] Open
Abstract
Parkinson's disease is a neurodegenerative disorder that affects more than 7 million people worldwide. Its aetiology is unknown, although the hypothesis of a genetic susceptibility to environmental agents is accepted. These environmental agents include fungi, bacteria, and viruses. Three microorganisms are directly associated with a significantly increased risk of developing Parkinson's disease: the fungal genus Malassezia, the bacterium Helicobacter pylori, and the hepatitis C virus. If the host is vulnerable due to genetic susceptibility or immune weakness, these microorganisms can access and infect the nervous system, causing chronic neuroinflammation with neurodegeneration. Other microorganisms show an epidemiological association with the disease, including the influenza type A, Japanese encephalitis type B, St Louis, and West Nile viruses. These viruses can affect the nervous system, causing encephalitis, which can result in parkinsonism. This article reviews the role of all these microorganisms in Parkinson's disease.
Collapse
Affiliation(s)
- E Fernández-Espejo
- Laboratorio de Neurología Molecular, Universidad de Sevilla, Sevilla, España; Red Andaluza de Investigación Clínica y Traslacional en Neurología (Neuro-RECA), Málaga, España.
| |
Collapse
|
197
|
Kellermayer R, Zilbauer M. The Gut Microbiome and the Triple Environmental Hit Concept of Inflammatory Bowel Disease Pathogenesis. J Pediatr Gastroenterol Nutr 2020; 71:589-595. [PMID: 33093364 DOI: 10.1097/mpg.0000000000002908] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The incidence of chronic inflammatory bowel diseases (IBDs), such as Crohn's disease (CD) and ulcerative colitis (UC) have significantly increased in recent decades implicating environmental effects. The developmental origin of disease concept provides a theoretical framework by which the complex interplay between environmental factors and host cells, particularly during vulnerable time periods, ultimately cause disease, such as IBD. Epigenetics has been proposed as the underlying mechanism within this concept, turning environmental triggers into stable changes of cellular function. Adding further to the complexity of IBD is the gut microbiome, which is equally responsive to the environment, and can impact host cell function, where recent findings underscore the stochastic and individualized nature of such effects. We review the microbiome literature through a novel triple environmental hit concept (priming, modulation, and trigger) of IBD pathogenesis. We propose that there are at least 3 distinct stages during an individual's lifespan where random/stochastic events driven by environmental influences are necessary for ultimately developing IBD. By this means, we speculate that microbiome-directed therapeutics carry potential for individualized prevention and dynamic treatment of IBD.
Collapse
Affiliation(s)
- Richard Kellermayer
- Section of Pediatric Gastroenterology, Texas Children's Hospital Baylor College of Medicine
- USDA/ARS Children's Nutrition Research Center, Houston, TX
| | | |
Collapse
|
198
|
Hong G, Li Y, Yang M, Li G, Qian W, Xiong H, Bai T, Song J, Zhang L, Hou X. Gut fungal dysbiosis and altered bacterial-fungal interaction in patients with diarrhea-predominant irritable bowel syndrome: An explorative study. Neurogastroenterol Motil 2020; 32:e13891. [PMID: 32449259 DOI: 10.1111/nmo.13891] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 03/11/2020] [Accepted: 04/30/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Little is known about intestinal fungi in IBS patients whose gut bacteria have been investigated a lot. In order to explore causal relationship between IBS and gut mycobiome, and use gut fungi to diagnose or even treat IBS, further characterization of it in IBS is required. METHODS Fifty-five diarrhea-predominant IBS (D-IBS) patients fulfilling Rome III criteria, and 16 healthy controls (HC) were recruited. Fresh fecal samples were collected and used for 16s rRNA and ITS2 high-throughput sequencing. Diversity and composition of gut bacteria and fungi, as well as bacterial-fungal interactions in D-IBS patients, were characterized. Specific fungal taxa differentiating D-IBS from HC were recognized by LEfSe and RandomForest methods, and their association with clinical symptoms was assessed by Spearman's correlation. RESULTS Diarrhea-predominant irritable bowel syndrome patients showed abnormal (IBS-dysbiosis) or normal (HC-like IBS) fecal bacterial structure and diversity compared with healthy controls. However, fecal fungal signatures differed absolutely between D-IBS and HC, which indicated a more susceptible alteration of gut fungi than bacteria in D-IBS. Fecal fungi showed significant correlations with IBS symptoms, especially Mycosphaerella, Aspergillus, Sporidiobolus, and Pandora which were identified to potentially differentiate D-IBS from HC. Moreover, compared with HC there were markedly declined bacterial-fungal interactions in D-IBS, in which Candida changed from negative to positive correlations with bacteria, and Eurotium changed from positive correlations to irrelevance, while Debaryomyces gained negative correlations with bacteria. CONCLUSIONS Gut fungal dysbiosis and altered bacterial-fungal interactions were present in patients with D-IBS, and gut fungi could be used to diagnose D-IBS.
Collapse
Affiliation(s)
- Gaichao Hong
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Li
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Min Yang
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Gangping Li
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Qian
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hanhua Xiong
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Bai
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jun Song
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lei Zhang
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaohua Hou
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|
199
|
Geuking MB, Burkhard R. Microbial modulation of intestinal T helper cell responses and implications for disease and therapy. Mucosal Immunol 2020; 13:855-866. [PMID: 32792666 DOI: 10.1038/s41385-020-00335-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/20/2020] [Accepted: 07/28/2020] [Indexed: 02/07/2023]
Abstract
Induction of intestinal T helper cell subsets by commensal members of the intestinal microbiota is an important component of the many immune adaptations required to establish host-microbial homeostasis. Importantly, altered intestinal T helper cell profiles can have pathological consequences that are not limited to intestinal sites. Therefore, microbial-mediated modulation of the intestinal T helper cell profile could have strong therapeutic potentials. However, in order to develop microbial therapies that specifically induce the desired alterations in the intestinal T helper cell compartment one has to first gain a detailed understanding of how microbial composition and the metabolites derived or induced by the microbiota impact on intestinal T helper cell responses. Here we summarize the milestone findings in the field of microbiota-intestinal T helper cell crosstalk with a focus on the role of specific commensal bacteria and their metabolites. We discuss mechanistic mouse studies and are linking these to human studies where possible. Moreover, we highlight recent advances in the field of microbial CD4 T cell epitope mimicry in autoimmune diseases and the role of microbially-induced CD4 T cells in cancer immune checkpoint blockade therapy.
Collapse
Affiliation(s)
- Markus B Geuking
- Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
| | - Regula Burkhard
- Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| |
Collapse
|
200
|
Ha CWY, Martin A, Sepich-Poore GD, Shi B, Wang Y, Gouin K, Humphrey G, Sanders K, Ratnayake Y, Chan KSL, Hendrick G, Caldera JR, Arias C, Moskowitz JE, Ho Sui SJ, Yang S, Underhill D, Brady MJ, Knott S, Kaihara K, Steinbaugh MJ, Li H, McGovern DPB, Knight R, Fleshner P, Devkota S. Translocation of Viable Gut Microbiota to Mesenteric Adipose Drives Formation of Creeping Fat in Humans. Cell 2020; 183:666-683.e17. [PMID: 32991841 PMCID: PMC7521382 DOI: 10.1016/j.cell.2020.09.009] [Citation(s) in RCA: 191] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 07/19/2020] [Accepted: 09/01/2020] [Indexed: 02/08/2023]
Abstract
A mysterious feature of Crohn's disease (CD) is the extra-intestinal manifestation of "creeping fat" (CrF), defined as expansion of mesenteric adipose tissue around the inflamed and fibrotic intestine. In the current study, we explore whether microbial translocation in CD serves as a central cue for CrF development. We discovered a subset of mucosal-associated gut bacteria that consistently translocated and remained viable in CrF in CD ileal surgical resections, and identified Clostridium innocuum as a signature of this consortium with strain variation between mucosal and adipose isolates, suggesting preference for lipid-rich environments. Single-cell RNA sequencing characterized CrF as both pro-fibrotic and pro-adipogenic with a rich milieu of activated immune cells responding to microbial stimuli, which we confirm in gnotobiotic mice colonized with C. innocuum. Ex vivo validation of expression patterns suggests C. innocuum stimulates tissue remodeling via M2 macrophages, leading to an adipose tissue barrier that serves to prevent systemic dissemination of bacteria.
Collapse
Affiliation(s)
- Connie W Y Ha
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Anthony Martin
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Gregory D Sepich-Poore
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA
| | - Baochen Shi
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Yizhou Wang
- Applied Genomics, Computation and Translational Core, Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Kenneth Gouin
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Applied Genomics, Computation and Translational Core, Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Gregory Humphrey
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Karenina Sanders
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | | | | | - Gustaf Hendrick
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - J R Caldera
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Christian Arias
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jacob E Moskowitz
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Shannan J Ho Sui
- Harvard Chan Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Shaohong Yang
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - David Underhill
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Matthew J Brady
- Department of Medicine, Section of Endocrinology and Metabolism, The University of Chicago, Chicago, IL 60637, USA
| | - Simon Knott
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Applied Genomics, Computation and Translational Core, Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | | | - Michael J Steinbaugh
- Harvard Chan Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Huiying Li
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Phillip Fleshner
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Division of Colorectal Surgery, Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Suzanne Devkota
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
| |
Collapse
|