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Nenciarini S, Renzi S, di Paola M, Meriggi N, Cavalieri D. Ascomycetes yeasts: The hidden part of human microbiome. WIREs Mech Dis 2024; 16:e1641. [PMID: 38228159 DOI: 10.1002/wsbm.1641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 12/17/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024]
Abstract
The fungal component of the microbiota, the mycobiota, has been neglected for a long time due to its poor richness compared to bacteria. Limitations in fungal detection and taxonomic identification arise from using metagenomic approaches, often borrowed from bacteriome analyses. However, the relatively recent discoveries of the ability of fungi to modulate the host immune response and their involvement in human diseases have made mycobiota a fundamental component of the microbial communities inhabiting the human host, deserving some consideration in host-microbe interaction studies and in metagenomics. Here, we reviewed recent data on the identification of yeasts of the Ascomycota phylum across human body districts, focusing on the most representative genera, that is, Saccharomyces and Candida. Then, we explored the key factors involved in shaping the human mycobiota across the lifespan, ranging from host genetics to environment, diet, and lifestyle habits. Finally, we discussed the strengths and weaknesses of culture-dependent and independent methods for mycobiota characterization. Overall, there is still room for some improvements, especially regarding fungal-specific methodological approaches and bioinformatics challenges, which are still critical steps in mycobiota analysis, and to advance our knowledge on the role of the gut mycobiota in human health and disease. This article is categorized under: Immune System Diseases > Genetics/Genomics/Epigenetics Immune System Diseases > Environmental Factors Infectious Diseases > Environmental Factors.
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Affiliation(s)
| | - Sonia Renzi
- Department of Biology, University of Florence, Florence, Italy
| | - Monica di Paola
- Department of Biology, University of Florence, Florence, Italy
| | - Niccolò Meriggi
- Department of Biology, University of Florence, Florence, Italy
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Jangi S, Hsia K, Zhao N, Kumamoto CA, Friedman S, Singh S, Michaud DS. Dynamics of the Gut Mycobiome in Patients With Ulcerative Colitis. Clin Gastroenterol Hepatol 2024; 22:821-830.e7. [PMID: 37802272 PMCID: PMC10960711 DOI: 10.1016/j.cgh.2023.09.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/10/2023] [Accepted: 09/19/2023] [Indexed: 10/08/2023]
Abstract
BACKGROUND & AIMS Intestinal fungi have been implicated in the pathogenesis of ulcerative colitis (UC). However, it remains unclear if fungal composition is altered during active versus quiescent disease. METHODS We analyzed clinical and metagenomic data from the Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease (SPARC IBD), available via the IBD Plexus Program of the Crohn's & Colitis Foundation. We evaluated the fungal composition of fecal samples from 421 patients with UC during clinical activity and remission. Within a longitudinal subcohort (n = 52), we assessed for dynamic taxonomic changes across alterations in clinical activity over time. We examined if fungal amplicon sequence variants and fungal-bacterial relationships were altered during activity versus remission. Finally, we classified activity in UC using a supervised machine learning random forest model trained on fungal abundance data. RESULTS During clinical activity, the relative abundance of genus Candida was increased 3.5-fold (P-adj < 1 × 10-4) compared with during remission. Patients with longitudinal reductions in clinical activity demonstrated parallel reductions in Candida relative abundance (P < .05). Candida relative abundance correlated with Parabacteroides diastonis, Faecalibacterium prausnitzii, and Bacteroides dorei relative abundance (P < .05) during remission; however, these correlations were disrupted during activity. Fungal abundance data successfully classified patients with active or quiescent UC (area under the curve ∼0.80), with Candida relative abundance critical to the success of the model. CONCLUSIONS Clinical activity in UC is associated with an increased relative abundance of Candida, cross-sectionally and dynamically over time. The role of fecal Candida as a target for therapeutics in UC should be evaluated.
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Affiliation(s)
- Sushrut Jangi
- Department of Medicine, Tufts Medical Center, Boston, Massachusetts.
| | - Katie Hsia
- Department of Medicine, Tufts Medical Center, Boston, Massachusetts
| | - Naisi Zhao
- Public Health and Community Medicine, Tufts University School of Medicine, Boston, Massachusetts
| | - Carol A Kumamoto
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts
| | - Sonia Friedman
- Department of Medicine, Tufts Medical Center, Boston, Massachusetts
| | - Siddharth Singh
- Division of Gastroenterology, Department of Medicine, University of California, San Diego, California
| | - Dominique S Michaud
- Public Health and Community Medicine, Tufts University School of Medicine, Boston, Massachusetts
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3
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Wang T, Lu Y, Wu J, Yu B. Composition and dynamics of intestinal fungi during the postnatal 2 months of very low birth weight infants. Eur J Pediatr 2024; 183:403-414. [PMID: 37906308 PMCID: PMC10857973 DOI: 10.1007/s00431-023-05257-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 09/29/2023] [Accepted: 10/03/2023] [Indexed: 11/02/2023]
Abstract
It has been found that intestinal fungi play a role in the composition of the intestinal microecology and in the formation and development of the immunity during childhood. We investigated the gut fungi composition of preterm infants to analysis composition and dynamics of intestinal fungi during the postnatal 2 months of very low birth weight infants. We collected feces from 34 very low birth weight infants (VLBWI) and 28 preterm infants with birth weight >1500 g. We extracted total fungal DNA from feces and analyzed the composition of gut fungus through ITS sequencing. The fungal detectable rate in the experimental group peaked on day 3 (85.19%), then gradually decreased and started to show an increasing trend again by day 28. There were significant differences in the alpha diversity of intestinal fungus between VLBWI and controls, and the VLBWI had its own characteristics at different time points in richness and diversity. A total of 10 phylums and 342 genera were identified in all VLBWI samples. The dominant fungal phylum of the VLBWI group is Ascomycota (50.3%)and Basidiomycota (48.8%). The functional metabolic activity of the experimental group was lower than that of the control group. CONCLUSION The composition and abundance of VLBWI intestinal fungal showed several alterations during the first 2 months of life. The prediction of gut microbiota function suggests that intestinal metabolic function may be altered in VLBWI. WHAT IS KNOWN • A limited number of studies has been found that symbiont fungi may be able to calibrate host immunological responses, promote development of peripheral lymphoid organs, promote T cell responses, and even may be associated with the development of certain diseases, such as inflammatory bowel disease (IBD), NEC, and allergic diseases. However, previous studies on intestinal microecology have mainly focused on adults while neglecting the role of fungi in the gut of children due to the much lower abundance of intestinal fungi than bacteria, limitations of techniques for detecting fungi, the difficulty of obtaining samples, and the absence of largescale reference databases. WHAT IS NEW • In recent years, the discovery and development of fungal detection technologies such as 18s rDNA sequencing technology, Internal Transcribed Spacer(ITS), and DNA fingerprinting technology have further broadened the perspective on the impact of intestinal fungal exposure in early life.
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Affiliation(s)
- Ting Wang
- Health Science Center, Ningbo University, Ningbo, Zhejiang, China
| | - Yanbo Lu
- Pediatrics, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, China
| | - Junhua Wu
- Pediatrics, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, China.
| | - Beirong Yu
- Pediatrics, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, China
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Govrins M, Lass-Flörl C. Candida parapsilosis complex in the clinical setting. Nat Rev Microbiol 2024; 22:46-59. [PMID: 37674021 DOI: 10.1038/s41579-023-00961-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2023] [Indexed: 09/08/2023]
Abstract
Representatives of the Candida parapsilosis complex are important yeast species causing human infections, including candidaemia as one of the leading diseases. This complex comprises C. parapsilosis, Candida orthopsilosis and Candida metapsilosis, and causes a wide range of clinical presentations from colonization to superficial and disseminated infections with a high prevalence in preterm-born infants and the potential to cause outbreaks in hospital settings. Compared with other Candida species, the C. parapsilosis complex shows high minimal inhibitory concentrations for echinocandin drugs due to a naturally occurring FKS1 polymorphism. The emergence of clonal outbreaks of strains with resistance to commonly used antifungals, such as fluconazole, is causing concern. In this Review, we present the latest medical data covering epidemiology, diagnosis, resistance and current treatment approaches for the C. parapsilosis complex. We describe its main clinical manifestations in adults and children and highlight new treatment options. We compare the three sister species, examining key elements of microbiology and clinical characteristics, including the population at risk, disease manifestation and colonization status. Finally, we provide a comprehensive resource for clinicians and researchers focusing on Candida species infections and the C. parapsilosis complex, aiming to bridge the emerging translational knowledge and future therapeutic challenges associated with this human pathogen.
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Affiliation(s)
- Miriam Govrins
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Cornelia Lass-Flörl
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria.
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Han Z, Min Y, Pang K, Wu D. Therapeutic Approach Targeting Gut Microbiome in Gastrointestinal Infectious Diseases. Int J Mol Sci 2023; 24:15654. [PMID: 37958637 PMCID: PMC10650060 DOI: 10.3390/ijms242115654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/20/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
While emerging evidence highlights the significance of gut microbiome in gastrointestinal infectious diseases, treatments like Fecal Microbiota Transplantation (FMT) and probiotics are gaining popularity, especially for diarrhea patients. However, the specific role of the gut microbiome in different gastrointestinal infectious diseases remains uncertain. There is no consensus on whether gut modulation therapy is universally effective for all such infections. In this comprehensive review, we examine recent developments of the gut microbiome's involvement in several gastrointestinal infectious diseases, including infection of Helicobacter pylori, Clostridium difficile, Vibrio cholerae, enteric viruses, Salmonella enterica serovar Typhimurium, Pseudomonas aeruginosa Staphylococcus aureus, Candida albicans, and Giardia duodenalis. We have also incorporated information about fungi and engineered bacteria in gastrointestinal infectious diseases, aiming for a more comprehensive overview of the role of the gut microbiome. This review will provide insights into the pathogenic mechanisms of the gut microbiome while exploring the microbiome's potential in the prevention, diagnosis, prediction, and treatment of gastrointestinal infections.
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Affiliation(s)
- Ziying Han
- Department of Gastroenterology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Dongcheng District, Beijing 100730, China
| | - Yiyang Min
- Peking Union Medical College, Beijing 100730, China
| | - Ke Pang
- Peking Union Medical College, Beijing 100730, China
| | - Dong Wu
- Department of Gastroenterology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Dongcheng District, Beijing 100730, China
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García-García J, Diez-Echave P, Yuste ME, Chueca N, García F, Cabeza-Barrera J, Fernández-Varón E, Gálvez J, Colmenero M, Rodríguez-Cabezas ME, Rodríguez-Nogales A, Morón R. Gut Microbiota Composition Can Predict Colonization by Multidrug-Resistant Bacteria in SARS-CoV-2 Patients in Intensive Care Unit: A Pilot Study. Antibiotics (Basel) 2023; 12:antibiotics12030498. [PMID: 36978365 PMCID: PMC10044413 DOI: 10.3390/antibiotics12030498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
The SARS-CoV-2 infection has increased the number of patients entering Intensive Care Unit (ICU) facilities and antibiotic treatments. Concurrently, the multi-drug resistant bacteria (MDRB) colonization index has risen. Considering that most of these bacteria are derived from gut microbiota, the study of its composition is essential. Additionally, SARS-CoV-2 infection may promote gut dysbiosis, suggesting an effect on microbiota composition. This pilot study aims to determine bacteria biomarkers to predict MDRB colonization risk in SARS-CoV-2 patients in ICUs. Seventeen adult patients with an ICU stay >48 h and who tested positive for SARS-CoV-2 infection were enrolled in this study. Patients were assigned to two groups according to routine MDRB colonization surveillance: non-colonized and colonized. Stool samples were collected when entering ICUs, and microbiota composition was determined through Next Generation Sequencing techniques. Gut microbiota from colonized patients presented significantly lower bacterial diversity compared with non-colonized patients (p < 0.05). Microbiota in colonized subjects showed higher abundance of Anaerococcus, Dialister and Peptoniphilus, while higher levels of Enterococcus, Ochrobactrum and Staphylococcus were found in non-colonized ones. Moreover, LEfSe analysis suggests an initial detection of Dialister propionicifaciens as a biomarker of MDRB colonization risk. This pilot study shows that gut microbiota profile can become a predictor biomarker for MDRB colonization in SARS-CoV-2 patients.
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Affiliation(s)
- Jorge García-García
- Department of Pharmacology, Center for Biomedical Research (CIBM), University of Granada, 18071 Granada, Spain
| | - Patricia Diez-Echave
- Department of Pharmacology, Center for Biomedical Research (CIBM), University of Granada, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain
| | - María Eugenia Yuste
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain
- Servicio de Medicina Intensiva, Hospital Universitario Clínico San Cecilio, 18016 Granada, Spain
| | - Natalia Chueca
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain
- Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERInfec), 18016 Granada, Spain
| | - Federico García
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain
- Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERInfec), 18016 Granada, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERInfec), 28029 Madrid, Spain
| | - Jose Cabeza-Barrera
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain
- Servicio Farmacia Hospitalaria, Hospital Universitario Clínico San Cecilio, 18016 Granada, Spain
| | - Emilio Fernández-Varón
- Department of Pharmacology, Center for Biomedical Research (CIBM), University of Granada, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain
| | - Julio Gálvez
- Department of Pharmacology, Center for Biomedical Research (CIBM), University of Granada, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
| | - Manuel Colmenero
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain
- Servicio de Medicina Intensiva, Hospital Universitario Clínico San Cecilio, 18016 Granada, Spain
- Correspondence: (M.C.); (M.E.R.-C.)
| | - Maria Elena Rodríguez-Cabezas
- Department of Pharmacology, Center for Biomedical Research (CIBM), University of Granada, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain
- Correspondence: (M.C.); (M.E.R.-C.)
| | - Alba Rodríguez-Nogales
- Department of Pharmacology, Center for Biomedical Research (CIBM), University of Granada, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain
| | - Rocío Morón
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain
- Servicio Farmacia Hospitalaria, Hospital Universitario Clínico San Cecilio, 18016 Granada, Spain
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Turunen J, Paalanne N, Reunanen J, Tapiainen T, Tejesvi MV. Development of gut mycobiome in infants and young children: a prospective cohort study. Pediatr Res 2023:10.1038/s41390-023-02471-y. [PMID: 36670159 PMCID: PMC10382308 DOI: 10.1038/s41390-023-02471-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/21/2022] [Accepted: 01/01/2023] [Indexed: 01/22/2023]
Abstract
BACKGROUND The composition of the gut fungal microbiome, mycobiome, is likely associated with human health. Yet, the development of gut mycobiome is poorly understood in infants and children. Here we investigate how perinatal events influence the development of gut mycobiome. METHODS In this prospective cohort study of 140 infants, we used ITS gene sequencing of fecal samples from birth to the age of 18 months. We compared gut mycobiome composition according to delivery mode and exposure to intrapartum antibiotics during vaginal delivery. RESULTS At birth, gut mycobiome were dominated by the genus Candida, at 6-month stool samples by Malassezia and Cystofilobasidium, and the 18-month stool samples by Trichosporon and unidentified fungi. Perinatal factors altered mycobiome. At 18 months, gut mycobiome of infants born vaginally consisted mostly of Trichosporon (32%) and unidentified fungi (31%), while those born via Cesarean section delivery samples had mycobiome dominated by Saccharomyces (50%). At the age of 18 months, those exposed to intrapartum antibiotics had mycobiome dominated by Trichosporon (66%) not seen in those unexposed to antibiotics. CONCLUSIONS Delivery mode and exposure to intrapartum antibiotic prophylaxis were markedly associated with gut mycobiome composition from birth to 18 months of age. IMPACT The composition of the gut mycobiome is likely associated with human health. Yet, the development of gut mycobiome is poorly understood in infants and children. In this prospective cohort study, delivery mode and exposure to intrapartum antibiotic prophylaxis were markedly associated with gut mycobiome composition from birth to 18 months of age. The impact of intrapartum antibiotic prophylaxis on fungal microbiome in vaginally born infants, previously shown to influence gut bacteriome composition, may be explained by the interaction between bacteria and fungi. Gut mycobiome composition likely deserves further investigation in relation to gut microbiome and health in children.
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Affiliation(s)
- Jenni Turunen
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland. .,Biocenter Oulu, University of Oulu, Oulu, Finland.
| | - Niko Paalanne
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland.,Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
| | - Justus Reunanen
- Biocenter Oulu, University of Oulu, Oulu, Finland.,Research Unit of Translational Medicine, University of Oulu, Oulu, Finland
| | - Terhi Tapiainen
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland.,Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
| | - Mysore V Tejesvi
- Biocenter Oulu, University of Oulu, Oulu, Finland.,Ecology and Genetics, Faculty of Science, University of Oulu, Oulu, Finland
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Azevedo MJ, Araujo R, Campos J, Campos C, Ferreira AF, Falcão-Pires I, Ramalho C, Zaura E, Pinto E, Sampaio-Maia B. Vertical Transmission and Antifungal Susceptibility Profile of Yeast Isolates from the Oral Cavity, Gut, and Breastmilk of Mother-Child Pairs in Early Life. Int J Mol Sci 2023; 24:ijms24021449. [PMID: 36674962 PMCID: PMC9867488 DOI: 10.3390/ijms24021449] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/06/2023] [Accepted: 01/07/2023] [Indexed: 01/13/2023] Open
Abstract
Yeast acquisition begins at birth; however, the contribution of the mother on yeast transmission to the offspring and associated resistance is yet to be clarified. The aim of this study was to explore the vertical transmission of yeasts and their antifungal susceptibility profile in early life. Oral, fecal, and breastmilk samples were collected from 73 mother-child pairs four to twelve weeks after delivery and cultured on Sabouraud dextrose agar with chloramphenicol. The isolates were identified by MALDI-TOF MS. The vertical transmission was studied by microsatellite genotyping. Antifungal susceptibility was determined for fluconazole, voriconazole, miconazole, anidulafungin, and nystatin by broth microdilution assay, following CLSI-M60 guidelines. A total of 129 isolates were identified from 53% mother-child pairs. We verified the vertical transmission of Candida albicans (n = three mother-child pairs) and Candida parapsilosis (n = one mother-child pair) strains, including an antifungal resistant strain transmitted from breastmilk to the gut of a child. Most isolates were susceptible to the tested antifungals, with the exception of four C. albicans isolates and one R. mucilaginosa isolate. The vertical transmission of yeasts happens in early life. This is the first work that demonstrated the role of the mother as a source of transmission of antifungal-resistant yeasts to the child.
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Affiliation(s)
- Maria João Azevedo
- INEB—Instituto Nacional de Engenharia Biomédica, 4150-177 Porto, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- Department of Preventive Dentistry, Academic Center for Dentistry Amsterdam, University of Amsterdam and Vrije Universiteit Amsterdam, 1081 LA Amsterdam, The Netherlands
| | - Ricardo Araujo
- INEB—Instituto Nacional de Engenharia Biomédica, 4150-177 Porto, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Joana Campos
- INEB—Instituto Nacional de Engenharia Biomédica, 4150-177 Porto, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Carla Campos
- Serviço de Patologia Clínica, Departamento de Patologia e Medicina Laboratorial, Instituto Português de Oncologia do Porto Francisco Gentil, 4200-072 Porto, Portugal
- Escola Superior de Saúde, Instituto Politécnico do Porto, 4200-072 Porto, Portugal
| | | | - Inês Falcão-Pires
- Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
| | - Carla Ramalho
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
- Department of Gynecology and Obstetrics, Centro Hospitalar Universitário de São João, 4200-319 Porto, Portugal
| | - Egija Zaura
- Department of Preventive Dentistry, Academic Center for Dentistry Amsterdam, University of Amsterdam and Vrije Universiteit Amsterdam, 1081 LA Amsterdam, The Netherlands
| | - Eugénia Pinto
- Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, 4450-208 Matosinhos, Portugal
| | - Benedita Sampaio-Maia
- INEB—Instituto Nacional de Engenharia Biomédica, 4150-177 Porto, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- Faculdade de Medicina Dentária, Universidade do Porto, 4200-393 Porto, Portugal
- Correspondence:
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Jacobsen ID. The Role of Host and Fungal Factors in the Commensal-to-Pathogen Transition of Candida albicans. CURRENT CLINICAL MICROBIOLOGY REPORTS 2023; 10:55-65. [PMID: 37151578 PMCID: PMC10154278 DOI: 10.1007/s40588-023-00190-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/16/2023] [Indexed: 05/09/2023]
Abstract
Abstract Purpose of Review The fungus Candida albicans has evolved to live in close association with warm-blooded hosts and is found frequently on mucosal surfaces of healthy humans. As an opportunistic pathogen, C. albicans can also cause mucosal and disseminated infections (candidiasis). This review describes the features that differentiate the fungus in the commensal versus pathogenic state and the main factors underlying C. albicans commensal-to-pathogen transition. Recent Findings Adhesion, invasion, and tissue damage are critical steps in the infection process. Especially invasion and damage require transcriptional and morphological changes that differentiate C. albicans in the pathogenic from the commensal state. While the commensal-to-pathogen transition has some conserved causes and features in the oral cavity, the female urogenital tract, and the gut, site-specific differences have been identified in recent years. Summary This review highlights how specific factors in the different mucosal niches affect development of candidiasis. Recent evidence suggests that colonization of the gut is not only a risk factor for systemic candidiasis but might also provide beneficial effects to the host.
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Affiliation(s)
- Ilse D. Jacobsen
- Research Group Microbial Immunology, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
- Institute of Microbiology, Friedrich Schiller University, Jena, Germany
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10
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Mochochoko BM, Pohl CH, O’Neill HG. Candida albicans-enteric viral interactions-The prostaglandin E 2 connection and host immune responses. iScience 2022; 26:105870. [PMID: 36647379 PMCID: PMC9839968 DOI: 10.1016/j.isci.2022.105870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The human microbiome comprises trillions of microorganisms residing within different mucosal cavities and across the body surface. The gut microbiota modulates host susceptibility to viral infections in several ways, and microbial interkingdom interactions increase viral infectivity within the gut. Candida albicans, a frequently encountered fungal species in the gut, produces highly structured biofilms and eicosanoids such as prostaglandin E2 (PGE2), which aid in viral protection and replication. These biofilms encompass viruses and provide a shield from antiviral drugs or the immune system. PGE2 is a key modulator of active inflammation with the potential to regulate interferon signaling upon microbial invasion or viral infections. In this review, we raise the perspective of gut interkingdom interactions involving C. albicans and enteric viruses, with a special focus on biofilms, PGE2, and viral replication. Ultimately, we discuss the possible implications of C. albicans-enteric virus associations on host immune responses, particularly the interferon signaling pathway.
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Affiliation(s)
- Bonang M. Mochochoko
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, 9301, South Africa
| | - Carolina H. Pohl
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, 9301, South Africa,Corresponding author
| | - Hester G. O’Neill
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, 9301, South Africa,Corresponding author
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Gehlhaar A, Inala A, Llivichuzhca-Loja D, Silva TN, Adegboye CY, O’Connell AE, Konnikova L. Insights into the Role of Commensal-Specific T Cells in Intestinal Inflammation. J Inflamm Res 2022; 15:1873-1887. [PMID: 35342295 PMCID: PMC8943607 DOI: 10.2147/jir.s288288] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/19/2022] [Indexed: 12/21/2022] Open
Abstract
Trillions of microorganisms exist in the human intestine as commensals and contribute to homeostasis through their interactions with the immune system. In this review, we use previous evidence from published papers to elucidate the involvement of commensal-specific T cells (CSTCs) in regulating intestinal inflammatory responses. CSTCs are generated centrally in the thymus or peripherally at mucosal interfaces and present as CD4+ or CD8+ T cells. Bacteria, fungi, and even viruses act commensally with humans, warranting consideration of CSTCs in this critical relationship. Dysregulation of this immunological balance can result in both intestinal inflammation or damaging autoimmune responses elsewhere in the body. Given the relative novelty of CSTCs in the literature, we aim to introduce the importance of their role in maintaining immune homeostasis at barrier sites such as the intestine.
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Affiliation(s)
- Arne Gehlhaar
- Department of Pediatrics, Yale University, New Haven, CT, USA
| | - Ashwin Inala
- Department of Pediatrics, Yale University, New Haven, CT, USA
| | | | - Tatiana N Silva
- Department of Pediatrics, Yale University, New Haven, CT, USA
| | - Comfort Y Adegboye
- Division of Newborn Medicine, Boston Children’s Hospital, Boston, MA, USA
| | - Amy E O’Connell
- Division of Newborn Medicine, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Liza Konnikova
- Department of Pediatrics, Yale University, New Haven, CT, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University, New Haven, CT, USA
- Program in Human and Translational Immunology, Yale University, New Haven, CT, USA
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12
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Musumeci S, Coen M, Leidi A, Schrenzel J. The human gut mycobiome and the specific role of Candida albicans: where do we stand, as clinicians? Clin Microbiol Infect 2021; 28:58-63. [PMID: 34363944 DOI: 10.1016/j.cmi.2021.07.034] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 07/08/2021] [Accepted: 07/22/2021] [Indexed: 12/21/2022]
Abstract
BACKGROUND The so-called 'mycobiome' has progressively acquired interest and increased the complexity of our understanding of the human gut microbiota. Several questions are arising concerning the role of fungi (and in particular of Candida albicans), the so-called 'mycobiome', that has been neglected for a long time and only recently gained interest within the scientific community. There is no consensus on mycobiome normobiosis because of its instability and variability. This review aims to raise awareness about this interesting topic and provide a framework to guide physicians faced with such questions. OBJECTIVES To summarize current knowledge and discuss current and potential implications of the mycobiome in clinical practice. SOURCES We performed a review of the existing literature in Medline Pubmed. CONTENT This review identifies several studies showing associations between specific mycobiome profiles and health. Fungi represent a significant biomass within the microbiota and several factors, such as diet, sex, age, co-morbidities, medications, immune status and inter-kingdom interactions, can influence its structure and population. The human gut mycobiota is indeed a key factor for several physiological processes (e.g. training of the immune system against infections) and pathological processes (e.g. immunological/inflammatory disorders, inflammatory bowel diseases, metabolic syndromes). Moreover, the mycobiome (and C. albicans in particular) could influence an even broader spectrum of conditions such as psychiatric diseases (depression, schizophrenia, bipolar disorder) or chronic viral infections (human immunodeficiency virus, hepatitis B virus); moreover, it could be implicated in tumorigenesis. IMPLICATIONS Candida albicans is a well-known opportunistic pathogen and a major component of the mycobiome but its role in the gastrointestinal tract is still poorly understood. From a potential screening biomarker to a key factor for several pathological processes, its presence could influence or even modify our clinical practice.
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Affiliation(s)
- Stefano Musumeci
- Service of Internal Medicine, Department of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Matteo Coen
- Service of Internal Medicine, Department of Medicine, Geneva University Hospitals, Geneva, Switzerland; Unit of Development and Research in Medical Education (UDREM), Faculty of Medicine, Geneva, Switzerland.
| | - Antonio Leidi
- Service of Internal Medicine, Department of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Jacques Schrenzel
- Bacteriology Laboratory, Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland; Genomic Research Laboratory, Department of Medicine, Geneva University Hospitals and University of Geneva, Geneva, Switzerland; Division of Infectious Diseases, Department of Medicine, Geneva University Hospitals, Geneva, Switzerland
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13
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Composition and Associations of the Infant Gut Fungal Microbiota with Environmental Factors and Childhood Allergic Outcomes. mBio 2021; 12:e0339620. [PMID: 34060330 PMCID: PMC8263004 DOI: 10.1128/mbio.03396-20] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Although often neglected in gut microbiota studies, recent evidence suggests that imbalanced, or dysbiotic, gut mycobiota (fungal microbiota) communities in infancy coassociate with states of bacterial dysbiosis linked to inflammatory diseases such as asthma. In the present study, we (i) characterized the infant gut mycobiota at 3 months and 1 year of age in 343 infants from the CHILD Cohort Study, (ii) defined associations among gut mycobiota community composition and environmental factors for the development of inhalant allergic sensitization (atopy) at age 5 years, and (iii) built a predictive model for inhalant atopy status at age 5 years using these data. We show that in Canadian infants, fungal communities shift dramatically in composition over the first year of life. Early-life environmental factors known to affect gut bacterial communities were also associated with differences in gut fungal community alpha diversity, beta diversity, and/or the relative abundance of specific fungal taxa. Moreover, these metrics differed among healthy infants and those who developed inhalant allergic sensitization (atopy) by age 5 years. Using a rationally selected set of early-life environmental factors in combination with fungal community composition at 1 year of age, we developed a machine learning logistic regression model that predicted inhalant atopy status at 5 years of age with 81% accuracy. Together, these data suggest an important role for the infant gut mycobiota in early-life immune development and indicate that early-life behavioral or therapeutic interventions have the potential to modify infant gut fungal communities, with implications for an infant's long-term health. IMPORTANCE Recent evidence suggests an immunomodulatory role for commensal fungi (mycobiota) in the gut, yet little is known about the composition and dynamics of early-life gut fungal communities. In this work, we show for the first time that the composition of the gut mycobiota of Canadian infants changes dramatically over the course of the first year of life, is associated with environmental factors such as geographical location, diet, and season of birth, and can be used in conjunction with knowledge of a small number of key early-life factors to predict inhalant atopy status at age 5 years. Our study highlights the importance of considering fungal communities as indicators or inciters of immune dysfunction preceding the onset of allergic disease and can serve as a benchmark for future studies aiming to examine infant gut fungal communities across birth cohorts.
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14
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Boutin RCT, Petersen C, Woodward SE, Serapio-Palacios A, Bozorgmehr T, Loo R, Chalanuchpong A, Cirstea M, Lo B, Huus KE, Barcik W, Azad MB, Becker AB, Mandhane PJ, Moraes TJ, Sears MR, Subbarao P, McNagny KM, Turvey SE, Finlay BB. Bacterial-fungal interactions in the neonatal gut influence asthma outcomes later in life. eLife 2021; 10:e67740. [PMID: 33876729 PMCID: PMC8075585 DOI: 10.7554/elife.67740] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 04/07/2021] [Indexed: 12/13/2022] Open
Abstract
Bacterial members of the infant gut microbiota and bacterial-derived short-chain fatty acids (SCFAs) have been shown to be protective against childhood asthma, but a role for the fungal microbiota in asthma etiology remains poorly defined. We recently reported an association between overgrowth of the yeast Pichia kudriavzevii in the gut microbiota of Ecuadorian infants and increased asthma risk. In the present study, we replicated these findings in Canadian infants and investigated a causal association between early life gut fungal dysbiosis and later allergic airway disease (AAD). In a mouse model, we demonstrate that overgrowth of P. kudriavzevii within the neonatal gut exacerbates features of type-2 and -17 inflammation during AAD later in life. We further show that P. kudriavzevii growth and adherence to gut epithelial cells are altered by SCFAs. Collectively, our results underscore the potential for leveraging inter-kingdom interactions when designing putative microbiota-based asthma therapeutics.
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Affiliation(s)
- Rozlyn CT Boutin
- Department of Microbiology and Immunology, University of British ColumbiaVancouverCanada
- Michael Smith Laboratories, University of British ColumbiaVancouverCanada
| | - Charisse Petersen
- Michael Smith Laboratories, University of British ColumbiaVancouverCanada
| | - Sarah E Woodward
- Department of Microbiology and Immunology, University of British ColumbiaVancouverCanada
- Michael Smith Laboratories, University of British ColumbiaVancouverCanada
| | | | - Tahereh Bozorgmehr
- Michael Smith Laboratories, University of British ColumbiaVancouverCanada
| | - Rachelle Loo
- Department of Microbiology and Immunology, University of British ColumbiaVancouverCanada
- Michael Smith Laboratories, University of British ColumbiaVancouverCanada
| | - Alina Chalanuchpong
- Department of Microbiology and Immunology, University of British ColumbiaVancouverCanada
- Michael Smith Laboratories, University of British ColumbiaVancouverCanada
| | - Mihai Cirstea
- Department of Microbiology and Immunology, University of British ColumbiaVancouverCanada
- Michael Smith Laboratories, University of British ColumbiaVancouverCanada
| | - Bernard Lo
- Department of Microbiology and Immunology, University of British ColumbiaVancouverCanada
| | - Kelsey E Huus
- Department of Microbiology and Immunology, University of British ColumbiaVancouverCanada
- Michael Smith Laboratories, University of British ColumbiaVancouverCanada
| | - Weronika Barcik
- Michael Smith Laboratories, University of British ColumbiaVancouverCanada
| | - Meghan B Azad
- Children’s Hospital Research Institute of Manitoba and Department of Pediatrics and Child Health, University of ManitobaWinnipegMBCanada
| | - Allan B Becker
- Children’s Hospital Research Institute of Manitoba and Department of Pediatrics and Child Health, University of ManitobaWinnipegMBCanada
| | - Piush J Mandhane
- Department of Pediatrics, University of AlbertaEdmontonCanada
- School of Public Health, University of AlbertaEdmontonCanada
| | | | | | - Padmaja Subbarao
- The Hospital for Sick ChildrenTorontoCanada
- Department of Pediatrics, University of TorontoTorontoCanada
| | - Kelly M McNagny
- Department of Biomedical Engineering, University of British ColumbiaVancouverCanada
- Department of Medical Genetics University of British ColumbiaVancouverCanada
| | - Stuart E Turvey
- Department of Microbiology and Immunology, University of British ColumbiaVancouverCanada
- Department of Pediatrics, University of British ColumbiaVancouverCanada
| | - B Brett Finlay
- Department of Microbiology and Immunology, University of British ColumbiaVancouverCanada
- Michael Smith Laboratories, University of British ColumbiaVancouverCanada
- Department of Biochemistry and Molecular Biology, University of British ColumbiaVancouverCanada
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15
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Scheffold A, Bacher P, LeibundGut-Landmann S. T cell immunity to commensal fungi. Curr Opin Microbiol 2020; 58:116-123. [PMID: 33120172 DOI: 10.1016/j.mib.2020.09.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/12/2020] [Accepted: 09/15/2020] [Indexed: 02/07/2023]
Abstract
Fungi are an important part of the microbiota in healthy barrier tissues. Fungal dysbiosis in turn is associated with local and distal inflammatory diseases. Recent advances have shed light on the antigen-specific IL-17-dependent mechanisms that regulate fungal commensalism and prevent fungal overgrowth during homeostasis. Progress in our understanding of species-specific differences in fungus-host interactions provides new hypotheses of why Candida albicans-targeting T cells exceed those directed against other fungal species in the human T cell repertoire. Importantly, C. albicans-specific Th17 cells can also contribute to immune pathology in distant organs such as the lung via cross-reaction with heterologous antigens.
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Affiliation(s)
- Alexander Scheffold
- Institute of Immunology, Christian-Albrechts Universität zu Kiel and Universitätsklinik Schleswig-Holstein, Kiel, Germany
| | - Petra Bacher
- Institute of Immunology, Christian-Albrechts Universität zu Kiel and Universitätsklinik Schleswig-Holstein, Kiel, Germany; Institute of Clinical Molecular Biology, Christian-Albrechts Universität zu Kiel, Kiel, Germany
| | - Salomé LeibundGut-Landmann
- Section of Immunology, Vetsuisse Faculty, University of Zürich, Switzerland; Institute of Experimental Immunology, University of Zürich, Switzerland.
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16
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Choy A, Freedberg DE. Impact of microbiome-based interventions on gastrointestinal pathogen colonization in the intensive care unit. Therap Adv Gastroenterol 2020; 13:1756284820939447. [PMID: 32733601 PMCID: PMC7370550 DOI: 10.1177/1756284820939447] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 06/15/2020] [Indexed: 02/04/2023] Open
Abstract
In the intensive care unit (ICU), colonization of the gastrointestinal tract by potentially pathogenic bacteria is common and often precedes clinical infection. Though effective in the short term, traditional antibiotic-based decolonization methods may contribute to rising resistance in the long term. Novel therapies instead focus on restoring gut microbiome equilibrium to achieve pathogen colonization resistance. This review summarizes the existing data regarding microbiome-based approaches to gastrointestinal pathogen colonization in ICU patients with a focus on prebiotics, probiotics, and synbiotics.
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Affiliation(s)
| | - Daniel E. Freedberg
- Division of Digestive and Liver Diseases, Columbia University Medical Center, New York, NY, USA
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17
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Romo JA, Kumamoto CA. On Commensalism of Candida. J Fungi (Basel) 2020; 6:jof6010016. [PMID: 31963458 PMCID: PMC7151168 DOI: 10.3390/jof6010016] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 01/13/2020] [Accepted: 01/15/2020] [Indexed: 01/09/2023] Open
Abstract
Candida species are both opportunistic fungal pathogens and common members of the human mycobiome. Over the years, the main focus of the fungal field has been on understanding the pathogenic potential and disease manifestation of these organisms. Therefore, understanding of their commensal lifestyle, interactions with host epithelial barriers, and initial transition into pathogenesis is less developed. In this review, we will describe the current knowledge on the commensal lifestyle of these fungi, how they are able to adhere to and colonize host epithelial surfaces, compete with other members of the microbiota, and interact with the host immune response, as well as their transition into opportunistic pathogens by invading the gastrointestinal epithelium.
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