601
|
Ghannoum MA, Mukherjee PK. The Human Mycobiome and its Impact on Health and Disease. CURRENT FUNGAL INFECTION REPORTS 2013. [DOI: 10.1007/s12281-013-0162-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
|
602
|
Sakko M, Moore C, Novak-Frazer L, Rautemaa V, Sorsa T, Hietala P, Järvinen A, Bowyer P, Tjäderhane L, Rautemaa R. 2-hydroxyisocaproic acid is fungicidal for Candida and Aspergillus species. Mycoses 2013; 57:214-21. [PMID: 24125484 DOI: 10.1111/myc.12145] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 09/05/2013] [Accepted: 09/13/2013] [Indexed: 11/30/2022]
Abstract
The amino acid derivative 2-hydroxyisocaproic acid (HICA) is a nutritional additive used to increase muscle mass. Low levels can be detected in human plasma as a result of leucine metabolism. It has broad antibacterial activity but its efficacy against pathogenic fungi is not known. The aim was to test the efficacy of HICA against Candida and Aspergillus species. Efficacy of HICA against 19 clinical and reference isolates representing five Candida and three Aspergillus species with variable azole antifungal sensitivity profiles was tested using a microdilution method. The concentrations were 18, 36 and 72 mg ml(-1) . Growth was determined spectrophotometrically for Candida isolates and by visual inspection for Aspergillus isolates, viability was tested by culture and impact on morphology by microscopy. HICA of 72 mg ml(-1) was fungicidal against all Candida and Aspergillus fumigatus and Aspergillus terreus isolates. Lower concentrations were fungistatic. Aspergillus flavus was not inhibited by HICA. HICA inhibited hyphal formation in susceptible Candida albicans and A. fumigatus isolates and affected cell wall integrity. In conclusion, HICA has broad antifungal activity against Candida and Aspergillus at concentrations relevant for topical therapy. As a fungicidal agent with broad-spectrum bactericidal activity, it may be useful in the topical treatment of multispecies superficial infections.
Collapse
Affiliation(s)
- M Sakko
- Finnish Doctoral Program of Oral Sciences, Turku, Finland; Institute of Dentistry, University of Oulu, Oulu, Finland; Institute of Dentistry, University of Helsinki, Helsinki, Finland
| | | | | | | | | | | | | | | | | | | |
Collapse
|
603
|
Murine models of Candida gastrointestinal colonization and dissemination. EUKARYOTIC CELL 2013; 12:1416-22. [PMID: 24036344 DOI: 10.1128/ec.00196-13] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Ninety-five percent of infectious agents enter through exposed mucosal surfaces, such as the respiratory and gastrointestinal (GI) tracts. The human GI tract is colonized with trillions of commensal microbes, including numerous Candida spp. Some commensal microbes in the GI tract can cause serious human infections under specific circumstances, typically involving changes in the gut environment and/or host immune conditions. Therefore, utilizing animal models of fungal GI colonization and dissemination can lead to significant insights into the complex pathophysiology of transformation from a commensal organism to a pathogen and host-pathogen interactions. This paper will review the methodologic approaches used for modeling GI colonization versus dissemination, the insights learned from these models, and finally, possible future directions using these animal modeling systems.
Collapse
|
604
|
Garsin DA, Lorenz MC. Candida albicans and Enterococcus faecalis in the gut: synergy in commensalism? Gut Microbes 2013; 4:409-15. [PMID: 23941906 PMCID: PMC3839987 DOI: 10.4161/gmic.26040] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The fungus Candida albicans and the gram-positive bacterium Enterococcus faecalis are both normal residents of the human gut microbiome and cause opportunistic disseminated infections in immunocompromised individuals. Using a nematode infection model, we recently showed that co-infection resulted in less pathology and less mortality than infection with either species alone and this was partly explained by an interkingdom signaling event in which a bacterial-derived product inhibits hyphal morphogenesis of C. albicans. In this addendum we discuss these findings in the contest of other described bacterial-fungal interactions and recent data suggesting a potentially synergistic relationship between these two species in the mouse gut as well. We suggest that E. faecalis and C. albicans promote a mutually beneficial association with the host, in effect choosing a commensal lifestyle over a pathogenic one.
Collapse
|
605
|
|
606
|
Huang YJ, Charlson ES, Collman RG, Colombini-Hatch S, Martinez FD, Senior RM. The role of the lung microbiome in health and disease. A National Heart, Lung, and Blood Institute workshop report. Am J Respir Crit Care Med 2013; 187:1382-7. [PMID: 23614695 DOI: 10.1164/rccm.201303-0488ws] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Study of the human lung microbiome in the context of pulmonary health and disease is an area of emerging research interest that is being driven by several contributing factors. These factors include increased recognition of the diversity of human-associated microbiota, their roles in health and in diseases associated with chronic inflammation, and advancements in technologies and tools that have facilitated such discoveries about the microbiota in organ systems outside of the lung. Therefore, the overarching goals of lung microbiome research are: to identify and characterize microbial populations associated with the respiratory tract and lungs; to understand their roles in lung health and disease; and, we hope, to allow the development of improved approaches for diagnosing and treating chronic respiratory diseases in which the microbiome has a role. Recent studies of the lung microbiome have yielded a number of interesting findings but also highlighted questions and challenges for researchers and clinicians. In December 2011, the National Heart, Lung, and Blood Institute convened a workshop to identify key issues and areas for further attention or development to advance research on the lung microbiome. Current knowledge and the state of research on the lung and related areas of human microbiome investigation were reviewed and discussed.
Collapse
Affiliation(s)
- Yvonne J Huang
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | | | | | | | | | | |
Collapse
|
607
|
Hoarau G, Colombel JF, Poulain D, Sendid B. Implication de la flore fongique intestinale dans le développement de la maladie de Crohn. Med Sci (Paris) 2013; 29:691-3. [DOI: 10.1051/medsci/2013298004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
608
|
Angebault C, Djossou F, Abélanet S, Permal E, Ben Soltana M, Diancourt L, Bouchier C, Woerther PL, Catzeflis F, Andremont A, d'Enfert C, Bougnoux ME. Candida albicans Is Not Always the Preferential Yeast Colonizing Humans: A Study in Wayampi Amerindians. J Infect Dis 2013; 208:1705-16. [DOI: 10.1093/infdis/jit389] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
609
|
Abstract
The mycobiome, referring primarily to the fungal biota in an environment, is an important component of the human microbiome. Despite its importance, it has remained understudied. New culture-independent approaches to determine microbial diversity, such as next-generation sequencing methods, are greatly broadening our view of fungal importance. An integrative analysis of current studies shows that different body sites harbor specific fungal populations, and that diverse mycobiome patterns are associated with various diseases. By interfacing with other biomes, as well as with the host, the mycobiome probably contributes to the progression of fungus-associated diseases and plays an important role in health and disease.
Collapse
Affiliation(s)
- Lijia Cui
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine; Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Elodie Ghedin
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
- Department of Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| |
Collapse
|
610
|
Abstract
The mycobiome, referring primarily to the fungal biota in an environment, is an important component of the human microbiome. Despite its importance, it has remained understudied. New culture-independent approaches to determine microbial diversity, such as next-generation sequencing methods, are greatly broadening our view of fungal importance. An integrative analysis of current studies shows that different body sites harbor specific fungal populations, and that diverse mycobiome patterns are associated with various diseases. By interfacing with other biomes, as well as with the host, the mycobiome probably contributes to the progression of fungus-associated diseases and plays an important role in health and disease.
Collapse
Affiliation(s)
- Lijia Cui
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine; Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Elodie Ghedin
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA ; Department of Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| |
Collapse
|
611
|
Erturk-Hasdemir D, Kasper DL. Resident commensals shaping immunity. Curr Opin Immunol 2013; 25:450-5. [PMID: 23830047 DOI: 10.1016/j.coi.2013.06.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Revised: 06/05/2013] [Accepted: 06/06/2013] [Indexed: 02/07/2023]
Abstract
All animals coexist with myriad commensal microorganisms in a symbiotic relationship that plays a key role in health and disease. Continuous commensal-host interactions profoundly affect the development and regulation of the host's immune system. The complex interaction of the commensal microbiota with the immune system is a topic of substantial interest. An understanding of these interactions and the mechanisms through which commensal microbes actively shape host immunity may yield new insights into the pathogenesis of many immune-mediated diseases and lead to new prophylactic and therapeutic interventions. This review examines recent advances in this field and their potential implications not just for the colonized tissues but also for the entire immune system.
Collapse
Affiliation(s)
- Deniz Erturk-Hasdemir
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Room 1056C, Boston, MA 02115, United States
| | | |
Collapse
|
612
|
Molecular fingerprints to identify Candida species. BIOMED RESEARCH INTERNATIONAL 2013; 2013:923742. [PMID: 23844370 PMCID: PMC3703398 DOI: 10.1155/2013/923742] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 05/30/2013] [Accepted: 06/06/2013] [Indexed: 11/17/2022]
Abstract
A wide range of molecular techniques have been developed for genotyping Candida species. Among them, multilocus sequence typing (MLST) and microsatellite length polymorphisms (MLP) analysis have recently emerged. MLST relies on DNA sequences of internal regions of various independent housekeeping genes, while MLP identifies microsatellite instability. Both methods generate unambiguous and highly reproducible data. Here, we review the results achieved by using these two techniques and also provide a brief overview of a new method based on high-resolution DNA melting (HRM). This method identifies sequence differences by subtle deviations in sample melting profiles in the presence of saturating fluorescent DNA binding dyes.
Collapse
|
613
|
Hoffmann C, Dollive S, Grunberg S, Chen J, Li H, Wu GD, Lewis JD, Bushman FD. Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents. PLoS One 2013; 8:e66019. [PMID: 23799070 PMCID: PMC3684604 DOI: 10.1371/journal.pone.0066019] [Citation(s) in RCA: 502] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 04/30/2013] [Indexed: 12/12/2022] Open
Abstract
Diet influences health as a source of nutrients and toxins, and by shaping the composition of resident microbial populations. Previous studies have begun to map out associations between diet and the bacteria and viruses of the human gut microbiome. Here we investigate associations of diet with fungal and archaeal populations, taking advantage of samples from 98 well-characterized individuals. Diet was quantified using inventories scoring both long-term and recent diet, and archaea and fungi were characterized by deep sequencing of marker genes in DNA purified from stool. For fungi, we found 66 genera, with generally mutually exclusive presence of either the phyla Ascomycota or Basiodiomycota. For archaea, Methanobrevibacter was the most prevalent genus, present in 30% of samples. Several other archaeal genera were detected in lower abundance and frequency. Myriad associations were detected for fungi and archaea with diet, with each other, and with bacterial lineages. Methanobrevibacter and Candida were positively associated with diets high in carbohydrates, but negatively with diets high in amino acids, protein, and fatty acids. A previous study emphasized that bacterial population structure was associated primarily with long-term diet, but high Candida abundance was most strongly associated with the recent consumption of carbohydrates. Methobrevibacter abundance was associated with both long term and recent consumption of carbohydrates. These results confirm earlier targeted studies and provide a host of new associations to consider in modeling the effects of diet on the gut microbiome and human health.
Collapse
Affiliation(s)
- Christian Hoffmann
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiania, Goiás, Brazil
| | - Serena Dollive
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Stephanie Grunberg
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Jun Chen
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Hongzhe Li
- Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Gary D. Wu
- Division of Gastroenterology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail: (GDW); (JDL); (FDB)
| | - James D. Lewis
- Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail: (GDW); (JDL); (FDB)
| | - Frederic D. Bushman
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail: (GDW); (JDL); (FDB)
| |
Collapse
|
614
|
Iliev ID, Underhill DM. Striking a balance: fungal commensalism versus pathogenesis. Curr Opin Microbiol 2013; 16:366-73. [PMID: 23756050 DOI: 10.1016/j.mib.2013.05.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 05/09/2013] [Accepted: 05/13/2013] [Indexed: 02/06/2023]
Abstract
The environment is suffused with nearly countless types of fungi, and our immune systems must be tuned to cope with constant exposure to them. In addition, it is becoming increasingly clear that many surfaces of our bodies are colonized with complex populations of fungi (the mycobiome) in the same way that they are colonized with complex populations of bacteria. The immune system must tolerate colonization with commensal fungi but defend against fungal invasion. Truly life-threatening fungal infections are common only when this balance is disrupted through, for example, profound immunosuppression or genetic mutation. Recent studies have begun to shed light on how this balance is established and maintained, and suggest future studies on the role of fungi in homeostatic conditions.
Collapse
Affiliation(s)
- Iliyan D Iliev
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
| | | |
Collapse
|
615
|
D'Amato-Palumbo S, Kaplan AA, Feinn RS, Lalla RV. Retrospective study of microorganisms associated with vascular access infections in hemodialysis patients. Oral Surg Oral Med Oral Pathol Oral Radiol 2013; 115:56-61. [PMID: 23217535 DOI: 10.1016/j.oooo.2012.08.445] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Revised: 08/08/2012] [Accepted: 08/11/2012] [Indexed: 12/17/2022]
Abstract
OBJECTIVE The aim of this study was to assess microorganisms associated with vascular access-associated infections (VAIs) in hemodialysis patients, with respect to possible origin from the mouth. STUDY DESIGN A retrospective and comparative analysis of the microbes associated with VAI in hemodialysis patients treated during a 10-year period was performed with the Human Oral Microbiome Database (HOMD). RESULTS Of 218 patient records identified, 65 patients collectively experienced 115 VAI episodes. The most common microorganisms involved were Staphylococcus aureus (49.6% of infections), Staphylococcus epidermidis (10.4%), Serratia marcescens (10.4%), Pseudomonas aeruginosa (9.6%), and Enterococcus faecalis/fecum (8.7%). None of these was found in ≥1% of HOMD clone libraries, indicating that they very rarely colonize the teeth or plaque. CONCLUSIONS Most VAIs were associated with microorganisms more likely to originate from other body sites than from the oral cavity. The risk of a VAI being caused by microorganisms originating from the oral cavity is very small.
Collapse
Affiliation(s)
- Sandra D'Amato-Palumbo
- Dental Hygiene Program, College of Arts and Sciences, University of New Haven, West Haven, Connecticut, USA
| | | | | | | |
Collapse
|
616
|
Topographic diversity of fungal and bacterial communities in human skin. Nature 2013; 498:367-70. [PMID: 23698366 PMCID: PMC3711185 DOI: 10.1038/nature12171] [Citation(s) in RCA: 765] [Impact Index Per Article: 69.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 04/09/2013] [Indexed: 02/07/2023]
Abstract
Traditional culture-based methods have incompletely defined the etiology of common recalcitrant human fungal skin diseases including athlete’s foot and toenail infections. Skin protects humans from invasion by pathogenic microorganisms, while providing a home for diverse commensal microbiota1. Bacterial genomic sequence data have generated novel hypotheses about species and community structures underlying human disorders2,3,4. However, microbial diversity is not limited to bacteria; microorganisms such as fungi also play major roles in microbial community stability, human health and disease5. Genomic methodologies to identify fungal species and communities have been limited compared with tools available for bacteria6. Fungal evolution can be reconstructed with phylogenetic markers, including ribosomal RNA gene regions and other highly conserved genes7. Here, we sequenced and analyzed fungal communities of 14 skin sites in 10 healthy adults. Eleven core body and arm sites were dominated by Malassezia fungi, with species-level classifications revealing greater topographical resolution between sites. By contrast, three foot sites, plantar heel, toenail, and toeweb, exhibited tremendous fungal diversity. Concurrent analysis of bacterial and fungal communities demonstrated that skin physiologic attributes and topography differentially shape these two microbial communities. These results provide a framework for future investigation of interactions between pathogenic and commensal fungal and bacterial communities in maintaining human health and contributing to disease pathogenesis.
Collapse
|
617
|
Huffnagle GB, Noverr MC. The emerging world of the fungal microbiome. Trends Microbiol 2013; 21:334-41. [PMID: 23685069 DOI: 10.1016/j.tim.2013.04.002] [Citation(s) in RCA: 351] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 03/27/2013] [Accepted: 04/15/2013] [Indexed: 02/06/2023]
Abstract
The study of the fungal microbiota ('mycobiome') is a new and rapidly emerging field that lags behind our understanding of the bacterial microbiome. Every human has fungi as part of their microbiota, but the total number of fungal cells is orders of magnitude smaller than that of the bacterial microbiota. However, the impact of the mycobiome on human health is significant, especially as a reservoir for blooms of pathogenic microbes when the host is compromised and as a potential cofactor in inflammatory diseases and metabolic disorders.
Collapse
Affiliation(s)
- Gary B Huffnagle
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.
| | | |
Collapse
|
618
|
Duarte S, Seena S, Bärlocher F, Pascoal C, Cássio F. A decade's perspective on the impact of DNA sequencing on aquatic hyphomycete research. FUNGAL BIOL REV 2013. [DOI: 10.1016/j.fbr.2013.02.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
619
|
Back-Brito GN, da Mota AJ, de Souza Bernardes LÂ, Takamune SS, Prado EDFGB, Cordás TA, Balducci I, da Nobrega FG, Koga-Ito CY. Effects of eating disorders on oral fungal diversity. Oral Surg Oral Med Oral Pathol Oral Radiol 2013; 113:512-7. [PMID: 22668429 DOI: 10.1016/j.oooo.2011.10.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Revised: 09/25/2011] [Accepted: 10/03/2011] [Indexed: 01/13/2023]
Abstract
BACKGROUND The eating disorders anorexia and bulimia nervosa can cause several systemic and oral alterations related to poor nutrition and induced vomiting; however, the oral microflora of these patients is poorly studied. OBJECTIVE The aim of this study was to evaluate fungal microflora in the oral cavity of these patients by culture-dependent and culture-independent methods. STUDY DESIGN Oral rinse samples were cultured to assess the prevalence of Candida species, and the isolates were identified by API system. Microorganism counts were compared by the Mann-Whitney test (5%). Ribotyping, a type of molecular analysis, was performed by sequencing the D1/D2 regions of 28S rRNA. RESULTS Our results demonstrated that the eating disorder group showed higher oral Candida spp. prevalence with culture-dependent methods and higher species diversity with culture-independent methods. CONCLUSIONS Eating disorders can lead to an increased oral Candida carriage. Culture-independent identification found greater fungal diversity than culture-dependent methods.
Collapse
Affiliation(s)
- Graziella Nuernberg Back-Brito
- Department of Biosciences and Oral Diagnosis, São José dos Campos Dental School, University Estadual Paulista, São José dos Campos, Brazil.
| | | | | | | | | | | | | | | | | |
Collapse
|
620
|
Rickerts V, McCormick Smith I, Mousset S, Kommedal O, Fredricks DN. Deciphering the aetiology of a mixed fungal infection by broad-range PCR with sequencing and fluorescence in situ hybridisation. Mycoses 2013; 56:681-6. [PMID: 23560622 DOI: 10.1111/myc.12083] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 03/18/2013] [Accepted: 03/21/2013] [Indexed: 11/30/2022]
Abstract
Simultaneous infections with multiple fungi may be misinterpreted as monomicrobial infections by current diagnostics with ramifications for the choice of antimicrobial agents that may impact patient outcomes. The application of molecular methods on tissue samples may be useful to decipher the aetiology of mixed fungal infections. We present a leukaemic patient who died from sepsis due to candidaemia. The postmortem examination documented fungal elements in lung tissue. Fungal DNA was amplified from the lung sample by broad-range PCR assays targeting the 28S ribosomal RNA gene or the internal transcribed spacer 2 (ITS-2). Fluorescence in situ hybridisation (FISH) using differentially labelled fungal probes was applied on the tissue. Sequencing identified the PCR amplicons as Aspergillus fumigatus (28S assay) and Candida tropicalis (ITS-2 assay). As a chromatogram suggested mixed amplicons, the Isentio ripseq(®) tool for in silico analysis was applied and confirmed the presence of both amplicons in the PCR products of both assays. FISH confirmed the presence of Aspergillus and Candida within the infectious process, a prerequisite for inferring a causal relationship with the infection. The combination of broad-range PCR with sequence analysis and FISH applied on tissue samples is a powerful approach to identify the aetiology of invasive fungal infections, including mixed infections.
Collapse
Affiliation(s)
- V Rickerts
- Robert Koch Institut, FG 16, Berlin, Germany
| | | | | | | | | |
Collapse
|
621
|
Abstract
The animal and bacterial kingdoms have coevolved and coadapted in response to environmental selective pressures over hundreds of millions of years. The meta'omics revolution in both sequencing and its analytic pipelines is fostering an explosion of interest in how the gut microbiome impacts physiology and propensity to disease. Gut microbiome studies are inherently interdisciplinary, drawing on approaches and technical skill sets from the biomedical sciences, ecology, and computational biology. Central to unraveling the complex biology of environment, genetics, and microbiome interaction in human health and disease is a deeper understanding of the symbiosis between animals and bacteria. Experimental model systems, including mice, fish, insects, and the Hawaiian bobtail squid, continue to provide critical insight into how host-microbiota homeostasis is constructed and maintained. Here we consider how model systems are influencing current understanding of host-microbiota interactions and explore recent human microbiome studies.
Collapse
Affiliation(s)
- Aleksandar D. Kostic
- Harvard School of Public Health, Boston, Massachusetts 02115, USA
- Harvard Medical School, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
- The Broad Institute of Harvard and Massachusetts Institute of Technology, Boston, Massachusetts 02141, USA
| | - Michael R. Howitt
- Harvard School of Public Health, Boston, Massachusetts 02115, USA
- Harvard Medical School, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Wendy S. Garrett
- Harvard School of Public Health, Boston, Massachusetts 02115, USA
- Harvard Medical School, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
- The Broad Institute of Harvard and Massachusetts Institute of Technology, Boston, Massachusetts 02141, USA
| |
Collapse
|
622
|
Pérez JC, Kumamoto CA, Johnson AD. Candida albicans commensalism and pathogenicity are intertwined traits directed by a tightly knit transcriptional regulatory circuit. PLoS Biol 2013; 11:e1001510. [PMID: 23526879 PMCID: PMC3601966 DOI: 10.1371/journal.pbio.1001510] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 02/06/2013] [Indexed: 12/21/2022] Open
Abstract
The identification of regulators, circuits, and target genes employed by the fungus Candida albicans to thrive in disparate niches in a mammalian host reveals interconnection between commensal and pathogenic lifestyles. Systemic, life-threatening infections in humans are often caused by bacterial or fungal species that normally inhabit a different locale in our body, particularly mucosal surfaces. A hallmark of these opportunistic pathogens, therefore, is their ability to thrive in disparate niches within the host. In this work, we investigate the transcriptional circuitry and gene repertoire that enable the human opportunistic fungal pathogen Candida albicans to proliferate in two different niches. By screening a library of transcription regulator deletion strains in mouse models of intestinal colonization and systemic infection, we identified eight transcription regulators that play roles in at least one of these models. Using genome-wide chromatin immunoprecipitation, we uncovered a network comprising ∼800 target genes and a tightly knit transcriptional regulatory circuit at its core. The network is enriched with genes upregulated in C. albicans cells growing in the host. Our findings indicate that many aspects of commensalism and pathogenicity are intertwined and that the ability of this microorganism to colonize multiple niches relies on a large, integrated circuit. Our skin and mouth, as well as our genital and gastrointestinal tracts, are laden with microorganisms belonging to all three domains of life (bacteria, archaea, and eukaryotes). Much of the time these commensal microorganisms are not only harmless but provide advantages to us. However, when the host's defenses are compromised, some members of the normal flora, such as the fungus C. albicans, can cross the host's protective barriers and colonize virtually every internal organ causing life-threatening conditions. The environment found in the bloodstream and internal organs is presumably distinct from the mucosal surfaces where our flora typically resides. Whether opportunistic pathogens such as C. albicans rely on common or separate gene repertoires to thrive in each of these locales is largely unknown. To address this question we carried out genetic screens in mouse models that recapitulate niches where C. albicans thrives and used genome-wide experimental approaches to uncover the genes required to proliferate in each environment. In fact, the ability of C. albicans to colonize disparate niches within a mammalian host relies on a large, integrated circuit. Our observations suggest that at least some key gene circuits are not dedicated to one niche or another. Rather, thriving in various locales of the host seems to involve the complex regulation of multiple processes, which may allow C. albicans to adjust to different environments.
Collapse
Affiliation(s)
- J Christian Pérez
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America.
| | | | | |
Collapse
|
623
|
Gouba N, Raoult D, Drancourt M. Plant and fungal diversity in gut microbiota as revealed by molecular and culture investigations. PLoS One 2013; 8:e59474. [PMID: 23555039 PMCID: PMC3598745 DOI: 10.1371/journal.pone.0059474] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 02/18/2013] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Few studies describing eukaryotic communities in the human gut microbiota have been published. The objective of this study was to investigate comprehensively the repertoire of plant and fungal species in the gut microbiota of an obese patient. METHODOLOGY/PRINCIPAL FINDINGS A stool specimen was collected from a 27-year-old Caucasian woman with a body mass index of 48.9 who was living in Marseille, France. Plant and fungal species were identified using a PCR-based method incorporating 25 primer pairs specific for each eukaryotic phylum and universal eukaryotic primers targeting 18S rRNA, internal transcribed spacer (ITS) and a chloroplast gene. The PCR products amplified using these primers were cloned and sequenced. Three different culture media were used to isolate fungi, and these cultured fungi were further identified by ITS sequencing. A total of 37 eukaryotic species were identified, including a Diatoms (Blastocystis sp.) species, 18 plant species from the Streptophyta phylum and 18 fungal species from the Ascomycota, Basidiomycota and Chytridiocomycota phyla. Cultures yielded 16 fungal species, while PCR-sequencing identified 7 fungal species. Of these 7 species of fungi, 5 were also identified by culture. Twenty-one eukaryotic species were discovered for the first time in human gut microbiota, including 8 fungi (Aspergillus flavipes, Beauveria bassiana, Isaria farinosa, Penicillium brevicompactum, Penicillium dipodomyicola, Penicillium camemberti, Climacocystis sp. and Malassezia restricta). Many fungal species apparently originated from food, as did 11 plant species. However, four plant species (Atractylodes japonica, Fibraurea tinctoria, Angelica anomala, Mitella nuda) are used as medicinal plants. CONCLUSIONS/SIGNIFICANCE Investigating the eukaryotic components of gut microbiota may help us to understand their role in human health.
Collapse
Affiliation(s)
- Nina Gouba
- Aix Marseille Université, URMITE, UMR63, CNRS 7278, IRD 198, Inserm 1095, Marseille, France
| | - Didier Raoult
- Aix Marseille Université, URMITE, UMR63, CNRS 7278, IRD 198, Inserm 1095, Marseille, France
| | - Michel Drancourt
- Aix Marseille Université, URMITE, UMR63, CNRS 7278, IRD 198, Inserm 1095, Marseille, France
- * E-mail:
| |
Collapse
|
624
|
|
625
|
|
626
|
von Rosenvinge EC, Song Y, White JR, Maddox C, Blanchard T, Fricke WF. Immune status, antibiotic medication and pH are associated with changes in the stomach fluid microbiota. ISME JOURNAL 2013; 7:1354-66. [PMID: 23466701 DOI: 10.1038/ismej.2013.33] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The stomach acts as a barrier to ingested microbes, thereby influencing the microbial ecology of the entire gastrointestinal (GI) tract. The stomach microbiota and the role of human host and environmental factors, such as health status or medications, in shaping its composition remain largely unknown. We sought to characterize the bacterial and fungal microbiota in the stomach fluid in order to gain insights into the role of the stomach in GI homeostasis. Gastric fluid was collected from 25 patients undergoing clinically indicated upper endoscopy. DNA isolates were used for PCR amplification of bacterial 16S ribosomal RNA (rRNA) genes and fungal internal transcribed spacers (ITS). RNA isolates were used for 16S rRNA cDNA generation and subsequent PCR amplification. While all stomach fluid samples are dominated by the phyla Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria and Fusobacteria (>99% of sequence reads), the transcriptionally active microbiota shows significant reduction in Actinobacteria (34%) and increase in Campylobacter (444%) (P<0.003), specifically the oral commensal and suspected intestinal pathogen Campylobacter concisus. Bacterial but not fungal diversity is reduced by antibiotic treatment (28%; P<0.02), immunosuppression in transplant recipients and HIV/AIDS patients (42%; P<0.001) and gastric fluid pH >4 (70%; P<0.05). Immunosuppression correlates with decreased abundance of Prevotella (24%), Fusobacterium (2%) and Leptotrichia (6%) and increased abundance of Lactobacillus (3844%) (P<0.003). We have generated the first in-depth characterization of the human gastric fluid microbiota, using bacterial 16S rRNA gene and transcript, and fungal ITS amplicon sequencing and provide evidence for a significant impact of the host immune status on its composition with likely consequences for human health.
Collapse
Affiliation(s)
- Erik C von Rosenvinge
- Division of Gastroenterology and Hepatology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | | | | | | | | | | |
Collapse
|
627
|
Clavaud C, Jourdain R, Bar-Hen A, Tichit M, Bouchier C, Pouradier F, El Rawadi C, Guillot J, Ménard-Szczebara F, Breton L, Latgé JP, Mouyna I. Dandruff is associated with disequilibrium in the proportion of the major bacterial and fungal populations colonizing the scalp. PLoS One 2013; 8:e58203. [PMID: 23483996 PMCID: PMC3590157 DOI: 10.1371/journal.pone.0058203] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 01/31/2013] [Indexed: 01/18/2023] Open
Abstract
The bacterial and fungal communities associated with dandruff were investigated using culture-independent methodologies in the French subjects. The major bacterial and fungal species inhabiting the scalp subject’s were identified by cloning and sequencing of the conserved ribosomal unit regions (16S for bacterial and 28S-ITS for fungal) and were further quantified by quantitative PCR. The two main bacterial species found on the scalp surface were Propionibacterium acnes and Staphylococcus epidermidis, while Malassezia restricta was the main fungal inhabitant. Dandruff was correlated with a higher incidence of M. restricta and S. epidermidis and a lower incidence of P. acnes compared to the control population (p<0.05). These results suggested for the first time using molecular methods, that dandruff is linked to the balance between bacteria and fungi of the host scalp surface.
Collapse
Affiliation(s)
| | - Roland Jourdain
- Advanced Research, L’Oréal Research and Innovation, Aulnay sous Bois, France
| | - Avner Bar-Hen
- MAP5, UFR de Mathématiques et Informatique, Université Paris Descartes, Paris, France
| | - Magali Tichit
- PF1, Plateforme génomique, Institut Pasteur, Paris, France
| | | | - Florence Pouradier
- International General Direction of Hair Metiers, L’Oréal Research and Innovation, Saint-Ouen, France
| | - Charles El Rawadi
- Advanced Research, L’Oréal Research and Innovation, Aulnay sous Bois, France
| | - Jacques Guillot
- UMR BIPAR, Ecopham, Ecole Nationale Vétérinaire d’Alfort (ENVA),Maisons-Alfort, France
| | | | - Lionel Breton
- Advanced Research, L’Oréal Research and Innovation, Aulnay sous Bois, France
| | - Jean-Paul Latgé
- Unité des Aspergillus, Institut Pasteur, Paris, France
- * E-mail: (JPL); (IM)
| | - Isabelle Mouyna
- Unité des Aspergillus, Institut Pasteur, Paris, France
- * E-mail: (JPL); (IM)
| |
Collapse
|
628
|
Monteiro-da-Silva F, Sampaio-Maia B, Pereira MDL, Araujo R. Characterization of the oral fungal microbiota in smokers and non-smokers. Eur J Oral Sci 2013; 121:132-5. [PMID: 23489903 DOI: 10.1111/eos.12030] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2013] [Indexed: 12/01/2022]
Abstract
This study aimed to assess the effect of smoking on the biodiversity of the oral fungal microbiota of healthy young subjects, using an improved culture method that assesses both total and pathogenic viable fungi. Forty individuals (20 smokers and 20 non-smokers) were selected. All individuals presented fungal growth (100% for molds and 92.5% for yeasts), a prevalence higher than previously reported. The most commonly occurring molds were Penicillium sp., Aspergillus sp., and Cladosporium sp. Smokers presented significantly higher levels of yeasts and pathogenic molds than did non-smokers. No differences in fungal prevalence and diversity were observed in smokers and non-smokers following a 30-wk observation period. In conclusion, tobacco smoking may alter the oral mycobiota and facilitate colonization of the oral cavity with yeasts and pathogenic molds. The effect of chronic fungal colonization on the oral health of tobacco smokers cannot be neglected.
Collapse
|
629
|
Bertini A, De Bernardis F, Hensgens LAM, Sandini S, Senesi S, Tavanti A. Comparison of Candida parapsilosis, Candida orthopsilosis, and Candida metapsilosis adhesive properties and pathogenicity. Int J Med Microbiol 2013; 303:98-103. [PMID: 23403338 DOI: 10.1016/j.ijmm.2012.12.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 11/29/2012] [Accepted: 12/02/2012] [Indexed: 11/27/2022] Open
Abstract
Retrospective studies indicate that Candida metapsilosis and Candida orthopsilosis each represents 1-10% of the infections/colonisations attributed to C. parapsilosis by conventional biochemical tests. Little is known on the virulence properties of these fungi and on their role in the establishment/progression of the infection. In this study, the adhesive properties of clinical isolates belonging to the 'psilosis' species were assessed in an in vitro model of co-incubation with human buccal epithelial cells (HBECs). Ectophosphatase activity was also measured for all isolates, since the activity of this enzyme has previously been linked to adhesion properties in C. parapsilosis. The results indicate that whilst C. parapsilosis and C. orthopsilosis strains showed similar adhesion abilities, C. metapsilosis isolates displayed a significantly lower ability to adhere to HBECs (P<0.05). No evidence of a correlation between ectophosphatase activity and adhesion was observed, and this finding was also confirmed by phosphatase inhibition experiments. Experimental vaginal candidiasis induced in oestrogen-treated mice with representative isolates of the 3 species indicated that mice infected with C. metapsilosis displayed a reduced vaginal fungal burden, especially in the early stages of the infection. The overall findings confirm that C. orthopsilosis has a comparable behaviour to C. parapsilosis, whilst C. metapsilosis seems to possess a reduced virulence potential.
Collapse
|
630
|
Heinrichs G, Hübner I, Schmidt CK, de Hoog GS, Haase G. Analysis of Black Fungal Biofilms Occurring at Domestic Water Taps (I): Compositional Analysis Using Tag-Encoded FLX Amplicon Pyrosequencing. Mycopathologia 2013; 175:387-97. [DOI: 10.1007/s11046-013-9618-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 01/17/2013] [Indexed: 02/02/2023]
|
631
|
White JR, Maddox C, White O, Angiuoli SV, Fricke WF. CloVR-ITS: Automated internal transcribed spacer amplicon sequence analysis pipeline for the characterization of fungal microbiota. MICROBIOME 2013; 1:6. [PMID: 24451270 PMCID: PMC3869194 DOI: 10.1186/2049-2618-1-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 11/21/2012] [Indexed: 05/16/2023]
Abstract
BACKGROUND Besides the development of comprehensive tools for high-throughput 16S ribosomal RNA amplicon sequence analysis, there exists a growing need for protocols emphasizing alternative phylogenetic markers such as those representing eukaryotic organisms. RESULTS Here we introduce CloVR-ITS, an automated pipeline for comparative analysis of internal transcribed spacer (ITS) pyrosequences amplified from metagenomic DNA isolates and representing fungal species. This pipeline performs a variety of steps similar to those commonly used for 16S rRNA amplicon sequence analysis, including preprocessing for quality, chimera detection, clustering of sequences into operational taxonomic units (OTUs), taxonomic assignment (at class, order, family, genus, and species levels) and statistical analysis of sample groups of interest based on user-provided information. Using ITS amplicon pyrosequencing data from a previous human gastric fluid study, we demonstrate the utility of CloVR-ITS for fungal microbiota analysis and provide runtime and cost examples, including analysis of extremely large datasets on the cloud. We show that the largest fractions of reads from the stomach fluid samples were assigned to Dothideomycetes, Saccharomycetes, Agaricomycetes and Sordariomycetes but that all samples were dominated by sequences that could not be taxonomically classified. Representatives of the Candida genus were identified in all samples, most notably C. quercitrusa, while sequence reads assigned to the Aspergillus genus were only identified in a subset of samples. CloVR-ITS is made available as a pre-installed, automated, and portable software pipeline for cloud-friendly execution as part of the CloVR virtual machine package (http://clovr.org). CONCLUSION The CloVR-ITS pipeline provides fungal microbiota analysis that can be complementary to bacterial 16S rRNA and total metagenome sequence analysis allowing for more comprehensive studies of environmental and host-associated microbial communities.
Collapse
Affiliation(s)
- James Robert White
- Institute for Genome Sciences, University of Maryland School of Medicine, BioPark II - 801 West Baltimore Street, Baltimore, MD, 21201, USA
| | - Cynthia Maddox
- Institute for Genome Sciences, University of Maryland School of Medicine, BioPark II - 801 West Baltimore Street, Baltimore, MD, 21201, USA
| | - Owen White
- Institute for Genome Sciences, University of Maryland School of Medicine, BioPark II - 801 West Baltimore Street, Baltimore, MD, 21201, USA
| | - Samuel V Angiuoli
- Institute for Genome Sciences, University of Maryland School of Medicine, BioPark II - 801 West Baltimore Street, Baltimore, MD, 21201, USA
| | - W Florian Fricke
- Institute for Genome Sciences, University of Maryland School of Medicine, BioPark II - 801 West Baltimore Street, Baltimore, MD, 21201, USA
| |
Collapse
|
632
|
Drell T, Lillsaar T, Tummeleht L, Simm J, Aaspõllu A, Väin E, Saarma I, Salumets A, Donders GGG, Metsis M. Characterization of the vaginal micro- and mycobiome in asymptomatic reproductive-age Estonian women. PLoS One 2013; 8:e54379. [PMID: 23372716 PMCID: PMC3553157 DOI: 10.1371/journal.pone.0054379] [Citation(s) in RCA: 167] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Accepted: 12/11/2012] [Indexed: 12/16/2022] Open
Abstract
The application of high-throughput sequencing methods has raised doubt in the concept of the uniform healthy vaginal microbiota consisting predominantly of lactobacilli by revealing the existence of more variable bacterial community composition. As this needs to be analyzed more extensively and there is little straightforward data regarding the vaginal mycobiome of asymptomatic women we aimed to define bacterial and fungal communities in vaginal samples from 494 asymptomatic, reproductive-age Estonian women. The composition of the vaginal microbiota was determined by amplifying bacterial 16S rRNA and fungal internal transcribed spacer-1 (ITS-1) regions and subsequently sequencing them using 454 Life Sciences pyrosequencing. We delineated five major bacterial community groups with distinctive diversity and species composition. Lactobacilli were among the most abundant bacteria in all groups, but also members of genus Gardnerella had high relative abundance in some of the groups. Microbial diversity increased with higher vaginal pH values, and was also higher when a malodorous discharge was present, indicating that some of the women who consider themselves healthy may potentially have asymptomatic bacterial vaginosis (BV). Our study is the first of its kind to analyze the mycobiome that colonizes the healthy vaginal environment using barcoded pyrosequencing technology. We observed 196 fungal operational taxonomic units (OTUs), including 16 OTUs of Candida spp., which is more diverse than previously recognized. However, assessing true fungal diversity was complicated because of the problems regarding the possible air-borne contamination and bioinformatics used for identification of fungal taxons as significant proportion of fungal sequences were assigned to unspecified OTUs.
Collapse
MESH Headings
- Adolescent
- Adult
- Asymptomatic Diseases
- Candida/classification
- Candida/genetics
- Candida/isolation & purification
- DNA, Intergenic/classification
- DNA, Intergenic/genetics
- Estonia/epidemiology
- Female
- Gardnerella vaginalis/classification
- Gardnerella vaginalis/genetics
- Gardnerella vaginalis/isolation & purification
- Humans
- Lactobacillus/classification
- Lactobacillus/genetics
- Lactobacillus/isolation & purification
- Metagenome/genetics
- Phylogeny
- Polymerase Chain Reaction
- RNA, Ribosomal, 16S/classification
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Vagina/microbiology
- Vaginal Discharge/microbiology
- Vaginosis, Bacterial/diagnosis
- Vaginosis, Bacterial/epidemiology
- Vaginosis, Bacterial/microbiology
Collapse
Affiliation(s)
- Tiina Drell
- Centre for Biology of Integrated Systems, Tallinn University of Technology, Tallinn, Estonia.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
633
|
Cavaleiro I, Proença L, Félix S, Salema-Oom M. Prevalence of Yeast Other than Candida albicans
in Denture Wearers. J Prosthodont 2013; 22:351-7. [DOI: 10.1111/jopr.12005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/13/2012] [Indexed: 11/26/2022] Open
Affiliation(s)
- Inês Cavaleiro
- Instituto Superior Ciências da Saúde Egas Moniz; Centro de Investigação Interdisciplinar Egas Moniz (CiiEM); Caparica Portugal
| | - Luis Proença
- Instituto Superior Ciências da Saúde Egas Moniz; Centro de Investigação Interdisciplinar Egas Moniz (CiiEM); Caparica Portugal
- Faculdade de Ciências da Universidade de Lisboa; Centro de Ciências Moleculares e Materiais (CCMM); Lisboa Portugal
| | - Sérgio Félix
- Instituto Superior Ciências da Saúde Egas Moniz; Centro de Investigação Interdisciplinar Egas Moniz (CiiEM); Caparica Portugal
| | - Madalena Salema-Oom
- Instituto Superior Ciências da Saúde Egas Moniz; Centro de Investigação Interdisciplinar Egas Moniz (CiiEM); Caparica Portugal
- Faculdade de Ciência e Tecnologia da Universidade Nova de Lisboa; Centro de Recursos Microbiológicos (CREM); Caparica Portugal
| |
Collapse
|
634
|
Merenstein D, Hu H, Wang C, Hamilton P, Blackmon M, Chen H, Calderone R, Li D. Colonization by Candida species of the oral and vaginal mucosa in HIV-infected and noninfected women. AIDS Res Hum Retroviruses 2013; 29:30-4. [PMID: 23098053 DOI: 10.1089/aid.2012.0269] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Candidiasis in HIV/AIDS patients continues to be a public health problem. Effective antifungal therapies are few in number and have inherent problems such as selecting for drug-resistant strains of Candida species. To evaluate the state of Candida colonization of the oral and vaginal mucosa, we recruited 80 women, both HIV-infected and HIV-uninfected, from the Women's Interagency HIV Study (WIHS). Diet diaries were collected by participants to examine the role of diet on fungal growth. Baseline studies were initially done in participants that followed the colonization of both mucosal sites over 0-90 days. The most common Candida species from both groups of patients were C. albicans and C. glabrata. Among the HIV-infected cohort, the percentage of participants who were positive for Candida spp. was higher than in the HIV-uninfected control group. Furthermore, the frequency of colonization (1 episode versus >1 episode) was also increased in the HIV-infected cohort. These data indicate that Candida species remain an important component of the microbial community in both populations.
Collapse
Affiliation(s)
- Daniel Merenstein
- Department of Family Medicine, Georgetown University Medical Center, Washington, District of Columbia
| | - Haihong Hu
- Department of Medicine, Georgetown University Medical Center, Washington, District of Columbia
| | - Cuiwei Wang
- Department of Medicine, Georgetown University Medical Center, Washington, District of Columbia
| | - Pilar Hamilton
- Department of Medicine, Georgetown University Medical Center, Washington, District of Columbia
| | - Mandy Blackmon
- Department of Medicine, Georgetown University Medical Center, Washington, District of Columbia
| | - Hui Chen
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, District of Columbia
| | - Richard Calderone
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, District of Columbia
| | - Dongmei Li
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, District of Columbia
| |
Collapse
|
635
|
Willner D, Hugenholtz P. Metagenomics and Community Profiling: Culture-Independent Techniques in the Clinical Laboratory. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.clinmicnews.2012.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
636
|
Tosun I, Akyuz Z, Guler NC, Gulmez D, Bayramoglu G, Kaklikkaya N, Arikan-Akdagli S, Aydin F. Distribution, virulence attributes and antifungal susceptibility patterns of Candida parapsilosis complex strains isolated from clinical samples. Med Mycol 2012; 51:483-92. [PMID: 23216051 DOI: 10.3109/13693786.2012.745953] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
It was recently proposed that Candida parapsilosis represents a complex composed of three closely related species, i.e., C. parapsilosis sensu stricto, C. orthopsilosis, and C. metapsilosis. The aim of this study was to describe the distribution of C. parapsilosis complex isolates among clinical samples. We also evaluated antifungal susceptibility profiles, in vitro presence of lipase and secreted aspartyl proteinase, as well as their ability to grow in total parenteral nutrition (TPN) solution, and biofilm production. A total of 413 non-C. albicans Candida isolates were obtained from various clinical samples between 2010 and 2011 in a Turkish Tertiary Care Hospital. Of them, 42 were identified as members of the C. parapsilosis complex. Among these, 38 (90.5%) were C. parapsilosis sensu stricto, 3 (7.1%) C. metapsilosis, and 1 (2.4%) C. orthopsilosis. All isolates recovered from blood were found to be C. parapsilosis sensu stricto and C. metapsilosis. In phenotypic tests, all 42 isolates grew in TPN solution and, although 26.2% of C. parapsilosis sensu stricto-isolates were capable of forming biofilms in vitro, neither C. orthopsilosis nor C. metapsilosis isolates were able to do so. Acid proteinase activity was detected in 31% of isolates and lipase activity in 33%. All isolates were sensitive to voriconazole, caspofungin, and anidulafungin, with only a single C. parapsilosis sensu stricto isolate showing dose-dependent susceptible to fluconazole. While the number of C. metapsilosis and C. orthopsilosis isolates remained low, there were no significant differences in antifungal MIC as compared to C. parapsilosis sensu stricto.
Collapse
Affiliation(s)
- Ilknur Tosun
- Department of Medical Microbiology, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey.
| | | | | | | | | | | | | | | |
Collapse
|
637
|
Abstract
The human mouth harbours one of the most diverse microbiomes in the human body, including viruses, fungi, protozoa, archaea and bacteria. The bacteria are responsible for the two commonest bacterial diseases of man: dental caries (tooth decay) and the periodontal (gum) diseases. Archaea are restricted to a small number of species of methanogens while around 1000 bacterial species have been found, with representatives from the phyla Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, Spirochaetes, Synergistetes and Tenericutes and the uncultured divisions GN02, SR1 and TM7. Around half of oral bacteria are as yet uncultured and culture-independent methods have been successfully used to comprehensively describe the oral bacterial community. The human oral microbiome database (HOMD, www.homd.org) provides a comprehensive resource consisting of descriptions of oral bacterial taxa, a 16S rRNA identification tool and a repository of oral bacterial genome sequences. Individuals' oral microbiomes are highly specific at the species level, although overall the human oral microbiome shows few geographical differences. Although caries and periodontitis are clearly bacterial diseases, they are not infectious diseases in the classical sense because they result from a complex interaction between the commensal microbiota, host susceptibility and environmental factors such as diet and smoking. Periodontitis, in particular, appears to result from an inappropriate inflammatory reaction to the normal microbiota, exacerbated by the presence of some disease-associated bacterial species. In functional terms, there appears to considerable redundancy among the oral microbiota and a focus on functional rather than phylogenetic diversity may be required in order to fully understand host-microbiome interactions.
Collapse
Affiliation(s)
- William G Wade
- King's College London Dental Institute, Microbiology Unit, Floor 17, Tower Wing, Guy's Campus, London SE1 9RT, UK.
| |
Collapse
|
638
|
Liu CM, Kachur S, Dwan MG, Abraham AG, Aziz M, Hsueh PR, Huang YT, Busch JD, Lamit LJ, Gehring CA, Keim P, Price LB. FungiQuant: a broad-coverage fungal quantitative real-time PCR assay. BMC Microbiol 2012; 12:255. [PMID: 23136846 PMCID: PMC3565980 DOI: 10.1186/1471-2180-12-255] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 10/24/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fungal load quantification is a critical component of fungal community analyses. Limitation of current approaches for quantifying the fungal component in the human microbiome suggests the need for new broad-coverage techniques. METHODS We analyzed 2,085 18S rRNA gene sequences from the SILVA database for assay design. We generated and quantified plasmid standards using a qPCR-based approach. We evaluated assay coverage against 4,968 sequences and performed assay validation following the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines. RESULTS We designed FungiQuant, a TaqMan® qPCR assay targeting a 351 bp region in the fungal 18S rRNA gene. Our in silico analysis showed that FungiQuant is a perfect sequence match to 90.0% of the 2,617 fungal species analyzed. We showed that FungiQuant's is 100% sensitive and its amplification efficiencies ranged from 76.3% to 114.5%, with r(2)-values of >0.99 against the 69 fungal species tested. Additionally, FungiQuant inter- and intra-run coefficients of variance ranged from <10% and <20%, respectively. We further showed that FungiQuant has a limit of quantification 25 copies and a limit of detection at 5 copies. Lastly, by comparing results from human-only background DNA with low-level fungal DNA, we showed that amplification in two or three of a FungiQuant performed in triplicate is statistically significant for true positive fungal detection. CONCLUSIONS FungiQuant has comprehensive coverage against diverse fungi and is a robust quantification and detection tool for delineating between true fungal detection and non-target human DNA.
Collapse
Affiliation(s)
- Cindy M Liu
- Division of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, AZ, 86011, USA
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Sergey Kachur
- Division of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, AZ, 86011, USA
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
- Current address: Ross University School of Medicine, Roseau, Dominica
| | - Michael G Dwan
- Division of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, AZ, 86011, USA
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Alison G Abraham
- Department of Epidemiology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21201, USA
| | - Maliha Aziz
- Division of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, AZ, 86011, USA
| | - Po-Ren Hsueh
- Departments of Laboratory Medicine and Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yu-Tsung Huang
- Department of Internal Medicine, Far Eastern Memorial Hospital, New Taipei City, Taiwan
| | - Joseph D Busch
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Louis J Lamit
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Catherine A Gehring
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Paul Keim
- Division of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, AZ, 86011, USA
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Lance B Price
- Division of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, AZ, 86011, USA
| |
Collapse
|
639
|
Moris DV, Melhem MSC, Martins MA, Souza LR, Kacew S, Szeszs MW, Carvalho LR, Pimenta-Rodrigues MV, Berghs HAM, Mendes RP. Prevalence and antifungal susceptibility of Candida parapsilosis complex isolates collected from oral cavities of HIV-infected individuals. J Med Microbiol 2012; 61:1758-1765. [PMID: 22956748 DOI: 10.1099/jmm.0.045112-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
At present, few data are available on the prevalence and antifungal susceptibility of Candida parapsilosis complex isolates from HIV-infected individuals. The C. parapsilosis complex comprises three species, C. parapsilosis sensu stricto, C. metapsilosis and C. orthopsilosis. Fifteen of 318 Candida isolates were identified as members of the C. parapsilosis complex by PCR and restriction fragment length polymorphism (RFLP). The prevalence of C. parapsilosis complex isolates was 4.7 %, 2.2 % being identified as C. parapsilosis sensu stricto and 2.5 % as C. metapsilosis, while no C. orthopsilosis was isolated. This is believed to be the first study that has identified isolates of C. metapsilosis obtained from the oral cavity of HIV-infected individuals. Antifungal susceptibility tests indicated that all the isolates were susceptible to amphotericin B (AMB), fluconazole (FLC), ketoconazole (KTC), itraconazole (ITC), voriconazole (VRC) and caspofungin (CASPO). Although isolates of C. parapsilosis sensu stricto and C. metapsilosis were susceptible to FLC, isolates of C. metapsilosis showed a tendency for higher MICs (≥1.0 µg ml(-1)). Based upon the frequency of candidiasis and the fact that certain isolates of the C. parapsilosis complex respond differently to FLC therapy, our data may be of therapeutic relevance with respect to susceptibility and potential resistance to specific antifungal agents. Our data suggest that C. metapsilosis can be a human commensal; its importance as a pathogen has yet to be confirmed.
Collapse
Affiliation(s)
- D V Moris
- Departamento de Doenças Tropicais e Diagnóstico por Imagem, Faculdade de Medicina de Botucatu, UNESP, Botucatu, São Paulo State, Brazil
| | | | | | - L R Souza
- Departamento de Doenças Tropicais e Diagnóstico por Imagem, Faculdade de Medicina de Botucatu, UNESP, Botucatu, São Paulo State, Brazil
| | - S Kacew
- Institute for Population Health, University of Ottawa, Ontario, Canada
| | - M W Szeszs
- Instituto Adolfo Lutz, São Paulo, Brazil
| | - L R Carvalho
- Departamento de Bioestatística, Instituto de Biociências, UNESP, Botucatu, São Paulo State, Brazil
| | - M V Pimenta-Rodrigues
- Departamento de Doenças Tropicais e Diagnóstico por Imagem, Faculdade de Medicina de Botucatu, UNESP, Botucatu, São Paulo State, Brazil
| | | | - R P Mendes
- Departamento de Doenças Tropicais e Diagnóstico por Imagem, Faculdade de Medicina de Botucatu, UNESP, Botucatu, São Paulo State, Brazil
| |
Collapse
|
640
|
Faran Ali SM, Tanwir F. Oral microbial habitat a dynamic entity. J Oral Biol Craniofac Res 2012; 2:181-7. [PMID: 25737863 PMCID: PMC3941266 DOI: 10.1016/j.jobcr.2012.07.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 07/30/2012] [Indexed: 01/03/2023] Open
Abstract
Oral microbial habitat is composed of wide variety of species. These species play a significant role in maintaining the well being of the oral cavity by contributing in various ways. However the proper functioning of these oral microbes can be detrimental for the human oral cavity if the conditions are not suitable such as redox potential (Eh), pH of a site, the activity of the host defenses, and the presence of antimicrobial agents. The oral microbial community represents the best-characterized group associated with the human host. There are strong correlations between the qualitative composition of the oral microbiota and clinically healthy or diseased states. Amongst the bacteria of more than 700 species now identified within the human oral microbiota, it is the streptococci that are numerically predominant. Interactions between mucosal surfaces and microbial microbiota are key to host defense, health, and disease. These surfaces are exposed to high numbers of microbes and must be capable of distinguishing between those that are beneficial or avirulent and those that will invade and cause disease. Our understanding of the mechanisms involved in these discriminatory processes has recently begun to expand as new studies bring to light the importance of epithelial cells and novel immune cell subsets such as T(h)17 T cells in these processes. In this review article we have tried to find out the factors responsible for maintaining oral microbial habitat intact and the reasons which cause changes in its composition.
Collapse
Affiliation(s)
- Syed Muhammad Faran Ali
- Department of Oral Biology, Ziauddin College of Dentistry, Ziauddin Medical University, 4/B Shahrah e Ghalib, Block 6, Clifton, Karachi 75600, Pakistan
| | - Farzeen Tanwir
- Department of Periodontology, Ziauddin College of Dentistry, Ziauddin Medical University, Karachi, Pakistan
| |
Collapse
|
641
|
Song J, Shi L, Li D, Sun Y, Niu Y, Chen Z, Luo H, Pang X, Sun Z, Liu C, Lv A, Deng Y, Larson-Rabin Z, Wilkinson M, Chen S. Extensive pyrosequencing reveals frequent intra-genomic variations of internal transcribed spacer regions of nuclear ribosomal DNA. PLoS One 2012; 7:e43971. [PMID: 22952830 PMCID: PMC3431384 DOI: 10.1371/journal.pone.0043971] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Accepted: 07/27/2012] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Internal transcribed spacer of nuclear ribosomal DNA (nrDNA) is already one of the most popular phylogenetic and DNA barcoding markers. However, the existence of its multiple copies has complicated such usage and a detailed characterization of intra-genomic variations is critical to address such concerns. METHODOLOGY/PRINCIPAL FINDINGS In this study, we used sequence-tagged pyrosequencing and genome-wide analyses to characterize intra-genomic variations of internal transcribed spacer 2 (ITS2) regions from 178 plant species. We discovered that mutation of ITS2 is frequent, with a mean of 35 variants per species. And on average, three of the most abundant variants make up 91% of all ITS2 copies. Moreover, we found different congeneric species share identical variants in 13 genera. Interestingly, different species across different genera also share identical variants. In particular, one minor variant of ITS2 in Eleutherococcus giraldii was found identical to the ITS2 major variant of Panax ginseng, both from Araliaceae family. In addition, DNA barcoding gap analysis showed that the intra-genomic distances were markedly smaller than those of the intra-specific or inter-specific variants. When each of 5543 variants were examined for its species discrimination efficiency, a 97% success rate was obtained at the species level. CONCLUSIONS Identification of identical ITS2 variants across intra-generic or inter-generic species revealed complex species evolutionary history, possibly, horizontal gene transfer and ancestral hybridization. Although intra-genomic multiple variants are frequently found within each genome, the usage of the major variants alone is sufficient for phylogeny construction and species determination in most cases. Furthermore, the inclusion of minor variants further improves the resolution of species identification.
Collapse
Affiliation(s)
- Jingyuan Song
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Linchun Shi
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Dezhu Li
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yongzhen Sun
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Yunyun Niu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Zhiduan Chen
- Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Hongmei Luo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Xiaohui Pang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Zhiying Sun
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Chang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Aiping Lv
- China Academy of Chinese Medical Sciences, Beijing, China
| | - Youping Deng
- Rush University Medical Center, Chicago, Illinois, United States of America
| | - Zachary Larson-Rabin
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | | | - Shilin Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| |
Collapse
|
642
|
The Changing Epidemiology of Oropharyngeal Candidiasis in Patients with HIV/AIDS in the Era of Antiretroviral Therapy. AIDS Res Treat 2012; 2012:262471. [PMID: 22970352 PMCID: PMC3434376 DOI: 10.1155/2012/262471] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 07/14/2012] [Indexed: 11/29/2022] Open
Abstract
The impact of antiretroviral therapy (ART) on opportunistic conditions in HIV patients continues to evolve. We specifically studied the changing epidemiology of oropharyngeal candidiasis (OPC) in 215 HIV/AIDS patients. Status of yeast colonization was assessed from oral rinse samples, and preliminary yeast identification was made using CHROMagar Candida and confirmed with standard microbiological techniques and/or molecular sequencing. Susceptibility to fluconazole was determined by CHROMagar Candida agar dilution screening and CLSI broth microdilution. 176 (82%) patients were colonized and 59 (27%) patients had symptomatic OPC. Candida albicans was the most prevalent species, though C. glabrata and C. dubliniensis were detected in 29% of isolates. Decreased fluconazole susceptibility occurred in 10% of isolates. Previous ART reduced the risk of OPC, while smoking increased the risk of colonization. Oral yeast colonization and symptomatic infection remain common even with advances in HIV therapy. C. albicans is the most common species, but other yeasts are prevalent and may have decreased susceptibility to fluconazole.
Collapse
|
643
|
Gainza-Cirauqui ML, Nieminen MT, Novak Frazer L, Aguirre-Urizar JM, Moragues MD, Rautemaa R. Production of carcinogenic acetaldehyde byCandida albicansfrom patients with potentially malignant oral mucosal disorders. J Oral Pathol Med 2012; 42:243-9. [DOI: 10.1111/j.1600-0714.2012.01203.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2012] [Indexed: 02/06/2023]
Affiliation(s)
| | | | - L. Novak Frazer
- Manchester Academic Health Science Centre; School of Translational Medicine and University Hospital of South Manchester; The University of Manchester; Manchester; UK
| | | | - M. D. Moragues
- School of Nursing; University of the Basque Country/EHU; Bilbao; Spain
| | | |
Collapse
|
644
|
Tissue Diagnosis of Invasive Fungal Infections: Current Limitations and the Emerging Use of Molecular Techniques. CURRENT FUNGAL INFECTION REPORTS 2012. [DOI: 10.1007/s12281-012-0098-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
645
|
Kraneveld EA, Buijs MJ, Bonder MJ, Visser M, Keijser BJF, Crielaard W, Zaura E. The relation between oral Candida load and bacterial microbiome profiles in Dutch older adults. PLoS One 2012; 7:e42770. [PMID: 22900048 PMCID: PMC3416775 DOI: 10.1371/journal.pone.0042770] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 07/11/2012] [Indexed: 11/18/2022] Open
Abstract
Currently there are no evidence-based ecological measures for prevention of overgrowth and subsequent infection by fungi in the oral cavity. The aim of this study was to increase our knowledge on fungal-bacterial ecological interactions. Salivary Candida abundance of 82 Dutch adults aged 58-80 years was established relative to the bacterial load by quantitative PCR analysis of the Internal Transcribed (ITS) region (Candida) and 16S rDNA gene (bacteria). The salivary microbiome was assessed using barcoded pyrosequencing of the bacterial hypervariable regions V5-V7 of 16S rDNA. Sequencing data was preprocessed by denoising and chimera removal, clustered in Operational Taxonomic Units (OTUs) and assigned to taxonomy. Both OTU-based (PCA, diversity statistics) and phylogeny-based analyses (UniFrac, PCoA) were performed. Saliva of Dutch older adults contained 0-4 × 10(8) CFU/mL Candida with a median Candida load of 0.06%. With increased Candida load the diversity of the salivary microbiome decreased significantly (p<0.001). Increase in the Candida load correlated positively with class Bacilli, and negatively with class Fusobacteria, Flavobacteria, and Bacteroidia. Microbiomes with high Candida load were less diverse and had a distinct microbial composition towards dominance by saccharolytic and acidogenic bacteria--streptococci. The control of the acidification of the oral environment may be a potential preventive measure for Candida outgrowth that should be evaluated in longitudinal clinical intervention trials.
Collapse
Affiliation(s)
- Eefje A. Kraneveld
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands
| | - Mark J. Buijs
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands
| | - Marc J. Bonder
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands
| | - Marjolein Visser
- Department of Health Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Bart J. F. Keijser
- Microbiology and Systems Biology, TNO Earth, Environmental and Life Sciences, Zeist, The Netherlands
| | - Wim Crielaard
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands
| | - Egija Zaura
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands
- * E-mail:
| |
Collapse
|
646
|
Charlson ES, Diamond JM, Bittinger K, Fitzgerald AS, Yadav A, Haas AR, Bushman FD, Collman RG. Lung-enriched organisms and aberrant bacterial and fungal respiratory microbiota after lung transplant. Am J Respir Crit Care Med 2012; 186:536-45. [PMID: 22798321 DOI: 10.1164/rccm.201204-0693oc] [Citation(s) in RCA: 226] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Long-term survival after lung transplantation is limited by infectious complications and by bronchiolitis obliterans syndrome (BOS), a form of chronic rejection linked in part to microbial triggers. OBJECTIVES To define microbial populations in the respiratory tract of transplant patients comprehensively using unbiased high-density sequencing. METHODS Lung was sampled by bronchoalveolar lavage (BAL) and upper respiratory tract by oropharyngeal wash (OW). Bacterial 16S rDNA and fungal internal transcribed spacer sequencing was used to profile organisms present. Outlier analysis plots defining taxa enriched in lung relative to OW were used to identify bacteria enriched in lung against a background of oropharyngeal carryover. MEASUREMENTS AND MAIN RESULTS Lung transplant recipients had higher bacterial burden in BAL than control subjects, frequent appearance of dominant organisms, greater distance between communities in BAL and OW indicating more distinct populations, and decreased respiratory tract microbial richness and diversity. Fungal populations were typically dominated by Candida in both sites or by Aspergillus in BAL but not OW. 16S outlier analysis identified lung-enriched taxa indicating bacteria replicating in the lower respiratory tract. In some cases this confirmed respiratory cultures but in others revealed enrichment by anaerobic organisms or mixed outgrowth of upper respiratory flora and provided quantitative data on relative abundances of bacteria found by culture. CONCLUSIONS Respiratory tract microbial communities in lung transplant recipients differ in structure and composition from healthy subjects. Outlier analysis can identify specific bacteria replicating in lung. These findings provide novel approaches to address the relationship between microbial communities and transplant outcome and aid in assessing lung infections.
Collapse
Affiliation(s)
- Emily S Charlson
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | | | | | | | | | | | | | | |
Collapse
|
647
|
Toju H, Tanabe AS, Yamamoto S, Sato H. High-coverage ITS primers for the DNA-based identification of ascomycetes and basidiomycetes in environmental samples. PLoS One 2012; 7:e40863. [PMID: 22808280 PMCID: PMC3395698 DOI: 10.1371/journal.pone.0040863] [Citation(s) in RCA: 585] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 06/14/2012] [Indexed: 01/30/2023] Open
Abstract
The kingdom Fungi is estimated to include 1.5 million or more species, playing key roles as decomposers, mutualists, and parasites in every biome on the earth. To comprehensively understand the diversity and ecology of this huge kingdom, DNA barcoding targeting the internal transcribed spacer (ITS) region of the nuclear ribosomal repeat has been regarded as a prerequisite procedure. By extensively surveying ITS sequences in public databases, we designed new ITS primers with improved coverage across diverse taxonomic groups of fungi compared to existing primers. An in silico analysis based on public sequence databases indicated that the newly designed primers matched 99% of ascomycete and basidiomycete ITS taxa (species, subspecies or varieties), causing little taxonomic bias toward either fungal group. Two of the newly designed primers could inhibit the amplification of plant sequences and would enable the selective investigation of fungal communities in mycorrhizal associations, soil, and other types of environmental samples. Optimal PCR conditions for the primers were explored in an in vitro investigation. The new primers developed in this study will provide a basis for ecological studies on the diversity and community structures of fungi in the era of massive DNA sequencing.
Collapse
Affiliation(s)
- Hirokazu Toju
- The Hakubi Center for Advanced Research, Kyoto University, Sakyo, Kyoto, Japan.
| | | | | | | |
Collapse
|
648
|
Santamaria M, Fosso B, Consiglio A, De Caro G, Grillo G, Licciulli F, Liuni S, Marzano M, Alonso-Alemany D, Valiente G, Pesole G. Reference databases for taxonomic assignment in metagenomics. Brief Bioinform 2012; 13:682-95. [PMID: 22786784 DOI: 10.1093/bib/bbs036] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Metagenomics is providing an unprecedented access to the environmental microbial diversity. The amplicon-based metagenomics approach involves the PCR-targeted sequencing of a genetic locus fitting different features. Namely, it must be ubiquitous in the taxonomic range of interest, variable enough to discriminate between different species but flanked by highly conserved sequences, and of suitable size to be sequenced through next-generation platforms. The internal transcribed spacers 1 and 2 (ITS1 and ITS2) of the ribosomal DNA operon and one or more hyper-variable regions of 16S ribosomal RNA gene are typically used to identify fungal and bacterial species, respectively. In this context, reliable reference databases and taxonomies are crucial to assign amplicon sequence reads to the correct phylogenetic ranks. Several resources provide consistent phylogenetic classification of publicly available 16S ribosomal DNA sequences, whereas the state of ribosomal internal transcribed spacers reference databases is notably less advanced. In this review, we aim to give an overview of existing reference resources for both types of markers, highlighting strengths and possible shortcomings of their use for metagenomics purposes. Moreover, we present a new database, ITSoneDB, of well annotated and phylogenetically classified ITS1 sequences to be used as a reference collection in metagenomic studies of environmental fungal communities. ITSoneDB is available for download and browsing at http://itsonedb.ba.itb.cnr.it/.
Collapse
Affiliation(s)
- Monica Santamaria
- Institute of Biomembranes and Bioenergetics, National Research Council, Bari, Italy
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
649
|
Dollive S, Peterfreund GL, Sherrill-Mix S, Bittinger K, Sinha R, Hoffmann C, Nabel CS, Hill DA, Artis D, Bachman MA, Custers-Allen R, Grunberg S, Wu GD, Lewis JD, Bushman FD. A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples. Genome Biol 2012; 13:R60. [PMID: 22759449 PMCID: PMC4053730 DOI: 10.1186/gb-2012-13-7-r60] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 07/03/2012] [Indexed: 11/23/2022] Open
Abstract
Eukaryotic microorganisms are important but understudied components of the human microbiome. Here we present a pipeline for analysis of deep sequencing data on single cell eukaryotes. We designed a new 18S rRNA gene-specific PCR primer set and compared a published rRNA gene internal transcribed spacer (ITS) gene primer set. Amplicons were tested against 24 specimens from defined eukaryotes and eight well-characterized human stool samples. A software pipeline https://sourceforge.net/projects/brocc/ was developed for taxonomic attribution, validated against simulated data, and tested on pyrosequence data. This study provides a well-characterized tool kit for sequence-based enumeration of eukaryotic organisms in human microbiome samples.
Collapse
|
650
|
Iliev ID, Funari VA, Taylor KD, Nguyen Q, Reyes CN, Strom SP, Brown J, Becker CA, Fleshner PR, Dubinsky M, Rotter JI, Wang HL, McGovern DPB, Brown GD, Underhill DM. Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis. Science 2012; 336:1314-7. [PMID: 22674328 DOI: 10.1126/science.1221789] [Citation(s) in RCA: 758] [Impact Index Per Article: 63.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The intestinal microflora, typically equated with bacteria, influences diseases such as obesity and inflammatory bowel disease. Here, we show that the mammalian gut contains a rich fungal community that interacts with the immune system through the innate immune receptor Dectin-1. Mice lacking Dectin-1 exhibited increased susceptibility to chemically induced colitis, which was the result of altered responses to indigenous fungi. In humans, we identified a polymorphism in the gene for Dectin-1 (CLEC7A) that is strongly linked to a severe form of ulcerative colitis. Together, our findings reveal a eukaryotic fungal community in the gut (the "mycobiome") that coexists with bacteria and substantially expands the repertoire of organisms interacting with the intestinal immune system to influence health and disease.
Collapse
Affiliation(s)
- Iliyan D Iliev
- Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|