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Katsoulis O, Pitts OR, Singanayagam A. The airway mycobiome and interactions with immunity in health and chronic lung disease. OXFORD OPEN IMMUNOLOGY 2024; 5:iqae009. [PMID: 39206335 PMCID: PMC11357796 DOI: 10.1093/oxfimm/iqae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 07/07/2024] [Accepted: 07/15/2024] [Indexed: 09/04/2024] Open
Abstract
The existence of commensal fungi that reside within the respiratory tract, termed the airway mycobiome, has only recently been discovered. Studies are beginning to characterize the spectrum of fungi that inhabit the human upper and lower respiratory tract but heterogeneous sampling and analysis techniques have limited the generalizability of findings to date. In this review, we discuss existing studies that have examined the respiratory mycobiota in healthy individuals and in those with inflammatory lung conditions such as asthma, chronic obstructive pulmonary disease and cystic fibrosis. Associations between specific fungi and features of disease pathogenesis are emerging but the precise functional consequences imparted by mycobiota upon the immune system remain poorly understood. It is imperative that further research is conducted in this important area as a more detailed understanding could facilitate the development of novel approaches to manipulating the mycobiome for therapeutic benefit.
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Affiliation(s)
- Orestis Katsoulis
- Centre for Bacterial Resistance Biology, Department of Infectious Disease, Imperial College London, London SW7 2DD, UK
| | - Oliver R Pitts
- Centre for Bacterial Resistance Biology, Department of Infectious Disease, Imperial College London, London SW7 2DD, UK
| | - Aran Singanayagam
- Centre for Bacterial Resistance Biology, Department of Infectious Disease, Imperial College London, London SW7 2DD, UK
- National Heart and Lung Institute, Imperial College London, London SW7 2DD, UK
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2
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Rojas OC, Amaral-Montesino C, Mendoza-Olazaran S, Carrión-Alvarez D, González-Álvarez R, Montoya AM. Isolation of Clavispora lusitaniae from the Oral Cavity of Immunocompetent Young Adults from the North of Mexico. Indian J Microbiol 2024; 64:475-481. [PMID: 39010992 PMCID: PMC11246318 DOI: 10.1007/s12088-023-01145-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 11/13/2023] [Indexed: 07/17/2024] Open
Abstract
The human oral cavity is normally colonized by microorganisms including bacteria, fungi, archaea, viruses and protozoa. The aim of this study was to determine the frequency of Candida spp., in de oral cavity in a group of medical students from the north of Mexico. Oral sample were obtained from 240 healthy students. The specimens were analyzed by traditional microbiology cultures and DNA sequencing. Candida spp., grew in Sabouraud dextrose agar from 57 samples and subsequently were isolated and phenotyped. The definitive identification to the species level was done by sequence analysis. The yeasts were identified as follow: 28 Clavispora lusitaniae, 20 Candida albicans, 5 Pichia kudriavzevii and 4 Candida parapsilosis. Our findings revealed that 23.75% of the healthy population has a potential pathogen in their mouth. Surprisingly, C. albicans is not the predominant yeast; instead other non-Candida species are the colonizers of the oral cavity as normal microbiota. C. lusitaniae is considered an emerging opportunistic pathogen in immunosuppressive patients. This paper pretends to highlight the presence of this yeast in the oral cavity in immunocompetent young adults. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-023-01145-x.
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Affiliation(s)
- Olga C Rojas
- Departamento de Microbiología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Av. Gonzalitos s/n, Colonia Mitras Centro, CP 64460 Monterrey, Nuevo León Mexico
- Departamento de Ciencia Básicas, Vicerrectoría de Ciencias de la Salud, Universidad de Monterrey, CP 66238 San Pedro Garza García, Mexico
| | - Cintia Amaral-Montesino
- Departamento de Ciencia Básicas, Vicerrectoría de Ciencias de la Salud, Universidad de Monterrey, CP 66238 San Pedro Garza García, Mexico
| | - Soraya Mendoza-Olazaran
- Departamento de Ciencia Básicas, Vicerrectoría de Ciencias de la Salud, Universidad de Monterrey, CP 66238 San Pedro Garza García, Mexico
| | - Diego Carrión-Alvarez
- Departamento de Ciencia Básicas, Vicerrectoría de Ciencias de la Salud, Universidad de Monterrey, CP 66238 San Pedro Garza García, Mexico
| | | | - Alexandra M Montoya
- Departamento de Microbiología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Av. Gonzalitos s/n, Colonia Mitras Centro, CP 64460 Monterrey, Nuevo León Mexico
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3
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Nenciarini S, Renzi S, di Paola M, Meriggi N, Cavalieri D. The yeast-human coevolution: Fungal transition from passengers, colonizers, and invaders. WIREs Mech Dis 2024; 16:e1639. [PMID: 38146626 DOI: 10.1002/wsbm.1639] [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: 05/19/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/27/2023]
Abstract
Fungi are the cause of more than a billion infections in humans every year, although their interactions with the host are still neglected compared to bacteria. Major systemic fungal infections are very unusual in the healthy population, due to the long history of coevolution with the human host. Humans are routinely exposed to environmental fungi and can host a commensal mycobiota, which is increasingly considered as a key player in health and disease. Here, we review the current knowledge on host-fungi coevolution and the factors that regulate their interaction. On one hand, fungi have learned to survive and inhabit the host organisms as a natural ecosystem, on the other hand, the host immune system finely tunes the response toward fungi. In turn, recognition of fungi as commensals or pathogens regulates the host immune balance in health and disease. In the human gut ecosystem, yeasts provide a fingerprint of the transient microbiota. Their status as passengers or colonizers is related to the integrity of the gut barrier and the risk of multiple disorders. Thus, the study of this less known component of the microbiota could unravel the rules of the transition from passengers to colonizers and invaders, as well as their dependence on the innate component of the host's immune response. This article is categorized under: Infectious Diseases > Environmental Factors Immune System Diseases > Environmental Factors Infectious Diseases > Molecular and Cellular Physiology.
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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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4
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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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Defta CL, Albu CC, Albu ŞD, Bogdan-Andreescu CF. Oral Mycobiota: A Narrative Review. Dent J (Basel) 2024; 12:115. [PMID: 38668027 PMCID: PMC11049401 DOI: 10.3390/dj12040115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/04/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Numerous studies have proven the important role of the oral microbiota in health and disease. The dysfunctionality of the oral microbiota, known as dysbiosis, is incriminated in dental caries, periodontal disease, oral infectious diseases, oral cancer, and systemic disease. The lesser-known component of the oral microbiota, the mycobiota, is now assiduously investigated. Recent technological developments have helped foster the identification of new fungal species based on genomic research. Next-generation sequencing has expanded our knowledge about the diversity, architecture, and relationships of oral microorganisms within the oral cavity. The mycobiome structure and relationships with the bacteriome have been studied to identify a mycobiotic signature. This review aimed to emphasize the latest knowledge of the oral mycobiome.
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Affiliation(s)
- Carmen Liliana Defta
- Department of Microbiology, Faculty of Dentistry, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania;
| | - Cristina-Crenguţa Albu
- Department of Genetics, Faculty of Dentistry, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Ştefan-Dimitrie Albu
- Department of Periodontology, Faculty of Dentistry, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania;
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Tsai FT, Yang CC, Lin YC, Hsu ML, Hong G, Yang MC, Wang DH, Huang LJ, Lin CT, Hsu WE, Tu HF. Temporal stability of tongue microbiota in older patients - A pilot study. J Dent Sci 2024; 19:1087-1095. [PMID: 38618132 PMCID: PMC11010706 DOI: 10.1016/j.jds.2024.01.012] [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] [Received: 12/19/2023] [Revised: 01/11/2024] [Indexed: 04/16/2024] Open
Abstract
Background/purpose Healthy states of human microbiota depend on a stable community of symbiotic microbes irrespective of external challenges from the environment. Thus, long-term stability of the oral microbiota is of importance, particularly for older patient populations. Materials and methods We used next-generation sequencing (NGS) to examine the tongue microbiota of 18 individuals receiving long-term care over a 10-month period. Results Beta diversity analysis demonstrated temporal stability of the tongue microbiota, as microbial compositions from all time points were indistinguishable from each other (P = 0.0887). However, significant individual variation in microbial composition (P = 0.0001) was observed, underscoring the presence of a unique microbial profile for each patient. Conclusion The temporal dynamics of tongue microbiota exhibit long-term stability, providing diagnostic implications for oral diseases within older patient populations.
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Affiliation(s)
- Fa-Tzu Tsai
- College of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Cheng-Chieh Yang
- College of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Stomatology, Oral & Maxillofacial Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yu-Cheng Lin
- College of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Oral Medicine Innovation Center (OMIC), National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ming-Lun Hsu
- College of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Guang Hong
- Division of Craniofacial Development and Tissue Biology, Tohoku University, Senda, Japan
| | - Mu-Chen Yang
- Division of Craniofacial Development and Tissue Biology, Tohoku University, Senda, Japan
| | - Ding-Han Wang
- College of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Oral Medicine Innovation Center (OMIC), National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Lin-Jack Huang
- Department of Dentistry, National Yang Ming Chiao Tung University Hospital, Yilan County, Taiwan
| | - Chiu-Tzu Lin
- Department of Dentistry, National Yang Ming Chiao Tung University Hospital, Yilan County, Taiwan
| | - Wun-Eng Hsu
- Department of Dentistry, Far Eastern Memorial Hospital, New Taipei City, Taiwan
| | - Hsi-Feng Tu
- College of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Dentistry, National Yang Ming Chiao Tung University Hospital, Yilan County, Taiwan
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Medeiros MJ, Seo L, Macias A, Price DK, Yew JY. Bacterial and fungal components of the gut microbiome have distinct, sex-specific roles in Hawaiian Drosophila reproduction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.14.549088. [PMID: 37503295 PMCID: PMC10370118 DOI: 10.1101/2023.07.14.549088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Gut microbiomes provide numerous physiological benefits for host animals. The role of bacterial members of microbiomes in host physiology is well-documented. However, much less is known about the contributions and interactions of fungal members of the microbiome even though fungi are significant components of many microbiomes, including those of humans and insects. Here, we used antibacterial and antifungal drugs to manipulate the gut microbiome of a Hawaiian picture-wing Drosophila species, D. grimshawi, and identified distinct, sex-specific roles for the bacteria and fungi in microbiome community stability and reproduction. Female oogenesis, fecundity and mating drive were significantly diminished when fungal communities were suppressed. By contrast, male fecundity was more strongly affected by bacterial but not fungal populations. For males and females, suppression of both bacteria and fungi severely reduced fecundity and altered fatty acid levels and composition, implicating the importance of interkingdom interactions on reproduction and lipid metabolism. Overall, our results reveal that bacteria and fungi have distinct, sexually-dimorphic effects on host physiology and interkingdom dynamics in the gut help to maintain microbiome community stability and enhance reproduction.
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Affiliation(s)
- Matthew J. Medeiros
- Pacific Biosciences Research Center, University of Hawaiʻi at Mānoa
- Department of Life Sciences, University of Nevada at Las Vegas
| | - Laura Seo
- Department of Life Sciences, University of Nevada at Las Vegas
| | - Aziel Macias
- Department of Life Sciences, University of Nevada at Las Vegas
| | - Donald K. Price
- Department of Life Sciences, University of Nevada at Las Vegas
| | - Joanne Y. Yew
- Pacific Biosciences Research Center, University of Hawaiʻi at Mānoa
- Department of Life Sciences, University of Nevada at Las Vegas
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Costa PDS, Prado A, Bagon NP, Negri M, Svidzinski TIE. Mixed Fungal Biofilms: From Mycobiota to Devices, a New Challenge on Clinical Practice. Microorganisms 2022; 10:microorganisms10091721. [PMID: 36144323 PMCID: PMC9506030 DOI: 10.3390/microorganisms10091721] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/19/2022] [Accepted: 08/24/2022] [Indexed: 11/29/2022] Open
Abstract
Most current protocols for the diagnosis of fungal infections are based on culture-dependent methods that allow the evaluation of fungal morphology and the identification of the etiologic agent of mycosis. Most current protocols for the diagnosis of fungal infections are based on culture-dependent methods that enable the examination of the fungi for further identification of the etiological agent of the mycosis. The isolation of fungi from pure cultures is typically recommended, as when more than one species is identified, the second agent is considered a contaminant. Fungi mostly survive in highly organized communities that provoke changes in phenotypic profile, increase resistance to antifungals and environmental stresses, and facilitate evasion from the immune system. Mixed fungal biofilms (MFB) harbor more than one fungal species, wherein exchange can occur that potentialize the effects of these virulence factors. However, little is known about MFB and their role in infectious processes, particularly in terms of how each species may synergistically contribute to the pathogenesis. Here, we review fungi present in MFB that are commensals of the human body, forming the mycobiota, and how their participation in MFB affects the maintenance of homeostasis. In addition, we discuss how MFB are formed on both biotic and abiotic surfaces, thus being a significant reservoir of microorganisms that have already been associated in infectious processes of high morbidity and mortality.
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A longitudinal study of the pulmonary mycobiome in subjects with and without chronic obstructive pulmonary disease. PLoS One 2022; 17:e0267195. [PMID: 35551278 PMCID: PMC9098062 DOI: 10.1371/journal.pone.0267195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 04/04/2022] [Indexed: 11/30/2022] Open
Abstract
Background Few studies have examined the stability of the pulmonary mycobiome. We report longitudinal changes in the oral and pulmonary mycobiome of participants with and without COPD in a large-scale bronchoscopy study (MicroCOPD). Methods Repeated sampling was performed in 30 participants with and 21 without COPD. We collected an oral wash (OW) and a bronchoalveolar lavage (BAL) sample from each participant at two time points. The internal transcribed spacer 1 region of the ribosomal RNA gene cluster was PCR amplified and sequenced on an Illumina HiSeq sequencer. Differences in taxonomy, alpha diversity, and beta diversity between the two time points were compared, and we examined the effect of intercurrent antibiotic use. Results Sample pairs were dominated by Candida. We observed less stability in the pulmonary taxonomy compared to the oral taxonomy, additionally emphasised by a higher Yue-Clayton measure in BAL compared to OW (0.69 vs 0.22). No apparent effect was visually seen on taxonomy from intercurrent antibiotic use or participant category. We found no systematic variation in alpha diversity by time either in BAL (p-value 0.16) or in OW (p-value 0.97), and no obvious clusters on bronchoscopy number in PCoA plots. Pairwise distance analyses showed that OW samples from repeated sampling appeared more stable compared to BAL samples using the Bray-Curtis distance metric (p-value 0.0012), but not for Jaccard. Conclusion Results from the current study propose that the pulmonary mycobiome is less stable than the oral mycobiome, and neither COPD diagnosis nor intercurrent antibiotic use seemed to influence the stability.
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Fungi—A Component of the Oral Microbiome Involved in Periodontal Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1373:113-138. [DOI: 10.1007/978-3-030-96881-6_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Mishra K, Bukavina L, Ghannoum M. Symbiosis and Dysbiosis of the Human Mycobiome. Front Microbiol 2021; 12:636131. [PMID: 34630340 PMCID: PMC8493257 DOI: 10.3389/fmicb.2021.636131] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 08/04/2021] [Indexed: 12/13/2022] Open
Abstract
The influence of microbiological species has gained increased visibility and traction in the medical domain with major revelations about the role of bacteria on symbiosis and dysbiosis. A large reason for these revelations can be attributed to advances in deep-sequencing technologies. However, the research on the role of fungi has lagged. With the continued utilization of sequencing technologies in conjunction with traditional culture assays, we have the opportunity to shed light on the complex interplay between the bacteriome and the mycobiome as they relate to human health. In this review, we aim to offer a comprehensive overview of the human mycobiome in healthy and diseased states in a systematic way. The authors hope that the reader will utilize this review as a scaffolding to formulate their understanding of the mycobiome and pursue further research.
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Affiliation(s)
- Kirtishri Mishra
- University Hospitals Cleveland Medical Center, Urology Institute, Cleveland, OH, United States.,Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH, United States
| | - Laura Bukavina
- University Hospitals Cleveland Medical Center, Urology Institute, Cleveland, OH, United States.,Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH, United States
| | - Mahmoud Ghannoum
- Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH, United States.,Center for Medical Mycology, and Integrated Microbiome Core, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH, United States.,Department of Dermatology, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH, United States
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12
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Villar CC, Dongari-Bagtzoglou A. Fungal diseases: Oral dysbiosis in susceptible hosts. Periodontol 2000 2021; 87:166-180. [PMID: 34463992 DOI: 10.1111/prd.12378] [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] [Indexed: 12/13/2022]
Abstract
The oral cavity is colonized by a large number of microorganisms that are referred to collectively as the oral microbiota. These indigenous microorganisms have evolved in symbiotic relationships with the oral mucosal immune system and are involved in maintaining homeostasis in the oral cavity. Although Candida species are commonly found in the healthy oral cavity without causing infection, these fungi can become pathogenic. Recents advances indicate that the development of oral candidiasis is driven both by Candida albicans overgrowth in a dysbiotic microbiome and by disturbances in the host's immune system. Perturbation of the oral microbiota triggered by host-extrinsic (ie, medications), host-intrinsic (ie, host genetics), and microbiome-intrinsic (ie, microbial interactions) factors may increase the risk of oral candidiasis. In this review, we provide an overview of the oral mycobiome, with a particular focus on the interactions of Candida albicans with some of the most common oral bacteria and the oral mucosal immune system. Also, we present a summary of our current knowledge of the host-intrinsic and host-extrinsic factors that can predispose to oral candidiasis.
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Affiliation(s)
- Cristina Cunha Villar
- Division of Periodontics, Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Anna Dongari-Bagtzoglou
- Department of Oral Health and Diagnostic Sciences, University of Connecticut School of Dental Medicine, Farmington, CT, USA
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13
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Pierre JF, Phillips GJ, Chandra LC, Rendina DN, Thomas-Gosain NF, Lubach GR, Lyte M, Coe CL, Gosain A. Lyticase Facilitates Mycobiome Resolution Without Disrupting Microbiome Fidelity in Primates. J Surg Res 2021; 267:336-341. [PMID: 34186310 PMCID: PMC8678161 DOI: 10.1016/j.jss.2021.06.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 05/03/2021] [Accepted: 06/08/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND Microbiome research has expanded to consider contributions of microbial kingdoms beyond bacteria, including fungi (i.e., the mycobiome). However, optimal specimen handling protocols are varied, including uncertainty of how enzymes utilized to facilitate fungal DNA recovery may interfere with bacterial microbiome sequencing from the same samples. METHODS With Institutional Animal Care and Use Committee approval, fecal samples were obtained from 20 rhesus macaques (10 males, 10 females; Macaca mulatta). DNA was extracted using commercially available kits, with or without lyticase enzyme treatment. 16S ribosomal RNA (bacterial) and Internal Transcribed Spacer (ITS; fungal) sequencing was performed on the Illumina MiSeq platform. Bioinformatics analysis was performed using Qiime and Calypso. RESULTS Inclusion of lyticase in the sample preparation pipeline significantly increased usable fungal ITS reads, community alpha diversity, and enhanced detection of numerous fungal genera that were otherwise poorly or not detected in primate fecal samples. Bacterial 16S ribosomal RNA amplicons obtained from library preparation were statistically unchanged by the presence of lyticase. CONCLUSIONS We demonstrate inclusion of the enzyme lyticase for fungal cell wall digestion markedly enhances mycobiota detection while maintaining fidelity of microbiome identification and community features in non-human primates. In restricted sample volumes, as are common in limited human samples, use of single sample DNA isolation will facilitate increased rigor and controlled approaches in future work.
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Affiliation(s)
- Joseph F Pierre
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee; Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, Tennessee.
| | - Greg J Phillips
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, Iowa
| | - Lawrance C Chandra
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, Iowa
| | - Danielle N Rendina
- Harlow Center, Department. of Psychology, University of Wisconsin, Madison, Wisconsin
| | - Neena F Thomas-Gosain
- Department. of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Gabriele R Lubach
- Harlow Center, Department. of Psychology, University of Wisconsin, Madison, Wisconsin
| | - Mark Lyte
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, Iowa
| | - Christopher L Coe
- Harlow Center, Department. of Psychology, University of Wisconsin, Madison, Wisconsin
| | - Ankush Gosain
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee; Children's Foundation Research Institute, Le Bonheur Children's Hospital, Memphis, Tennessee; Department of Surgery, University of Tennessee Health Science Center, Memphis, Tennessee.
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14
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Shaimaa, Zainab H, Hugar D, Sultana A. A comparative study to assess risk of oral candidiasis in pregnant and nonpregnant women. J Oral Maxillofac Pathol 2021; 25:118-123. [PMID: 34349421 PMCID: PMC8272470 DOI: 10.4103/jomfp.jomfp_255_20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 10/07/2020] [Accepted: 03/10/2021] [Indexed: 11/05/2022] Open
Abstract
Background: The major hormonal changes observed in pregnant women lead to an imbalance in the oral environment. Hence, recent studies suggest that the placenta may harbor a unique microbiome that may have originated in the maternal oral microbiome. Aim: The present study aimed to assess the risk factor of oral candidiasis in pregnancy and to evaluate the prevalence of Candida species in the oral cavity of pregnant women in all three trimesters. The comparison was also done between pregnant and nonpregnant women to evaluate the cause of the prevalence of candidal species. Materials and Methods: Thirty pregnant and thirty nonpregnant women aged between 20 and 30 years were included in the study that were healthy and who did not have any obvious lesion in the oral cavity. The sterile swabs were used to collect samples from the oral cavity from both the groups by brushing the dorsum of the tongue and buccal mucosa. The pregnant women were followed throughout the pregnancy, i.e., in every trimester, for the sample collection. The samples were then cultured on Sabouraud Dextrose Agar media. The positive growth on culture plates was then inoculated on HiCrome agar differential agar media for speciation. Results: Statistical analysis was done by comparing the positive growth in pregnant and nonpregnant women using Fisher's exact test. The pregnant women were compared in three trimesters using the McNemar Chi-square test. Conclusion: The study concludes that there was no significant presence of Candidal species when compared between pregnant and nonpregnant groups. The prevalence of Candida species also remained the same.
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Affiliation(s)
- Shaimaa
- Department of Oral and Maxillofacial Pathology and Microbiology, Al Badar Dental College and Hospital, Gulbarga, Karnataka, India
| | - Heena Zainab
- Department of Oral and Maxillofacial Pathology and Microbiology, Al Badar Dental College and Hospital, Gulbarga, Karnataka, India
| | - Deepa Hugar
- Department of Oral and Maxillofacial Pathology and Microbiology, Al Badar Dental College and Hospital, Gulbarga, Karnataka, India
| | - Ameena Sultana
- Department of Oral and Maxillofacial Pathology and Microbiology, Al Badar Dental College and Hospital, Gulbarga, Karnataka, India
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Crossing Kingdoms: How the Mycobiota and Fungal-Bacterial Interactions Impact Host Health and Disease. Infect Immun 2021; 89:IAI.00648-20. [PMID: 33526565 PMCID: PMC8090948 DOI: 10.1128/iai.00648-20] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The term “microbiota” invokes images of mucosal surfaces densely populated with bacteria. These surfaces and the luminal compartments they form indeed predominantly harbor bacteria. The term “microbiota” invokes images of mucosal surfaces densely populated with bacteria. These surfaces and the luminal compartments they form indeed predominantly harbor bacteria. However, research from this past decade has started to complete the picture by focusing on important but largely neglected constituents of the microbiota: fungi, viruses, and archaea. The community of commensal fungi, also called the mycobiota, interacts with commensal bacteria and the host. It is thus not surprising that changes in the mycobiota have significant impact on host health and are associated with pathological conditions such as inflammatory bowel disease (IBD). In this review we will give an overview of why the mycobiota is an important research area and different mycobiota research tools. We will specifically focus on distinguishing transient and actively colonizing fungi of the oral and gut mycobiota and their roles in health and disease. In addition to correlative and observational studies, we will discuss mechanistic studies on specific cross-kingdom interactions of fungi, bacteria, and the host.
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16
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Candida prevalence in saliva before and after oral cancer treatment. Surgeon 2021; 19:e446-e451. [PMID: 33608227 DOI: 10.1016/j.surge.2021.01.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/28/2020] [Accepted: 01/07/2021] [Indexed: 01/24/2023]
Abstract
BACKGROUND Previous studies have shown an increased prevalence of candidiasis in patients receiving radiotherapy for head and neck cancer. However, little is known of the effect the different cancer treatment modalities have on the oral Candida status. OBJECTIVE AND HYPOTHESIS The objective of this study was to investigate the change in salivary Candida status of oral squamous cell carcinoma (OSCC) patients undergoing cancer treatment. The hypothesis was that cancer treatments change the oral microbial environment favouring an increase in the prevalence of more pathogenic non-albicans Candida (NAC). METHODS We collected paraffin-stimulated saliva from 44 OSCC patients before surgery and after a minimum of 19 months of follow-up. Chromagar, Bichro-Dupli-test and API ID 32 C were used for identification of different Candida species and results were analysed statistically. RESULTS At both timepoints, 75% of samples were Candida positive with C. albicans being the most common yeast. NAC strains were present in 16% of the pre-operative samples and 14% of the follow-up samples. The NAC species found were C. dubliniensis, C. krusei, C. guilliermondii (preoperatively only) and C. glabrata (at follow-up only). In 73% of the cases, the salivary Candida status remained unchanged. There was an 18% increase in the prevalence of candidiasis. However, the different treatment modalities did not statistically significantly affect the Candida status of the patients. CONCLUSION The intraindividual prevalence of salivary Candida among OSCC patients seems to be stable and different treatment modalities have little to no effect on the salivary Candida status.
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Abstract
The microbial communities that inhabit the gingival crevice are responsible for the pathological processes that affect the periodontium. The changes in composition and function of subgingival bacteria as disease develops have been extensively studied. Subgingival communities, however, also contain fungi, Archaea, and viruses, which could contribute to the dysbiotic processes associated with periodontal diseases. High-throughput DNA sequencing has facilitated a better understanding of the mycobiome, archaeome, and virome. However, the number of studies available on the nonbacterial components of the subgingival microbiome remains limited in comparison with publications focusing on bacteria. Difficulties in characterizing fungal, archaeal, and viral populations arise from the small portion of the total metagenome mass they occupy and lack of comprehensive reference genome databases. In addition, specialized approaches potentially introducing bias are required to enrich for viral particles, while harsh methods of cell lysis are needed to recover nuclei acids from certain fungi. While the characterization of the subgingival diversity of fungi, Archaea and viruses is incomplete, emerging evidence suggests that they could contribute in different ways to subgingival dysbiosis. Certain fungi, such as Candida albicans are suggested to facilitate colonization of bacterial pathogens. Methanogenic Archaea are associated with periodontitis severity and are thought to partner synergistically with bacterial fermenters, while viruses may affect immune responses or shape microbial communities in ways incompletely understood. This review describes the manner in which omics approaches have improved our understanding of the diversity of fungi, Archaea, and viruses within subgingival communities. Further characterization of these understudied components of the subgingival microbiome is required, together with mechanistic studies to unravel their ecological role and potential contributions to dysbiosis.
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Affiliation(s)
- Patricia I Diaz
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, Buffalo, NY
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18
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Oba PM, Holscher HD, Mathai RA, Kim J, Swanson KS. Diet Influences the Oral Microbiota of Infants during the First Six Months of Life. Nutrients 2020; 12:nu12113400. [PMID: 33167488 PMCID: PMC7694519 DOI: 10.3390/nu12113400] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/26/2020] [Accepted: 10/31/2020] [Indexed: 12/31/2022] Open
Abstract
Background: Oral microorganisms contribute to oral health and disease, but few have studied how infant feeding methods affect their establishment. Methods: Infant (n = 12) feeding records and tongue and cheek swabs were collected within 48 h of birth, and after 2, 4, and 6 mo. DNA was extracted from samples, bacterial and fungal amplicons were generated and sequenced using Illumina MiSeq, and sequences were analyzed using Quantitative Insights Into Microbial Ecology (QIIME) and Statistical Analysis System (SAS) to evaluate differences over time and among breast-fed, formula-fed, mixed-fed, and solid food-fed infants. Results: Considering all time points, breast milk- and mixed-fed infants had lower oral species richness than solid food-fed infants (p = 0.006). Regardless of feeding mode, species richness was lower at birth than at other time points (p = 0.006). Principal coordinates analysis (PCoA) of unique fraction metric (UniFrac) distances indicated that bacterial communities were impacted by feeding method (p < 0.005). Considering all time points, breast-fed infants had higher Streptococcus, while formula-fed infants had higher Actinomyces and Prevotella. Regardless of feeding mode, Propionibacterium, Porphyromonas, Prevotella, Gemella, Granulicatella, Veillonella, Fusobacterium, Leptotrichia, Neisseria, and Haemophilus increased with age, while Cloacibacterium and Dechloromonas decreased with age. Oral fungi were detected in infants but were not impacted by diet. Conclusions: These findings demonstrate that the establishment of oral bacteria depends on dietary composition and age. More research is necessary to determine whether this affects risk of oral caries and other health outcomes later in life.
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Affiliation(s)
- Patrícia M. Oba
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;
| | - Hannah D. Holscher
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Rose Ann Mathai
- Department of Nutrition, Dominican University, River Forest, IL 60305, USA;
| | - Juhee Kim
- Department of Nutrition, East Carolina State University, Greenville, NC 27834, USA;
| | - Kelly S. Swanson
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Correspondence: ; Tel.: +1-(217)-333-4189
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19
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Gerós-Mesquita Â, Carvalho-Pereira J, Franco-Duarte R, Alves A, Gerós H, Pais C, Sampaio P. Oral Candida albicans colonization in healthy individuals: prevalence, genotypic diversity, stability along time and transmissibility. J Oral Microbiol 2020; 12:1820292. [PMID: 33062200 PMCID: PMC7534343 DOI: 10.1080/20002297.2020.1820292] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/31/2020] [Accepted: 09/03/2020] [Indexed: 11/17/2022] Open
Abstract
In this study, 181 healthy individuals, including 29 couples, were analysed regarding oral yeast colonization using a culture-based approach. Results showed that 39% of the individuals were yeast carriers, 89% being colonized with Candida albicans, 5% with C. guilliermondi, 3% with C. lusitaniae and 3% with C. parapsilosis. Sixty-two percent of the couples had at least one member colonized. Colonization and CFU counts were higher in the couples´ group. Eighty percent of the volunteers were colonized with C. albicans strains with only one CAI genotype, while two but similar CAI genotypes inhabited the oral cavity of the remaining 20% individuals. The same CAI genotypes were found in 66.6% of the couples when both were colonized. Our results indicate that the intimacy among couples increases the probability of heavy cross-colonization, which is potentiated when one member of the couple is a smoker.
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Affiliation(s)
- Ângela Gerós-Mesquita
- CBMA (Centre of Molecular and Environmental Biology) / Department of Biology / University of Minho, Braga, Portugal
| | - Joana Carvalho-Pereira
- CBMA (Centre of Molecular and Environmental Biology) / Department of Biology / University of Minho, Braga, Portugal
| | - Ricardo Franco-Duarte
- CBMA (Centre of Molecular and Environmental Biology) / Department of Biology / University of Minho, Braga, Portugal
| | | | - Hernâni Gerós
- CBMA (Centre of Molecular and Environmental Biology) / Department of Biology / University of Minho, Braga, Portugal
- CITAB (Centre for the Research and Technology of Agro-Environmental and Biological Sciences) / University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
- CEB (Centre of Biological Engineering) /Department of Biological Engineering / University of Minho, Braga, Portugal
| | - Célia Pais
- CBMA (Centre of Molecular and Environmental Biology) / Department of Biology / University of Minho, Braga, Portugal
| | - Paula Sampaio
- CBMA (Centre of Molecular and Environmental Biology) / Department of Biology / University of Minho, Braga, Portugal
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20
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Diaz PI, Dongari-Bagtzoglou A. Critically Appraising the Significance of the Oral Mycobiome. J Dent Res 2020; 100:133-140. [PMID: 32924741 DOI: 10.1177/0022034520956975] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Recent efforts to understand the oral microbiome have focused on its fungal component. Since fungi occupy a low proportion of the oral microbiome biomass, mycobiome studies rely on sequencing of internal transcribed spacer (ITS) amplicons. ITS-based studies usually detect hundreds of fungi in oral samples. Here, we review the oral mycobiome, critically appraising the significance of such large fungal diversity. When harsh lysis methods are used to extract DNA, 2 oral mycobiome community types (mycotypes) are evident, each dominated by only 1 genus, either Candida or Malassezia. The rest of the diversity in ITS surveys represents low-abundance fungi possibly acquired from the environment and ingested food. So far, Candida is the only genus demonstrated to reach a significant biomass in the oral cavity and clearly shown to be associated with a distinct oral ecology. Candida thrives in the presence of lower oral pH and is enriched in caries, with mechanistic studies in animal models suggesting it participates in the disease process by synergistically interacting with acidogenic bacteria. Candida serves as the main etiological agent of oral mucosal candidiasis, in which a Candida-bacteriome partnership plays a key role. The function of other potential oral colonizers, such as lipid-dependent Malassezia, is still unclear, with further studies needed to establish whether Malassezia are metabolically active oral commensals. Low-abundance oral mycobiome members acquired from the environment may be viable in the oral cavity, and although they may not play a significant role in microbiome communities, they could serve as opportunistic pathogens in immunocompromised hosts. We suggest that further work is needed to ascertain the significance of oral mycobiome members beyond Candida. ITS-based surveys should be complemented with other methods to determine the in situ biomass and metabolic state of fungi thought to play a role in the oral environment.
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Affiliation(s)
- P I Diaz
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, State University of New York, Buffalo, NY, USA.,UB Microbiome Center, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - A Dongari-Bagtzoglou
- Division of Periodontology, Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, UConn Health, Farmington, CT, USA
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21
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Panteli N, Mastoraki M, Nikouli E, Lazarina M, Antonopoulou E, Kormas KA. Imprinting statistically sound conclusions for gut microbiota in comparative animal studies: A case study with diet and teleost fishes. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 36:100738. [PMID: 32896688 DOI: 10.1016/j.cbd.2020.100738] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022]
Abstract
Despite the technical progress in high-throughput sequencing technologies, defining the sample size which is capable of yielding representative inferences in metabarcoding analysis still remains debatable. The present study addresses the influence of individual variability in assessing dietary effects on fish gut microbiota parameters and estimates the biological sample size that is sufficient to imprint a statistically secure outcome. European sea bass (Dicentrarchus labrax) and gilthead sea bream (Sparus aurata) were fed three alternative animal protein diets and a fishmeal control diet. Gut microbiota data from 12 individuals per diet, derived from Illumina sequencing of the V3-V4 region of the 16S rRNA gene, were randomized in all possible combinations of n-1 individuals. Results in this study showcased that increasing the sample size can limit the prevalence of individuals with high microbial load on the outcome and can ensure the statistical confidence required for an accurate validation of dietary-induced microbe shifts. Inter-individual variability was evident in the four dietary treatments where consequently misleading inferences arose from insufficient biological replication. These findings have critical implications for the design of future metabarcoding studies and highlight the urgency in selecting an adequate sample size able to safely elucidate the dietary effects on fish gut microbial communities.
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Affiliation(s)
- Nikolas Panteli
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Maria Mastoraki
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Eleni Nikouli
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46 Volos, Greece
| | - Maria Lazarina
- Department of Ecology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Efthimia Antonopoulou
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece.
| | - Konstantinos A Kormas
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46 Volos, Greece
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22
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Hong BY, Hoare A, Cardenas A, Dupuy AK, Choquette L, Salner AL, Schauer PK, Hegde U, Peterson DE, Dongari-Bagtzoglou A, Strausbaugh LD, Diaz PI. The Salivary Mycobiome Contains 2 Ecologically Distinct Mycotypes. J Dent Res 2020; 99:730-738. [PMID: 32315566 DOI: 10.1177/0022034520915879] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A broad range of fungi has been detected in molecular surveys of the oral mycobiome. However, knowledge is still lacking on interindividual variability of these communities and the ecologic and clinical significance of oral fungal commensals. In this cross-sectional study, we use internal transcribed spacer 1 amplicon sequencing to evaluate the salivary mycobiome in 59 subjects, 36 of whom were scheduled to receive cancer chemotherapy. Analysis of the broad population structure of fungal communities in the whole cohort identified 2 well-demarcated genus-level community types (mycotypes), with Candida and Malassezia as the main taxa driving cluster partitioning. The Candida mycotype had lower diversity than the Malassezia mycotype and was positively correlated with cancer and steroid use in these subjects, smoking, caries, utilizing a removable prosthesis, and plaque index. Mycotypes were also associated with metabolically distinct bacteria indicative of divergent oral environments, with aciduric species enriched in the Candida mycotype and inflammophilic bacteria increased in the Malassezia mycotype. Similar to their fungal counterparts, coexisting bacterial communities associated with the Candida mycotype showed lower diversity than those associated with the Malassezia mycotype, suggesting that common environmental pressures affected bacteria and fungi. Mycotypes were also seen in an independent cohort of 24 subjects, in which cultivation revealed Malassezia as viable oral mycobiome members, although the low-abundance Malassezia sympodialis was the only Malassezia species recovered. There was a high degree of concordance between the molecular detection and cultivability of Candida, while cultivation showed low sensitivity for detection of the Malassezia mycotype. Overall, our work provides insights into the oral mycobiome landscape, revealing 2 community classes with apparently distinct ecologic constraints and specific associations with coexisting bacteria and clinical parameters. The utility of mycotypes as biomarkers for oral diseases warrants further study.
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Affiliation(s)
- B Y Hong
- Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, UConn Health, Farmington, CT, USA.,The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - A Hoare
- Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, UConn Health, Farmington, CT, USA.,Laboratorio de Microbiología Oral, Facultad de Odontología, Universidad de Chile, Santiago, Chile
| | - A Cardenas
- Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, UConn Health, Farmington, CT, USA
| | - A K Dupuy
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - L Choquette
- Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, UConn Health, Farmington, CT, USA.,The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - A L Salner
- Hartford Healthcare Cancer Institute at Hartford Hospital, Hartford, CT, USA
| | - P K Schauer
- Hartford Healthcare Cancer Institute at Hartford Hospital, Hartford, CT, USA
| | - U Hegde
- Department of Medicine, UConn Health, Farmington, CT, USA
| | - D E Peterson
- Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, UConn Health, Farmington, CT, USA
| | - A Dongari-Bagtzoglou
- Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, UConn Health, Farmington, CT, USA
| | - L D Strausbaugh
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - P I Diaz
- Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, UConn Health, Farmington, CT, USA
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23
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Observational Cohort Study of Oral Mycobiome and Interkingdom Interactions over the Course of Induction Therapy for Leukemia. mSphere 2020; 5:5/2/e00048-20. [PMID: 32295867 PMCID: PMC7160678 DOI: 10.1128/msphere.00048-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Although the term "microbiome" refers to all microorganisms, the majority of microbiome studies focus on the bacteriome. Here, we characterize the oral mycobiome, including mycobiome-bacteriome interactions, in the setting of remission-induction chemotherapy (RIC) for acute myeloid leukemia (AML). Oral samples (n = 299) were prospectively collected twice weekly from 39 AML patients during RIC until neutrophil recovery. Illumina MiSeq 16S rRNA gene (V4) and internal transcribed spacer 2 (ITS2) sequencing were used to determine bacterial and fungal diversity and community composition. Intrakingdom and interkingdom network connectivity at baseline (T1) and at midpoint (T3) and a later time point (T6) were assessed via SPIEC-EASI (sparse inverse covariance estimation for ecological association inference). In this exploratory study, mycobiome α-diversity was not significantly associated with antibiotic or antifungal receipt. However, postchemotherapy mycobiome α-diversity was lower in subjects receiving high-intensity chemotherapy. Additionally, greater decreases in Malassezia levels were seen over time among patients on high-intensity RIC compared to low-intensity RIC (P = 0.003). A significantly higher relative abundance of Candida was found among patients who had infection (P = 0.008), while a significantly higher relative abundance of Fusarium was found among patients who did not get an infection (P = 0.03). Analyses of intrakingdom and interkingdom relationships at T1, T3, and T6 indicated that interkingdom connectivity increased over the course of IC as bacterial α-diversity diminished. In (to our knowledge) the first longitudinal mycobiome study performed during AML RIC, we found that mycobiome-bacteriome interactions are highly dynamic. Our study data suggest that inclusion of mycobiome analysis in the design of microbiome studies may be necessary to optimally understand the ecological and functional role of microbial communities in clinical outcomes.IMPORTANCE This report highlights the importance of longitudinal, parallel characterization of oral fungi and bacteria in order to better elucidate the dynamic changes in microbial community structure and interkingdom functional interactions during the injury of chemotherapy and antibiotic exposure as well as the clinical consequences of these interrelated alterations.
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24
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Handschuh Briones RA, Silva Arcos EN, Urrutia M, Godoy-Martínez P. Actividad antifúngica de los enjuagues bucales frente a Candida albicans y Rhodotorula mucilaginosa: un estudio in vitro. Rev Iberoam Micol 2020; 37:47-52. [DOI: 10.1016/j.riam.2019.10.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 10/03/2019] [Accepted: 10/30/2019] [Indexed: 10/23/2022] Open
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25
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Azevedo MJ, Pereira MDL, Araujo R, Ramalho C, Zaura E, Sampaio-Maia B. Influence of delivery and feeding mode in oral fungi colonization - a systematic review. MICROBIAL CELL (GRAZ, AUSTRIA) 2020; 7:36-45. [PMID: 32025512 PMCID: PMC6993125 DOI: 10.15698/mic2020.02.706] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/19/2019] [Accepted: 12/02/2019] [Indexed: 12/18/2022]
Abstract
Postnatal acquisition of microorganisms from maternal and environmental sources contributes to the child microbiome development. Several studies showed that the mode of delivery and breastfeeding may have impact on the oral bacterial colonization, however, the influence on oral fungal colonization is still unknown. We performed a systematic literature review on mother to child oral fungi transmission, namely regarding the association between the mode of delivery and breastfeeding in oral yeast colonization. Our analysis revealed no significant differences between the oral mycobiome of breastfed and bottle-fed children. As for the delivery mode, the majority of studies found a relation between fungal colonization and vaginal delivery. Candida albicans was the most commonly isolated fungi species. Our analysis suggests that maternal breastfeeding does not seem to influence oral mycology, but vaginal delivery appears to promote oral yeast colonization in early life.
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Affiliation(s)
- Maria Joao Azevedo
- Faculdade de Medicina Dentária, Universidade do Porto, Portugal
- INEB – Instituto Nacional de Engenharia Biomédica, Universidade do Porto, Portugal
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
- Academic Center for Dentistry Amsterdam (ACTA), University of Amsterdam and Vrije Universiteit Amsterdam, the Netherlands
| | - Maria de Lurdes Pereira
- Faculdade de Medicina Dentária, Universidade do Porto, Portugal
- EpiUnit- Instituto de Saúde Pública, Universidade do Porto
| | - Ricardo Araujo
- INEB – Instituto Nacional de Engenharia Biomédica, Universidade do Porto, Portugal
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
- Dept. Medical Biotechnology, College of Medicine and Public Health, Flinders University of South Australia
| | - Carla Ramalho
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
- Faculdade de Medicina, Universidade do Porto, Portugal
- Centro Hospitalar São João, Porto, Portugal
| | - Egija Zaura
- Academic Center for Dentistry Amsterdam (ACTA), University of Amsterdam and Vrije Universiteit Amsterdam, the Netherlands
| | - Benedita Sampaio-Maia
- Faculdade de Medicina Dentária, Universidade do Porto, Portugal
- INEB – Instituto Nacional de Engenharia Biomédica, Universidade do Porto, Portugal
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
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26
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Diaz P, Valm A. Microbial Interactions in Oral Communities Mediate Emergent Biofilm Properties. J Dent Res 2020; 99:18-25. [PMID: 31590609 PMCID: PMC6927214 DOI: 10.1177/0022034519880157] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Oral microbial communities are extraordinarily complex in taxonomic composition and comprise interdependent biological systems. The bacteria, archaea, fungi, and viruses that thrive within these communities engage in extensive cell-cell interactions, which are both beneficial and antagonistic. Direct physical interactions among individual cells mediate large-scale architectural biofilm arrangements and provide spatial proximity for chemical communication and metabolic cooperation. In this review, we summarize recent work in identifying specific molecular components that mediate cell-cell interactions and describe metabolic interactions, such as cross-feeding and exchange of electron acceptors and small molecules, that modify the growth and virulence of individual species. We argue, however, that although pairwise interaction models have provided useful information, complex community-like systems are needed to study the properties of oral communities. The networks of multiple synergistic and antagonistic interactions within oral biofilms give rise to the emergent properties of persistence, stability, and long-range spatial structure, with these properties mediating the dysbiotic transitions from health to oral diseases. A better understanding of the fundamental properties of interspecies networks will lead to the development of effective strategies to manipulate oral communities.
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Affiliation(s)
- P.I. Diaz
- Division of Periodontology, Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, UConn Health, Farmington, CT, USA
| | - A.M. Valm
- Department of Biological Sciences, University at Albany, SUNY, Albany, NY, USA,A.M. Valm, Department of Biological Sciences, University at Albany, SUNY, 1400 Washington Ave., Albany, NY 12222, USA.
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27
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Azzam SZ, Cayme GJ, Martinez LR. Polymicrobial interactions involving fungi and their importance for the environment and in human disease. Microb Pathog 2019; 140:103942. [PMID: 31881258 DOI: 10.1016/j.micpath.2019.103942] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 01/08/2023]
Abstract
Understanding polymicrobial interactions involving fungi in the environment and the human mycobiome is necessary to address environmental and medically related problems such as drought or antimicrobial resistance. The diversity of these interactions highlights the complexity of fungi, considering how some interactions can be antagonistic, while others synergistic. Over the years, an increase in studies on the mycobiome have revealed similarities between the human and environmental hosts. More recently, studies have focused on microbial commensal relationships and identifying causative agents of human disease. The overlap of some of these interactions is impossible to ignore, indicating that there are areas for medical exploitation that need to be further investigated. This review provides the latest advances in polymicrobial interactions involving fungi and discusses the importance of the fungal lifestyle in the environment and in human disease.
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Affiliation(s)
- Seham Z Azzam
- Department of Biological Sciences, The Border Biomedical Research Center, University of Texas at El Paso, TX, USA
| | - Ginelle J Cayme
- Department of Biological Sciences, The Border Biomedical Research Center, University of Texas at El Paso, TX, USA
| | - Luis R Martinez
- Department of Biological Sciences, The Border Biomedical Research Center, University of Texas at El Paso, TX, USA; Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA.
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28
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Abstract
The oral microbiota is complex, multikingdom, interactive, and involves extensive biofilm formation. While dominated by bacteria, Candida is a frequent member of this microbiota; however, several other potentially pathogenic fungi (among around 100 identified species) appear to reside in some individuals, including Cryptococcus, Aspergillus, and Fusarium. Oral candidiasis may manifest as a variety of disease entities in normal hosts and in the immunocompromised. These include pseudomembranous candidiasis (thrush), hyperplastic or atrophic (denture) candidiasis, linear gingival erythema, median rhomboid glossitis, and angular cheilitis. The purpose of this review is to describe the oral fungal microbiota (ie, oral mycobiota), common mouth diseases caused by its members, predisposing factors and treatment, and the potential for causing disseminated disease like their bacterial counterparts.
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Affiliation(s)
- Dennis J Baumgardner
- Department of Family Medicine, Aurora UW Medical Group, Aurora Health Care, Milwaukee, WI; Department of Family Medicine and Community Health, University of Wisconsin School of Medicine and Public Health, Madison, WI; Center for Urban Population Health, Milwaukee, WI
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Miller DP, Fitzsimonds ZR, Lamont RJ. Metabolic Signaling and Spatial Interactions in the Oral Polymicrobial Community. J Dent Res 2019; 98:1308-1314. [PMID: 31356756 DOI: 10.1177/0022034519866440] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Oral supra- and subgingival biofilms are complex communities in which hundreds of bacteria, viruses, and fungi reside and interact. In these social environments, microbes compete and cooperate for resources, such as living space and nutrients. The metabolic activities of bacteria can transform their microenvironment and dynamically influence the fitness and growth of cohabitating organisms. Biofilm communities are temporally and spatially organized largely due to cell-to-cell communication, which promotes synergistic interactions. Metabolic interactions maintain biofilm homeostasis through mutualistic cross-feeding, metabolic syntrophy, and cross-respiration. These interactions include reciprocal metabolite exchanges that promote the growth of physiologically compatible bacteria, processive catabolism of complex substrates, and unidirectional interactions that are globally important for the polymicrobial community. Additionally, oral bacterial interactions can lead to detoxification of oxidative compounds, which will provide protection to the community at large. It has also been established that specific organisms provide terminal electron acceptors to partner species that result in a shift from fermentation to respiration, thus increasing ATP yields and improving fitness. Indeed, many interspecies relationships are multidimensional, and the net outcome can be spatially and temporally dependent. Cross-kingdom interactions also occur as oral yeast are antagonistic to some oral bacteria, while numerous mutualistic interactions contribute to yeast-bacterial colonization, fitness in the oral community, and the pathogenesis of caries. Consideration of this social environment reveals behaviors and phenotypes that are not apparent through the study of microbes in isolation. Here, we provide a comprehensive overview of the metabolic interactions that shape the oral microbial community.
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Affiliation(s)
- D P Miller
- Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, KY, USA
| | - Z R Fitzsimonds
- Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, KY, USA
| | - R J Lamont
- Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, KY, USA
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30
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Krüger W, Vielreicher S, Kapitan M, Jacobsen ID, Niemiec MJ. Fungal-Bacterial Interactions in Health and Disease. Pathogens 2019; 8:E70. [PMID: 31117285 PMCID: PMC6630686 DOI: 10.3390/pathogens8020070] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/02/2019] [Accepted: 05/16/2019] [Indexed: 12/28/2022] Open
Abstract
Fungi and bacteria encounter each other in various niches of the human body. There, they interact directly with one another or indirectly via the host response. In both cases, interactions can affect host health and disease. In the present review, we summarized current knowledge on fungal-bacterial interactions during their commensal and pathogenic lifestyle. We focus on distinct mucosal niches: the oral cavity, lung, gut, and vagina. In addition, we describe interactions during bloodstream and wound infections and the possible consequences for the human host.
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Affiliation(s)
- Wibke Krüger
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena 07745, Germany.
| | - Sarah Vielreicher
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena 07745, Germany.
| | - Mario Kapitan
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena 07745, Germany.
- Center for Sepsis Control and Care, Jena 07747, Germany.
| | - Ilse D Jacobsen
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena 07745, Germany.
- Center for Sepsis Control and Care, Jena 07747, Germany.
- Institute of Microbiology, Friedrich Schiller University, Jena 07743, Germany.
| | - Maria Joanna Niemiec
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena 07745, Germany.
- Center for Sepsis Control and Care, Jena 07747, Germany.
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31
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Zakrzewski M, Simms LA, Brown A, Appleyard M, Irwin J, Waddell N, Radford-Smith GL. IL23R-Protective Coding Variant Promotes Beneficial Bacteria and Diversity in the Ileal Microbiome in Healthy Individuals Without Inflammatory Bowel Disease. J Crohns Colitis 2019; 13:451-461. [PMID: 30445599 DOI: 10.1093/ecco-jcc/jjy188] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND AND AIMS This study aimed to characterize the mucosa-associated microbiota in ileal Crohn's disease [CD] patients and in healthy controls in terms of host genotype and inflammation status. METHODS The mucosa-associated microbiotas of intestinal pinch biopsies from 15 ileal CD patients with mild and moderate disease and from 58 healthy controls were analysed based on 16S ribosomal sequencing to determine microbial profile differences between [1] IL23R, NOD2 and ATG16L1 genotypes in healthy subjects, [2] ileal CD patients and control subjects, and [3] inflamed and non-inflamed mucosal tissue in CD patients. RESULTS The protective variant of the IL23R gene [rs11209026] significantly impacted the microbial composition in the ileum of healthy subjects and was associated with an increased abundance of phylotypes within the family Christensenellaceae as well as increases in diversity and richness. Comparative analysis of healthy and non-inflamed CD microbiome samples indicated a notable decrease in the abundance of Faecalibacterium prausnitzii as well as Shannon diversity and richness. Inflamed and non-inflamed ileal samples of CD subjects had high intra-individual stability and inter-individual variability, but no significant alterations in diversity, richness or taxa were identified. Calprotectin correlated positively with the abundance of Proteobacteria and negatively with diversity in the samples from healthy subjects. CONCLUSIONS The observation of low diversity and low abundance of beneficial bacteria in healthy control subjects carrying the IL23R [rs11209026] wild-type GG genotype indicates that the gut microbiome is influenced by host genetics and is altered prior to disease diagnosis. Faecal calprotectin may be a potential non-invasive screening tool for dysbiosis in subjects without disorders of intestinal inflammation.
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Affiliation(s)
- Martha Zakrzewski
- Medical Genomics, QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, Australia
| | - Lisa A Simms
- Gut Health, QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, Australia
| | - Allison Brown
- Gut Health, QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, Australia.,Department of Gastroenterology and Hepatology, Royal Brisbane and Women's Hospital, Herston, Brisbane 4029, Australia
| | - Mark Appleyard
- Department of Gastroenterology and Hepatology, Royal Brisbane and Women's Hospital, Herston, Brisbane 4029, Australia
| | - James Irwin
- Gut Health, QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, Australia.,Department of Gastroenterology, Palmerston North Hospital, Palmerston North, New Zealand
| | - Nicola Waddell
- Medical Genomics, QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, Australia
| | - Graham L Radford-Smith
- Gut Health, QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, Australia.,Department of Gastroenterology and Hepatology, Royal Brisbane and Women's Hospital, Herston, Brisbane 4029, Australia.,University of Queensland School of Medicine, Herston, Brisbane 4029, Australia
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32
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Detection and identification of fungi in bronchoalveolar lavage fluid from immunocompromised patients using panfungal PCR. Folia Microbiol (Praha) 2018; 64:421-428. [PMID: 30535753 DOI: 10.1007/s12223-018-00669-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 11/29/2018] [Indexed: 01/24/2023]
Abstract
Rapid diagnostics of fungal pneumonia and initiation of appropriate therapy are still challenging. In this study, we used two panfungal assays to test bronchoalveolar lavage fluid (BALF) samples to prove their ability to confirm invasive fungal disease diagnosis and identify causative agents. Two methods targeting different fungal rDNA regions were used, and the obtained PCR products were sequenced directly or after cloning. In total, 106 BALF samples from 104 patients were tested. After sequencing, we obtained 578 sequences. Four hundred thirty-seven sequences were excluded from further analysis due to duplication (n = 335) or similarity with sequences detected in the extraction control sample (n = 102); 141 unique sequences were analyzed. Altogether, 23/141 (16%) of the fungi detected belonged to pathogenic species, and 63/141 (45%) were identified as various yeasts; a variety of environmental or very rare fungal human pathogens represented 29/141 (21%) of the total and 26/141 (18%) were described as uncultured fungus. Panfungal PCR detected fungal species that would be missed by specific methods in only one case (probable cryptococcosis). Panfungal PCR followed by sequencing has limited use for testing BALF samples due to frequent commensal or environmental fungal species pickup.
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33
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Fechney JM, Browne GV, Prabhu N, Irinyi L, Meyer W, Hughes T, Bockmann M, Townsend G, Salehi H, Adler CJ. Preliminary study of the oral mycobiome of children with and without dental caries. J Oral Microbiol 2018; 11:1536182. [PMID: 30598729 PMCID: PMC6225480 DOI: 10.1080/20002297.2018.1536182] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 09/23/2018] [Accepted: 10/01/2018] [Indexed: 12/31/2022] Open
Abstract
Children’s oral health is in a dire state, with dental decay (caries) being one of the most common chronic diseases. While the role of bacteria in the oral microbiome and dental caries is established, the contribution of fungi is relatively unknown. We assessed the oral mycobiome in childhood (n = 17), to determine if the composition of fungi varies between children with and without caries. Oral mycobiome composition was assessed by using Illumina MiSeq to sequence the ITS2 region, which was amplified from dental plaque. This revealed that the oral mycobiome in the investigated children contained 46 fungal species. Candida albicans was the most abundant species and was ubiquitous in all samples, indicating this species may not be involved in caries development as previously suggested. While the overall diversity of fungi was similar, independent of caries status (p > 0.05), we found caries influenced the abundance of specific fungi. Children without caries had a significantly higher abundance of 17 species compared to children with caries, which had three enriched species (p < 0.001). While the differentially abundant species between health and caries may be specific to an Australian population, our findings indicate the mycobiome plays a role in oral health.
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Affiliation(s)
- Jacquelyn M Fechney
- Discipline of Pediatric Dentistry, Westmead Centre for Oral Health, University of Sydney, Sydney, Australia
| | - Gina V Browne
- Institute of Dental Research, School of Dentistry, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Neeta Prabhu
- Discipline of Pediatric Dentistry, Westmead Centre for Oral Health, University of Sydney, Sydney, Australia
| | - Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Hospital, Faculty of Medicine and Health, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia.,Westmead Institute for Medical Research, Sydney, Australia
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Hospital, Faculty of Medicine and Health, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia.,Westmead Institute for Medical Research, Sydney, Australia
| | - Toby Hughes
- Adelaide Dental School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
| | - Michelle Bockmann
- Adelaide Dental School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
| | - Grant Townsend
- Adelaide Dental School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
| | - Hanieh Salehi
- Institute of Dental Research, School of Dentistry, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Christina J Adler
- Institute of Dental Research, School of Dentistry, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
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34
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De-La-Torre J, Quindós G, Marcos-Arias C, Marichalar-Mendia X, Gainza ML, Eraso E, Acha-Sagredo A, Aguirre-Urizar JM. Oral Candida colonization in patients with chronic periodontitis. Is there any relationship? Rev Iberoam Micol 2018; 35:134-139. [PMID: 30082174 DOI: 10.1016/j.riam.2018.03.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 02/13/2018] [Accepted: 03/14/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Candida can be implicated in the pathology of chronic periodontitis. AIMS To analyze the oral Candida carriage in patients suffering from chronic periodontitis (CP) and its correlation with the severity of this condition. METHODS Microbiological samples were taken from 155 patients using the oral rinse (OR) technique and by using paper points in the periodontal pockets (GPP). These patients were divided into 3 groups: 89 patients without CP (control), 47 with moderate CP, and 19 with severe CP. Samples were cultured in a Candida chromogenic agar for Candida. Species were identified by microbiological and molecular methods. RESULTS Candida was isolated in the OR of 45 (50.6%), 21 (44.7%), and 11 (57.9%) patients, respectively, and in the GPP of 32 (36%), 14 (29.2%), and 10 (42.6%) patients from the control, moderate CP and severe CP groups, respectively. Candida was isolated more frequently and in a greater burden in OR than in GPP (p<0.01). Candida albicans was the most prevalent species. GPP of patients with CP had poor fungal biodiversity (p<0.01). CONCLUSIONS Colonization by Candida was present in the samples of patients without CP, and with both moderate and severe CP. Nonetheless, patients with severe CP had a higher rate of Candida colonization, especially by C. albicans.
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Affiliation(s)
- Janire De-La-Torre
- Department of Immunology, Microbiology and Parasitology, Unidad de formación e investigación multidisciplinar "Microbios y Salud" (UFI 11/25), Faculty of Medicine and Dentistry, University of the Basque Country/Euskal Herriko Unibertsitatea, Leioa, Spain; Department of Stomatology II, Unidad de formación e investigación multidisciplinar "Microbios y Salud" (UFI 11/25), Faculty of Medicine and Dentistry, University of the Basque Country/Euskal Herriko Unibertsitatea, Leioa, Spain.
| | - Guillermo Quindós
- Department of Immunology, Microbiology and Parasitology, Unidad de formación e investigación multidisciplinar "Microbios y Salud" (UFI 11/25), Faculty of Medicine and Dentistry, University of the Basque Country/Euskal Herriko Unibertsitatea, Leioa, Spain
| | - Cristina Marcos-Arias
- Department of Immunology, Microbiology and Parasitology, Unidad de formación e investigación multidisciplinar "Microbios y Salud" (UFI 11/25), Faculty of Medicine and Dentistry, University of the Basque Country/Euskal Herriko Unibertsitatea, Leioa, Spain
| | - Xabier Marichalar-Mendia
- Department of Stomatology II, Unidad de formación e investigación multidisciplinar "Microbios y Salud" (UFI 11/25), Faculty of Medicine and Dentistry, University of the Basque Country/Euskal Herriko Unibertsitatea, Leioa, Spain
| | - María Luisa Gainza
- Department of Dental Surgery, Faculty of Dental Surgery, University of Malta, Malta
| | - Elena Eraso
- Department of Immunology, Microbiology and Parasitology, Unidad de formación e investigación multidisciplinar "Microbios y Salud" (UFI 11/25), Faculty of Medicine and Dentistry, University of the Basque Country/Euskal Herriko Unibertsitatea, Leioa, Spain
| | - Amelia Acha-Sagredo
- Department of Stomatology II, Unidad de formación e investigación multidisciplinar "Microbios y Salud" (UFI 11/25), Faculty of Medicine and Dentistry, University of the Basque Country/Euskal Herriko Unibertsitatea, Leioa, Spain
| | - José Manuel Aguirre-Urizar
- Department of Stomatology II, Unidad de formación e investigación multidisciplinar "Microbios y Salud" (UFI 11/25), Faculty of Medicine and Dentistry, University of the Basque Country/Euskal Herriko Unibertsitatea, Leioa, Spain
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Bandara HMHN, Panduwawala CP, Samaranayake LP. Biodiversity of the human oral mycobiome in health and disease. Oral Dis 2018; 25:363-371. [PMID: 29786923 DOI: 10.1111/odi.12899] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 05/14/2018] [Accepted: 05/15/2018] [Indexed: 01/01/2023]
Abstract
The organisms that colonize the human body over a lifetime are diverse, extensive and gargantuan. A fair proportion of the microbiota that constitutes this human microbiome live within our oral cavities mostly as harmonious associates causing only sporadic disease. An important core constituent of the microbiome is the mycobiome, representing various fungal genera. Up until recently, only a few species of fungi, mainly Candida species, were thought to constitute the human oral mycobiome. The reasons for this are manifold, although the uncultivable nature of many fungi in conventional laboratory media, and their complex genetic composition seem to be the major factors which eluded their detection over the years. Nevertheless, recent advances in computing and high-throughput sequencing such as next-generation sequencing (NGS) platforms have provided us a panoramic view of a totally new world of fungi that are human oral cohabitués. Their diversity is perplexing, and functionality yet to be deciphered. Here, we provide a glimpse of what is currently known of the oral mycobiome, in health and disease, with some future perspectives.
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Affiliation(s)
| | - Chamila P Panduwawala
- Department of Oral and Craniofacial Health Sciences, College of Dental Medicine, University of Sharjah, Sharjah, UAE
| | - Lakshman Perera Samaranayake
- Department of Oral and Craniofacial Health Sciences, College of Dental Medicine, University of Sharjah, Sharjah, UAE
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36
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Oral Yeast Colonization and Fungal Infections in Peritoneal Dialysis Patients: A Pilot Study. CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2017; 2017:4846363. [PMID: 29430252 PMCID: PMC5753011 DOI: 10.1155/2017/4846363] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 11/06/2017] [Indexed: 01/24/2023]
Abstract
Peritonitis and exit-site infections are important complications in peritoneal dialysis (PD) patients that are occasionally caused by opportunistic fungi inhabiting distant body sites. In this study, the oral yeast colonization of PD patients and the antifungal susceptibility profile of the isolated yeasts were accessed and correlated with fungal infection episodes in the following 4 years. Saliva yeast colonization was accessed in 21 PD patients and 27 healthy controls by growth in CHROMagar-Candida® and 18S rRNA/ITS sequencing. PD patients presented a lower oral yeast prevalence when compared to controls, namely, Candida albicans. Other species were also isolated, Candida glabrata and Candida carpophila. The antifungal susceptibility profiles of these isolates revealed resistance to itraconazole, variable susceptibility to caspofungin, and higher MIC values of posaconazole compared to previous reports. The 4-year longitudinal evaluation of these patients revealed Candida parapsilosis and Candida zeylanoides as PD-related exit-site infectious agents, but no correlation was found with oral yeast colonization. This pilot study suggests that oral yeast colonization may represent a limited risk for fungal infection development in PD patients. Oral yeast isolates presented a variable antifungal susceptibility profile, which may suggest resistance to some second-line drugs, highlighting the importance of antifungal susceptibility assessment in the clinical practice.
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37
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Nash AK, Auchtung TA, Wong MC, Smith DP, Gesell JR, Ross MC, Stewart CJ, Metcalf GA, Muzny DM, Gibbs RA, Ajami NJ, Petrosino JF. The gut mycobiome of the Human Microbiome Project healthy cohort. MICROBIOME 2017; 5:153. [PMID: 29178920 PMCID: PMC5702186 DOI: 10.1186/s40168-017-0373-4] [Citation(s) in RCA: 519] [Impact Index Per Article: 74.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 11/14/2017] [Indexed: 05/02/2023]
Abstract
BACKGROUND Most studies describing the human gut microbiome in healthy and diseased states have emphasized the bacterial component, but the fungal microbiome (i.e., the mycobiome) is beginning to gain recognition as a fundamental part of our microbiome. To date, human gut mycobiome studies have primarily been disease centric or in small cohorts of healthy individuals. To contribute to existing knowledge of the human mycobiome, we investigated the gut mycobiome of the Human Microbiome Project (HMP) cohort by sequencing the Internal Transcribed Spacer 2 (ITS2) region as well as the 18S rRNA gene. RESULTS Three hundred seventeen HMP stool samples were analyzed by ITS2 sequencing. Fecal fungal diversity was significantly lower in comparison to bacterial diversity. Yeast dominated the samples, comprising eight of the top 15 most abundant genera. Specifically, fungal communities were characterized by a high prevalence of Saccharomyces, Malassezia, and Candida, with S. cerevisiae, M. restricta, and C. albicans operational taxonomic units (OTUs) present in 96.8, 88.3, and 80.8% of samples, respectively. There was a high degree of inter- and intra-volunteer variability in fungal communities. However, S. cerevisiae, M. restricta, and C. albicans OTUs were found in 92.2, 78.3, and 63.6% of volunteers, respectively, in all samples donated over an approximately 1-year period. Metagenomic and 18S rRNA gene sequencing data agreed with ITS2 results; however, ITS2 sequencing provided greater resolution of the relatively low abundance mycobiome constituents. CONCLUSIONS Compared to bacterial communities, the human gut mycobiome is low in diversity and dominated by yeast including Saccharomyces, Malassezia, and Candida. Both inter- and intra-volunteer variability in the HMP cohort were high, revealing that unlike bacterial communities, an individual's mycobiome is no more similar to itself over time than to another person's. Nonetheless, several fungal species persisted across a majority of samples, evidence that a core gut mycobiome may exist. ITS2 sequencing data provided greater resolution of the mycobiome membership compared to metagenomic and 18S rRNA gene sequencing data, suggesting that it is a more sensitive method for studying the mycobiome of stool samples.
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Affiliation(s)
- Andrea K. Nash
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
| | - Thomas A. Auchtung
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
| | - Matthew C. Wong
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
| | - Daniel P. Smith
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
| | - Jonathan R. Gesell
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
| | - Matthew C. Ross
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
| | - Christopher J. Stewart
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
| | - Ginger A. Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Nadim J. Ajami
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
| | - Joseph F. Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX USA
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Bourgeois D, David A, Inquimbert C, Tramini P, Molinari N, Carrouel F. Quantification of carious pathogens in the interdental microbiota of young caries-free adults. PLoS One 2017; 12:e0185804. [PMID: 29016613 PMCID: PMC5634565 DOI: 10.1371/journal.pone.0185804] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 09/19/2017] [Indexed: 11/06/2022] Open
Abstract
Background The majority of caries lesions in adults occur on the proximal tooth surfaces of the posterior teeth. A comprehensive study of the composition of the oral microbiota is fundamental for a better understanding of the etiology of interdental caries. Methods Twenty-five caries-free subjects (20–35 years old) were enrolled in the study. The interdental biofilm of four interdental sites were collected. The real-time polymerase chain reaction (PCR) methodology were used to quantify (i) the following bacteria: Streptococcus spp., Streptococcus mutans, Lactobacillus spp., Enterococcus spp., and Enterococcus faecalis; (ii) the fungus Candida albicans; and (iii) total bacteria. Results Streptococcus spp. was the most abundant species, followed by Lactobacillus spp. and Enterococcus spp. Streptococcus spp. and Lactobacillus spp. were detected at all tested sites and Enterococcus spp. at 99% of sites. S. mutans was detected at only 28% of the tested sites and C. albicans was detected at 11% of sites. E. faecalis was never detected. In 54.5% of the biofilm inhabited by C. albicans, S. mutans was present. Moreover, 28% of the ID sites co-expressed S. mutans and Lactobacillus spp. The studied pathogens were organized into two correlated groups of species. Strikingly, the fungus C. albicans and the bacteria Enterococcus spp. cluster together, whereas Streptococcus spp., S. mutans and Lactobacillus spp. form one distinct cluster. Conclusion The interdental biofilm of young caries-free adults is comprised of pathogens that are able to induce interproximal caries. That several of these pathogens are implicated in heart disease or other systemic diseases is an argument for the disruption of interdental biofilms using daily oral hygiene.
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Affiliation(s)
- Denis Bourgeois
- Laboratory "Systemic Health Care" EA4129, University Lyon 1, Lyon, France
- Department of Prevention and Public Health, Faculty of Dentistry, University Lyon 1, Lyon, France
- * E-mail:
| | - Alexandra David
- Laboratory "Systemic Health Care" EA4129, University Lyon 1, Lyon, France
| | - Camille Inquimbert
- Laboratory "Systemic Health Care" EA4129, University Lyon 1, Lyon, France
| | - Paul Tramini
- Department of Dental Public Health, University of Montpellier, Montpellier, France
| | - Nicolas Molinari
- Service DIM, CHU de Montpellier, UMR 5149 IMAG, University of Montpellier, Montpellier, France
| | - Florence Carrouel
- Laboratory "Systemic Health Care" EA4129, University Lyon 1, Lyon, France
- Department Basic and Clinical Biological Sciences, Faculty of Dentistry, University Lyon 1, Lyon, France
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39
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Lof M, Janus MM, Krom BP. Metabolic Interactions between Bacteria and Fungi in Commensal Oral Biofilms. J Fungi (Basel) 2017; 3:jof3030040. [PMID: 29371557 PMCID: PMC5715944 DOI: 10.3390/jof3030040] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 07/10/2017] [Accepted: 07/12/2017] [Indexed: 12/14/2022] Open
Abstract
Oral health is more than just the absence of disease. The key to oral health is a diverse microbiome in an ecological balance. The oral microbiota is one of the most complex and diverse microbial communities in the human body. To maintain oral health, balance between the human host and the intrinsic microorganisms is essential. The healthy oral cavity is represented by a great microbial diversity, including both bacteria and fungi. The bacterial microbiome is very well studied. In contrast, fungi inhabiting the oral cavity are often overlooked. All microbial species in the oral cavity form communities which establish a variety of micro-niches and inter- and intra-species interactions. These interactions can be classified into three main groups: physical, chemical and metabolic interactions. Different metabolic interactions are reviewed in this report, among which are the metabolism of sugars, carbon, lactate and oxygen. This review set out with the aim of assessing the importance of metabolic interactions between fungi and bacteria in the healthy oral cavity.
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Affiliation(s)
- Marloes Lof
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), Vrije Universiteit Amsterdam and the University of Amsterdam, Amsterdam, 1081 LA, The Netherlands.
| | - Marleen M Janus
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), Vrije Universiteit Amsterdam and the University of Amsterdam, Amsterdam, 1081 LA, The Netherlands.
| | - Bastiaan P Krom
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), Vrije Universiteit Amsterdam and the University of Amsterdam, Amsterdam, 1081 LA, The Netherlands.
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Rio R, Simões-Silva L, Garro S, Silva MJ, Azevedo Á, Sampaio-Maia B. Oral yeast colonization throughout pregnancy. Med Oral Patol Oral Cir Bucal 2017; 22:e144-e148. [PMID: 28160578 PMCID: PMC5359706 DOI: 10.4317/medoral.21413] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 12/06/2016] [Indexed: 01/11/2023] Open
Abstract
Background Recent studies suggest that placenta may harbour a unique microbiome that may have origin in maternal oral microbiome. Although the major physiological and hormonal adjustments observed in pregnant women lead to biochemical and microbiological modifications of the oral environment, very few studies evaluated the changes suffered by the oral microbiota throughout pregnancy. So, the aim of our study was to evaluate oral yeast colonization throughout pregnancy and to compare it with non-pregnant women. Material and Methods The oral yeast colonization was assessed in saliva of 30 pregnant and non-pregnant women longitudinally over a 6-months period. Demographic information was collected, a non-invasive intra-oral examination was performed and saliva flow and pH were determined. Results Pregnant and non-pregnant groups were similar regarding age and level of education. Saliva flow rate did not differ, but saliva pH was lower in pregnant than in non-pregnant women. Oral yeast prevalence was higher in pregnant than in non-pregnant women, either in the first or in the third trimester, but did not attain statistical significance. In individuals colonized with yeast, the total yeast quantification (Log10CFU/mL) increase from the 1st to the 3rd trimester in pregnant women, but not in non-pregnant women. Conclusions Pregnancy may favour oral yeast growth that may be associated with an acidic oral environment. Key words:Oral yeast, fungi, pregnancy, saliva pH.
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Affiliation(s)
- R Rio
- Faculdade de Medicina, Dentária da Universidade do Porto, Rua Dr. Manuel Pereira da Silva, 4200-393 Porto, Portugal,
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Persoon IF, Crielaard W, Özok AR. Prevalence and nature of fungi in root canal infections: a systematic review and meta-analysis. Int Endod J 2017; 50:1055-1066. [PMID: 27987307 DOI: 10.1111/iej.12730] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 11/28/2016] [Indexed: 12/14/2022]
Abstract
The role of bacteria in causing apical periodontitis has been widely established, whilst the role of other microorganisms is studied less thoroughly. This systematic review and meta-analysis reviewed the literature for the prevalence and diversity of fungi in root canal infections. An extensive literature search was carried out in the Cochrane databases, EMBASE, MEDLINE, LILACS, SciELO and Web of Science. Additional studies were identified from six endodontic journals, four main endodontic textbooks and references of relevant papers. Selected clinical studies included sampling of necrotic pulps in permanent teeth and microbial analysis of these samples. Studies were critically appraised using the Joanna Briggs Institute Prevalence Critical Appraisal Checklist. Meta-analysis was performed using MetaXL. The screening of 1041 titles and abstracts and full-text reading yielded 54 studies. The overall prevalence of fungi in root canal infections was 7.5% (CI 95%: 3.6-11.8%) in the inverse variance fixed effect heterogeneity model. Candida albicans was the most frequently isolated species. Significant heterogeneity was observed (P < 0.001, I2 = 85.04%). Subgroup analyses based on geographical location, period of publication, type of infection, state of general health, communication with the oral cavity, type of sample and identification method revealed no factor influencing the prevalence. Better standardized techniques and a comprehensive analysis will reveal a more detailed and accurate representation of the prevalence and nature of fungi in root canal infections.
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Affiliation(s)
- I F Persoon
- Department of Preventive Dentistry, University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - W Crielaard
- Department of Preventive Dentistry, University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - A R Özok
- Department of Endodontology, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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42
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Diaz PI, Hong BY, Dupuy AK, Strausbaugh LD. Mining the oral mycobiome: Methods, components, and meaning. Virulence 2016; 8:313-323. [PMID: 27791473 DOI: 10.1080/21505594.2016.1252015] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Research on oral fungi has centered on Candida. However, recent internal transcribed spacer (ITS)-based studies revealed a vast number of fungal taxa as potential oral residents. We review DNA-based studies of the oral mycobiome and contrast them with cultivation-based surveys, showing that most genera encountered by cultivation have also been detected molecularly. Some taxa such as Malassezia, however, appear in high prevalence and abundance in molecular studies but have not been cultivated. Important technical and bioinformatic challenges to ITS-based oral mycobiome studies are discussed. These include optimization of sample lysis, variability in length of ITS amplicons, high intra-species ITS sequence variability, high inter-species variability in ITS copy number and challenges in nomenclature and maintenance of curated reference databases. Molecular surveys are powerful first steps to characterize the oral mycobiome but further research is needed to unravel which fungi detected by DNA are true oral residents and what role they play in oral homeostasis.
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Affiliation(s)
- Patricia I Diaz
- a Division of Periodontology, Department of Oral Health and Diagnostic Sciences , School of Dental Medicine, UConn Health , Farmington , CT , USA
| | - Bo-Young Hong
- a Division of Periodontology, Department of Oral Health and Diagnostic Sciences , School of Dental Medicine, UConn Health , Farmington , CT , USA
| | - Amanda K Dupuy
- b Institute for Systems Genomics, University of Connecticut , Storrs , CT , USA
| | - Linda D Strausbaugh
- b Institute for Systems Genomics, University of Connecticut , Storrs , CT , USA
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Sampaio-Maia B, Caldas IM, Pereira ML, Pérez-Mongiovi D, Araujo R. The Oral Microbiome in Health and Its Implication in Oral and Systemic Diseases. ADVANCES IN APPLIED MICROBIOLOGY 2016; 97:171-210. [PMID: 27926431 DOI: 10.1016/bs.aambs.2016.08.002] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The oral microbiome can alter the balance between health and disease, locally and systemically. Within the oral cavity, bacteria, archaea, fungi, protozoa, and viruses may all be found, each having a particular role, but strongly interacting with each other and with the host, in sickness or in health. A description on how colonization occurs and how the oral microbiome dynamically evolves throughout the host's life is given. In this chapter the authors also address oral and nonoral conditions in which oral microorganisms may play a role in the etiology and progression, presenting the up-to-date knowledge on oral dysbiosis as well as the known underlying pathophysiologic mechanisms involving oral microorganisms in each condition. In oral pathology, oral microorganisms are associated with several diseases, namely dental caries, periodontal diseases, endodontic infections, and also oral cancer. In systemic diseases, nonoral infections, adverse pregnancy outcomes, cardiovascular diseases, and diabetes are among the most prevalent pathologies linked with oral cavity microorganisms. The knowledge on how colonization occurs, how oral microbiome coevolves with the host, and how oral microorganisms interact with each other may be a key factor to understand diseases etiology and progression.
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Affiliation(s)
| | - I M Caldas
- Universidade do Porto, Portugal; Institute of Research and Advanced Training in Health Sciences and Technologies, University Institute of Health Sciences (IUCS), CESPU, CRL, Gandra, Portugal; Universidade de Coimbra, Portugal
| | | | - D Pérez-Mongiovi
- Institute of Research and Advanced Training in Health Sciences and Technologies, University Institute of Health Sciences (IUCS), CESPU, CRL, Gandra, Portugal
| | - R Araujo
- Universidade do Porto, Portugal; Flinders University, Adelaide, SA, Australia
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Sheth CC, Makda K, Dilmahomed Z, González R, Luzi A, Jovani-Sancho MDM, Veses V. Alcohol and tobacco consumption affect the oral carriage of Candida albicans and mutans streptococci. Lett Appl Microbiol 2016; 63:254-9. [PMID: 27450704 DOI: 10.1111/lam.12620] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 06/02/2016] [Accepted: 06/02/2016] [Indexed: 11/29/2022]
Abstract
UNLABELLED This study sought to determine if there is a relationship between the consumption of alcohol and tobacco and oral colonization by mutans streptococci and Candida species. Subjects were recruited from the University Dental Clinic of CEU Cardenal Herrera University (Moncada, Valencia). Information on alcohol and tobacco consumption was obtained by questionnaire. Individual stimulated saliva samples from 105 patients were obtained and selective media was used to isolate and quantify mutans streptococci and Candida spp. colony forming units per millilitre of saliva (CFU ml(-1) ). Samples were stratified by duration and quantity of alcohol and tobacco consumption. Alcohol consumption statistically significantly decreased oral carriage of mutans streptococci, whereas there was no effect on Candida albicans colonization levels. Tobacco users were found to harbour elevated levels of C. albicans; however, there was no observed effect on bacterial colonization by mutans streptococci. The carriage of other species investigated, such as Candida krusei, Candida tropicalis and lactobacilli, do not show a response to the consumption of the stimulants analysed. Microbial colonization of the oral cavity changes in a species-specific manner in response to dietary and social habits such as drinking alcohol and smoking. SIGNIFICANCE AND IMPACT OF THE STUDY In this paper, we evaluate the effect of alcohol and tobacco consumption on key species of the oral microflora. Our results show species-specific changes in two major opportunistic pathogens, such as Candida albicans and mutans streptococci, whereas other members of oral microflora are not affected by the consumption of the stimulants studied. We believe this original paper will contribute to raise awareness among the dental community towards a more personalized oral health assessment, taking in consideration alcohol and tobacco consumption in the prevention of specific oral and systemic pathologies.
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Affiliation(s)
- C C Sheth
- Department of Biomedical Sciences, School of Health Sciences, Universidad CEU Cardenal Herrera, Moncada, Valencia, Spain
| | - K Makda
- Dentistry Department, School of Health Sciences, Universidad CEU Cardenal Herrera, Moncada, Valencia, Spain
| | - Z Dilmahomed
- Dentistry Department, School of Health Sciences, Universidad CEU Cardenal Herrera, Moncada, Valencia, Spain
| | - R González
- Dentistry Department, School of Health Sciences, Universidad CEU Cardenal Herrera, Moncada, Valencia, Spain
| | - A Luzi
- Dentistry Department, School of Health Sciences, Universidad CEU Cardenal Herrera, Moncada, Valencia, Spain
| | - M Del M Jovani-Sancho
- Dentistry Department, School of Health Sciences, Universidad CEU Cardenal Herrera, Moncada, Valencia, Spain
| | - V Veses
- Department of Biomedical Sciences, School of Health Sciences, Universidad CEU Cardenal Herrera, Moncada, Valencia, Spain.
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Madhwani T, McBain AJ. The Application of Magnetic Bead Selection to Investigate Interactions between the Oral Microbiota and Salivary Immunoglobulins. PLoS One 2016; 11:e0158288. [PMID: 27483159 PMCID: PMC4970730 DOI: 10.1371/journal.pone.0158288] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 06/13/2016] [Indexed: 11/19/2022] Open
Abstract
The effect of humoral immunity on the composition of the oral microbiota is less intensively investigated than hygiene and diet, in part due to a lack of simple and robust systems for investigating interactions between salivary immunoglobulins and oral bacteria. Here we report the application of an ex situ method to investigate the specificity of salivary immunoglobulins for salivary bacteria. Saliva collected from six volunteers was separated into immunoglobulin and microbial fractions, and the microbial fractions were then directly exposed to salivary immunoglobulins of "self" and "non-self" origin. Antibody-selected bacteria were separated from their congeners using a magnetic bead system, selective for IgA or IgG isotypes. The positively selected fractions were then characterized using gel-based eubacterial-specific DNA profiling. The eubacterial profiles of positively selected fractions diverged significantly from profiles of whole salivary consortia based on volunteer (P≤ 0.001%) and immunoglobulin origin (P≤ 0.001%), but not immunoglobulin isotype (P = 0.2). DNA profiles of separated microbial fractions were significantly (p≤ 0.05) less diverse than whole salivary consortia and included oral and environmental bacteria. Consortia selected using self immunoglobulins were generally less diverse than those selected with immunoglobulins of non-self origin. Magnetic bead separation facilitated the testing of interactions between salivary antibodies and oral bacteria, showing that these interactions are specific and may reflect differences in recognition by self and non-self immunoglobulins. Further development of this system could improve understanding of the relationship between the oral microbiota and the host immune system and of mechanisms underlying the compositional stability of the oral microbiota.
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Affiliation(s)
- Tejal Madhwani
- Manchester Pharmacy School, The University of Manchester, Manchester, M13 9PT, United Kingdom
| | - Andrew J. McBain
- Manchester Pharmacy School, The University of Manchester, Manchester, M13 9PT, United Kingdom
- * E-mail:
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Brilhante RSN, Oliveira JSD, Evangelista AJDJ, Serpa R, Silva ALD, Aguiar FRMD, Pereira VS, Castelo-Branco DDSCM, Pereira-Neto WA, Cordeiro RDA, Sidrim JJC, Rocha MFG. Candida tropicalis from veterinary and human sources shows similar in vitro hemolytic activity, antifungal biofilm susceptibility and pathogenesis against Caenorhabditis elegans. Vet Microbiol 2016; 192:213-219. [PMID: 27527785 DOI: 10.1016/j.vetmic.2016.07.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 07/26/2016] [Accepted: 07/27/2016] [Indexed: 10/21/2022]
Abstract
The aim of this study was to evaluate the in vitro hemolytic activity and biofilm antifungal susceptibility of veterinary and human Candida tropicalis strains, as well as their pathogenesis against Caenorhabditis elegans. Twenty veterinary isolates and 20 human clinical isolates of C. tropicalis were used. The strains were evaluated for their hemolytic activity and biofilm production. Biofilm susceptibility to itraconazole, fluconazole, voriconazole, amphotericin B and caspofungin was assessed using broth microdilution assay. The in vivo evaluation of strain pathogenicity was investigated using the nematode C. elegans. Hemolytic factor was observed in 95% of the strains and 97.5% of the isolates showed ability to form biofilm. Caspofungin and amphotericin B showed better results than azole antifungals against mature biofilms. Paradoxical effect on mature biofilm metabolic activity was observed at elevated concentrations of caspofungin (8-64μg/mL). Azole antifungals were not able to inhibit mature C. tropicalis biofilms, even at the higher tested concentrations. High mortality rates of C. elegans were observed when the worms were exposed to with C. tropicalis strains, reaching up to 96%, 96h after exposure of the worms to C. tropicalis strains. These results reinforce the high pathogenicity of C. tropicalis from veterinary and human sources and show the effectiveness of caspofungin and amphotericin B against mature biofilms of this species.
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Affiliation(s)
- Raimunda Sâmia Nogueira Brilhante
- Department of Pathology and Legal Medicine, School of Medicine, Specialized Medical Mycology Center, Postgraduate Program in Medical Microbiology, Federal University of Ceará, Fortaleza, CE, Brazil; Postgraduate Program in Medical Sciences, Federal University of Ceará, Fortaleza, CE, Brazil.
| | - Jonathas Sales de Oliveira
- Department of Pathology and Legal Medicine, School of Medicine, Specialized Medical Mycology Center, Postgraduate Program in Medical Microbiology, Federal University of Ceará, Fortaleza, CE, Brazil
| | | | - Rosana Serpa
- Department of Pathology and Legal Medicine, School of Medicine, Specialized Medical Mycology Center, Postgraduate Program in Medical Microbiology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Aline Lobão da Silva
- School of Veterinary, Postgraduate Program in Veterinary Sciences, State University of Ceará, Fortaleza, CE, Brazil
| | - Felipe Rodrigues Magalhães de Aguiar
- Department of Pathology and Legal Medicine, School of Medicine, Specialized Medical Mycology Center, Postgraduate Program in Medical Microbiology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Vandbergue Santos Pereira
- Department of Pathology and Legal Medicine, School of Medicine, Specialized Medical Mycology Center, Postgraduate Program in Medical Microbiology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Débora de Souza Collares Maia Castelo-Branco
- Department of Pathology and Legal Medicine, School of Medicine, Specialized Medical Mycology Center, Postgraduate Program in Medical Microbiology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Waldemiro Aquino Pereira-Neto
- Department of Pathology and Legal Medicine, School of Medicine, Specialized Medical Mycology Center, Postgraduate Program in Medical Microbiology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Rossana de Aguiar Cordeiro
- Department of Pathology and Legal Medicine, School of Medicine, Specialized Medical Mycology Center, Postgraduate Program in Medical Microbiology, Federal University of Ceará, Fortaleza, CE, Brazil; Postgraduate Program in Medical Sciences, Federal University of Ceará, Fortaleza, CE, Brazil
| | - José Júlio Costa Sidrim
- Department of Pathology and Legal Medicine, School of Medicine, Specialized Medical Mycology Center, Postgraduate Program in Medical Microbiology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Marcos Fábio Gadelha Rocha
- Department of Pathology and Legal Medicine, School of Medicine, Specialized Medical Mycology Center, Postgraduate Program in Medical Microbiology, Federal University of Ceará, Fortaleza, CE, Brazil; School of Veterinary, Postgraduate Program in Veterinary Sciences, State University of Ceará, Fortaleza, CE, Brazil
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Watkins RR, Mukherjee PK, Chandra J, Retuerto MA, Guidry C, Haller N, Paranjape C, Ghannoum MA. Admission to the Intensive Care Unit is Associated With Changes in the Oral Mycobiome. J Intensive Care Med 2016; 32:278-282. [PMID: 26893317 DOI: 10.1177/0885066615627757] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A prospective exploratory study was conducted to characterize the oral mycobiome at baseline and determine whether changes occur after admission to the intensive care unit (ICU). We found that ICU admission is associated with alterations in the oral mycobiome, including an overall increase in Candida albicans.
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Affiliation(s)
- Richard R Watkins
- 1 Department of Internal Medicine, Northeast Ohio Medical University, Rootstown, OH, USA.,2 Division of Infectious Diseases, Akron General Medical Center, Akron, OH, USA
| | - Pranab K Mukherjee
- 3 Department of Dermatology, Center for Medical Mycology, University Hospitals Case Medical Center, Case Western Reserve University, Cleveland, OH, USA
| | - Jyotsna Chandra
- 3 Department of Dermatology, Center for Medical Mycology, University Hospitals Case Medical Center, Case Western Reserve University, Cleveland, OH, USA
| | - Mauricio A Retuerto
- 4 OHARA/ACTG Mycology Unit, Department of Dermatology, Case Western Reserve University, Cleveland, OH, USA
| | - Chrissy Guidry
- 5 Department of Surgery, Akron General Medical Center, Akron, OH, USA
| | - Nairmeen Haller
- 6 Department of Research, Akron General Medical Center, Akron, OH, USA
| | | | - Mahmoud A Ghannoum
- 7 Department of Dermatology, Center for Medical Microbiology, Case Western Reserve University School of Medicine, University Hospitals Case Medical Center, Cleveland, OH, USA
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Muraille E. The Unspecific Side of Acquired Immunity Against Infectious Disease: Causes and Consequences. Front Microbiol 2016; 6:1525. [PMID: 26793171 PMCID: PMC4707229 DOI: 10.3389/fmicb.2015.01525] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 12/18/2015] [Indexed: 11/13/2022] Open
Abstract
Acquired immunity against infectious disease (AIID) has long been considered as strictly dependent on the B and T lymphocytes of the adaptive immune system. Consequently, AIID has been viewed as highly specific to the antigens expressed by pathogens. However, a growing body of data motivates revision of this central paradigm of immunology. Unrelated past infection, vaccination, and chronic infection have been found to induce cross-protection against numerous pathogens. These observations can be partially explained by the poly-specificity of antigenic T and B receptors, the Mackaness effect and trained immunity. In addition, numerous studies highlight the importance of microbiota composition on resistance to infectious disease via direct competition or modulation of the immune response. All of these data support the idea that a non-negligible part of AIID in nature can be nonspecific to the pathogens encountered and even of the antigens expressed by pathogens. As this protection may be dependent on the private T and B repertoires produced by the random rearrangement of genes, past immune history, chronic infection, and microbiota composition, it is largely unpredictable at the individual level. However, we can reasonably expect that a better understanding of the underlying mechanisms will allow us to statistically predict cross-protection at the population level. From an evolutionary perspective, selection of immune mechanisms allowing for partially nonspecific AIID would appear to be advantageous against highly polymorphic and rapidly evolving pathogens. This new emerging paradigm may have several important consequences on our understanding of individual infectious disease susceptibility and our conception of tolerance, vaccination and therapeutic strategies against infection and cancer. It also underscores the importance of viewing the microbiota and persisting infectious agents as integral parts of the immune system.
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Affiliation(s)
- Eric Muraille
- Laboratoire de Parasitologie, Faculté de Médecine, Université Libre de BruxellesBruxelles, Belgium
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Candida albicans in Multispecies Oral Communities; A Keystone Commensal? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 931:13-20. [DOI: 10.1007/5584_2016_5] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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50
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Sampaio-Maia B, Simões-Silva L, Pestana M, Araujo R, Soares-Silva IJ. The Role of the Gut Microbiome on Chronic Kidney Disease. ADVANCES IN APPLIED MICROBIOLOGY 2016; 96:65-94. [PMID: 27565581 DOI: 10.1016/bs.aambs.2016.06.002] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Chronic kidney disease (CKD) is estimated to affect nearly 500 million people worldwide and cardiovascular (CV) disease is a major cause of death in this population. However, therapeutic interventions targeting traditional CV risks are not effective at lowering the incidence of CV events or at delaying the progression of the disease in CKD patients. In recent years, disturbances of normal gut microbiome were recognized in the pathogenesis of diverse chronic diseases. Gut dysbiosis is being unraveled in CKD and pointed as a nontraditional risk factor for CV risk and CKD progression. The most often reported changes in gut microbiome in CKD are related to the lower levels of Bifidobacteriaceae and Lactobacillaceae and to higher levels of Enterobacteriaceae. Although metagenomics brought us an amplified vision on the microbial world that inhabits the human host, it still lacks the sensitivity to characterize the microbiome up to species level, not revealing alterations that occur within specific genus. Here, we review the current state-of-the-art concerning gut dysbiosis in CKD and its role in pathophysiological mechanisms in CKD, particularly in relation with CV risk. Also, the strategies towards prevention and treatment of gut dysbiosis in CKD progression will be discussed.
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Affiliation(s)
| | | | - M Pestana
- University of Porto, Porto, Portugal; São João Hospital Center, Porto, EPE, Portugal
| | - R Araujo
- University of Porto, Porto, Portugal; Flinders University, Adelaide, SA, Australia
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