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Cena JAD, Belmok A, Kyaw CM, Dame-Teixeira N. The Archaea domain: Exploring historical and contemporary perspectives with in silico primer coverage analysis for future research in Dentistry. Arch Oral Biol 2024; 161:105936. [PMID: 38422909 DOI: 10.1016/j.archoralbio.2024.105936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/07/2024] [Accepted: 02/21/2024] [Indexed: 03/02/2024]
Abstract
OBJECTIVE The complete picture of how the human microbiome interacts with its host is still largely unknown, particularly concerning microorganisms beyond bacteria. Although existing in very low abundance and not directly linked to causing diseases, archaea have been detected in various sites of the human body, including the gastrointestinal tract, oral cavity, skin, eyes, respiratory and urinary systems. But what exactly are these microorganisms? In the early 1990 s, archaea were classified as a distinct domain of life, sharing a more recent common ancestor with eukaryotes than with bacteria. While archaea's presence and potential significance in Dentistry remain under-recognized, there are concerns that they may contribute to oral dysbiosis. However, detecting archaea in oral samples presents challenges, including difficulties in culturing, the selection of DNA extraction methods, primer design, bioinformatic analysis, and databases. DESIGN This is a comprehensive review on the oral archaeome, presenting an in-depth in silico analysis of various primers commonly used for detecting archaea in human body sites. RESULTS Among several primer pairs used for detecting archaea in human samples across the literature, only one specifically designed for detecting methanogenic archaea in stool samples, exhibited exceptional coverage levels for the domain and various archaea phyla. CONCLUSIONS Our in silico analysis underscores the need for designing new primers targeting not only methanogenic archaea but also nanoarchaeal and thaumarchaeota groups to gain a comprehensive understanding of the archaeal oral community. By doing so, researchers can pave the way for further advancements in the field of oral archaeome research.
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Affiliation(s)
| | - Aline Belmok
- Institute of Biology, University of Brasilia, Brazil
| | | | - Naile Dame-Teixeira
- Department of Dentistry, School of Health Sciences, University of Brasilia, Brazil; Division of Oral Biology, School of Dentistry, University of Leeds, UK.
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2
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Kuehnast T, Kumpitsch C, Mohammadzadeh R, Weichhart T, Moissl-Eichinger C, Heine H. Exploring the human archaeome: its relevance for health and disease, and its complex interplay with the human immune system. FEBS J 2024. [PMID: 38555566 DOI: 10.1111/febs.17123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 02/23/2024] [Accepted: 03/11/2024] [Indexed: 04/02/2024]
Abstract
This Review aims to coalesce existing knowledge on the human archaeome, a less-studied yet critical non-bacterial component of the human microbiome, with a focus on its interaction with the immune system. Despite a largely bacteria-centric focus in microbiome research, archaea present unique challenges and opportunities for understanding human health. We examine the archaeal distribution across different human body sites, such as the lower gastrointestinal tract (LGT), upper aerodigestive tract (UAT), urogenital tract (UGT), and skin. Variability in archaeal composition exists between sites; methanogens dominate the LGT, while Nitrososphaeria are prevalent on the skin and UAT. Archaea have yet to be classified as pathogens but show associations with conditions such as refractory sinusitis and vaginosis. In the LGT, methanogenic archaea play critical metabolic roles by converting bacterial end-products into methane, correlating with various health conditions, including obesity and certain cancers. Finally, this work looks at the complex interactions between archaea and the human immune system at the molecular level. Recent research has illuminated the roles of specific archaeal molecules, such as RNA and glycerolipids, in stimulating immune responses via innate immune receptors like Toll-like receptor 8 (TLR8) and 'C-type lectin domain family 4 member E' (CLEC4E; also known as MINCLE). Additionally, metabolic by-products of archaea, specifically methane, have demonstrated immunomodulatory effects through anti-inflammatory and anti-oxidative pathways. Despite these advancements, the mechanistic underpinnings of how archaea influence immune activity remain a fertile area for further investigation.
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Affiliation(s)
- Torben Kuehnast
- D&R Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Austria
| | - Christina Kumpitsch
- D&R Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Austria
| | - Rokhsareh Mohammadzadeh
- D&R Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Austria
| | - Thomas Weichhart
- Institute of Medical Genetics, Medical University of Vienna, Austria
| | - Christine Moissl-Eichinger
- D&R Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Austria
- BioTechMed Graz, Austria
| | - Holger Heine
- Research Center Borstel - Leibniz Lung Center, Division of Innate Immunity, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Borstel, Germany
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3
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Guerra A. Human associated Archaea: a neglected microbiome worth investigating. World J Microbiol Biotechnol 2024; 40:60. [PMID: 38172371 DOI: 10.1007/s11274-023-03842-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 11/14/2023] [Indexed: 01/05/2024]
Abstract
The majority of research in the field of human microbiota has predominantly focused on bacterial and fungal communities. Conversely, the human archaeome has received scant attention and remains poorly studied, despite its potential role in human diseases. Archaea have the capability to colonize various human body sites, including the gastrointestinal tract, skin, vagina, breast milk, colostrum, urinary tract, lungs, nasal and oral cavities. This colonization can occur through vertical transmission, facilitated by the transfer of breast milk or colostrum from mother to child, as well as through the consumption of dairy products, organic produce, salty foods, and fermented items. The involvement of these microorganisms in diseases, such as periodontitis, might be attributed to their production of toxic compounds and the detoxification of growth inhibitors for pathogens. However, the precise mechanisms through which these contributions occur remain incompletely understood, necessitating further studies to assess their impact on human health.
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4
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Soza-Bolaños AI, Domínguez-Pérez RA, Ayala-Herrera JL, Pérez-Serrano RM, Soto-Barreras U, Espinosa-Cristóbal LF, Rivera-Albarrán CA, Zaldívar-Lelo de Larrea G. Presence of methanogenic archaea in necrotic root canals of patients with or without type 2 diabetes mellitus. AUST ENDOD J 2023; 49:641-647. [PMID: 37715368 DOI: 10.1111/aej.12797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 08/11/2023] [Accepted: 09/04/2023] [Indexed: 09/17/2023]
Abstract
Theoretically, a necrotic root canal fulfils all requirements as a niche for methanogens to inhabit. However, their presence in it and its implication in apical periodontitis (AP) is controversial. Therefore, to contribute to ending the controversy, this study aimed to detect and compare methanogens' presence in two distinct niches with supposedly different microenvironments; both were necrotic root canals associated with AP but one from patients with type 2 diabetes mellitus (T2DM) while the other from non-diabetic patients. A clinical examination was performed on 65 T2DM patients and 73 non-diabetic controls. Samples from necrotic root canals were obtained, and methanogens were identified. The presence of methanogens was three times higher (27.6%) in the T2DM group than in non-diabetic patients (8.2%). In addition, methanogens' presence was associated with a higher prevalence of periapical symptoms.
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Affiliation(s)
- Ana I Soza-Bolaños
- Laboratory of Multidisciplinary Dentistry Research, Facultad de Medicina, Universidad Autónoma de Querétaro, Santiago de Querétaro, Mexico
- Department of Endodontics, Facultad de Medicina, Universidad Autónoma de Querétaro, Santiago de Querétaro, Mexico
| | - Rubén A Domínguez-Pérez
- Laboratory of Multidisciplinary Dentistry Research, Facultad de Medicina, Universidad Autónoma de Querétaro, Santiago de Querétaro, Mexico
- Department of Endodontics, Facultad de Medicina, Universidad Autónoma de Querétaro, Santiago de Querétaro, Mexico
| | | | - Rosa M Pérez-Serrano
- Laboratorio de Genética y Biología Molecular (GENBIOM), Facultad de Medicina, Universidad Autónoma de Querétaro, Santiago de Querétaro, Mexico
| | | | - León F Espinosa-Cristóbal
- Master Program in Dental Sciences, Stomatology Department, Institute of Biomedical Sciences, Autonomous University of Juarez, Ciudad Juarez, Mexico
| | - Claudia A Rivera-Albarrán
- Laboratory of Multidisciplinary Dentistry Research, Facultad de Medicina, Universidad Autónoma de Querétaro, Santiago de Querétaro, Mexico
| | - Guadalupe Zaldívar-Lelo de Larrea
- Laboratorio de Genética y Biología Molecular (GENBIOM), Facultad de Medicina, Universidad Autónoma de Querétaro, Santiago de Querétaro, Mexico
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5
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Saha S, Boesch C, Maycock J, Wood S, Do T. Sweet Orange Juice Processing By-Product Extracts: A Caries Management Alternative to Chlorhexidine. Biomolecules 2023; 13:1607. [PMID: 38002290 PMCID: PMC10669069 DOI: 10.3390/biom13111607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
Dental caries is one of the most prevalent chronic diseases globally in both children and adults. This study investigated the potential of industrial sweet orange waste extracts (ISOWE) as a substitute for chlorhexidine (CHX) in managing dental caries. First, the cytotoxicity of ISOWE (40, 80, 120 mg/mL) and CHX (0.1 and 0.2%) on buccal epithelial cells was determined. ISOWE exhibited no overall toxicity, whereas CHX strongly affected cell viability. The combination of ISOWE and CHX significantly enhanced cell proliferation compared to CHX alone. Next, the antimicrobial efficacy of ISOWE, CHX, and their combination was assessed against a 7-day complex biofilm model inoculated with oral samples from human volunteers. CHX exhibited indiscriminate antimicrobial action, affecting both pathogenic and health-associated oral microorganisms. ISOWE demonstrated lower antimicrobial efficacy than CHX but showed enhanced efficacy against pathogenic species while preserving the oral microbiome's balance. When applied to a cariogenic biofilm, the combined treatment of ISOWE with 0.1% CHX showed similar efficacy to 0.2% CHX treatment alone. Overall, the findings suggest that ISOWE is a promising natural anti-cariogenic agent with lower toxicity and enhanced selectivity for pathogenic species compared to CHX.
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Affiliation(s)
- Suvro Saha
- School of Food Science and Nutrition, Faculty of Environment, University of Leeds, Leeds LS2 9JT, UK; (S.S.)
- School of Dentistry, Division of Oral Biology, Faculty of Medicine & Health, University of Leeds, Leeds LS9 7TF, UK
| | - Christine Boesch
- School of Food Science and Nutrition, Faculty of Environment, University of Leeds, Leeds LS2 9JT, UK; (S.S.)
| | - Joanne Maycock
- School of Food Science and Nutrition, Faculty of Environment, University of Leeds, Leeds LS2 9JT, UK; (S.S.)
| | - Simon Wood
- School of Dentistry, Division of Oral Biology, Faculty of Medicine & Health, University of Leeds, Leeds LS9 7TF, UK
| | - Thuy Do
- School of Dentistry, Division of Oral Biology, Faculty of Medicine & Health, University of Leeds, Leeds LS9 7TF, UK
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6
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Antezack A, Etchecopar-Etchart D, La Scola B, Monnet-Corti V. New putative periodontopathogens and periodontal health-associated species: A systematic review and meta-analysis. J Periodontal Res 2023; 58:893-906. [PMID: 37572051 DOI: 10.1111/jre.13173] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/14/2023] [Accepted: 08/01/2023] [Indexed: 08/14/2023]
Abstract
To investigate the existence of any association between new putative periodontal pathogens and periodontitis. Two independent reviewers conducted electronic literature searches in the MEDLINE (PubMed), EMBASE, DOSS and Google Scholar databases as well as a manual search to identify eligible clinical studies prior to November 2022. Studies comparing the prevalence of microorganisms other than the already-known periodontal pathogens in subgingival plaque and/or saliva samples between subjects with periodontitis and subject with periodontal health were included. Meta-analyses were performed on data provided by the included studies. Fifty studies including a total of 2739 periodontitis subjects and 1747 subjects with periodontal health were included. The Archaea domain and 25 bacterial species (Anaeroglobus geminatus, Bacteroidales [G-2] bacterium HMT 274, Desulfobulbus sp. HMT 041, Dialister invisus, Dialister pneumosintes, Eubacterium brachy, Enterococcus faecalis, Eubacterium nodatum, Eubacterium saphenum, Filifactor alocis, Fretibacterium sp. HMT 360, Fretibacterium sp. HMT 362, Mogibacterium timidum, Peptoniphilaceae sp. HMT 113, Peptostreptococcus stomatis, Porphyromonas endodontalis, Slackia exigua, Streptococcus gordonii, Selenomonas sputigena, Treponema amylovorum, Treponema lecithinolyticum, Treponema maltophilum, Treponema medium, Treponema parvum and Treponema socranskii) were found to be statistically significantly associated with periodontitis. Network studies should be conducted to investigate the role of these newly identified periodontitis-associated microorganisms through interspecies interaction and host-microbe crosstalk analyses.
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Affiliation(s)
- Angéline Antezack
- Faculté des Sciences Médicales et Paramédicales, Ecole de Médecine Dentaire, Aix-Marseille Univ, Marseille, France
- AP-HM, Hôpital Timone, Pôle Odontologie, Service de Parodontologie, Marseille, France
- MEPHI, IRD, AP-HM, IHU Méditerranée Infection, Aix Marseille Univ, Marseille, France
| | - Damien Etchecopar-Etchart
- EA 3279: CEREeSS-Health Service Research and Quality of Life Center, Aix-Marseille Univ, Marseille, France
- Département de Psychiatrie, Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
- FondaMental Foundation, Creteil, France
| | - Bernard La Scola
- MEPHI, IRD, AP-HM, IHU Méditerranée Infection, Aix Marseille Univ, Marseille, France
| | - Virginie Monnet-Corti
- Faculté des Sciences Médicales et Paramédicales, Ecole de Médecine Dentaire, Aix-Marseille Univ, Marseille, France
- AP-HM, Hôpital Timone, Pôle Odontologie, Service de Parodontologie, Marseille, France
- MEPHI, IRD, AP-HM, IHU Méditerranée Infection, Aix Marseille Univ, Marseille, France
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7
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Krawczyk KT, Locht C, Kowalewicz-Kulbat M. Halophilic Archaea Halorhabdus Rudnickae and Natrinema Salaciae Activate Human Dendritic Cells and Orient T Helper Cell Responses. Front Immunol 2022; 13:833635. [PMID: 35720372 PMCID: PMC9204267 DOI: 10.3389/fimmu.2022.833635] [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: 12/11/2021] [Accepted: 04/28/2022] [Indexed: 12/03/2022] Open
Abstract
Halophilic archaea are procaryotic organisms distinct from bacteria, known to thrive in hypersaline environments, including salt lakes, salterns, brines and salty food. They have also been identified in the human microbiome. The biological significance of halophiles for human health has rarely been examined. The interactions between halophilic archaea and human dendritic cells (DCs) and T cells have not been identified so far. Here, we show for the first time that the halophilic archaea Halorhabdus rudnickae and Natrinema salaciae activate human monocyte-derived DCs, induce DC maturation, cytokine production and autologous T cell activation. In vitro both strains induced DC up-regulation of the cell-surface receptors CD86, CD80 and CD83, and cytokine production, including IL-12p40, IL-10 and TNF-α, but not IL-23 and IL-12p70. Furthermore, autologous CD4+ T cells produced significantly higher amounts of IFN-γ and IL-13, but not IL-17A when co-cultured with halophile-stimulated DCs in comparison to T cells co-cultured with unstimulated DCs. IFN-γ was almost exclusively produced by naïve T cells, while IL-13 was produced by both naïve and memory CD4+ T cells. Our findings thus show that halophilic archaea are recognized by human DCs and are able to induce a balanced cytokine response. The immunomodulatory functions of halophilic archaea and their potential ability to re-establish the immune balance may perhaps participate in the beneficial effects of halotherapies.
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Affiliation(s)
- Krzysztof T Krawczyk
- Department of Immunology and Infectious Biology, Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Camille Locht
- Department of Immunology and Infectious Biology, Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland.,Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Magdalena Kowalewicz-Kulbat
- Department of Immunology and Infectious Biology, Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
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8
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Li Z, Liu Y, Zhang L. Role of the microbiome in oral cancer occurrence, progression and therapy. Microb Pathog 2022; 169:105638. [PMID: 35718272 DOI: 10.1016/j.micpath.2022.105638] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 06/07/2022] [Accepted: 06/10/2022] [Indexed: 02/07/2023]
Abstract
The oral cavity, like other digestive or mucosal sites, contains a site-specific microbiome that plays a significant role in maintaining health and homeostasis. Strictly speaking, the gastrointestinal tract starts from the oral cavity, with special attention paid to the specific flora of the oral cavity. In healthy people, the microbiome of the oral microenvironment is governed by beneficial bacteria, that benefit the host by symbiosis. When a microecological imbalance occurs, changes in immune and metabolic signals affect the characteristics of cancer, as well as chronic inflammation, disruption of the epithelial barrier, changes in cell proliferation and cell apoptosis, genomic instability, angiogenesis, and epithelial barrier destruction and metabolic regulation. These pathophysiological changes could result in oral cancer. Rising evidence suggests that oral dysbacteriosis and particular microbes may play a positive role in the evolution, development, progression, and metastasis of oral cancer, for instance, oral squamous cell carcinoma (OSCC) through direct or indirect action.
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Affiliation(s)
- Zhengrui Li
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200000, China.
| | - Yuan Liu
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200000, China.
| | - Ling Zhang
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200000, China.
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9
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Djemai K, Drancourt M, Tidjani Alou M. Bacteria and Methanogens in the Human Microbiome: a Review of Syntrophic Interactions. MICROBIAL ECOLOGY 2022; 83:536-554. [PMID: 34169332 DOI: 10.1007/s00248-021-01796-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
Methanogens are microorganisms belonging to the Archaea domain and represent the primary source of biotic methane. Methanogens encode a series of enzymes which can convert secondary substrates into methane following three major methanogenesis pathways. Initially recognized as environmental microorganisms, methanogens have more recently been acknowledged as host-associated microorganisms after their detection and initial isolation in ruminants in the 1950s. Methanogens have also been co-detected with bacteria in various pathological situations, bringing their role as pathogens into question. Here, we review reported associations between methanogens and bacteria in physiological and pathological situations in order to understand the metabolic interactions explaining these associations. To do so, we describe the origin of the metabolites used for methanogenesis and highlight the central role of methanogens in the syntrophic process during carbon cycling. We then focus on the metabolic abilities of co-detected bacterial species described in the literature and infer from their genomes the probable mechanisms of their association with methanogens. The syntrophic interactions between bacteria and methanogens are paramount to gut homeostasis. Therefore, any dysbiosis affecting methanogens might impact human health. Thus, the monitoring of methanogens may be used as a bio-indicator of dysbiosis. Moreover, new therapeutic approaches can be developed based on their administration as probiotics. We thus insist on the importance of investigating methanogens in clinical microbiology.
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Affiliation(s)
- Kenza Djemai
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-University, 19-12 Bd Jean Moulin, 13005, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Michel Drancourt
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-University, 19-12 Bd Jean Moulin, 13005, Marseille, France
| | - Maryam Tidjani Alou
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-University, 19-12 Bd Jean Moulin, 13005, Marseille, France.
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10
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Meta-analyses on the Periodontal Archaeome. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1373:69-93. [DOI: 10.1007/978-3-030-96881-6_4] [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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11
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The Role of the Microbiome in Oral Squamous Cell Carcinoma with Insight into the Microbiome-Treatment Axis. Int J Mol Sci 2020; 21:ijms21218061. [PMID: 33137960 PMCID: PMC7662318 DOI: 10.3390/ijms21218061] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/06/2020] [Accepted: 10/12/2020] [Indexed: 12/24/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is one of the leading presentations of head and neck cancer (HNC). The first part of this review will describe the highlights of the oral microbiome in health and normal development while demonstrating how both the oral and gut microbiome can map OSCC development, progression, treatment and the potential side effects associated with its management. We then scope the dynamics of the various microorganisms of the oral cavity, including bacteria, mycoplasma, fungi, archaea and viruses, and describe the characteristic roles they may play in OSCC development. We also highlight how the human immunodeficiency viruses (HIV) may impinge on the host microbiome and increase the burden of oral premalignant lesions and OSCC in patients with HIV. Finally, we summarise current insights into the microbiome–treatment axis pertaining to OSCC, and show how the microbiome is affected by radiotherapy, chemotherapy, immunotherapy and also how these therapies are affected by the state of the microbiome, potentially determining the success or failure of some of these treatments.
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12
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Montenegro SCL, Retamal-Valdes B, Bueno-Silva B, Duarte PM, Faveri M, Figueiredo LC, Feres M. Do patients with aggressive and chronic periodontitis exhibit specific differences in the subgingival microbial composition? A systematic review. J Periodontol 2020; 91:1503-1520. [PMID: 32233092 DOI: 10.1002/jper.19-0586] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/15/2020] [Accepted: 02/27/2020] [Indexed: 12/23/2022]
Abstract
BACKGROUND The 2017 World Workshop on the Classification of Periodontal and Peri-Implant Diseases and Conditions grouped the diseases previously recognized as chronic (CP) or aggressive (AgP) periodontitis under a single category named periodontitis. The rationale for this decision was the lack of specific patterns of immune-inflammatory response or microbial profiles associated with CP or AgP. However, no previous studies have compiled the results of all studies comparing subgingival microbial data between these clinical conditions. Thus, this systematic review aimed to answer the following focused question: "Do patients with AgP periodontitis present differences in the subgingival microbiota when compared with patients with CP?" METHODS A systematic review was conducted according to the PRISMA statement. The MEDLINE, EMBASE, and Cochrane databases were searched up to June 2019 for studies of any design (except case reports, case series, and reviews) comparing subgingival microbial data from patients with CP and AgP. RESULTS A total of 488 articles were identified and 56 were included. Thirteen studies found Aggregatibacter actinomycetemcomitans elevated in AgP in comparison with CP, while Fusobacterium nucleatum, Parvimonas micra, and Campylobacter rectus were elevated in AgP in a few studies. None of these species were elevated in CP. However, the number of studies not showing statistically significant differences between CP and AgP was always higher than that of studies showing differences. CONCLUSION These results suggested an association of A. actinomycetemcomitans with AgP, but neither this species nor the other species studied to date were unique to or could differentiate between CP and AgP (PROSPERO #CRD42016039385).
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Affiliation(s)
| | - Belen Retamal-Valdes
- Department of Periodontology, Dental Research Division, Guarulhos University, Guarulhos, SP, Brazil
| | - Bruno Bueno-Silva
- Department of Periodontology, Dental Research Division, Guarulhos University, Guarulhos, SP, Brazil
| | - Poliana Mendes Duarte
- Department of Periodontology, Dental Research Division, Guarulhos University, Guarulhos, SP, Brazil.,Department of Periodontology, School of Advanced Dental Sciences, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Marcelo Faveri
- Department of Periodontology, Dental Research Division, Guarulhos University, Guarulhos, SP, Brazil
| | | | - Magda Feres
- Department of Periodontology, Dental Research Division, Guarulhos University, Guarulhos, SP, Brazil
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Abstract
The Archaea domain was recognized as a separate phylogenetic lineage in the tree of life nearly 3 decades ago. It is now known as part of the human microbiome; however, given that its roles in oral sites are still poorly understood, this review aimed to establish the current level of evidence regarding archaea in the oral cavity to guide future research, providing insights on the present knowledge about the human oral archaeome. A scoping review was conducted with the PRISMA Extension for Scoping Reviews checklist. Five electronic databases were searched, as well as gray literature. Two independent reviewers performed the selection and characterization of the studies. Clinical studies were included when the target population consisted of humans of any age who were donors of samples from the oral cavity. A qualitative analysis was performed, based on the type of oral site and by considering the methods employed for archaeal identification and taxonomy, including the DNA extraction protocols, primers, and probes used. Fifty articles were included in the final scoping review, published from 1987 to 2019. Most studies sampled periodontal sites. Methanogens were the most abundant archaea in those sites, and their presence could be associated with other periodontal pathogens. No consistent relationship with different disease conditions was observed in studies that evaluated the microbiota surviving in endodontic sites. Few articles analyzed the presence of archaea in dental caries, saliva, or tongue microbiota, as well as in archaeologic samples, also showing a relationship with healthy microbiota. Archaea have been detected in different oral niches of individuals from diverse geographic locations and clinical conditions, suggesting potential roles in oral diseases. Methodological limitations may hamper our current knowledge about archaeal diversity and prevalence in oral samples, and future research with diversified methodological approaches may lead to a better comprehension of the human oral archaeome.
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Affiliation(s)
- A Belmok
- Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, Brazil
| | - J A de Cena
- Department of Dentistry, Faculty of Heath Sciences, University of Brasília, Brasília, Brazil
| | - C M Kyaw
- Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, Brazil
| | - N Damé-Teixeira
- Department of Dentistry, Faculty of Heath Sciences, University of Brasília, Brasília, Brazil
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Armitage GC. A brief history of periodontics in the United States of America: Pioneers and thought-leaders of the past, and current challenges. Periodontol 2000 2019; 82:12-25. [PMID: 31850629 DOI: 10.1111/prd.12303] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This paper summarizes historical events in periodontology in the United States over the past 200 years. The contributions of some of the key thought-leaders of the past are highlighted. Throughout the 20th century, the evolution of thought, leading to the views currently held regarding the pathogenesis and treatment of periodontal diseases, was significantly influenced by: (1) major changes in health-care education; (2) the emergence of periodontics as a specialty of dentistry; (3) the publication of peer-reviewed journals with an emphasis on periodontology; (4) formation of the National Institute of Dental and Craniofacial Research (NIDCR); and (5) expansion of periodontal research programs by the NIDCR. The two major future challenges facing periodontal research are development of a better understanding of the ecological complexities of host-microbial interactions in periodontal health and disease, and identification of the relevant mechanisms involved in the predictable regeneration of damaged periodontal tissues.
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Affiliation(s)
- Gary C Armitage
- Division of Periodontology, Department of Orofacial Sciences, University of California San Francisco, San Francisco, California, USA
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Sogodogo E, Doumbo O, Aboudharam G, Kouriba B, Diawara O, Koita H, Togora S, Drancourt M. First characterization of methanogens in oral cavity in Malian patients with oral cavity pathologies. BMC Oral Health 2019; 19:232. [PMID: 31666044 PMCID: PMC6820998 DOI: 10.1186/s12903-019-0929-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/16/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The oral cavity of humans is inhabited by several hundreds of bacterial species and other microorganisms such as fungi and archaeal methanogens. Regarding methanogens, data have been obtained from oral cavity samples collected in Europe, America and Asia. There is no study published on the presence of methanogens in the oral cavity in persons living in Africa. The objective of our study was to bring new knowledge on the distribution of oral methanogens in persons living in Mali, Africa. METHODS A total of 31 patients were included in the study during a 15-day collection period in September. Bacterial investigations consisted in culturing the bacteria in 5% sheep blood-enriched Columbia agar and PolyViteX agar plates. For archaeal research, we used various methods including culture, molecular biology and fluorescent in situ hybridization (FISH). RESULTS Eight of 31 (26%) oral samples collected in eight patients consulting for stomatology diseases tested positive in polymerase chain-reaction (PCR)-based assays for methanogens including five cases of Methanobrevibacter oralis and one case each of Methanobrevibacter smithii, Methanobrevibacter massiliense and co-infection Methanobrevibacter oralis and Methanobrevibacter massiliense. CONCLUSIONS In this pilot study, we are reporting here the first characterization of methanogens in the oral cavity in eight patients in Mali. These methanogen species have already been documented in oral specimens collected from individuals in Europe, Asia, North America and Brazil.
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Affiliation(s)
- Elisabeth Sogodogo
- Aix Marseille University, IRD, MEPHI, IHU-Méditerranée Infection, 19-21, Boulevard Jean Moulin, 13005, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - Ogobara Doumbo
- Department of Epidemiology of Parasitic Diseases, Malaria Research and Training Center, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Gérard Aboudharam
- Aix Marseille University, IRD, MEPHI, IHU-Méditerranée Infection, 19-21, Boulevard Jean Moulin, 13005, Marseille, France.,Aix-Marseille-University, UFR Odontology, Marseille, France
| | - Bourema Kouriba
- Department of Epidemiology of Parasitic Diseases, Malaria Research and Training Center, University of Science, Techniques and Technologies of Bamako, Bamako, Mali.,Centre d'Infectiologie Charles-Mérieux (CICM), Bamako, Mali
| | - Ousseynou Diawara
- National Center of Odonto Stomatology, Faculty of Medicine and Odonto Stomatology, Bamako, Mali
| | - Hapssa Koita
- National Center of Odonto Stomatology, Faculty of Medicine and Odonto Stomatology, Bamako, Mali
| | - Souleymane Togora
- National Center of Odonto Stomatology, Faculty of Medicine and Odonto Stomatology, Bamako, Mali
| | - Michel Drancourt
- Aix Marseille University, IRD, MEPHI, IHU-Méditerranée Infection, 19-21, Boulevard Jean Moulin, 13005, Marseille, France.
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Ramos TN, Borsanelli AC, Saraiva JR, Vaccari J, Schweitzer CM, Gaetti-Jardim Jr E, Dutra IS. Efficacy of virginiamycin for the control of periodontal disease in calves. PESQUISA VETERINÁRIA BRASILEIRA 2019. [DOI: 10.1590/1678-5150-pvb-5922] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
ABSTRACT: Periodontal diseases are multifactorial infectious processes caused by complexes of microorganisms, with damage to health, production, and animal welfare. The aim of the present study was to evaluate the efficacy of virginiamycin in the prevention and control of two early forms of periodontal disease: gingivitis and necrotizing gingivitis. Ten weaned calves, aged four to six months, were permanently kept in a single lot under the same rotational grazing regime in a newly reformed area of Panicum maximum. Five of the calves were orally administered 340mg of virginiamycin (Virginiamycin Group) daily for a period of 18 weeks, while the remaining five calves (Control Group) remained under the same food management but did not receive virginiamycin. During this period, animals underwent 18 weekly evaluations regarding periodontal health, with monitoring and recording of clinical parameters of the eight deciduous incisor teeth on the labial and lingual faces. At approximately two-week intervals, nine collections of subgingival sulcus material from five sites of the four right incisor teeth of each animal were performed and subjected to microbiological evaluation using polymerase chain reaction with primers of 25 microorganisms considered potentially pathogenic. After 1440 periodontal clinical evaluations of incisor teeth of the 10 calves, a total of 395 episodes of gingivitis were recorded, of which 267 occurred in the Control Group and 128 in the Virginiamycin Group. Similarly, 89 episodes of necrotizing gingivitis were recorded; 58 in the Control Group and 31 in the Virginiamycin Group. Comparison of between-group means found significant differences for teeth with gingivitis and necrotizing gingivitis (t test; p<0.05). The total number of teeth with gingivitis (p<0.01) and necrotizing gingivitis (p<0.01) in Control Group was significantly higher than that of gingivitis (p<0.01) and necrotizing gingivitis (p<0.05) in the Virginiamycin Group. There was a positive correlation between total occurrence of gingivitis and necrotizing gingivitis in the Virginiamycin Group by Pearson’s test. Virginiamycin had a protective effect on treated animals compared with the Control Group (OR = 0.36: CI (95%) = 0.27-0.43). In the Control Group, Actinomyces israelli (4.74%), domain Archaea (1.58%), Eikenella corrodens (1.05%), Fusobacterium nucleatum (27.37%), class Mollicutes (5.26%); Porphyromonas endodontalis(5.26%); Porphyromonas gulae(0.53%), Prevotella buccae (6.32%), Prevotella loescheii (3.68%), Prevotella nigrescens (8.42%), Prevotella oralis (1.58%), Tannerella forsythia (0.53%), and Treponema denticola (4.21%) were detected at healthy sites, and gingivitis or necrotizing gingivitis samples. In the Virginiamycin Group, A. israelli (3.41%), domain Archaea (0.98%), F. nucleatum (9.27%), class Mollicutes(4.39%), P. endodontalis (4.39%), P. gulae (0.49%), P. buccae (8.29%), P. loescheii (6.83%), P. nigrescens (15.61%), P. oralis (1.46%), Selenomonas sputigena (0.49%), T. forsythia (0.49%), and T. denticola (2.44%) were detected. In conclusion, virginiamycin administered at a dosage of 340mg/animal/day significantly reduced the occurrence of gingivitis and necrotizing gingivitis in cattle maintained on reformed pastures, and was revealed to have action against periodontal bacterial microbiota considered to be potentially pathogenic.
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Belkacemi S, Mazel A, Tardivo D, Tavitian P, Stephan G, Bianca G, Terrer E, Drancourt M, Aboudharam G. Peri-implantitis-associated methanogens: a preliminary report. Sci Rep 2018; 8:9447. [PMID: 29930395 PMCID: PMC6013440 DOI: 10.1038/s41598-018-27862-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 06/07/2018] [Indexed: 01/30/2023] Open
Abstract
Methanogens have already been described in periodontitis but not in peri-implantitis. Thirty peri-implantitis samples and 28 control samples were collected in 28 consenting peri-implantitis patients. PCR-sequencing of the 16S rRNA gene was used as a broad-spectrum screening method and results were further confirmed by real-time quantitative PCR targeting the mcrA genes. Results showed a methanogen community dominated by Methanobrevibacter oralis in 31/58 (51%) samples including 16/28 (57%) control samples and 15/30 (50%) peri-implantitis samples. Methanobrevibacter massiliense was detected in 5/58 (8.6%) samples including 3/28 (1%) control samples and 2/30 (6.7%) peri-implantitis samples. The prevalence of M. oralis or M. massiliense did not significantly differ in peri-implantitis and control samples (exact Fisher test, P = 0.61 and P = 0.67, respectively). Further ponderation of the methanogen load by the real-time quantitative PCR for actin human gene again indicated non-significant difference (Wilcoxon-Mann-Whitney test, P = 0.48 and P = 0.40, respectively). These data show that the prevalence of methanogens does not differ in peri-implantitis lesions and healthy sites, when individuals are their own control. These data do not allow assigning a specific pathogenic role to methanogens in peri-implantitis; methanogens rather are part of the commensal and normal flora of the oral cavity.
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Affiliation(s)
- Souad Belkacemi
- Aix-Marseille Univ, IRD, MEPHI, IHU Méditerranée-Infection, Marseille, France
| | - Anthony Mazel
- UFR Odontologie, Aix-Marseille Université, Marseille, France
| | | | | | - Grégory Stephan
- UFR Odontologie, Aix-Marseille Université, Marseille, France
| | | | - Elodie Terrer
- Aix-Marseille Univ, IRD, MEPHI, IHU Méditerranée-Infection, Marseille, France
- UFR Odontologie, Aix-Marseille Université, Marseille, France
| | - Michel Drancourt
- Aix-Marseille Univ, IRD, MEPHI, IHU Méditerranée-Infection, Marseille, France.
| | - Gérard Aboudharam
- Aix-Marseille Univ, IRD, MEPHI, IHU Méditerranée-Infection, Marseille, France
- UFR Odontologie, Aix-Marseille Université, Marseille, France
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Comparison of Oral Microbe Quantities from Tongue Samples and Subgingival Pockets. Int J Dent 2018; 2018:2048390. [PMID: 29853892 PMCID: PMC5944217 DOI: 10.1155/2018/2048390] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 03/08/2018] [Accepted: 03/22/2018] [Indexed: 12/17/2022] Open
Abstract
Objectives To improve understanding of periodontitis pathology, we need more profound knowledge of relative abundances of single prokaryotic species and colonization dynamics between habitats. Thus, we quantified oral microbes from two oral habitats to gain insights into colonization variability and correlation to the clinical periodontal status. Methods We analyzed tongue scrapings and subgingival pocket samples from 237 subjects (35–54 years) with at least 10 teeth and no recent periodontal treatment from the 11-year follow-up of the Study of Health in Pomerania. Relative abundances of Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, Fusobacterium nucleatum, Streptococcus sanguinis, total bacteria, and Archaea were correlated to clinically assessed pocket depths (PD) and clinical attachment levels (CAL). Results Increased relative abundances of P. gingivalis, A. actinomycetemcomitans, and F. nucleatum were linked to increased levels of PD and CAL (i) on the subject level (mean PD, mean CAL) and (ii) in subgingival pockets. Relative abundances of Archaea from tongue samples correlated negatively with mean PD or mean CAL. Detection and quantity of bacterial species correlated weakly to moderately between the tongue and subgingival pocket, except for Archaea. Conclusions Relative abundances of specific oral species correlated weakly to moderately between habitats. Single species, total bacteria, and Archaea were linked to clinically assessed severity of periodontitis in a habitat-dependent manner.
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Metaorganisms in extreme environments: do microbes play a role in organismal adaptation? ZOOLOGY 2018; 127:1-19. [DOI: 10.1016/j.zool.2018.02.004] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 02/08/2018] [Accepted: 02/12/2018] [Indexed: 02/06/2023]
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Guilhot E, Khelaifia S, La Scola B, Raoult D, Dubourg G. Methods for culturing anaerobes from human specimen. Future Microbiol 2018; 13:369-381. [PMID: 29446650 DOI: 10.2217/fmb-2017-0170] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Anaerobes represent the dominating population in the human gut microbiota and play a key role in gut homeostasis. In addition, several anaerobes are now considered as probiotics and they remain essential to several processes in the field of biotechnology. With the implementation of MALDI-TOF MS in routine laboratories, anaerobes are no longer neglected in clinical microbiology, as their identification is made easy. However, the isolation and identification of anaerobic bacteria, remains time consuming, fastidious and costly. Various strategies have been developed, from sampling to culturing human specimens, which will be discussed in this paper. Also, particular attention is paid to isolating species with special medical importance, as for contribution to the field of culturomics.
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Affiliation(s)
- Elodie Guilhot
- Aix Marseille Univ., IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Saber Khelaifia
- Aix Marseille Univ., IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Bernard La Scola
- Aix Marseille Univ., IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix Marseille Univ., IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Grégory Dubourg
- Aix Marseille Univ., IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Marseille, France
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Abstract
Though seemingly distinct and autonomous, emerging evidence suggests there is a bidirectional interaction between the intestinal microbiota and the brain. This crosstalk may play a substantial role in neurologic diseases, including anxiety, depression, autism, multiple sclerosis, Parkinson's disease, and, potentially, Alzheimer's disease. Long hypothesized by Metchnikoff and others well over 100 years ago, investigations into the mind-microbe axis is now seeing a rapid resurgence of research. If specific pathways and mechanisms of interaction are understood, it could have broad therapeutic potential, as the microbiome is environmentally acquired and can be modified to promote health. This review will discuss immune, endocrine, and neural system pathways that interconnect the gut microbiota to central nervous system and discuss how these findings might be applied to neurologic disease.
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Affiliation(s)
- Laura M Cox
- Ann Romney Center for Neurologic Diseases, Brigham & Women's Hospital, Harvard Medical School, 60 Fenwood Road, Boston, MA, 02446, USA
| | - Howard L Weiner
- Ann Romney Center for Neurologic Diseases, Brigham & Women's Hospital, Harvard Medical School, 60 Fenwood Road, Boston, MA, 02446, USA.
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Isoshima D, Yamashiro K, Matsunaga K, Shinobe M, Nakanishi N, Nakanishi I, Omori K, Yamamoto T, Takashiba S. Assessment of pathogenesis of infective endocarditis by plasma IgG antibody titer test against periodontal bacteria. Clin Case Rep 2017; 5:1580-1586. [PMID: 29026549 PMCID: PMC5628203 DOI: 10.1002/ccr3.1066] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 06/02/2017] [Indexed: 12/02/2022] Open
Abstract
Oral bacteria cause infective endocarditis (IE), so severe periodontitis is thought to be high risk for IE. We suggest the identification of high-risk patients by an IgG antibody titer test against periodontal bacteria might become common screening test.
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Affiliation(s)
- Daichi Isoshima
- Department of Pathophysiology‐Periodontal ScienceOkayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences2‐5‐1 Shikata‐choKita‐kuOkayama700‐8525Japan
| | - Keisuke Yamashiro
- Department of Pathophysiology‐Periodontal ScienceOkayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences2‐5‐1 Shikata‐choKita‐kuOkayama700‐8525Japan
| | - Kazuyuki Matsunaga
- Department of Pathophysiology‐Periodontal ScienceOkayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences2‐5‐1 Shikata‐choKita‐kuOkayama700‐8525Japan
| | | | - Nagako Nakanishi
- Miyoshi Renal Clinic3‐13‐2 Miyoshi‐choFuchu‐shiTokyo183‐0045Japan
| | - Izumi Nakanishi
- Machidakeisen Hospital2‐1‐47 Minami‐machidaMachida‐shiTokyo194‐0005Japan
| | - Kazuhiro Omori
- Department of Periodontics and EndodonticsOkayama University Hospital2‐5‐1 Shikata‐choKita‐kuOkayama700‐8558Japan
| | - Tadashi Yamamoto
- Department of Periodontics and EndodonticsOkayama University Hospital2‐5‐1 Shikata‐choKita‐kuOkayama700‐8558Japan
| | - Shogo Takashiba
- Department of Pathophysiology‐Periodontal ScienceOkayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences2‐5‐1 Shikata‐choKita‐kuOkayama700‐8525Japan
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Hoedt EC, Cuív PÓ, Morrison M. Methane matters: from blue-tinged moos, to boozy roos, and the health of humans too. Anim Front 2016. [DOI: 10.2527/af.2016-0029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Emily C. Hoedt
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072 Australia
| | - Páraic Ó Cuív
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, QLD, 4102 Australia
| | - Mark Morrison
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, QLD, 4102 Australia
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Alterations of the human gut microbiome in multiple sclerosis. Nat Commun 2016; 7:12015. [PMID: 27352007 PMCID: PMC4931233 DOI: 10.1038/ncomms12015] [Citation(s) in RCA: 821] [Impact Index Per Article: 102.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 05/20/2016] [Indexed: 02/07/2023] Open
Abstract
The gut microbiome plays an important role in immune function and has been implicated in several autoimmune disorders. Here we use 16S rRNA sequencing to investigate the gut microbiome in subjects with multiple sclerosis (MS, n=60) and healthy controls (n=43). Microbiome alterations in MS include increases in Methanobrevibacter and Akkermansia and decreases in Butyricimonas, and correlate with variations in the expression of genes involved in dendritic cell maturation, interferon signalling and NF-kB signalling pathways in circulating T cells and monocytes. Patients on disease-modifying treatment show increased abundances of Prevotella and Sutterella, and decreased Sarcina, compared with untreated patients. MS patients of a second cohort show elevated breath methane compared with controls, consistent with our observation of increased gut Methanobrevibacter in MS in the first cohort. Further study is required to assess whether the observed alterations in the gut microbiome play a role in, or are a consequence of, MS pathogenesis. The gut microbiome has been implicated in several autoimmune disorders. Here, the authors study the gut microbiome of patients with multiple sclerosis, and find correlations between altered abundance of certain gut microorganisms and changes in expression of immune defence genes.
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Restricted diversity of dental calculus methanogens over five centuries, France. Sci Rep 2016; 6:25775. [PMID: 27166431 PMCID: PMC4863154 DOI: 10.1038/srep25775] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 04/05/2016] [Indexed: 11/08/2022] Open
Abstract
Methanogens are acknowledged archaeal members of modern dental calculus microbiota and dental pathogen complexes. Their repertoire in ancient dental calculus is poorly known. We therefore investigated archaea in one hundred dental calculus specimens collected from individuals recovered from six archaeological sites in France dated from the 14(th) to 19(th) centuries AD. Dental calculus was demonstrated by macroscopic and cone-beam observations. In 56 calculus specimens free of PCR inhibition, PCR sequencing identified Candidatus Methanobrevibacter sp. N13 in 44.6%, Methanobrevibacter oralis in 19.6%, a new Methanomassiliicoccus luminyensis-like methanogen in 12.5%, a Candidatus Nitrososphaera evergladensis-like in one and Methanoculleus bourgensis in one specimen, respectively. One Candidatus Methanobrevibacter sp. N13 dental calculus was further documented by fluorescent in situ hybridization. The prevalence of dental calculus M. oralis was significantly lower in past populations than in modern populations (P = 0.03, Chi-square test). This investigation revealed a previously unknown repertoire of archaea found in the oral cavity of past French populations as reflected in preserved dental calculus.
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Abstract
For decades, Aggregatibacter actinomycetemcomitans has been considered the most likely etiologic agent in aggressive periodontitis. Implementation of DNA-based microbiologic methodologies has considerably improved our understanding of the composition of subgingival biofilms, and advanced open-ended molecular techniques even allow for genome mapping of the whole bacterial spectrum in a sample and characterization of both the cultivable and not-yet-cultivable microbiota associated with periodontal health and disease. Currently, A. actinomycetemcomitans is regarded as a minor component of the resident oral microbiota and as an opportunistic pathogen in some individuals. Its specific JP2 clone, however, shows properties of a true exogenous pathogen and has an important role in the development of aggressive periodontitis in certain populations. Still, limited data exist on the impact of other microbes specifically in aggressive periodontitis. Despite a wide heterogeneity of bacteria, especially in subgingival samples collected from patients, bacteria of the red complex in particular, and those of the orange complex, are considered as potential pathogens in generalized aggressive periodontitis. These types of bacterial findings closely resemble those found for chronic periodontitis, representing a mixed polymicrobial infection without a clear association with any specific microorganism. In aggressive periodontitis, the role of novel and not-yet-cultivable bacteria has not yet been elucidated. There are geographic and ethnic differences in the carriage of periodontitis-associated microorganisms, and they need to be taken into account when comparing study reports on periodontal microbiology in different study populations. In the present review, we provide an overview on the colonization of potential periodontal pathogens in childhood and adolescence, and on specific microorganisms that have been suspected for their role in the initiation and progression of aggressive forms of periodontal disease.
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Abstract
Archaea have been detected in several ecological niches of the human body such as the large intestine, skin, vagina as well as the oral cavity. At present, archaea are recognized as nonpathogenic microorganisms. However, some data indicate that they may be involved in the etiopathogenesis of several diseases, including intestinal diseases as well as oral diseases: periodontitis, peri-implantitis and endodontitis. In this study, on the basis of 16S rRNA gene sequence analysis, we examined whether archaea might be present in inflamed pulp tissues and contribute to the development of endodontic infection. In comparison, we also determined selected bacterial species associated with endodontitis. We detected archaea in 85% of infected endodontic samples. In addition, Prevotella intermedia, Porphyromonas gingivalis, Tannerella forsythia and Treponema denticola were present in inflamed pulp tissue samples and Treponema denticola occurred with the highest frequency (70%). Further analysis revealed the presence of methanogenic archaea in analyzed samples. Direct sequencing of archaeal 16S rRNA gene PCR products indicated the occurrence of methanogenic archaea in inflamed pulp tissues; phylogenetically most similar were Methanobrevibacter oralis and Methanobrevibacter smithii. Therefore, our results show that methanogenic archaea are present in inflamed pulp tissues and may participate in the development of endodontic infection.
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Bang C, Schmitz RA. Archaea associated with human surfaces: not to be underestimated. FEMS Microbiol Rev 2015; 39:631-48. [DOI: 10.1093/femsre/fuv010] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2015] [Indexed: 12/18/2022] Open
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Li CL, Jiang YT, Liu DL, Qian J, Liang JP, Shu R. Prevalence and quantification of the uncommon Archaea phylotype Thermoplasmata in chronic periodontitis. Arch Oral Biol 2014; 59:822-8. [PMID: 24859768 DOI: 10.1016/j.archoralbio.2014.05.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 03/28/2014] [Accepted: 05/05/2014] [Indexed: 11/28/2022]
Abstract
OBJECTIVE Chronic periodontitis is a chronic inflammatory disease of the periodontal tissues and is caused by invasion of certain types of bacteria and Archaea, with Methanobrevibacter oralis as the predominant archaeon. In this study, we investigated the prevalence and quantity of the newly discovered Archaea phylotype Thermoplasmata in patients with chronic periodontitis. METHODS Subgingival plaque samples were obtained from 49 patients with chronic periodontitis and 45 periodontally healthy subjects. Qualitative analyses of Archaea and class Thermoplasmata were carried out by amplification of 16S rRNA genes in DNA extracts from plaque samples, and all the samples were quantitatively analyzed by real-time polymerase chain reaction (PCR). RESULTS The prevalence of Archaea in patients with chronic periodontitis was 69.4% according to the conventional PCR results, but was 87.8% according to real-time PCR. In the control group, three samples were detected as positive, but none of these were confirmed in qualitative analyses. The prevalence of class Thermoplasmata was 18.4% by nested PCR and 24.5% by quantitative PCR in the chronic periodontitis group. The prevalence of Thermoplasmata was significantly lower than that of total Archaea. The relative abundances of Archaea and Thermoplasmata varied among samples. Thermoplasmata were not the predominant archaeons in the subgingival dental plaque. Among the clinical parameters of patients with periodontitis, probing depth was positively associated with Archaea detection. CONCLUSIONS The existence of Archaea was correlated closely with the presence of chronic periodontitis. Thermoplasmata represented a minor archaeon in periodontal infection.
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Affiliation(s)
- Chao Lun Li
- Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Yun Tao Jiang
- Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Da Li Liu
- Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - JieLei Qian
- Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Jing Ping Liang
- Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Rong Shu
- Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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Hirai K, Maeda H, Omori K, Yamamoto T, Kokeguchi S, Takashiba S. Serum antibody response to group II chaperonin from Methanobrevibacter oralis and human chaperonin CCT. Pathog Dis 2014; 68:12-9. [PMID: 23620386 DOI: 10.1111/2049-632x.12041] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 03/02/2013] [Accepted: 03/29/2013] [Indexed: 01/06/2023] Open
Abstract
Both group I (HSP60) and group II (CCT) chaperonins are targets of autoantibodies. Autoimmune reactions to HSP60 have been well characterized, while immune reactions to group II chaperonin have not been clarified. Methanobrevibacter oralis is a suspected periodontal pathogen with group II chaperonin. In this study, serum responses to M. oralis chaperonin, human HSP60, and CCT subunits were examined using sera from patients with periodontitis and autoimmune diseases. In comparison with healthy controls, periodontitis patients showed significantly higher responses to CCT4 and CCT8 on dot blot analysis. Signals for CCT3 and CCT8 in autoimmune disease patients were significantly higher than in controls. Significant differences were also demonstrated by Western blotting in anti-CCT4 response in both patient groups. All subjects showed strong reactivity to M. oralis chaperonin and faint signals to human HSP60. Autoantibodies were raised against CCT rather than HSP60; and CCT3, CCT4, and CCT8 were shown to be the main targets. Host immune systems may be frequently exposed to chaperonins of Archaea in various habitats. Although further studies of the cross-reactivity between M. oralis chaperonin and human CCT are required, anti-CCT autoantibodies may be involved in the pathogenesis of periodontitis and autoimmune diseases.
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Affiliation(s)
- Kimito Hirai
- Department of Pathophysiology-Periodontal Science, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
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Lira EAG, Ramiro FS, Chiarelli FM, Dias RR, Feres M, Figueiredo LC, Faveri M. Reduction in prevalence of Archaea after periodontal therapy in subjects with generalized aggressive periodontitis. Aust Dent J 2014; 58:442-7. [PMID: 24320900 DOI: 10.1111/adj.12123] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2013] [Indexed: 12/12/2022]
Abstract
BACKGROUND There is evidence of a possible relationship between Archaea and periodontal disease; however, to date few studies have assessed the changes in prevalence of this domain after periodontal therapy. The aim of this randomized double-blind and placebo-controlled study was to assess if periodontal treatment with or without systemic antibiotic would change the prevalence of Archaea after periodontal therapy. METHODS Thirty subjects were randomly assigned to receive scaling and root planing (SRP) alone or combined with metronidazole (MTZ) + amoxicillin (AMX) for 14 days. Clinical and microbiological examinations were performed at baseline and at six months post-SRP. Nine subgingival plaque samples per subject were analysed for the presence of Archaea. RESULTS SRP alone or combined with MTZ + AMX significantly reduced the prevalence of subjects colonized by Archaea at six months post-therapy. However, no significant differences between treatment groups were observed (p > 0.05). Both therapies led to a statistically significant decrease in the mean percentage of sites colonized by Archaea (p < 0.05). A negative Spearman correlation was observed between the presence of Archaea and the mean clinical attachment gain at six months post-therapy (r(2) = -0.61; 95% CI -0.80- -0.31; p = 0.003). CONCLUSIONS SRP alone or combined with MTZ + AMX provides a similar reduction in the prevalence of Archaea in the subgingival biofilm of subjects with generalized aggressive periodontitis.
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Affiliation(s)
- E A G Lira
- Department of Periodontology, Dental Research Division, Guarulhos University, Guarulhos, São Paulo, Brazil
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Blais Lecours P, Marsolais D, Cormier Y, Berberi M, Haché C, Bourdages R, Duchaine C. Increased prevalence of Methanosphaera stadtmanae in inflammatory bowel diseases. PLoS One 2014; 9:e87734. [PMID: 24498365 PMCID: PMC3912014 DOI: 10.1371/journal.pone.0087734] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 12/28/2013] [Indexed: 12/12/2022] Open
Abstract
Background The gut microbiota is associated with the modulation of mucosal immunity and the etiology of inflammatory bowel diseases (IBD). Previous studies focused on the impact of bacterial species on IBD but seldom suspected archaea, which can be a major constituent of intestinal microbiota, to be implicated in the diseases. Recent evidence supports that two main archaeal species found in the digestive system of humans, Methanobrevibacter smithii (MBS) and Methanosphaera stadtmanae (MSS) can have differential immunogenic properties in lungs of mice; with MSS but not MBS being a strong inducer of the inflammatory response. We thus aimed at documenting the immunogenic potential of MBS and MSS in humans and to explore their association with IBD. Methods To validate the immunogenicity of MBS and MSS in humans, peripheral blood mononuclear cells from healthy subjects were stimulated with these two microorganisms and the production of inflammatory cytokine TNF was measured by ELISA. To verify MBS and MSS prevalence in IBD, stool samples from 29 healthy control subjects and 29 patients suffering from IBD were collected for DNA extraction. Plasma was also collected from these subjects to measure antigen-specific IgGs by ELISA. Quantitative PCR was used for bacteria, methanogens, MBS and MSS quantification. Results Mononuclear cells stimulated with MSS produced higher concentrations of TNF (39.5 ng/ml) compared to MBS stimulation (9.1 ng/ml). Bacterial concentrations and frequency of MBS-containing stools were similar in both groups. However, the number of stool samples positive for the inflammatory archaea MSS was higher in patients than in controls (47% vs 20%). Importantly, only IBD patients developed a significant anti-MSS IgG response. Conclusion The prevalence of MSS is increased in IBD patients and is associated with an antigen-specific IgG response.
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Affiliation(s)
- Pascale Blais Lecours
- Centre de recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, Québec, Canada
| | - David Marsolais
- Centre de recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, Québec, Canada
- Département de médecine, Faculté de médecine, Université Laval, Québec, QC, Canada
| | - Yvon Cormier
- Centre de recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, Québec, Canada
- Département de médecine, Faculté de médecine, Université Laval, Québec, QC, Canada
| | | | | | | | - Caroline Duchaine
- Centre de recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, Québec, Canada
- Département de biochimie, de microbiologie et de bioinformatique, Faculté des sciences et de génie, Université Laval, Québec, Québec, Canada
- * E-mail:
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Khelaifia S, Ramonet PY, Bedotto Buffet M, Drancourt M. A semi-automated protocol for Archaea DNA extraction from stools. BMC Res Notes 2013; 6:186. [PMID: 23651536 PMCID: PMC3662635 DOI: 10.1186/1756-0500-6-186] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 04/17/2013] [Indexed: 02/01/2023] Open
Abstract
Background The PCR-based detection of archaea DNA in human specimens relies on efficient DNA extraction. We previously designed one such protocol involving only manual steps. In an effort to reduce the workload involved, we compared this manual protocol to semi-automated and automated protocols for archaea DNA extraction from human specimens. Findings We tested 110 human stool specimens using each protocol. An automated protocol using the EZ1 Advanced XL extractor with the V 1.066069118 Qiagen DNA bacteria card and the EZ1® DNA Tissue Kit (Qiagen, Courtaboeuf, France) yielded 35/110 (32%) positives for the real-time PCR detection of the Methanobrevibacter smithii 16S rRNA gene, with average Ct values of 36.1. A semi-automated protocol combining glass-powder crushing, overnight proteinase K digestion and lysis in the buffer from the EZ1 kit yielded 90/110 (82%) positive specimens (P = 0.001) with an average Ct value of 27.4 (P = 0.001). The manual protocol yielded 100/110 (91%) positive specimens (P = 0.001) with an average Ct value of 30.33 (P = 0.001). However, neither the number of positive specimens nor the Ct values were significantly different between the manual protocol and the semi-automated protocol (P > 0.1 and P > 0.1). Conclusion Proteinase K digestion and glass powder crushing dramatically increase the extraction yield of archaea DNA from human stools. The semi-automated protocol described here was more rapid than the manual protocol and yielded significantly more archaeal DNA. It could be applied for extracting total stool DNA for further PCR amplification.
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Affiliation(s)
- Saber Khelaifia
- Aix Marseille Université, URMITE, UMR63 CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
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Medical microbiological approach to Archaea in oral infectious diseases. JAPANESE DENTAL SCIENCE REVIEW 2013. [DOI: 10.1016/j.jdsr.2013.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Khelaifia S, Raoult D, Drancourt M. A versatile medium for cultivating methanogenic archaea. PLoS One 2013; 8:e61563. [PMID: 23613876 PMCID: PMC3629087 DOI: 10.1371/journal.pone.0061563] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 03/11/2013] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Methanobrevibacter smithii, Methanobrevibacter oralis, Methanosphaera stadtmanae, Methanomassilicoccus luminyensis and Methanobrevibacter arboriphilicus have been cultured from human digestive microbiota. Each one of these fastidious methanogenic archaea requires a specific medium for its growth, hampering their routine isolation and the culture. METHODOLOGY/PRINCIPAL FINDINGS A new culture medium here referred as SAB medium was optimized and tested to cultivate methanogens associated with human microbiota, as well as two mesophile methanogens Methanobacterium beijingense and Methanosaeta concilii. It was further tested for the isolation of archaea from 20 human stool specimens including 10 specimens testing positive for PCR detection of M. smithii. After inoculating 10(5) colony-forming-unit archaea/mL or 1 g stool specimen in parallel in SAB medium and reference DSMZ medium in the presence of negative controls, growth of archaea was determined by optical microscopy and the measurement of methane production by gas chromatography. While the negative controls remained sterile, all tested archaea grew significantly more rapidly in SAB medium than in reference medium in 1-3 days (P<0.05, Student test). Among PCR-positive stool specimens, 10/10 grew in the SAB medium, 6/10 in DSMZ 119 medium, 5/10 in DSMZ 322 medium and 3/10 in DSMZ 334 c medium. Four out of ten PCR-negative stool specimens grew after a 3-week incubation in the SAB-medium whereas no growth was detected in any of the reference media. 16S rRNA gene sequencing yielded 99-100% sequence similarity with reference M. smithii except for one specimen that yielded 99-100% sequence similarity with reference Methanobrevibacter millerae. CONCLUSIONS/SIGNIFICANCE SAB medium allows for the versatile isolation and growth of methanogenic archaea associated with human gut microbiota including the archaea missed by inoculation of reference media. Implementation of the SAB medium in veterinary and medical microbiology laboratories will ease the routine culture-based detection of methanogenic archaea in clinical and environmental specimens.
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Affiliation(s)
- Saber Khelaifia
- Aix Marseille Université, URMITE, UMR63 CNRS 7278, IRD 198, Inserm 1095, 13005, Marseille, France
| | - Didier Raoult
- Aix Marseille Université, URMITE, UMR63 CNRS 7278, IRD 198, Inserm 1095, 13005, Marseille, France
| | - Michel Drancourt
- Aix Marseille Université, URMITE, UMR63 CNRS 7278, IRD 198, Inserm 1095, 13005, Marseille, France
- * E-mail:
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Khelaifia S, Brunel JM, Raoult D, Drancourt M. Hydrophobicity of imidazole derivatives correlates with improved activity against human methanogenic archaea. Int J Antimicrob Agents 2013; 41:544-7. [PMID: 23561316 DOI: 10.1016/j.ijantimicag.2013.02.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 02/05/2013] [Accepted: 02/08/2013] [Indexed: 11/24/2022]
Abstract
Methanogenic archaea are involved in periodontitis in humans. They have also been implicated in digestive tract pathologies and obesity. These microorganisms are broadly resistant to antibiotics, except for metronidazole and ornidazole. In this study, eight imidazole derivatives were synthesised and their in vitro cytotoxicity and activity against six species of methanogenic archaea, including Methanobrevibacter smithii, Methanobrevibacter oralis, Methanosphaera stadtmanae, Methanobacterium beijingense, Methanosaeta concilii and Methanomassiliicoccus luminyensis, were tested. Whilst the effective half-maximum cytotoxic concentrations (EC50 values) of all compounds were ≤50 mg/L, minimum inhibitory concentrations (MICs) were 0.05-0.8 mg/L for most methanogenic archaea and 0.1-1mg/L for M. stadtmanae. These results indicated a >20-400 therapeutic index (EC50/MIC) for these compounds, which compared with metronidazole exhibited 1-log increased activity against methanogenic archaea cultured from the human microbiota. These compounds are therefore promising molecules for the treatment of methanogenic archaea-related infections.
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Affiliation(s)
- Saber Khelaifia
- Unité de recherche sur les maladies infectieuses et tropicales émergentes, UMR CNRS 6236 IRD 3R198, FR IDMM, Méditerranée Infection, Aix-Marseille Université, Marseille, France
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Saengkerdsub S, Ricke SC. Ecology and characteristics of methanogenic archaea in animals and humans. Crit Rev Microbiol 2013; 40:97-116. [PMID: 23425063 DOI: 10.3109/1040841x.2013.763220] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this review, the molecular techniques used in animal-based-methanogen studies will be discussed along with how methanogens interact not only with other microorganisms but with their animal hosts as well. These methods not only indicate the diversity and levels of methanogens, but also provide insight on their ecological functions. Most molecular techniques have been based on either 16S rRNA genes or methyl-coenzyme M reductase, a ubiquitous enzyme in methanogens. The most predominant methanogens in animals belong to the genus Methanobrevibacter. Besides methanogens contributing to overall H2 balance, methanogens also have mutual interactions with other bacteria. In addition to shared metabolic synergism, the host animal retrieves additional energy from the diet when methanogens are co-colonized with other normal flora. By comparing genes in methanogens with other bacteria, possible gene transfer between methanogens and other bacteria in the same environments appears to occur. Finally, diets in conjunction with the genetics of methanogens and hosts may represent the biological framework that dictate the extent of methanogen prevalence in these ecosystems. In addition, host evolution including the immune system could serve as an additional selective pressure for methanogen colonization.
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Affiliation(s)
- Suwat Saengkerdsub
- Department of Food Science, Center for Food Safety, University of Arkansas , Fayetteville, AR , USA , and
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Real-time PCR quantification of Methanobrevibacter oralis in periodontitis. J Clin Microbiol 2012; 51:993-4. [PMID: 23254133 DOI: 10.1128/jcm.02863-12] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A real-time PCR assay developed to quantify Methanobrevibacter oralis indicated that its inoculum significantly correlated with periodontitis severity (P = 0.003), despite a nonsignificant difference in prevalence between controls (3/10) and patients (12/22) (P = 0.2, Fisher test). The M. oralis load can be used as a biomarker for periodontitis.
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Nguyen-Hieu T. Microbial sampling process can change results of microbiological analysis in periodontitis diagnosis. A minireview. ACTA ACUST UNITED AC 2012. [PMID: 23188761 DOI: 10.1111/jicd.12010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This minireview aims to verify the supposition that the microbial sampling process can change results of microbiological analysis in periodontitis diagnosis. The literature search via Pubmed yielded 52 appropriate articles for analysis. Of which 38% (20/52) described that the sampling sites were isolated from saliva, whereas 62% (32/52) did not. Also, 29% (15/52) declared that the microbial sampling was performed before probing pocket depth (PPD), whereas 71% (37/52) did not. Comparison of the results of microbiological analysis in these studies showed that the bacteria most frequently detected in periodontal pockets was variable. Therefore, a sampling process that includes both the microbial sample being taken before PPD and saliva isolation of the sampling sites is needed to ensure the accuracy of microbiological analysis in periodontitis diagnosis.
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Affiliation(s)
- Tung Nguyen-Hieu
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, Marseille, France.
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40
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Nguyen-Hieu T, Khelaifia S, Aboudharam G, Drancourt M. Methanogenic archaea in subgingival sites: a review. APMIS 2012; 121:467-77. [PMID: 23078250 DOI: 10.1111/apm.12015] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 09/20/2012] [Indexed: 02/06/2023]
Abstract
Archaea are non-bacterial prokaryotes associated with oral microbiota in humans, but their roles in oral pathologies remain controversial. Several studies reported the molecular detection of methanogenic archaea from periodontitis, but the significance of this association has not been confirmed yet. An electronic search was therefore conducted in MEDLINE-Pubmed to identify all papers published in English connecting archaea and periodontal infections. Data analysis of the selected studies showed that five genera of methanogenic archaea have been detected in the subgingival microbiota, Methanobrevibacter oralis being the most frequently detected species in 41% of periodontitis patients and 55% of periodontal pockets compared to 6% of healthy subjects and 5% of periodontally-healthy sites (p < 10(-5) , Chi-squared test). Based on the five determination-criteria proposed by Socransky (association with disease, elimination of the organism, host response, animal pathogenicity and mechanisms of pathogenicity), M. oralis is a periodontal pathogen. The methanogenic archaea load correlating with periodontitis severity further supports the pathogenic role of methanogenic archaea in periodontitis. Therefore, detection and quantification of M. oralis in periodontal pockets could help the laboratory diagnosis and follow-up of periodontitis. Determining the origin, diversity and pathogenesis of archaea in periodontal infections warrants further investigations.
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Affiliation(s)
- Tung Nguyen-Hieu
- URMITE, UMR63, CNRS 7278, IRD 198, Inserm 1095, Aix-Marseille Université, Marseille, France
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Khelaifia S, Drancourt M. Susceptibility of archaea to antimicrobial agents: applications to clinical microbiology. Clin Microbiol Infect 2012; 18:841-8. [DOI: 10.1111/j.1469-0691.2012.03913.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Matarazzo F, Ribeiro AC, Faveri M, Taddei C, Martinez MB, Mayer MPA. The domain Archaea in human mucosal surfaces. Clin Microbiol Infect 2012; 18:834-40. [PMID: 22827611 DOI: 10.1111/j.1469-0691.2012.03958.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Archaea present distinct features from bacteria and eukaryotes, and thus constitute one of the branches of the phylogenetic tree of life. Members of this domain colonize distinct niches in the human body, arranged in complex communities, especially in the intestines and the oral cavity. The diversity of archaea within these niches is limited to a few phylotypes, constituted in particular by methane-producing archaeal organisms. Although they are possibly symbionts, methanogens may play a role in the establishment of mucosal diseases by favouring the growth of certain bacterial groups.
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Affiliation(s)
- F Matarazzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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43
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Microbiota associated with infections of the jaws. Int J Dent 2012; 2012:369751. [PMID: 22829824 PMCID: PMC3399405 DOI: 10.1155/2012/369751] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2012] [Revised: 05/09/2012] [Accepted: 05/18/2012] [Indexed: 01/28/2023] Open
Abstract
The microbial infections involving the craniofacial skeleton, particularly maxilla and mandible, have direct relationship with the dental biofilm, with predominance of obligate anaerobes. In some patients, these infections may spread to bone marrow or facial soft tissues, producing severe and life-threatening septic conditions. In such cases, local treatment associated with systemic antimicrobials should be used in order to eradicate the sources of contamination. This paper discuss the possibility of spread of these infections and their clinical implications for dentistry, as well as their etiology and aspects related to microbial virulence and pathogenesis.
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Blais Lecours P, Duchaine C, Taillefer M, Tremblay C, Veillette M, Cormier Y, Marsolais D. Immunogenic properties of archaeal species found in bioaerosols. PLoS One 2011; 6:e23326. [PMID: 21858070 PMCID: PMC3155538 DOI: 10.1371/journal.pone.0023326] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 07/13/2011] [Indexed: 11/24/2022] Open
Abstract
The etiology of bioaerosol-related pulmonary diseases remains poorly understood. Recently, archaea emerged as prominent airborne components of agricultural environments, but the consequences of airway exposure to archaea remain unknown. Since subcomponents of archaea can be immunogenic, we used a murine model to study the pulmonary immune responses to two archaeal species found in agricultural facilities: Methanobrevibacter smithii (MBS) and Methanosphaera stadtmanae (MSS). Mice were administered intranasally with 6.25, 25 or 100 µg of MBS or MSS, once daily, 3 days a week, for 3 weeks. MSS induced more severe histopathological alterations than MBS with perivascular accumulation of granulocytes, pronounced thickening of the alveolar septa, alveolar macrophages accumulation and increased perivascular mononucleated cell accumulation. Analyses of bronchoalveolar lavage fluids revealed up to 3 times greater leukocyte accumulation with MSS compared to MBS. Instillation of 100 µg of MBS or MSS caused predominant accumulation of monocyte/macrophages (4.5×10(5) and 4.8×10(5) cells/ml respectively) followed by CD4(+) T cells (1.38×10(5) and 1.94×10(5) cells/ml respectively), B cells (0.73×10(5) and 1.28×10(5) cells/ml respectively), and CD8(+) T cells (0.20×10(5) and 0.31×10(5) cells/ml respectively) in the airways. Both archaeal species induced similar titers of antigen-specific IgGs in plasma. MSS but not MBS caused an accumulation of eosinophils and neutrophils in the lungs, which surprisingly, correlated inversely with the size of the inoculum. Stronger immunogenicity of MSS was confirmed by a 3 fold higher accumulation of myeloid dendritic cells in the airways, compared to MBS. Thus, the dose and species of archaea determine the magnitude and nature of the pulmonary immune response. This is the first report of an immunomodulatory role of archaeal species found in bioaerosols.
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Affiliation(s)
- Pascale Blais Lecours
- Centre de recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, Canada
| | - Caroline Duchaine
- Centre de recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, Canada
- Département de biochimie, de microbiologie et de bioinformatique, Faculté des sciences et de génie, Université Laval, Québec, Canada
| | - Michel Taillefer
- Centre de recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, Canada
| | | | - Marc Veillette
- Centre de recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, Canada
| | - Yvon Cormier
- Centre de recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, Canada
- Départment de médecine, Faculté de médecine, Université Laval, Québec, Canada
| | - David Marsolais
- Centre de recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, Canada
- Départment de médecine, Faculté de médecine, Université Laval, Québec, Canada
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Fernandez y Mostajo M, Zaura E, Crielaard W, Beertsen W. Does routine analysis of subgingival microbiota in periodontitis contribute to patient benefit? Eur J Oral Sci 2011; 119:259-64. [PMID: 21726285 DOI: 10.1111/j.1600-0722.2011.00828.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In clinical periodontology it is common practice to sample subgingival plaque from periodontitis patients and to search for the presence of alleged periodontal pathogens using routine laboratory techniques such as culture, DNA-DNA hybridization or real-time PCR. Usually, special attention is given to the recognition of 'red complex' microorganisms and to Aggregatibacter actinomycetemcomitans. Recently, molecular open-ended techniques have been introduced which are distinct from the more 'classical' approaches in that they do not preselect for certain species. In this study, we investigated to what extent the outcome of these techniques has changed our insight into the composition of the subgingival microbiota and whether this has consequences on clinical decision making. The open-ended approaches showed that the composition of subgingival plaque is much more complex than previously thought. Next to the 'classical' putative periodontal pathogens, several non-culturable and fastidious species are now recognized as being associated with periodontitis, thus enlarging the group of suspected periodontal pathogens. We conclude that routine analyses of subgingival plaque in the clinic are not necessarily of benefit to the patient.
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46
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Matarazzo F, Ribeiro AC, Feres M, Faveri M, Mayer MPA. Diversity and quantitative analysis of Archaea in aggressive periodontitis and periodontally healthy subjects. J Clin Periodontol 2011; 38:621-7. [DOI: 10.1111/j.1600-051x.2011.01734.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Horz HP, Conrads G. Methanogenic Archaea and oral infections - ways to unravel the black box. J Oral Microbiol 2011; 3. [PMID: 21541092 PMCID: PMC3086593 DOI: 10.3402/jom.v3i0.5940] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 01/25/2011] [Accepted: 01/26/2011] [Indexed: 02/06/2023] Open
Abstract
Archaea, organisms that make up the third domain of cellular life are members of the human oral microflora. They are strikingly less diverse than oral bacteria and appear to be relatively rare with respect to their numerical abundance. Since they have been exclusively found in association with oral infections such as periodontitis and apical periodontitis and given their unique physiology and energy metabolism, it is highly plausible that they are more than just secondary colonizers of infected areas, but instead are actively involved in the overall poly-microbial infection process. Conversely, it is a highly challenging task to clearly demonstrate their possible active participation – mostly due to the difficulty to grow them in routine microbiology laboratories. This current review points out the importance for understanding the medical impact of methanogens and aims at devising strategies for elucidating the true function of archaea in the oral ecosystem.
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Affiliation(s)
- Hans-Peter Horz
- Division of Oral Microbiology and Immunology, RWTH Aachen University Hospital, Aachen, Germany
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Faveri M, Gonçalves LFH, Feres M, Figueiredo LC, Gouveia LA, Shibli JA, Mayer MPA. Prevalence and microbiological diversity of Archaea in peri-implantitis subjects by 16S ribosomal RNA clonal analysis. J Periodontal Res 2011; 46:338-44. [PMID: 21338359 DOI: 10.1111/j.1600-0765.2011.01347.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND AND OBJECTIVE This study evaluated the prevalence and the molecular diversity of Archaea in the subgingival biofilm samples of subjects with peri-implantitis. MATERIAL AND METHODS Fifty subjects were assigned into two groups: Control (n = 25), consisting of subjects with healthy implants; and Test (n = 25), consisting of subjects with peri-implantitis sites, as well as a healthy implant. In the Test group, subgingival biofilm samples were taken from the deepest sites of the diseased implant. In both groups, subgingival biofilm was collected from one site with a healthy implant and from one site with a periodontally healthy tooth. DNA was extracted and the 16S ribosomal RNA gene was amplified with universal primer pairs for Archaea. Amplified genes were cloned and sequenced, and the phylotypes were identified by comparison with known 16S ribosomal RNA sequences. RESULTS In the Control group, Archaea were detected in two and three sites of the implant and the tooth, respectively. In the Test group, Archaea were detected in 12, 4 and 2 sites of diseased implants, healthy implants and teeth, respectively. Diseased implants presented a significantly higher prevalence of Archaea in comparison with healthy implants and natural teeth, irrespective of group. Over 90% of the clone libraries were formed by Methanobrevibacter oralis, which was detected in both groups. Methanobacterium congelense/curvum was detected in four subjects from the Test group and in two subjects from the Control group. CONCLUSION Although M. oralis was the main species of Archaea associated with both healthy and diseased implant sites, the data indicated an increased prevalence of Archaea in peri-implantitis sites, and their role in pathogenesis should be further investigated.
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Affiliation(s)
- M Faveri
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Brazil.
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Jarrell KF, Walters AD, Bochiwal C, Borgia JM, Dickinson T, Chong JPJ. Major players on the microbial stage: why archaea are important. MICROBIOLOGY-SGM 2011; 157:919-936. [PMID: 21330437 DOI: 10.1099/mic.0.047837-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
As microbiology undergoes a renaissance, fuelled in part by developments in new sequencing technologies, the massive diversity and abundance of microbes becomes yet more obvious. The Archaea have traditionally been perceived as a minor group of organisms forced to evolve into environmental niches not occupied by their more 'successful' and 'vigorous' counterparts, the bacteria. Here we outline some of the evidence gathered by an increasingly large and productive group of scientists that demonstrates not only that the Archaea contribute significantly to global nutrient cycling, but also that they compete successfully in 'mainstream' environments. Recent data suggest that the Archaea provide the major routes for ammonia oxidation in the environment. Archaea also have huge economic potential that to date has only been fully realized in the production of thermostable polymerases. Archaea have furnished us with key paradigms for understanding fundamentally conserved processes across all domains of life. In addition, they have provided numerous exemplars of novel biological mechanisms that provide us with a much broader view of the forms that life can take and the way in which micro-organisms can interact with other species. That this information has been garnered in a relatively short period of time, and appears to represent only a small proportion of what the Archaea have to offer, should provide further incentives to microbiologists to investigate the underlying biology of this fascinating domain.
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Affiliation(s)
- Ken F Jarrell
- Department of Microbiology and Immunology, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Alison D Walters
- Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK
| | - Chitvan Bochiwal
- Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK
| | - Juliet M Borgia
- Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK
| | - Thomas Dickinson
- Sheffield Hallam University, City Campus, Howard Street, Sheffield S1 1WB, UK
| | - James P J Chong
- Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK
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The discussion goes on: What is the role of Euryarchaeota in humans? ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2010; 2010:967271. [PMID: 21253553 PMCID: PMC3021867 DOI: 10.1155/2010/967271] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Accepted: 11/11/2010] [Indexed: 02/06/2023]
Abstract
The human body (primarily the intestinal tract, the oral cavity, and the skin) harbours approximately 1,000 different bacterial species. However, the number of archaeal species known to colonize man seems to be confined to a handful of organisms within the class Euryarchaeota (including Methanobrevibacter smithii, M. oralis, and Methanosphaera stadtmanae). In contrast to this conspicuously low diversity of Archaea in humans their unique physiology in conjunction with the growing number of reports regarding their occurrence at sites of infection has made this issue an emerging field of study. While previous review articles in recent years have addressed the putative role of particularly methanogenic archaea for human health and disease, this paper compiles novel experimental data that have been reported since then. The aim of this paper is to inspire the scientific community of “Archaea experts” for those unique archaeal organisms that have successfully participated in the human-microbe coevolution.
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