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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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Pilliol V, Morsli M, Terlier L, Hassani Y, Malat I, Guindo CO, Davoust B, Lamglait B, Drancourt M, Aboudharam G, Grine G, Terrer E. Candidatus Methanosphaera massiliense sp. nov., a methanogenic archaeal species found in a human fecal sample and prevalent in pigs and red kangaroos. Microbiol Spectr 2024; 12:e0514122. [PMID: 38189277 PMCID: PMC10845953 DOI: 10.1128/spectrum.05141-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 11/24/2023] [Indexed: 01/09/2024] Open
Abstract
Methanosphaera stadtmanae was the sole Methanosphaera representative to be cultured and detected by molecular methods in the human gut microbiota, further associated with digestive and respiratory diseases, leaving unknown the actual diversity of human-associated Methanosphaera species. Here, a novel Methanosphaera species, Candidatus Methanosphaera massiliense (Ca. M. massiliense) sp. nov. was isolated by culture using a hydrogen- and carbon dioxide-free medium from one human feces sample. Ca. M. massiliense is a non-motile, 850 nm Gram-positive coccus autofluorescent at 420 nm. Whole-genome sequencing yielded a 29.7% GC content, gapless 1,785,773 bp genome sequence with an 84.5% coding ratio, encoding for alcohol and aldehyde dehydrogenases promoting the growth of Ca. M. massiliense without hydrogen. Screening additional mammal and human feces using a specific genome sequence-derived DNA-polymerase RT-PCR system yielded a prevalence of 22% in pigs, 12% in red kangaroos, and no detection in 149 other human samples. This study, extending the diversity of Methanosphaera in human microbiota, questions the zoonotic sources of Ca. M. massiliense and possible transfer between hosts.IMPORTANCEMethanogens are constant inhabitants in the human gut microbiota in which Methanosphaera stadtmanae was the only cultivated Methanosphaera representative. We grew Candidatus Methanosphaera massiliense sp. nov. from one human feces sample in a novel culture medium under a nitrogen atmosphere. Systematic research for methanogens in human and animal fecal samples detected Ca. M. massiliense in pig and red kangaroo feces, raising the possibility of its zoonotic acquisition. Host specificity, source of acquisition, and adaptation of methanogens should be further investigated.
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Affiliation(s)
- Virginie Pilliol
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, Ecole de Médecine Dentaire, Marseille, France
| | - Madjid Morsli
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Laureline Terlier
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Yasmine Hassani
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Ihab Malat
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Cheick Oumar Guindo
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Bernard Davoust
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | | | - Michel Drancourt
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Gérard Aboudharam
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, Ecole de Médecine Dentaire, Marseille, France
| | | | - Elodie Terrer
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
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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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Volmer JG, McRae H, Morrison M. The evolving role of methanogenic archaea in mammalian microbiomes. Front Microbiol 2023; 14:1268451. [PMID: 37727289 PMCID: PMC10506414 DOI: 10.3389/fmicb.2023.1268451] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 08/18/2023] [Indexed: 09/21/2023] Open
Abstract
Methanogenic archaea (methanogens) represent a diverse group of microorganisms that inhabit various environmental and host-associated microbiomes. These organisms play an essential role in global carbon cycling given their ability to produce methane, a potent greenhouse gas, as a by-product of their energy production. Recent advances in culture-independent and -dependent studies have highlighted an increased prevalence of methanogens in the host-associated microbiome of diverse animal species. Moreover, there is increasing evidence that methanogens, and/or the methane they produce, may play a substantial role in human health and disease. This review addresses the expanding host-range and the emerging view of host-specific adaptations in methanogen biology and ecology, and the implications for host health and disease.
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Affiliation(s)
- James G. Volmer
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, QLD, Australia
| | - Harley McRae
- Faculty of Medicine, University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Mark Morrison
- Faculty of Medicine, University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, QLD, Australia
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Sereme Y, Michel M, Mezouar S, Guindo CO, Kaba L, Grine G, Mura T, Mège JL, Tran TA, Corbeau P, Filleron A, Vitte J. A Non-Invasive Neonatal Signature Predicts Later Development of Atopic Diseases. J Clin Med 2022; 11:jcm11102749. [PMID: 35628877 PMCID: PMC9143112 DOI: 10.3390/jcm11102749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 02/01/2023] Open
Abstract
Background: Preterm birth is a major cause of morbidity and mortality in infants and children. Non-invasive methods for screening the neonatal immune status are lacking. Archaea, a prokaryotic life domain, comprise methanogenic species that are part of the neonatal human microbiota and contribute to early immune imprinting. However, they have not yet been characterized in preterm neonates. Objective: To characterize the gut immunological and methanogenic Archaeal (MA) signature in preterm neonates, using the presence or absence of atopic conditions at the age of one year as a clinical endpoint. Methods: Meconium and stool were collected from preterm neonates and used to develop a standardized stool preparation method for the assessment of mediators and cytokines and characterize the qPCR kinetics of gut MA. Analysis addressed the relationship between immunological biomarkers, Archaea abundance, and atopic disease at age one. Results: Immunoglobulin E, tryptase, calprotectin, EDN, cytokines, and MA were detectable in the meconium and later samples. Atopic conditions at age of one year were positively associated with neonatal EDN, IL-1β, IL-10, IL-6, and MA abundance. The latter was negatively associated with neonatal EDN, IL-1β, and IL-6. Conclusions: We report a non-invasive method for establishing a gut immunological and Archaeal signature in preterm neonates, predictive of atopic diseases at the age of one year.
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Affiliation(s)
- Youssouf Sereme
- IHU Méditerranée Infection, 13005 Marseille, France; (Y.S.); (M.M.); (S.M.); (C.O.G.); (L.K.); (G.G.); (J.-L.M.)
- IRD, APHM, MEPHI, Aix-Marseille Université, 13284 Marseille, France
| | - Moïse Michel
- IHU Méditerranée Infection, 13005 Marseille, France; (Y.S.); (M.M.); (S.M.); (C.O.G.); (L.K.); (G.G.); (J.-L.M.)
- IRD, APHM, MEPHI, Aix-Marseille Université, 13284 Marseille, France
- Immunology Department, University Hospital Nîmes, 30900 Nîmes, France
| | - Soraya Mezouar
- IHU Méditerranée Infection, 13005 Marseille, France; (Y.S.); (M.M.); (S.M.); (C.O.G.); (L.K.); (G.G.); (J.-L.M.)
- IRD, APHM, MEPHI, Aix-Marseille Université, 13284 Marseille, France
| | - Cheick Oumar Guindo
- IHU Méditerranée Infection, 13005 Marseille, France; (Y.S.); (M.M.); (S.M.); (C.O.G.); (L.K.); (G.G.); (J.-L.M.)
- IRD, APHM, MEPHI, Aix-Marseille Université, 13284 Marseille, France
| | - Lanceï Kaba
- IHU Méditerranée Infection, 13005 Marseille, France; (Y.S.); (M.M.); (S.M.); (C.O.G.); (L.K.); (G.G.); (J.-L.M.)
- IRD, AP-HM, SSA, VITROME, Aix-Marseille Université, 13284 Marseille, France
| | - Ghiles Grine
- IHU Méditerranée Infection, 13005 Marseille, France; (Y.S.); (M.M.); (S.M.); (C.O.G.); (L.K.); (G.G.); (J.-L.M.)
- IRD, APHM, MEPHI, Aix-Marseille Université, 13284 Marseille, France
- UFR Odontologie, Aix-Marseille Université, 13284 Marseille, France
| | - Thibault Mura
- INSERM, University of Montpellier, U1061, Neuropsychiatry: Epidemiological and Clinical Research, 34093 Montpellier, France;
- Laboratoire de Biostatistique, Epidémiologie Clinique, Santé Publique Innovation et Méthodologie (BESPIM), Groupe Hospitalier Caremeau, CHU de Nîmes, Nîmes University Hospital, 30900 Nîmes, France
| | - Jean-Louis Mège
- IHU Méditerranée Infection, 13005 Marseille, France; (Y.S.); (M.M.); (S.M.); (C.O.G.); (L.K.); (G.G.); (J.-L.M.)
- IRD, APHM, MEPHI, Aix-Marseille Université, 13284 Marseille, France
| | - Tu Anh Tran
- Paediatrics Department, University Hospital Nîmes, 30900 Nîmes, France;
- INSERM U1183, Institute for Regenerative Medicine & Biotherapy, 34295 Montpellier, France
- Faculty de Medicine, Montpellier University, 34000 Montpellier, France
| | - Pierre Corbeau
- Immunology Department, University Hospital Nîmes, 30900 Nîmes, France
- Faculty de Medicine, Montpellier University, 34000 Montpellier, France
- CNRS UMR 9002, Institute of Human Genetics, 34090 Montpellier, France
- Correspondence: (P.C.); (A.F.); (J.V.); Tel.: +33-4-13-73-20-51 (J.V.); Fax: +33-4-13-73-20-52 (J.V.)
| | - Anne Filleron
- Paediatrics Department, University Hospital Nîmes, 30900 Nîmes, France;
- INSERM U1183, Institute for Regenerative Medicine & Biotherapy, 34295 Montpellier, France
- Faculty de Medicine, Montpellier University, 34000 Montpellier, France
- Correspondence: (P.C.); (A.F.); (J.V.); Tel.: +33-4-13-73-20-51 (J.V.); Fax: +33-4-13-73-20-52 (J.V.)
| | - Joana Vitte
- IHU Méditerranée Infection, 13005 Marseille, France; (Y.S.); (M.M.); (S.M.); (C.O.G.); (L.K.); (G.G.); (J.-L.M.)
- IRD, APHM, MEPHI, Aix-Marseille Université, 13284 Marseille, France
- Faculty de Medicine, Montpellier University, 34000 Montpellier, France
- IDESP, INSERM UMR UA11, Institut Desbrest d’Epidemiologie et de Santé Publique (IDESP) Campus Sante, 34093 Montpellier, France
- Correspondence: (P.C.); (A.F.); (J.V.); Tel.: +33-4-13-73-20-51 (J.V.); Fax: +33-4-13-73-20-52 (J.V.)
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Sabey KA, Song SJ, Jolles A, Knight R, Ezenwa VO. Coinfection and infection duration shape how pathogens affect the African buffalo gut microbiota. THE ISME JOURNAL 2021; 15:1359-1371. [PMID: 33328653 PMCID: PMC8115229 DOI: 10.1038/s41396-020-00855-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 11/10/2020] [Accepted: 11/20/2020] [Indexed: 01/07/2023]
Abstract
Changes in the gut microbiota during pathogen infection are often predicted to influence disease outcomes. However, studies exploring whether pathogens induce microbiota shifts have yielded inconsistent results. This suggests that variation in infection, rather than the presence of infection alone, might shape pathogen-microbiota relationships. For example, most hosts are coinfected with multiple pathogens simultaneously, and hosts vary in how long they are infected, which may amplify or diminish microbial shifts expected in response to a focal pathogen. We used a longitudinal anthelmintic treatment study of free-ranging African buffalo (Syncerus caffer) to examine whether (i) coinfection with bovine tuberculosis (Mycobacterium bovis, TB) and gastrointestinal nematodes, and (ii) the duration of TB infection, modified effects of single pathogens on the gut microbiota. By accounting for the interaction between TB and nematodes, we found that coinfection affected changes in microbial abundance associated with single infections. Furthermore, the duration of TB infection predicted more microbiota variation than the presence of TB. Importantly, coinfection and infection duration had nearly as much influence on microbial patterns as demographic and environmental factors commonly examined in microbiota research. These findings demonstrate that acknowledging infection heterogeneities may be crucial to understanding relationships between pathogens and the gut microbiota.
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Affiliation(s)
- Kate A Sabey
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Se Jin Song
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Anna Jolles
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR, USA
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Vanessa O Ezenwa
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA.
- Odum School of Ecology, University of Georgia, Athens, GA, USA.
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Brassard J, Marsolais D, Blanchet MR. Mutant Mice and Animal Models of Airway Allergic Disease. Methods Mol Biol 2021; 2241:59-74. [PMID: 33486728 DOI: 10.1007/978-1-0716-1095-4_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Eosinophilia is a hallmark of allergic airway inflammation, and eosinophils represent an integral effector leukocyte through their release of various granule-stored cytokines and proteins. Numerous mouse models have been developed to mimic clinical disease and they have been instrumental in furthering our understanding of the role of eosinophils in disease. Most of these models consist of intranasal (i.n.) administration of antigenic proteases including papain and house dust mite (HDM) or the neo-antigen ovalbumin, with a resulting Th2-biased immune response and airway eosinophilia. These models have been particularly informative when combined with the numerous transgenic mice available that modulate eosinophil frequency or the mechanisms involved in their migration. Here, we describe the current models of allergic airway inflammation and outline some of the transgenic mice available to study eosinophil disease.
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Affiliation(s)
- Julyanne Brassard
- Centre de Recherche, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC, Canada
| | - David Marsolais
- Centre de Recherche, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC, Canada
| | - Marie-Renee Blanchet
- Centre de Recherche, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC, Canada.
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Sereme Y, Mezouar S, Grine G, Mege JL, Drancourt M, Corbeau P, Vitte J. Methanogenic Archaea: Emerging Partners in the Field of Allergic Diseases. Clin Rev Allergy Immunol 2020; 57:456-466. [PMID: 31522353 DOI: 10.1007/s12016-019-08766-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Archaea, which form one of four domains of life alongside Eukarya, Bacteria, and giant viruses, have long been neglected as components of the human microbiota and potential opportunistic infectious pathogens. In this review, we focus on methanogenic Archaea, which rely on hydrogen for their metabolism and growth. On one hand, methanogenic Archaea in the gut are functional associates of the fermentative digestion of dietary fibers, favoring the production of beneficial short-chain fatty acids and likely contributing to the weaning reaction during the neonatal window of opportunity. On the other hand, methanogenic Archaea trigger the activation of innate and adaptive responses and the generation of specific T and B cells in animals and humans. In mouse models, lung hypersensitivity reactions can be induced by inhaled methanogenic Archaea mimicking human professional exposure to organic dust. Changes in methanogenic Archaea of the microbiota are detected in an array of dysimmune conditions comprising inflammatory bowel disease, obesity, malnutrition, anorexia, colorectal cancer, and diverticulosis. At the subcellular level, methanogenic Archaea are activators of the TLR8-dependent NLRP3 inflammasome, modulate the release of antimicrobial peptides and drive the production of proinflammatory, Th-1, Th-2, and Th-17 cytokines. Our objective was to introduce the most recent and major pieces of evidence supporting the involvement of Archaea in the balance between health and dysimmune diseases, with a particular focus on atopic and allergic conditions.
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Affiliation(s)
- Youssouf Sereme
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille, France
- IRD, APHM, MEPHI, Aix Marseille University, Marseille, France
| | - Soraya Mezouar
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille, France
- IRD, APHM, MEPHI, Aix Marseille University, Marseille, France
| | - Ghiles Grine
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille, France
- IRD, APHM, MEPHI, Aix Marseille University, Marseille, France
| | - Jean Louis Mege
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille, France
- IRD, APHM, MEPHI, Aix Marseille University, Marseille, France
- APHM, Hôpital Timone, Service de Bactériologie - Epidémiologie - Hygiène hospitalière, Aix-Marseille University, Marseille, France
| | - Michel Drancourt
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille, France
- IRD, APHM, MEPHI, Aix Marseille University, Marseille, France
| | - Pierre Corbeau
- Institute of Human Genetics, UMR9002, CNRS-Montpellier University, Montpellier, France
- Montpellier University, Montpellier, France
- Immunology Department, University Hospital, Nîmes, France
| | - Joana Vitte
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille, France.
- IRD, APHM, MEPHI, Aix Marseille University, Marseille, France.
- APHM, Hôpital Timone, Service de Bactériologie - Epidémiologie - Hygiène hospitalière, Aix-Marseille University, Marseille, France.
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Piovesana S, Capriotti AL, Foglia P, Montone CM, La Barbera G, Zenezini Chiozzi R, Laganà A, Cavaliere C. Development of an Analytical Method for the Metaproteomic Investigation of Bioaerosol from Work Environments. Proteomics 2019; 19:e1900152. [PMID: 31315163 DOI: 10.1002/pmic.201900152] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/21/2019] [Indexed: 11/10/2022]
Abstract
The metaproteomic analysis of air particulate matter provides valuable information about the properties of bioaerosols in the atmosphere and their influence on climate and public health. In this work, a new method for the extraction and analysis of proteins in airborne particulate matter from quartz microfiber filters is developed. Different protein extraction procedures are tested to select the best extraction protocol based on protein recovery. The optimized method is tested for the extraction of proteins from spores of ubiquitous bacteria species and used for the metaproteomic characterization of filters from three work environments. In particular, ambient aerosol samples are collected in a composting plant, in a wastewater treatment plant, and in an agricultural holding. A total of 179, 15, 205, and 444 proteins are identified in composting plant, wastewater treatment plant, and agricultural holding, (cow stable and blending plant), respectively. In agreement with the major categories of primary biological aerosol particles, all identified proteins originated primarily from fungi, bacteria, and plants. The paper is the first metaproteomic study applied to bioaerosol samples collected in occupationally relevant environmental sites and, even though not aimed at monitoring the risk exposure of workers, it provides information on the possible exposure in the working environmental sites.
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Affiliation(s)
- Susy Piovesana
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Anna Laura Capriotti
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Patrizia Foglia
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Carmela Maria Montone
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Giorgia La Barbera
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | | | - Aldo Laganà
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Chiara Cavaliere
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
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Intestinal archaea inversely associated with childhood asthma. J Allergy Clin Immunol 2019; 143:2305-2307. [PMID: 30796982 DOI: 10.1016/j.jaci.2019.02.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 01/24/2019] [Accepted: 02/14/2019] [Indexed: 11/23/2022]
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Vierbuchen T, Stein K, Heine H. RNA is taking its Toll: Impact of RNA-specific Toll-like receptors on health and disease. Allergy 2019; 74:223-235. [PMID: 30475385 DOI: 10.1111/all.13680] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/08/2018] [Accepted: 11/20/2018] [Indexed: 12/13/2022]
Abstract
RNA-sensing Toll-like receptors (TLRs) are often described as antiviral receptors of the innate immune system. However, the past decade has shown that the function and relevance of these receptors are far more complex. They were found to be essential for the detection of various bacterial, archaeal, and eukaryotic microorganisms and facilitate the discrimination between dead and living microbes. The cytokine and interferon response profile that is triggered has the potential to improve the efficacy of next-generation vaccines and may prevent the development of asthma and allergy. Nevertheless, the ability to recognize foreign RNA comes with a cost as also damaged host cells can release nucleic acids that might induce an inappropriate immune response. Thus, it is not surprising that RNA-sensing TLRs play a key role in various autoimmune diseases. However, promising new inhibitors and antagonists are on the horizon to improve their treatment.
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Affiliation(s)
- Tim Vierbuchen
- Division of Innate Immunity Research Center Borstel – Leibniz Lung Center Borstel Germany
| | - Karina Stein
- Division of Innate Immunity Research Center Borstel – Leibniz Lung Center Borstel Germany
- Airway Research Center North (ARCN) German Center for Lung Research (DZL) Borstel Germany
| | - Holger Heine
- Division of Innate Immunity Research Center Borstel – Leibniz Lung Center Borstel Germany
- Airway Research Center North (ARCN) German Center for Lung Research (DZL) Borstel Germany
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12
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Hoedt EC, Parks DH, Volmer JG, Rosewarne CP, Denman SE, McSweeney CS, Muir JG, Gibson PR, Cuív PÓ, Hugenholtz P, Tyson GW, Morrison M. Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size. ISME JOURNAL 2018; 12:2942-2953. [PMID: 30068938 DOI: 10.1038/s41396-018-0225-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 04/27/2018] [Accepted: 06/03/2018] [Indexed: 11/09/2022]
Abstract
The genus Methanosphaera is a well-recognized but poorly characterized member of the mammalian gut microbiome, and distinctive from Methanobrevibacter smithii for its ability to induce a pro-inflammatory response in humans. Here we have used a combination of culture- and metagenomics-based approaches to expand the representation and information for the genus, which has supported the examination of their phylogeny and physiological capacity. Novel isolates of the genus Methanosphaera were recovered from bovine rumen digesta and human stool, with the bovine isolate remarkable for its large genome size relative to other Methanosphaera isolates from monogastric hosts. To substantiate this observation, we then recovered seven high-quality Methanosphaera-affiliated population genomes from ruminant and human gut metagenomic datasets. Our analyses confirm a monophyletic origin of Methanosphaera spp. and that the colonization of monogastric and ruminant hosts favors representatives of the genus with different genome sizes, reflecting differences in the genome content needed to persist in these different habitats.
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Affiliation(s)
- Emily C Hoedt
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - Donovan H Parks
- Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - James G Volmer
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Carly P Rosewarne
- Commonwealth Scientific and Industrial Research Organisation, Kintore Avenue, Adelaide, Australia
| | - Stuart E Denman
- Commonwealth Scientific and Industrial Research Organisation, Queensland Bioscience Precinct, St Lucia, Australia
| | - Christopher S McSweeney
- Commonwealth Scientific and Industrial Research Organisation, Queensland Bioscience Precinct, St Lucia, Australia
| | - Jane G Muir
- Department of Gastroenterology, Central Clinical School, The Alfred Centre, Monash University, Melbourne, Victoria, Australia
| | - Peter R Gibson
- Department of Gastroenterology, Central Clinical School, The Alfred Centre, Monash University, Melbourne, Victoria, Australia
| | - Páraic Ó Cuív
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - Philip Hugenholtz
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia.,Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Gene W Tyson
- Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Mark Morrison
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia. .,Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Australia.
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13
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Peachey LE, Molena RA, Jenkins TP, Di Cesare A, Traversa D, Hodgkinson JE, Cantacessi C. The relationships between faecal egg counts and gut microbial composition in UK Thoroughbreds infected by cyathostomins. Int J Parasitol 2018; 48:403-412. [PMID: 29432771 PMCID: PMC5946844 DOI: 10.1016/j.ijpara.2017.11.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 11/23/2017] [Accepted: 11/26/2017] [Indexed: 12/31/2022]
Abstract
We profiled the faecal microbial communities of horses with cyathostomin infections, pre- and post-anthelmintic treatment. Methanomicrobia and Dehalobacterium were expanded in the microbiota of horses with low cyathostomin faecal egg counts. A reduction in TM7 and an expansion in Adlercreutzia followed anthelmintic treatment in horses with high faecal egg counts. Novel intervention strategies against cyathostomins based on the manipulation of the gut flora may be developed.
A growing body of evidence, particularly in humans and rodents, supports the existence of a complex network of interactions occurring between gastrointestinal (GI) helminth parasites and the gut commensal bacteria, with substantial effects on both host immunity and metabolic potential. However, little is known of the fundamental biology of such interactions in other animal species; nonetheless, given the considerable economic losses associated with GI parasites, particularly in livestock and equines, as well as the global threat of emerging anthelmintic resistance, further explorations of the complexities of host-helminth-microbiota interactions in these species are needed. This study characterises the composition of the equine gut commensal flora associated with the presence, in faecal samples, of low (Clow) and high (Chigh) numbers of eggs of an important group of GI parasites (i.e. the cyathostomins), prior to and following anthelmintic treatment. High-throughput sequencing of bacterial 16S rRNA amplicons and associated bioinformatics and statistical analyses of sequence data revealed strong clustering according to faecal egg counts (P = 0.003). A trend towards increased populations of Methanomicrobia (class) and Dehalobacterium (genus) was observed in Clow in comparison with Chigh. Anthelmintic treatment in Chigh was associated with a significant reduction of the bacterial Phylum TM7 14 days post-ivermectin administration, as well as a transient expansion of Adlercreutzia spp. at 2 days post-treatment. This study provides a first known insight into the discovery of the intimate mechanisms governing host-parasite-microbiota interactions in equines, and sets a basis for the development of novel, biology-based intervention strategies against equine GI helminths based on the manipulation of the commensal gut flora.
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Affiliation(s)
- L E Peachey
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, CB3 0ES, United Kingdom.
| | - R A Molena
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, CB3 0ES, United Kingdom
| | - T P Jenkins
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, CB3 0ES, United Kingdom
| | - A Di Cesare
- Faculty of Veterinary Medicine, University of Teramo, Teramo, 64100, Italy
| | - D Traversa
- Faculty of Veterinary Medicine, University of Teramo, Teramo, 64100, Italy
| | - J E Hodgkinson
- Department of Infection Biology, University of Liverpool, Leahurst, Neston CH64 7TE, United Kingdom
| | - C Cantacessi
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, CB3 0ES, United Kingdom.
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14
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Bernatchez E, Gold MJ, Langlois A, Blais-Lecours P, Boucher M, Duchaine C, Marsolais D, McNagny KM, Blanchet MR. Methanosphaera stadtmanae induces a type IV hypersensitivity response in a mouse model of airway inflammation. Physiol Rep 2017; 5:5/7/e13163. [PMID: 28364028 PMCID: PMC5392504 DOI: 10.14814/phy2.13163] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 01/20/2017] [Indexed: 12/13/2022] Open
Abstract
Despite improved awareness of work‐related diseases and preventive measures, many workers are still at high risk of developing occupational hypersensitivity airway diseases. This stems from a lack of knowledge of bioaerosol composition and their potential effects on human health. Recently, archaea species were identified in bioaerosols, raising the possibility that they play a major role in exposure‐related pathology. Specifically, Methanosphaera stadtmanae (MSS) and Methanobrevibacter smithii (MBS) are found in high concentrations in agricultural environments and respiratory exposure to crude extract demonstrates immunomodulatory activity in mice. Nevertheless, our knowledge of the specific impact of methanogens exposure on airway immunity and their potential to induce airway hypersensitivity responses in workers remains scant. Analysis of the lung mucosal response to methanogen crude extracts in mice demonstrated that MSS and MBS predominantly induced TH17 airway inflammation, typical of a type IV hypersensitivity response. Furthermore, the response to MSS was associated with antigen‐specific IgG1 and IgG2a production. However, despite the presence of eosinophils after MSS exposure, only a weak TH2 response and no airway hyperresponsiveness were observed. Finally, using eosinophil and mast cell‐deficient mice, we confirmed that these cells are dispensable for the TH17 response to MSS, although eosinophils likely contribute to the exacerbation of inflammatory processes induced by MSS crude extract exposure. We conclude that, as MSS induces a clear type IV hypersensitivity lung response, it has the potential to be harmful to workers frequently exposed to this methanogen, and that preventive measures should be taken to avoid chronic hypersensitivity disease development in workers.
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Affiliation(s)
- Emilie Bernatchez
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Quebec City, Quebec, Canada
| | - Matthew J Gold
- The Biomedical Research Center, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anick Langlois
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Quebec City, Quebec, Canada
| | - Pascale Blais-Lecours
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Quebec City, Quebec, Canada
| | - Magali Boucher
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Quebec City, Quebec, Canada
| | - Caroline Duchaine
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Quebec City, Quebec, Canada
| | - David Marsolais
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Quebec City, Quebec, Canada
| | - Kelly M McNagny
- The Biomedical Research Center, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marie-Renée Blanchet
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Quebec City, Quebec, Canada
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15
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Vierbuchen T, Bang C, Rosigkeit H, Schmitz RA, Heine H. The Human-Associated Archaeon Methanosphaera stadtmanae Is Recognized through Its RNA and Induces TLR8-Dependent NLRP3 Inflammasome Activation. Front Immunol 2017; 8:1535. [PMID: 29181003 PMCID: PMC5694038 DOI: 10.3389/fimmu.2017.01535] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 10/27/2017] [Indexed: 01/04/2023] Open
Abstract
The archaeon Methanosphaera stadtmanae is a member of the gut microbiota; yet, the molecular cross-talk between archaea and the human immune system and its potential contribution to inflammatory diseases has not been evaluated. Although archaea are as bacteria prokaryotes, they form a distinct domain having unique features such as different cell wall structures and membrane lipids. So far, no microbe-associated molecular patterns of archaea which activate innate immune receptors have been identified. By stimulating human myeloid cells with M. stadtmanae and purified archaeal nucleic acids, we identified both the microorganism and its RNA as potent stimuli for the innate immune system. To dissect the recognition and activation pathways induced by M. stadtmanae, human monocytic BLaER1 knockout cells were generated using the CRISPR/Cas9 system targeting components of TLR and inflammasome signaling. While the recognition of M. stadtmanae is mediated by TLR7 and TLR8, activation of the NLRP3 inflammasome depends solely on TLR8 engagement. Notably, this process resembles hallmarks of both the canonical and the recently described alternative inflammasome activation. Thus, we have demonstrated for the first time the specific recognition of and response to an archaeon by human cells at the molecular level.
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Affiliation(s)
- Tim Vierbuchen
- Division of Innate Immunity, Research Center Borstel, Borstel, Germany
| | - Corinna Bang
- Institute for General Microbiology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Hanna Rosigkeit
- Division of Innate Immunity, Research Center Borstel, Borstel, Germany
| | - Ruth A Schmitz
- Institute for General Microbiology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Holger Heine
- Division of Innate Immunity, Research Center Borstel, Borstel, Germany.,Airway Research Center North (ARCN), German Center for Lung Research (DZL), Borstel, Germany
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