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Duller S, Moissl-Eichinger C. Archaea in the Human Microbiome and Potential Effects on Human Infectious Disease. Emerg Infect Dis 2024; 30. [PMID: 39043386 PMCID: PMC11286065 DOI: 10.3201/eid3008.240181] [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] [Indexed: 07/25/2024] Open
Abstract
Archaea represent a separate domain of life, next to bacteria and eukarya. As components of the human microbiome, archaea have been associated with various diseases, including periodontitis, endodontic infections, small intestinal bacterial overgrowth, and urogenital tract infections. Archaea are generally considered nonpathogenic; the reasons are speculative because of limited knowledge and gene annotation challenges. Nevertheless, archaeal syntrophic principles that shape global microbial networks aid both archaea and potentially pathogenic bacteria. Evaluating archaea interactions remains challenging, requiring clinical studies on inflammatory potential and the effects of archaeal metabolism. Establishing a culture collection is crucial for investigating archaea functions within the human microbiome, which could improve health outcomes in infectious diseases. We summarize potential reasons for archaeal nonpathogenicity, assess the association with infectious diseases in humans, and discuss the necessary experimental steps to enable mechanistic studies involving archaea.
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Bork F, Greve CL, Youn C, Chen S, N C Leal V, Wang Y, Fischer B, Nasri M, Focken J, Scheurer J, Engels P, Dubbelaar M, Hipp K, Zalat B, Szolek A, Wu MJ, Schittek B, Bugl S, Kufer TA, Löffler MW, Chamaillard M, Skokowa J, Kramer D, Archer NK, Weber ANR. naRNA-LL37 composite DAMPs define sterile NETs as self-propagating drivers of inflammation. EMBO Rep 2024; 25:2914-2949. [PMID: 38783164 PMCID: PMC11239898 DOI: 10.1038/s44319-024-00150-5] [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: 08/24/2023] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 05/25/2024] Open
Abstract
Neutrophil extracellular traps (NETs) are a key antimicrobial feature of cellular innate immunity mediated by polymorphonuclear neutrophils (PMNs). NETs counteract microbes but are also linked to inflammation in atherosclerosis, arthritis, or psoriasis by unknown mechanisms. Here, we report that NET-associated RNA (naRNA) stimulates further NET formation in naive PMNs via a unique TLR8-NLRP3 inflammasome-dependent pathway. Keratinocytes respond to naRNA with expression of psoriasis-related genes (e.g., IL17, IL36) via atypical NOD2-RIPK signaling. In vivo, naRNA drives temporary skin inflammation, which is drastically ameliorated by genetic ablation of RNA sensing. Unexpectedly, the naRNA-LL37 'composite damage-associated molecular pattern (DAMP)' is pre-stored in resting neutrophil granules, defining sterile NETs as inflammatory webs that amplify neutrophil activation. However, the activity of the naRNA-LL37 DAMP is transient and hence supposedly self-limiting under physiological conditions. Collectively, upon dysregulated NET release like in psoriasis, naRNA sensing may represent both a potential cause of disease and a new intervention target.
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Affiliation(s)
- Francesca Bork
- Institute of Immunology, Department of Innate Immunity, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Carsten L Greve
- Institute of Immunology, Department of Innate Immunity, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Christine Youn
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Sirui Chen
- Institute of Immunology, Department of Innate Immunity, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Vinicius N C Leal
- Institute of Immunology, Department of Innate Immunity, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
- Laboratory of Immunogenetics, Department of Immunology, Institute of Biomedical Science, University of São Paulo (USP), São Paulo, SP, Brazil
| | - Yu Wang
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Berenice Fischer
- Department of Dermatology, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Masoud Nasri
- Division of Translational Oncology, Department of Oncology, Hematology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Otfried-Müller Str. 10, 72076, Tübingen, Germany
| | - Jule Focken
- Department of Dermatology, University Hospital Tübingen, Liebermeisterstr. 25, 72076, Tübingen, Germany
| | - Jasmin Scheurer
- Department of Dermatology, University Hospital Tübingen, Liebermeisterstr. 25, 72076, Tübingen, Germany
| | - Pujan Engels
- Institute of Immunology, Department of Innate Immunity, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Marissa Dubbelaar
- Institute of Immunology, Department of Peptide-based Immunotherapy, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
- Quantitative Biology Center (QBiC), University of Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
| | - Katharina Hipp
- Electron Microscopy Facility, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076, Tübingen, Germany
| | - Baher Zalat
- Institute of Immunology, Department of Innate Immunity, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Andras Szolek
- Institute of Immunology, Department of Innate Immunity, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Meng-Jen Wu
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Birgit Schittek
- Department of Dermatology, University Hospital Tübingen, Liebermeisterstr. 25, 72076, Tübingen, Germany
- iFIT - Cluster of Excellence (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- CMFI - Cluster of Excellence (EXC 2124) "Controlling microbes to fight infection", University of Tübingen, Tübingen, Germany
| | - Stefanie Bugl
- Institute of Immunology, Department of Innate Immunity, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Thomas A Kufer
- Institute of Nutritional Medicine, Department of Immunology, University of Hohenheim, Fruwirthstr. 12, 70593, Stuttgart, Germany
| | - Markus W Löffler
- Institute of Immunology, Department of Peptide-based Immunotherapy, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
- iFIT - Cluster of Excellence (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Institute for Clinical and Experimental Transfusion Medicine, Medical Faculty, University of Tübingen, Otfried-Müller-Str. 4/1, 72076, Tübingen, Germany
| | - Mathias Chamaillard
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, F-59000, Lille, France
| | - Julia Skokowa
- Division of Translational Oncology, Department of Oncology, Hematology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Otfried-Müller Str. 10, 72076, Tübingen, Germany
- iFIT - Cluster of Excellence (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Daniela Kramer
- Department of Dermatology, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Nathan K Archer
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Alexander N R Weber
- Institute of Immunology, Department of Innate Immunity, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany.
- iFIT - Cluster of Excellence (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.
- CMFI - Cluster of Excellence (EXC 2124) "Controlling microbes to fight infection", University of Tübingen, Tübingen, Germany.
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3
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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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Volkmar K, Jaedtka M, Baars I, Walber B, Philipp MS, Bagola K, Müller AJ, Heine H, van Zandbergen G. Investigating pyroptosis as a mechanism of L. major cell-to-cell spread in the human BLaER1 infection model. Mol Microbiol 2024; 121:453-469. [PMID: 37612878 DOI: 10.1111/mmi.15142] [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: 03/14/2023] [Revised: 07/04/2023] [Accepted: 08/03/2023] [Indexed: 08/25/2023]
Abstract
Leishmania is the causative agent of the tropical neglected disease leishmaniasis and infects macrophages as its definitive host cell. In order to sustain and propagate infections, Leishmania parasites have to complete cycles of exit and re-infection. Yet, the mechanism driving the parasite spread to other cells remains unclear. Recent studies reported pro-inflammatory monocytes as replicative niche of Leishmania major and showed prolonged expression of IL-1β at the site of infection, indicating an activation of the NLRP3 inflammasome and pointing toward pyroptosis as a possible mechanism of parasite spread. To address the species-specific inflammasome activation of human cells, we characterized the BLaER1 monocytes as a model for L. major infection. We found that BLaER1 monocytes support infection and activation by Leishmania parasites to the same extent as primary human macrophages. Harnessing the possibilities of this infection model, we first showed that BLaER1 GSDMD-/- cells, which carry a deletion of the pore-forming protein gasdermin D, are more resistant to pyroptotic cell death and, concomitantly, display a strongly delayed release of intracellular parasite. Using that knockout in a co-incubation assay in comparison with wild-type BLaER1 cells, we demonstrate that impairment of the pyroptosis pathway leads to lower rates of parasite spread to new host cells, thus, implicating pyroptotic cell death as a possible exit mechanism of L. major in pro-inflammatory microenvironments.
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Affiliation(s)
- Kerren Volkmar
- Division of Immunology, Paul-Ehrlich-Institut Langen, Langen, Germany
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Moritz Jaedtka
- Division of Immunology, Paul-Ehrlich-Institut Langen, Langen, Germany
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Iris Baars
- Experimental Immunodynamics, Institute of Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Bianca Walber
- Division of Immunology, Paul-Ehrlich-Institut Langen, Langen, Germany
| | | | - Katrin Bagola
- Division of Immunology, Paul-Ehrlich-Institut Langen, Langen, Germany
| | - Andreas J Müller
- Experimental Immunodynamics, Institute of Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Holger Heine
- Division of Innate Immunity, Research Center Borstel-Leibniz Lung Center, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Borstel, Germany
| | - Ger van Zandbergen
- Division of Immunology, Paul-Ehrlich-Institut Langen, Langen, Germany
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University of Mainz, Mainz, Germany
- Research Center for Immunotherapy (FZI), University Medical Center, Johannes Gutenberg-University Mainz, Mainz, Germany
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Cisek AA, Szymańska E, Aleksandrzak-Piekarczyk T, Cukrowska B. The Role of Methanogenic Archaea in Inflammatory Bowel Disease-A Review. J Pers Med 2024; 14:196. [PMID: 38392629 PMCID: PMC10890621 DOI: 10.3390/jpm14020196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/28/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024] Open
Abstract
Methanogenic archaea are a part of the commensal gut microbiota responsible for hydrogen sink and the efficient production of short-chain fatty acids. Dysbiosis of methanogens is suspected to play a role in pathogenesis of variety of diseases, including inflammatory bowel disease (IBD). Unlike bacteria, the diversity of archaea seems to be higher in IBD patients compared to healthy subjects, whereas the prevalence and abundance of gut methanogens declines in IBD, especially in ulcerative colitis. To date, studies focusing on methanogens in pediatric IBD are very limited; nevertheless, the preliminary results provide some evidence that methanogens may be influenced by the chronic inflammatory process in IBD. In this review, we demonstrated the development and diversity of the methanogenic community in IBD, both in adults and children.
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Affiliation(s)
- Agata Anna Cisek
- Department of Pathomorphology, The Children's Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland
| | - Edyta Szymańska
- Department of Gastroenterology, Hepatology, Nutritional Disorders and Pediatrics, The Children's Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland
| | | | - Bożena Cukrowska
- Department of Pathomorphology, The Children's Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland
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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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Cisek AA, Szymańska E, Wierzbicka-Rucińska A, Aleksandrzak-Piekarczyk T, Cukrowska B. Methanogenic Archaea in the Pediatric Inflammatory Bowel Disease in Relation to Disease Type and Activity. Int J Mol Sci 2024; 25:673. [PMID: 38203843 PMCID: PMC10779203 DOI: 10.3390/ijms25010673] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/25/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
The inflammatory bowel disease (IBD) is associated with gut microbiota dysbiosis; however, studies on methanogens-especially those focused on children-are extremely limited. The aim of this study was to determine the abundance of total methanogenic archaea and their three subgroups: Methanobrevibacter (Mb.) smithii, Methanosphaera (Ms.) stadtmanae, and Methanomassiliicoccales, in the feces of children with both active and inactive Crohn's disease (CD) and ulcerative colitis (UC). The results of a quantitative real-time PCR were cross-referenced with the disease type (CD vs. UC) and activity assessed with the use of Pediatric Crohn's Disease Activity Index (PCDAI) and Pediatric Ulcerative Colitis Activity Index (PUCAI) indices, and fecal calprotectin (FCP) concentration, and compared with controls. There was a significant decrease in the number of total methanogens in CD and UC compared to controls. The prevalence of total methanogens was also lower in UC compared to controls. Furthermore, patients from the inactive UC group were colonized by a lower number of Mb. smithii, and demonstrated the most pronounced positive correlation between the number of Ms. stadtmanae and the FCP concentration. Our results demonstrate that gut methanogens are related to the type and activity of pediatric IBD.
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Affiliation(s)
- Agata Anna Cisek
- Department of Pathomorphology, The Children’s Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland;
| | - Edyta Szymańska
- Department of Gastroenterology, Hepatology, Nutritional Disorders and Pediatrics, The Children’s Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland;
| | - Aldona Wierzbicka-Rucińska
- Department of Biochemistry, Radioimmunology and Experimental Medicine, The Children’s Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland;
| | | | - Bożena Cukrowska
- Department of Pathomorphology, The Children’s Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland;
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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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Oka S, Watanabe M, Ito E, Takeyama A, Matsuoka T, Takahashi M, Izumi Y, Arichi N, Ohno H, Yamasaki S, Inuki S. Archaeal Glycerolipids Are Recognized by C-Type Lectin Receptor Mincle. J Am Chem Soc 2023; 145:18538-18548. [PMID: 37555666 DOI: 10.1021/jacs.3c05473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Recently, various metabolites derived from host microbes have been reported to modulate the immune system, with potential involvement in health or diseases. Archaea, prokaryotic organisms, are present in the human body, but their connection with the host is largely unknown when compared to other microorganisms such as bacteria. This study focused on unique glycerolipids from symbiotic methanogenic archaea and evaluated their activities toward an innate immune receptor. The results revealed that archaeal lipids were recognized by the C-type lectin receptor Mincle and induced immune responses. A concurrent structure-activity relationship study identified the key structural features of archaeal lipids required for recognition by Mincle. Subsequent gene expression profiling suggested qualitative differences between the symbiotic archaeal lipid and the pathogenic bacteria-derived lipid. These findings have broad implications for understanding the function of symbiotic archaea in host health and diseases.
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Affiliation(s)
- Shiori Oka
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Miyuki Watanabe
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
- Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka 565-0871, Japan
| | - Emi Ito
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
- Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka 565-0871, Japan
| | - Ami Takeyama
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
- Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka 565-0871, Japan
| | - Takuro Matsuoka
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Masatomo Takahashi
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
| | - Yoshihiro Izumi
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
| | - Norihito Arichi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Hiroaki Ohno
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Sho Yamasaki
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
- Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka 565-0871, Japan
| | - Shinsuke Inuki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Kyoto 606-8501, Japan
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10
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Campbell GR, Rawat P, Teodorof-Diedrich C, Spector SA. IRAK1 inhibition blocks the HIV-1 RNA mediated pro-inflammatory cytokine response from microglia. J Gen Virol 2023; 104:001858. [PMID: 37256770 PMCID: PMC10336426 DOI: 10.1099/jgv.0.001858] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/10/2023] [Indexed: 06/02/2023] Open
Abstract
Human immunodeficiency virus (HIV)-associated neurocognitive disorders (HAND) are a common source of morbidity in people living with HIV (PLWH). Although antiretroviral therapy (ART) has lessened the severity of neurocognitive disorders, cognitive impairment still occurs in PLWH receiving ART. The pathogenesis of HAND is likely multifaceted, but common factors include the persistence of HIV transcription within the central nervous system, higher levels of pro-inflammatory cytokines in the cerebrospinal fluid, and the presence of activated microglia. Toll-like receptor (TLR) 7 and TLR8 are innate pathogen recognition receptors located in microglia and other immune and non-immune cells that can recognise HIV RNA and trigger pro-inflammatory responses. IL-1 receptor-associated kinase (IRAK) 1 is key to these signalling pathways. Here, we show that IRAK1 inhibition inhibits the TLR7 and TLR8-dependent pro-inflammatory response to HIV RNA. Using genetic and pharmacological inhibition, we demonstrate that inhibition of IRAK1 prevents IRAK1 phosphorylation and ubiquitination, and the subsequent recruitment of TRAF6 and the TAK1 complex to IRAK1, resulting in the inhibition of downstream signalling and the suppression of pro-inflammatory cytokine and chemokine release.
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Affiliation(s)
- Grant R. Campbell
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA
| | - Pratima Rawat
- Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Present address: Microbiologics Inc, San Diego, CA, USA
| | - Carmen Teodorof-Diedrich
- Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Stephen A. Spector
- Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Rady Children’s Hospital, San Diego, CA, USA
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11
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Bonvegna S, Cilia R. Disease mechanisms as subtypes: Microbiome. HANDBOOK OF CLINICAL NEUROLOGY 2023; 193:107-131. [PMID: 36803806 DOI: 10.1016/b978-0-323-85555-6.00006-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Abnormalities in gut microbiota have been suggested to be involved in the pathophysiology and progression of Parkinson's disease (PD). Gastrointestinal nonmotor symptoms often precede the onset of motor features in PD, suggesting a role for gut dysbiosis in neuroinflammation and α-synuclein (α-syn) aggregation. In the first part of this chapter, we analyze critical features of healthy gut microbiota and factors (environmental and genetic) that modify its composition. In the second part, we focus on the mechanisms underlying the gut dysbiosis and how it alters anatomically and functionally the mucosal barrier, triggering neuroinflammation and subsequently α-syn aggregation. In the third part, we describe the most common alterations in the gut microbiota of PD patients, dividing the gastrointestinal system in higher and lower tract to examine the association between microbiota abnormalities and clinical features. In the final section, we report on current and future therapeutic approaches to gut dysbiosis aiming to either reduce the risk for PD, modify the disease course, or improve the pharmacokinetic profile of dopaminergic therapies. We also suggest that further studies will be needed to clarify the role of the microbiome in PD subtyping and of pharmacological and nonpharmacological interventions in modifying specific microbiota profiles in individualizing disease-modifying treatments in PD.
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Affiliation(s)
- Salvatore Bonvegna
- Fondazione IRCCS Istituto Neurologico Carlo Besta, Department of Clinical Neurosciences, Parkinson and Movement Disorders Unit, Milan, Italy
| | - Roberto Cilia
- Fondazione IRCCS Istituto Neurologico Carlo Besta, Department of Clinical Neurosciences, Parkinson and Movement Disorders Unit, Milan, Italy.
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12
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Gut Microbiota and Metabolome Changes in Three Pulmonary Hypertension Rat Models. Microorganisms 2023; 11:microorganisms11020472. [PMID: 36838437 PMCID: PMC9959815 DOI: 10.3390/microorganisms11020472] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
Dysbiosis of the gut microbiota and metabolites is found in both pulmonary hypertension patients and pulmonary hypertension rodent models. However, the exact changes in gut microbiota during the development of pulmonary hypertension is unclear. The function of the gut microbiota is also ambiguous. Here, this study showed that the gut microbiota was disrupted in rats with hypoxia (Hyp)-, hypoxia/Sugen5416 (HySu)-, and monocrotaline (MCT)-induced pulmonary hypertension. The gut microbiota is dynamically changed during the development of Hyp-, HySu-, and MCT-induced rat pulmonary hypertension. The variation in the α diversity of the gut microbiota in Hyp-induced pulmonary hypertension rats was similar to that in rats with MCT-induced pulmonary hypertension and different from that in rats with HySu-induced pulmonary hypertension. In addition, six plasma biomarkers, His, Ala, Ser, ADMA, 2-hydroxybutyric acid, and cystathionine, were identified in Hyp-induced pulmonary hypertension rats. Furthermore, a disease-associated network connecting Streptococcus with Hyp-induced pulmonary hypertension-associated metabolites was described here, including trimethylamine N-oxide, Asp, Asn, Lys, His, Ser, Pro, and Ile.
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13
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Huang HI, Chio CC, Lin JY, Chou CJ, Lin CC, Chen SH, Yu LS. EV-A71 induced IL-1β production in THP-1 macrophages is dependent on NLRP3, RIG-I, and TLR3. Sci Rep 2022; 12:21425. [PMID: 36503883 PMCID: PMC9741760 DOI: 10.1038/s41598-022-25458-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022] Open
Abstract
Enterovirus A71 (EV-A71) is an emerging enterovirus that can cause neurological complications. Enhanced serum IL-1β levels were observed in EV-A71 patients with severe neurological symptoms. However, the roles of sensors in enterovirus-induced IL-1β production are unclear. In this study, we identified that pattern recognition receptors, including RIG-I, TLR3, and TLR8, are implicated in EV-A71-triggered IL-1β release in human macrophages. EV-A71 infection results in caspase-1 and caspase-8, which act as regulators of EV-A71-induced NLRP3 and RIG-I inflammasome activation. Moreover, knockdown of the expression of TLR3 and TLR8 decreased the released IL-1β in an NLRP3-dependent manner. Since TLR3 and TLR8 ligands promote NLRP3 inflammasome activation via caspase-8, the alternative pathway may be involved. In summary, these results indicate that activation of the NLRP3 and RIG-I inflammasomes in EV-A71-infected macrophages is mediated by caspase-1 and caspase-8 and affected by TLRs, including TLR3 and TLR8.
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Affiliation(s)
- Hsing-I Huang
- grid.145695.a0000 0004 1798 0922Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan ,grid.145695.a0000 0004 1798 0922Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan ,grid.145695.a0000 0004 1798 0922Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan ,grid.454211.70000 0004 1756 999XDepartment of Pediatrics, Linkou Chang Gung Memorial Hospital, Kwei-Shan, Tao-Yuan, Taiwan
| | - Chi-Chong Chio
- grid.145695.a0000 0004 1798 0922Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan ,grid.145695.a0000 0004 1798 0922Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan ,grid.145695.a0000 0004 1798 0922Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan
| | - Jhao-Yin Lin
- grid.145695.a0000 0004 1798 0922Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan ,grid.145695.a0000 0004 1798 0922Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan
| | - Chia-Jung Chou
- grid.145695.a0000 0004 1798 0922Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan
| | - Chia-Chen Lin
- grid.145695.a0000 0004 1798 0922Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan
| | - Shih-Hsiang Chen
- grid.454211.70000 0004 1756 999XDivision of Pediatric Hematology/Oncology, Linkou Chang Gung Memorial Hospital, Kwei-Shan, Tao-Yuan, Taiwan ,grid.145695.a0000 0004 1798 0922College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan
| | - Liang-Sheng Yu
- grid.145695.a0000 0004 1798 0922Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Kwei-Shan, Tao-Yuan, Taiwan
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14
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Hoegenauer C, Hammer HF, Mahnert A, Moissl-Eichinger C. Methanogenic archaea in the human gastrointestinal tract. Nat Rev Gastroenterol Hepatol 2022; 19:805-813. [PMID: 36050385 DOI: 10.1038/s41575-022-00673-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/26/2022] [Indexed: 12/24/2022]
Abstract
The human microbiome is strongly interwoven with human health and disease. Besides bacteria, viruses and eukaryotes, numerous archaea are located in the human gastrointestinal tract and are responsible for methane production, which can be measured in clinical methane breath analyses. Methane is an important readout for various diseases, including intestinal methanogen overgrowth. Notably, the archaea responsible for methane production are largely overlooked in human microbiome studies due to their non-bacterial biology and resulting detection issues. As such, their importance for health and disease remains largely unclear to date, in particular as not a single archaeal representative has been deemed to be pathogenic. In this Perspective, we discuss the current knowledge on the clinical relevance of methanogenic archaea. We explain the archaeal unique response to antibiotics and their negative and positive effects on human physiology, and present the current understanding of the use of methane as a diagnostic marker.
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Affiliation(s)
- Christoph Hoegenauer
- Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Heinz F Hammer
- Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Alexander Mahnert
- Diagnostic and Research Department of Microbiology, Hygiene and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Christine Moissl-Eichinger
- Diagnostic and Research Department of Microbiology, Hygiene and Environmental Medicine, Medical University of Graz, Graz, Austria.
- BioTechMed Graz, Graz, Austria.
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15
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Moitinho-Silva L, Degenhardt F, Rodriguez E, Emmert H, Juzenas S, Möbus L, Uellendahl-Werth F, Sander N, Baurecht H, Tittmann L, Lieb W, Gieger C, Peters A, Ellinghaus D, Bang C, Franke A, Weidinger S, Rühlemann MC. Host genetic factors related to innate immunity, environmental sensing and cellular functions are associated with human skin microbiota. Nat Commun 2022; 13:6204. [PMID: 36261456 PMCID: PMC9582029 DOI: 10.1038/s41467-022-33906-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 10/06/2022] [Indexed: 12/24/2022] Open
Abstract
Despite the increasing knowledge about factors shaping the human microbiome, the host genetic factors that modulate the skin-microbiome interactions are still largely understudied. This contrasts with recent efforts to characterize host genes that influence the gut microbiota. Here, we investigated the effect of genetics on skin microbiota across three different skin microenvironments through meta-analyses of genome-wide association studies (GWAS) of two population-based German cohorts. We identified 23 genome-wide significant loci harboring 30 candidate genes involved in innate immune signaling, environmental sensing, cell differentiation, proliferation and fibroblast activity. However, no locus passed the strict threshold for study-wide significance (P < 6.3 × 10-10 for 80 features included in the analysis). Mendelian randomization (MR) analysis indicated the influence of staphylococci on eczema/dermatitis and suggested modulating effects of the microbiota on other skin diseases. Finally, transcriptional profiles of keratinocytes significantly changed after in vitro co-culturing with Staphylococcus epidermidis, chosen as a representative of skin commensals. Seven candidate genes from the GWAS were found overlapping with differential expression in the co-culturing experiments, warranting further research of the skin commensal and host genetic makeup interaction.
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Affiliation(s)
- Lucas Moitinho-Silva
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Frauke Degenhardt
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Elke Rodriguez
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Hila Emmert
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Simonas Juzenas
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
- Institute of Biotechnology, Life Science Centre, Vilnius University, Vilnius, Lithuania
| | - Lena Möbus
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Nicole Sander
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Hansjörg Baurecht
- Department for Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
| | - Lukas Tittmann
- Biobank PopGen and Institute of Epidemiology, Kiel University, Kiel, Germany
| | - Wolfgang Lieb
- Institute of Epidemiology, Kiel University, Kiel, Germany
| | - Christian Gieger
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany.
| | - Stephan Weidinger
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Kiel, Germany.
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16
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Abstract
The human gut microbiome produces a functional complex of biomolecules, including nucleic acids, (poly)peptides, structural molecules, and metabolites. This impacts human physiology in multiple ways, especially by triggering inflammatory pathways in disease. At present, much remains to be learned about the identity of key effectors and their causal roles.
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17
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Gut Non-Bacterial Microbiota: Emerging Link to Irritable Bowel Syndrome. Toxins (Basel) 2022; 14:toxins14090596. [PMID: 36136534 PMCID: PMC9503233 DOI: 10.3390/toxins14090596] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/18/2022] [Accepted: 08/25/2022] [Indexed: 11/20/2022] Open
Abstract
As a common functional gastrointestinal disorder, irritable bowel syndrome (IBS) significantly affects personal health and imposes a substantial economic burden on society, but the current understanding of its occurrence and treatment is still inadequate. Emerging evidence suggests that IBS is associated with gut microbial dysbiosis, but most studies focus on the bacteria and neglect other communities of the microbiota, including fungi, viruses, archaea, and other parasitic microorganisms. This review summarizes the latest findings that link the nonbacterial microbiota with IBS. IBS patients show less fungal and viral diversity but some alterations in mycobiome, virome, and archaeome, such as an increased abundance of Candida albicans. Moreover, fungi and methanogens can aid in diagnosis. Fungi are related to distinct IBS symptoms and induce immune responses, intestinal barrier disruption, and visceral hypersensitivity via specific receptors, cells, and metabolites. Novel therapeutic methods for IBS include fungicides, inhibitors targeting fungal pathogenic pathways, probiotic fungi, prebiotics, and fecal microbiota transplantation. Additionally, viruses, methanogens, and parasitic microorganisms are also involved in the pathophysiology and treatment. Therefore, the gut nonbacterial microbiota is involved in the pathogenesis of IBS, which provides a novel perspective on the noninvasive diagnosis and precise treatment of this disease.
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18
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Tian W, Zhang T, Wang X, Zhang J, Ju J, Xu H. Global research trends in atherosclerosis: A bibliometric and visualized study. Front Cardiovasc Med 2022; 9:956482. [PMID: 36082127 PMCID: PMC9445883 DOI: 10.3389/fcvm.2022.956482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundIncreasing evidence has spurred a considerable evolution of concepts related to atherosclerosis, prompting the need to provide a comprehensive view of the growing literature. By retrieving publications in the Web of Science Core Collection (WoSCC) of Clarivate Analytics, we conducted a bibliometric analysis of the scientific literature on atherosclerosis to describe the research landscape.MethodsA search was conducted of the WoSCC for articles and reviews serving exclusively as a source of information on atherosclerosis published between 2012 and 2022. Microsoft Excel 2019 was used to chart the annual productivity of research relevant to atherosclerosis. Through CiteSpace and VOSviewer, the most prolific countries or regions, authors, journals, and resource-, intellectual-, and knowledge-sharing in atherosclerosis research, as well as co-citation analysis of references and keywords, were analyzed.ResultsA total of 20,014 publications were retrieved. In terms of publications, the United States remains the most productive country (6,390, 31,93%). The most publications have been contributed by Johns Hopkins Univ (730, 3.65%). ALVARO ALONSO produced the most published works (171, 0.85%). With a betweenness centrality of 0.17, ERIN D MICHOS was the most influential author. The most prolific journal was identified as Atherosclerosis (893, 4.46%). Circulation received the most co-citations (14,939, 2.79%). Keywords with the ongoing strong citation bursts were “nucleotide-binding oligomerization (NOD), Leucine-rich repeat (LRR)-containing protein (NLRP3) inflammasome,” “short-chain fatty acids (SCFAs),” “exosome,” and “homeostasis,” etc.ConclusionThe research on atherosclerosis is driven mostly by North America and Europe. Intensive research has focused on the link between inflammation and atherosclerosis, as well as its complications. Specifically, the NLRP3 inflammasome, interleukin-1β, gut microbiota and SCFAs, exosome, long non-coding RNAs, autophagy, and cellular senescence were described to be hot issues in the field.
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Affiliation(s)
- Wende Tian
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Graduate School, China Academy of Chinese Medical Sciences, Beijing, China
- National Clinical Research Center for Chinese Medicine Cardiology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Tai Zhang
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Graduate School, China Academy of Chinese Medical Sciences, Beijing, China
- Department of Gastroenterology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xinyi Wang
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Graduate School, China Academy of Chinese Medical Sciences, Beijing, China
- National Clinical Research Center for Chinese Medicine Cardiology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jie Zhang
- National Clinical Research Center for Chinese Medicine Cardiology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Graduate School, Beijing University of Chinese Medicine, Beijing, China
| | - Jianqing Ju
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- National Clinical Research Center for Chinese Medicine Cardiology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- *Correspondence: Jianqing Ju,
| | - Hao Xu
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- National Clinical Research Center for Chinese Medicine Cardiology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Hao Xu,
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19
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Campbell GR, Rawat P, Spector SA. Pacritinib Inhibition of IRAK1 Blocks Aberrant TLR8 Signalling by SARS-CoV-2 and HIV-1-Derived RNA. J Innate Immun 2022; 15:96-106. [PMID: 35785771 PMCID: PMC10643889 DOI: 10.1159/000525292] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/27/2022] [Indexed: 11/19/2022] Open
Abstract
Macrophages promote an early host response to infection by releasing pro-inflammatory cytokines such as interleukin (IL) 1β (IL-1β), tumour necrosis factor (TNF), and IL-6. One of the mechanisms through which cells sense pathogenic microorganisms is through Toll-like receptors (TLRs). IL-1 receptor-associated kinase (IRAK) 1, IRAK2, IRAK3, and IRAK4 are integral to TLR and IL-1 receptor signalling pathways. Recent studies suggest a role for aberrant TLR8 and NLRP3 inflammasome activation during both COVID-19 and HIV-1 infection. Here, we show that pacritinib inhibits the TLR8-dependent pro-inflammatory cytokine response elicited by GU-rich single-stranded RNA derived from SARS-CoV-2 and HIV-1. Using genetic and pharmacologic inhibition, we demonstrate that pacritinib inhibits IRAK1 phosphorylation and ubiquitination which then inhibits the recruitment of the TAK1 complex to IRAK1, thus inhibiting the activation of downstream signalling and the production of pro-inflammatory cytokines.
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Affiliation(s)
- Grant R. Campbell
- Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Pratima Rawat
- Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Stephen A. Spector
- Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Rady Children's Hospital, San Diego, California, USA
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20
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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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21
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Zhang XN, Yu ZL, Chen JY, Li XY, Wang ZP, Wu M, Liu LT. The crosstalk between NLRP3 inflammasome and gut microbiome in atherosclerosis. Pharmacol Res 2022; 181:106289. [PMID: 35671922 DOI: 10.1016/j.phrs.2022.106289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/22/2022] [Accepted: 06/01/2022] [Indexed: 01/29/2023]
Abstract
Atherosclerosis (AS) is chronic pathological process based on the inflammatory reaction associated with factors including vascular endothelial dysfunction, inflammation, and autoimmunity. Inflammasomes are known to be at the core of the inflammatory response. As a pattern recognition receptor of innate immunity, the NLRP3 inflammasome mediates the secretion of inflammatory factors by activating the Caspase-1, which is important for maintaining the immune system and regulating the gut microbiome, and participates in the occurrence and development of AS. The intestinal microecology is composed of a large number of complex structures of gut microbiota and its metabolites, which play an important role in AS. The gut microbiota and its metabolites regulate the activation of the NLRP3 inflammasome. Targeting the NLRP3 inflammasome and regulating intestinal microecology represent a new direction for the treatment of AS. This paper systematically reviews the interaction between the NLRP3 inflammasome and gut microbiome in AS, strategies for targeting the NLRP3 inflammasome and gut microbiome for the treatment of AS, and provides new ideas for the research and development of drugs for the treatment of AS.
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Affiliation(s)
- Xiao-Nan Zhang
- Department of Cardiovascular Medicine, National Clinical Research Center for Chinese Medicine Cardiology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100093, China
| | - Zong-Liang Yu
- Department of Cardiovascular Medicine, National Clinical Research Center for Chinese Medicine Cardiology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100093, China
| | - Ji-Ye Chen
- Department of Cardiovascular Medicine, National Clinical Research Center for Chinese Medicine Cardiology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100093, China
| | - Xiao-Ya Li
- Department of Cardiovascular Medicine, National Clinical Research Center for Chinese Medicine Cardiology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100093, China; Department of Cardiovascular Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Ze-Ping Wang
- Department of Cardiovascular Medicine, National Clinical Research Center for Chinese Medicine Cardiology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100093, China; Department of Cardiovascular Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Min Wu
- Department of comprehensive Internal Medicine, Guang'an Men Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, China.
| | - Long-Tao Liu
- Department of Cardiovascular Medicine, National Clinical Research Center for Chinese Medicine Cardiology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100093, China.
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22
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Mohammadzadeh R, Mahnert A, Duller S, Moissl-Eichinger C. Archaeal key-residents within the human microbiome: characteristics, interactions and involvement in health and disease. Curr Opin Microbiol 2022; 67:102146. [PMID: 35427870 DOI: 10.1016/j.mib.2022.102146] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/25/2022] [Accepted: 03/01/2022] [Indexed: 12/13/2022]
Abstract
Since the introduction of Archaea as new domain of life more than 40 years ago, they are no longer regarded as eccentric inhabitants of extreme ecosystems. These microorganisms are widespread in various moderate ecosystems, including eukaryotic hosts such as humans. Indeed, members of the archaeal community are now recognized as paramount constituents of human microbiome, while their definite role in disease or health is not fully elucidated and no archaeal pathogen has been reported. Here, we present a brief overview of archaea residing in and on the human body, with a specific focus on common lineages including Methanobrevibacter, Methanosphaeraand Methanomassilococcales.
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Affiliation(s)
- Rokhsareh Mohammadzadeh
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
| | - Alexander Mahnert
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
| | - Stefanie Duller
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
| | - Christine Moissl-Eichinger
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria; BioTechMed, 8010 Graz, Austria.
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23
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Köllisch G, Solis FV, Obermann HL, Eckert J, Müller T, Vierbuchen T, Rickmeyer T, Muche S, Przyborski JM, Heine H, Kaufmann A, Baumeister S, Lingelbach K, Bauer S. TLR8 is activated by 5'-methylthioinosine, a Plasmodium falciparum-derived intermediate of the purine salvage pathway. Cell Rep 2022; 39:110691. [PMID: 35417716 DOI: 10.1016/j.celrep.2022.110691] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 02/02/2022] [Accepted: 03/25/2022] [Indexed: 12/31/2022] Open
Abstract
The innate immune recognition of the malaria-causing pathogen Plasmodium falciparum (P. falciparum) is not fully explored. Here, we identify the nucleoside 5'-methylthioinosine (MTI), a Plasmodium-specific intermediate of the purine salvage pathway, as a pathogen-derived Toll-like receptor 8 (TLR8) agonist. Co-incubation of MTI with the TLR8 enhancer poly(dT) as well as synthetic or P. falciparum-derived RNA strongly increase its stimulatory activity. Of note, MTI generated from methylthioadenosine (MTA) by P. falciparum lysates activates TLR8 when MTI metabolism is inhibited by immucillin targeting the purine nucleoside phosphorylase (PfPNP). Importantly, P. falciparum-infected red blood cells incubated with MTI or cultivated with MTA and immucillin lead to TLR8-dependent interleukin-6 (IL-6) production in human monocytes. Our data demonstrate that the nucleoside MTI is a natural human TLR8 ligand with possible in vivo relevance for innate sensing of P. falciparum.
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Affiliation(s)
- Gabriele Köllisch
- Department of Parasitology, Philipps University Marburg, 35043 Marburg, Germany
| | | | - Hannah-Lena Obermann
- Institute for Immunology, Philipps University Marburg, BMFZ, 35043 Marburg, Germany
| | - Jeannine Eckert
- Department of Parasitology, Philipps University Marburg, 35043 Marburg, Germany
| | - Thomas Müller
- Institute for Medical Microbiology, Immunology und Hygiene, Technical University Munich, Munich, Germany
| | - Tim Vierbuchen
- Division of Innate Immunity, Research Center Borstel, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Borstel, Germany
| | - Thomas Rickmeyer
- Institute for Pharmaceutical Chemistry, Philipps University Marburg, 35043 Marburg, Germany
| | - Simon Muche
- Department of Chemistry, Philipps University Marburg, 35043 Marburg, Germany
| | - Jude M Przyborski
- Department of Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, Giessen, Germany
| | - Holger Heine
- Division of Innate Immunity, Research Center Borstel, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Borstel, Germany
| | - Andreas Kaufmann
- Institute for Immunology, Philipps University Marburg, BMFZ, 35043 Marburg, Germany
| | - Stefan Baumeister
- Department of Parasitology, Philipps University Marburg, 35043 Marburg, Germany
| | - Klaus Lingelbach
- Department of Parasitology, Philipps University Marburg, 35043 Marburg, Germany
| | - Stefan Bauer
- Institute for Immunology, Philipps University Marburg, BMFZ, 35043 Marburg, Germany.
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24
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Obermann HL, Lederbogen II, Steele J, Dorna J, Sander LE, Engelhardt K, Bakowsky U, Kaufmann A, Bauer S. RNA-Cholesterol Nanoparticles Function as Potent Immune Activators via TLR7 and TLR8. Front Immunol 2022; 12:658895. [PMID: 35126343 PMCID: PMC8814444 DOI: 10.3389/fimmu.2021.658895] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 12/27/2021] [Indexed: 12/30/2022] Open
Abstract
The innate immune system senses viral and bacterial ribonucleic acid (RNA) via pattern recognition receptors (PRR) leading to subsequent activation of the immune system. One group of RNA sensors is formed by endosomal/lysosomal Toll-like receptors (TLR) such as TLR7 and TLR8. During viral or bacterial infection, immunostimulatory RNA is part of the pathogen reaching the endosomal/lysosomal compartment after cellular uptake. Synthetic single-stranded or double-stranded oligoribonucleotides (ORN) can mimic RNA from pathogens and are widely used as activating ligands for TLR7 and TLR8. However, one limitation in the use of synthetic ORN driven immune stimulation is the need for transfection reagents for RNA delivery into cells. Here we demonstrate that the conjugation of cholesterol to a double-stranded version of immunostimulatory RNA40 strongly enhanced RNA uptake into monocytes and plasmacytoid dendritic cells when compared to naked RNA. Cholesterol-conjugated RNA (RNA-chol) formed nanoparticles that were superior to RNA-liposomes complexes in regard to induction of type I interferon from human and murine plasmacytoid dendritic cells as well as proinflammatory cytokine production (e.g. TNF-α, IL12p70 or IL-6) in human monocytes. Furthermore, the RNA40-chol induced cytokines in human monocyte cultures supported TH1 and TFH cell differentiation underscoring a strong adjuvant function of RNA-chol nanoparticles for adaptive immune responses. In summary, cholesterol-conjugated immunostimulatory RNA forms nanoparticles and functions as a potent immune adjuvant in human and murine immune cells. It further simplifies the use of immunostimulatory RNA by avoiding the need for liposomal transfection reagents.
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Affiliation(s)
| | - Ines I Lederbogen
- Institute for Immunology, Philipps-University Marburg, Marburg, Germany
| | - Jenny Steele
- Department of Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Jens Dorna
- Institute for Immunology, Philipps-University Marburg, Marburg, Germany
| | - Leif Erik Sander
- Department of Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Konrad Engelhardt
- Department of Pharmaceutics and Biopharmaceutics, Philipps-University Marburg, Marburg, Germany
| | - Udo Bakowsky
- Department of Pharmaceutics and Biopharmaceutics, Philipps-University Marburg, Marburg, Germany
| | - Andreas Kaufmann
- Institute for Immunology, Philipps-University Marburg, Marburg, Germany
| | - Stefan Bauer
- Institute for Immunology, Philipps-University Marburg, Marburg, Germany
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25
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Abstract
Intestinal microbiota, dominated by bacteria, plays an important role in the occurrence and the development of alcohol-associated liver disease (ALD), which is one of the most common liver diseases around the world. With sufficient studies focusing on the gut bacterial community, chronic alcohol consumption is now known as a key factor that alters the composition of gut bacterial community, increases intestinal permeability, causes intestinal dysfunction, induces bacterial translocation, and exacerbates the process of ALD via gut-liver axis. However, gut non-bacterial communities including fungi, viruses, and archaea, which may also participate in the disease, has received little attention relative to the gut bacterial community. This paper will systematically collect the latest literatures reporting non-bacterial communities in mammalian health and disease, and review their mechanisms in promoting the development of ALD including CLEC7A pathway, Candidalysin (a peptide toxin secreted by Candida albicans), metabolites, and other chemical substances secreted or regulated by gut commensal mycobiome, virome, and archaeome, hoping to bring novel insights on our current knowledge of ALD.
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Affiliation(s)
- Wenkang Gao
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yixin Zhu
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Jin Ye
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huikuan Chu
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China,CONTACT Huikuan Chu Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, China
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26
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Youngblut ND, de la Cuesta-Zuluaga J, Ley RE. Incorporating genome-based phylogeny and functional similarity into diversity assessments helps to resolve a global collection of human gut metagenomes. Environ Microbiol 2022; 24:3966-3984. [PMID: 35049120 DOI: 10.1111/1462-2920.15910] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 01/15/2022] [Indexed: 11/29/2022]
Abstract
Tree-based diversity measures incorporate phylogenetic or functional relatedness into comparisons of microbial communities. This can improve the identification of explanatory factors compared to tree-agnostic diversity measures. However, applying tree-based diversity measures to metagenome data is more challenging than for single-locus sequencing (e.g., 16S rRNA gene). Utilizing the Genome Taxonomy Database (GTDB) for species-level metagenome profiling allows for functional diversity measures based on genomic content or traits inferred from it. Still, it is unclear how metagenome-based assessments of microbiome diversity benefit from incorporating phylogeny or function into measures of diversity. We assessed this by measuring phylogeny-based, function-based, and tree-agnostic diversity measures from a large, global collection of human gut metagenomes composed of 30 studies and 2943 samples. We found tree-based measures to explain phenotypic variation (e.g., westernization, disease status, and gender) better or equivalent to tree-agnostic measures. Ecophylogenetic and functional diversity measures provided unique insight into how microbiome diversity was partitioned by phenotype. Tree-based measures greatly improved machine learning model performance for predicting westernization, disease status, and gender, relative to models trained solely on tree-agnostic measures. Our findings illustrate the usefulness of tree- and function-based measures for metagenomic assessments of microbial diversity, which is a fundamental component of microbiome science. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Nicholas D Youngblut
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max Planck Ring 5, 72076, Tübingen, Germany
| | - Jacobo de la Cuesta-Zuluaga
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max Planck Ring 5, 72076, Tübingen, Germany
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max Planck Ring 5, 72076, Tübingen, Germany
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27
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Contreras G, Thomsen J, Pfitzer M, Hafenbradl D, Kostner D, Holtmann D, Schmitz R, Rother M, Molitor B. New perspectives for biotechnological applications of methanogens. CURRENT RESEARCH IN BIOTECHNOLOGY 2022. [DOI: 10.1016/j.crbiot.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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28
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Chibani CM, Mahnert A, Borrel G, Almeida A, Werner A, Brugère JF, Gribaldo S, Finn RD, Schmitz RA, Moissl-Eichinger C. A catalogue of 1,167 genomes from the human gut archaeome. Nat Microbiol 2022; 7:48-61. [PMID: 34969981 PMCID: PMC8727293 DOI: 10.1038/s41564-021-01020-9] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 11/10/2021] [Indexed: 12/19/2022]
Abstract
The human gut microbiome plays an important role in health, but its archaeal diversity remains largely unexplored. In the present study, we report the analysis of 1,167 nonredundant archaeal genomes (608 high-quality genomes) recovered from human gastrointestinal tract, sampled across 24 countries and rural and urban populations. We identified previously undescribed taxa including 3 genera, 15 species and 52 strains. Based on distinct genomic features, we justify the split of the Methanobrevibacter smithii clade into two separate species, with one represented by the previously undescribed 'Candidatus Methanobrevibacter intestini'. Patterns derived from 28,581 protein clusters showed significant associations with sociodemographic characteristics such as age groups and lifestyle. We additionally show that archaea are characterized by specific genomic and functional adaptations to the host and carry a complex virome. Our work expands our current understanding of the human archaeome and provides a large genome catalogue for future analyses to decipher its impact on human physiology.
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Affiliation(s)
- Cynthia Maria Chibani
- grid.9764.c0000 0001 2153 9986Institute for Microbiology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Alexander Mahnert
- grid.11598.340000 0000 8988 2476Diagnostic & Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria
| | - Guillaume Borrel
- grid.428999.70000 0001 2353 6535Department of Microbiology, Unit of Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France
| | - Alexandre Almeida
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK ,grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | - Almut Werner
- grid.9764.c0000 0001 2153 9986Institute for Microbiology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Jean-François Brugère
- grid.494717.80000000115480420Institut Universitaire de Technologie Clermont Auvergne, Université Clermont Auvergne, CNRS, UMR 6023 Laboratoire Microorganismes: Genome et Environnement, Clermont-Ferrand, France
| | - Simonetta Gribaldo
- grid.428999.70000 0001 2353 6535Department of Microbiology, Unit of Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France
| | - Robert D. Finn
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Ruth A. Schmitz
- grid.9764.c0000 0001 2153 9986Institute for Microbiology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Christine Moissl-Eichinger
- Diagnostic & Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria. .,BioTechMed, Graz, Austria.
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29
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Systematic characterization of human gut microbiome-secreted molecules by integrated multi-omics. ISME COMMUNICATIONS 2021; 1:82. [PMID: 35106519 PMCID: PMC7612290 DOI: 10.1038/s43705-021-00078-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The human gut microbiome produces a complex mixture of biomolecules that interact with human physiology and play essential roles in health and disease. Crosstalk between micro-organisms and host cells is enabled by different direct contacts, but also by the export of molecules through secretion systems and extracellular vesicles. The resulting molecular network, comprised of various biomolecular moieties, has so far eluded systematic study. Here we present a methodological framework, optimized for the extraction of the microbiome-derived, extracellular biomolecular complement, including nucleic acids, (poly)peptides, and metabolites, from flash-frozen stool samples of healthy human individuals. Our method allows simultaneous isolation of individual biomolecular fractions from the same original stool sample, followed by specialized omic analyses. The resulting multi-omics data enable coherent data integration for the systematic characterization of this molecular complex. Our results demonstrate the distinctiveness of the different extracellular biomolecular fractions, both in terms of their taxonomic and functional composition. This highlights the challenge of inferring the extracellular biomolecular complement of the gut microbiome based on single-omic data. The developed methodological framework provides the foundation for systematically investigating mechanistic links between microbiome-secreted molecules, including those that are typically vesicle-associated, and their impact on host physiology in health and disease.
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30
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Small Intestinal Bacterial Overgrowth as Potential Therapeutic Target in Parkinson's Disease. Int J Mol Sci 2021; 22:ijms222111663. [PMID: 34769091 PMCID: PMC8584211 DOI: 10.3390/ijms222111663] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/17/2021] [Accepted: 10/25/2021] [Indexed: 12/15/2022] Open
Abstract
Increasing evidence suggests that the gut microbiota and the brain are closely connected via the so-called gut–brain axis. Small intestinal bacterial overgrowth (SIBO) is a gut dysbiosis in which the small intestine is abundantly colonized by bacteria that are typically found in the colon. Though not a disease, it may result in intestinal symptoms caused by the accumulation of microbial gases in the intestine. Intestinal inflammation, malabsorption and vitamin imbalances may also develop. SIBO can be eradicated by one or several courses of antibiotics but reappears if the predisposing condition persists. Parkinson’s disease (PD) is a common neurodegenerative proteinopathy for which disease modifying interventions are not available. Sporadic forms may start in the gut years before the development of clinical features. Increased gastrointestinal transit time is present in most people with PD early during the course of the disease, predisposing to gut dysbiosis, including SIBO. The role that gut dysbiosis may play in the etiopathogenesis of PD is not fully understood yet. Here, we discuss the possibility that SIBO could contribute to the progression of PD, by promoting or preventing neurodegeneration, thus being a potential target for treatments aiming at slowing down the progression of PD. The direct symptomatic impact of SIBO and its impact on symptomatic medication are also briefly discussed.
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31
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Brandenburg J, Marwitz S, Tazoll SC, Waldow F, Kalsdorf B, Vierbuchen T, Scholzen T, Gross A, Goldenbaum S, Hölscher A, Hein M, Linnemann L, Reimann M, Kispert A, Leitges M, Rupp J, Lange C, Niemann S, Behrends J, Goldmann T, Heine H, Schaible UE, Hölscher C, Schwudke D, Reiling N. WNT6/ACC2-induced storage of triacylglycerols in macrophages is exploited by Mycobacterium tuberculosis. J Clin Invest 2021; 131:e141833. [PMID: 34255743 DOI: 10.1172/jci141833] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 07/06/2021] [Indexed: 11/17/2022] Open
Abstract
In view of emerging drug-resistant tuberculosis (TB), host-directed adjunct therapies are urgently needed to improve treatment outcomes with currently available anti-TB therapies. One approach is to interfere with the formation of lipid-laden "foamy" macrophages in the host, as they provide a nutrient-rich host cell environment for Mycobacterium tuberculosis (Mtb). Here, we provide evidence that Wnt family member 6 (WNT6), a ligand of the evolutionarily conserved Wingless/Integrase 1 (WNT) signaling pathway, promotes foam cell formation by regulating key lipid metabolic genes including acetyl-CoA carboxylase 2 (ACC2) during pulmonary TB. Using genetic and pharmacological approaches, we demonstrated that lack of functional WNT6 or ACC2 significantly reduced intracellular triacylglycerol (TAG) levels and Mtb survival in macrophages. Moreover, treatment of Mtb-infected mice with a combination of a pharmacological ACC2 inhibitor and the anti-TB drug isoniazid (INH) reduced lung TAG and cytokine levels, as well as lung weights, compared with treatment with INH alone. This combination also reduced Mtb bacterial numbers and the size of mononuclear cell infiltrates in livers of infected mice. In summary, our findings demonstrate that Mtb exploits WNT6/ACC2-induced storage of TAGs in macrophages to facilitate its intracellular survival, a finding that opens new perspectives for host-directed adjunctive treatment of pulmonary TB.
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Affiliation(s)
- Julius Brandenburg
- Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany.,German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Sebastian Marwitz
- Pathology, Research Center Borstel, Borstel, Germany.,Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Grosshansdorf, Germany
| | - Simone C Tazoll
- Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Franziska Waldow
- German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany.,Bioanalytical Chemistry
| | - Barbara Kalsdorf
- German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany.,Clinical Infectious Diseases
| | | | | | - Annette Gross
- Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Svenja Goldenbaum
- Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | | | | | - Lara Linnemann
- Cellular Microbiology, Research Center Borstel, Borstel, Germany
| | | | - Andreas Kispert
- Institute for Molecular Biology, Hannover Medical School, Hannover, Germany
| | - Michael Leitges
- Division of BioMedical Sciences/Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Jan Rupp
- German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany.,Department of Infectious Diseases and Microbiology and
| | - Christoph Lange
- German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany.,Clinical Infectious Diseases.,Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany.,Baylor College of Medicine and Texas Children's Hospital, Houston, Texas, USA
| | - Stefan Niemann
- German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany.,Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | | | - Torsten Goldmann
- Pathology, Research Center Borstel, Borstel, Germany.,Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Grosshansdorf, Germany
| | | | - Ulrich E Schaible
- German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany.,Cellular Microbiology, Research Center Borstel, Borstel, Germany
| | - Christoph Hölscher
- German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany.,Infection Immunology, and
| | - Dominik Schwudke
- German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany.,Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Grosshansdorf, Germany.,Bioanalytical Chemistry
| | - Norbert Reiling
- Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany.,German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
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32
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Wegner J, Zillinger T, Schlee-Guimaraes TM, Bartok E, Schlee M. An epigenetic GPI anchor defect impairs TLR4 signaling in the B cell transdifferentiation model for primary human monocytes BLaER1. Sci Rep 2021; 11:14983. [PMID: 34294787 PMCID: PMC8298422 DOI: 10.1038/s41598-021-94386-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/07/2021] [Indexed: 11/24/2022] Open
Abstract
Antigen-presenting myeloid cells like monocytes detect invading pathogens via pattern recognition receptors (PRRs) and initiate adaptive and innate immune responses. As analysis of PRR signaling in primary human monocytes is hampered by their restricted expandability, human monocyte models like THP-1 cells are commonly used for loss-of-function studies, such as with CRISPR-Cas9 editing. A recently developed transdifferentiation cell culture system, BLaER1, enables lineage conversion from malignant B cells to monocytes and was found superior to THP-1 in mimicking PRR signaling, thus being the first model allowing TLR4 and inflammasome pathway analysis. Here, we identified an important caveat when investigating TLR4-driven signaling in BLaER1 cells. We show that this model contains glycosylphosphatidylinositol (GPI) anchor-deficient cells, which lack CD14 surface expression when differentiated to monocytes, resulting in diminished LPS/TLR4 but not TLR7/TLR8 responsiveness. This GPI anchor defect is caused by epigenetic silencing of PIGH, leading to a random distribution of intact and PIGH-deficient clones after single-cell cloning. Overexpressing PIGH restored GPI-anchored protein (including CD14) expression and LPS responsiveness. When studying CD14- or other GPI-anchored protein-dependent pathways, researchers should consider this anomaly and ensure equal GPI-anchored protein expression when comparing cells that have undergone single-cell cloning, e. g. after CRISPR-Cas9 editing.
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Affiliation(s)
- Julia Wegner
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany.
| | - Thomas Zillinger
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany.,Institute of Immunology, Philipps-University Marburg, Marburg, Germany
| | | | - Eva Bartok
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany.,Unit of Experimental Immunology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Martin Schlee
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
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33
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Campbell GR, Spector SA. Induction of Autophagy to Achieve a Human Immunodeficiency Virus Type 1 Cure. Cells 2021; 10:cells10071798. [PMID: 34359967 PMCID: PMC8307643 DOI: 10.3390/cells10071798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/13/2021] [Accepted: 07/13/2021] [Indexed: 02/06/2023] Open
Abstract
Effective antiretroviral therapy has led to significant human immunodeficiency virus type 1 (HIV-1) suppression and improvement in immune function. However, the persistence of integrated proviral DNA in latently infected reservoir cells, which drive viral rebound post-interruption of antiretroviral therapy, remains the major roadblock to a cure. Therefore, the targeted elimination or permanent silencing of this latently infected reservoir is a major focus of HIV-1 research. The most studied approach in the development of a cure is the activation of HIV-1 expression to expose latently infected cells for immune clearance while inducing HIV-1 cytotoxicity—the “kick and kill” approach. However, the complex and highly heterogeneous nature of the latent reservoir, combined with the failure of clinical trials to reduce the reservoir size casts doubt on the feasibility of this approach. This concern that total elimination of HIV-1 from the body may not be possible has led to increased emphasis on a “functional cure” where the virus remains but is unable to reactivate which presents the challenge of permanently silencing transcription of HIV-1 for prolonged drug-free remission—a “block and lock” approach. In this review, we discuss the interaction of HIV-1 and autophagy, and the exploitation of autophagy to kill selectively HIV-1 latently infected cells as part of a cure strategy. The cure strategy proposed has the advantage of significantly decreasing the size of the HIV-1 reservoir that can contribute to a functional cure and when optimised has the potential to eradicate completely HIV-1.
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Affiliation(s)
- Grant R. Campbell
- Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA;
- Correspondence: ; Tel.: +1-858-534-7477
| | - Stephen A. Spector
- Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA;
- Rady Children’s Hospital, San Diego, CA 92123, USA
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Metagenomic Analysis of the Fecal Archaeome in Suckling Piglets Following Perinatal Tulathromycin Metaphylaxis. Animals (Basel) 2021; 11:ani11061825. [PMID: 34207278 PMCID: PMC8235425 DOI: 10.3390/ani11061825] [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: 05/11/2021] [Revised: 06/14/2021] [Accepted: 06/16/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The archaeal population, or ‘archaeome’, is comprised of unicellular microorganisms with a distinct biology compared with bacteria and has been shown to be an important component of host-associated microbes. While the impact of antimicrobial administration on gastrointestinal microbiota has been widely evaluated, no metagenomics-based analysis has been performed to assess the impact of an early life antimicrobials intervention on the fecal archaeome in swine. The aim of this study was therefore to investigate the impact of perinatal tulathromycin (TUL) administration on the fecal archaeome composition and diversity in suckling piglets using metagenomic sequencing analysis. Our results suggest that perinatal TUL metaphylaxis seems to have a minimal effect on the gut archaeome composition and diversity in sucking piglets. Abstract The gastrointestinal microbiome plays an important role in swine health and wellbeing, but the gut archaeome structure and function in swine remain largely unexplored. To date, no metagenomics-based analysis has been done to assess the impact of an early life antimicrobials intervention on the gut archaeome. The aim of this study was to investigate the effects of perinatal tulathromycin (TUL) administration on the fecal archaeome composition and diversity in suckling piglets using metagenomic sequencing analysis. Sixteen litters were administered one of two treatments (TUL; 2.5 mg/kg IM and control (CONT); saline 1cc IM) soon after birth. Deep fecal swabs were collected from all piglets on days 0 (prior to treatment), 5, and 20 post intervention. Each piglet’s fecal archaeome was composed of rich and diverse communities that showed significant changes over time during the suckling period. At the phylum level, 98.24% of the fecal archaeome across all samples belonged to Euryarchaeota. At the genus level, the predominant archaeal genera across all samples were Methanobrevibacter (43.31%), Methanosarcina (10.84%), Methanococcus (6.51%), and Methanocorpusculum (6.01%). The composition and diversity of the fecal archaeome between the TUL and CONT groups at the same time points were statistically insignificant. Our findings indicate that perinatal TUL metaphylaxis seems to have a minimal effect on the gut archaeome composition and diversity in sucking piglets. This study improves our current understanding of the fecal archaeome structure in sucking piglets and provides a rationale for future studies to decipher its role in and impact on host robustness during this critical phase of production.
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Campbell GR, To RK, Hanna J, Spector SA. SARS-CoV-2, SARS-CoV-1, and HIV-1 derived ssRNA sequences activate the NLRP3 inflammasome in human macrophages through a non-classical pathway. iScience 2021; 24:102295. [PMID: 33718825 PMCID: PMC7939994 DOI: 10.1016/j.isci.2021.102295] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/11/2021] [Accepted: 03/05/2021] [Indexed: 12/29/2022] Open
Abstract
Macrophages promote an early host response to infection by releasing pro-inflammatory cytokines such as interleukin-1β (IL-1β), TNF, and IL-6. The bioactivity of IL-1β is classically dependent on NLRP3 inflammasome activation, which culminates in caspase-1 activation and pyroptosis. Recent studies suggest a role for NLRP3 inflammasome activation in lung inflammation and fibrosis in both COVID-19 and SARS, and there is evidence of NLRP3 involvement in HIV-1 disease. Here, we show that GU-rich single-stranded RNA (GU-rich RNA) derived from SARS-CoV-2, SARS-CoV-1, and HIV-1 trigger a TLR8-dependent pro-inflammatory cytokine response from human macrophages in the absence of pyroptosis, with GU-rich RNA from the SARS-CoV-2 spike protein triggering the greatest inflammatory response. Using genetic and pharmacological inhibition, we show that the induction of mature IL-1β is through a non-classical pathway dependent on caspase-1, caspase-8, the NLRP3 inflammasome, potassium efflux, and autophagy while being independent of TRIF (TICAM1), vitamin D3, and pyroptosis.
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Affiliation(s)
- Grant R. Campbell
- Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Rachel K. To
- Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Jonathan Hanna
- Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Stephen A. Spector
- Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
- Rady Children's Hospital, San Diego, CA 92123, USA
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Chuphal N, Singha KP, Sardar P, Sahu NP, Shamna N, Kumar V. Scope of Archaea in Fish Feed: a New Chapter in Aquafeed Probiotics? Probiotics Antimicrob Proteins 2021; 13:1668-1695. [PMID: 33821466 DOI: 10.1007/s12602-021-09778-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2021] [Indexed: 12/21/2022]
Abstract
The outbreak of diseases leading to substantial loss is a major bottleneck in aquaculture. Over the last decades, the concept of using feed probiotics was more in focus to address the growth and health of cultivable aquatic organisms. The objective of this review is to provide an overview of the distinct functionality of archaea from conventional probiotics in nutrient utilization, specific caloric contribution, evading immune response and processing thermal resistance. The prime limitation of conventional probiotics is the viability of desired microbes under harsh feed processing conditions. To overcome the constraints of commercial probiotics pertaining to incompatibility towards industrial processing procedure, a super microbe, archaea, appears to be a potential alternative approach in aquaculture. The peculiarity of the archaeal cell wall provides them with heat stability and rigidity under industrial processing conditions. Besides, archaea being one of the gut microbial communities participates in various health-oriented biological functions in animals. Thus, the current review devoted that administration of archaea in aquafeed could be a promising strategy in aquaculture. Archaea may be used as a potential probiotic with the possible modes of functions and advantages over conventional probiotics in aquafeed preparation. The present review also provides the challenges associated with the use of archaea for aquaculture and a brief outline of the patents on archaea to highlight the various use of archaea in different sectors.
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Affiliation(s)
- Nisha Chuphal
- Fish Nutrition, Biochemistry and Physiology Division, ICAR-Central Institute of Fisheries Education, Versova, Mumbai, 400 061, India
| | - Krishna Pada Singha
- Fish Nutrition, Biochemistry and Physiology Division, ICAR-Central Institute of Fisheries Education, Versova, Mumbai, 400 061, India.,Aquaculture Research Institute, Department of Animal Veterinary and Food Sciences, University of Idaho, Moscow, ID, 83844-3020, USA
| | - Parimal Sardar
- Fish Nutrition, Biochemistry and Physiology Division, ICAR-Central Institute of Fisheries Education, Versova, Mumbai, 400 061, India.
| | - Narottam Prasad Sahu
- Fish Nutrition, Biochemistry and Physiology Division, ICAR-Central Institute of Fisheries Education, Versova, Mumbai, 400 061, India
| | - Naseemashahul Shamna
- Fish Nutrition, Biochemistry and Physiology Division, ICAR-Central Institute of Fisheries Education, Versova, Mumbai, 400 061, India
| | - Vikas Kumar
- Aquaculture Research Institute, Department of Animal Veterinary and Food Sciences, University of Idaho, Moscow, ID, 83844-3020, USA.
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Gong B, Wang C, Meng F, Wang H, Song B, Yang Y, Shan Z. Association Between Gut Microbiota and Autoimmune Thyroid Disease: A Systematic Review and Meta-Analysis. Front Endocrinol (Lausanne) 2021; 12:774362. [PMID: 34867823 PMCID: PMC8635774 DOI: 10.3389/fendo.2021.774362] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 10/29/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Autoimmune thyroid disease (AITD) is characterized by thyroid dysfunction and deficits in the autoimmune system. Growing attention has been paid toward the field of gut microbiota over the last few decades. Several recent studies have found that gut microbiota composition in patients with AITD has altered, but no studies have conducted systematic reviews on the association between gut microbiota and ATID. METHODS We searched PubMed, Web of Science, Embase, and Cochrane databases without language restrictions and conducted a systematic review and meta-analysis of eight studies, including 196 patients with AITD. RESULTS The meta-analysis showed that the alpha diversity and abundance of certain gut microbiota were changed in patients with AITD compared to the controls. Chao1,the index of the microflora richness, was increased in the Hashimoto's thyroiditis group compared to controls (SMD, 0.68, 95%CI: 0.16 to 1.20), while it was decreased in the Graves' disease group (SMD, -0.87, 95%CI: -1.46 to -0.28). In addition, we found that some beneficial bacteria like Bifidobacterium and Lactobacillus were decreased in the AITD group, and harmful microbiota like Bacteroides fragilis was significantly increased compared with the controls. Furthermore, the percentage of relevant abundance of other commensal bacteria such as Bacteroidetes, Bacteroides, and Lachnospiraceae was increased compared with the controls. CONCLUSIONS This meta-analysis indicates an association between AITD and alteration of microbiota composition at the family, genus, and species levels. SYSTEMATIC REVIEW REGISTRATION PROSPERO, identifier CRD42021251557.
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Galvanin A, Vogt LM, Grober A, Freund I, Ayadi L, Bourguignon-Igel V, Bessler L, Jacob D, Eigenbrod T, Marchand V, Dalpke A, Helm M, Motorin Y. Bacterial tRNA 2'-O-methylation is dynamically regulated under stress conditions and modulates innate immune response. Nucleic Acids Res 2020; 48:12833-12844. [PMID: 33275131 PMCID: PMC7736821 DOI: 10.1093/nar/gkaa1123] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/03/2020] [Indexed: 12/23/2022] Open
Abstract
RNA modifications are a well-recognized way of gene expression regulation at the post-transcriptional level. Despite the importance of this level of regulation, current knowledge on modulation of tRNA modification status in response to stress conditions is far from being complete. While it is widely accepted that tRNA modifications are rather dynamic, such variations are mostly assessed in terms of total tRNA, with only a few instances where changes could be traced to single isoacceptor species. Using Escherichia coli as a model system, we explored stress-induced modulation of 2'-O-methylations in tRNAs by RiboMethSeq. This analysis and orthogonal analytical measurements by LC-MS show substantial, but not uniform, increase of the Gm18 level in selected tRNAs under mild bacteriostatic antibiotic stress, while other Nm modifications remain relatively constant. The absence of Gm18 modification in tRNAs leads to moderate alterations in E. coli mRNA transcriptome, but does not affect polysomal association of mRNAs. Interestingly, the subset of motility/chemiotaxis genes is significantly overexpressed in ΔTrmH mutant, this corroborates with increased swarming motility of the mutant strain. The stress-induced increase of tRNA Gm18 level, in turn, reduced immunostimulation properties of bacterial tRNAs, which is concordant with the previous observation that Gm18 is a suppressor of Toll-like receptor 7 (TLR7)-mediated interferon release. This documents an effect of stress induced modulation of tRNA modification that acts outside protein translation.
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Affiliation(s)
- Adeline Galvanin
- Université de Lorraine, CNRS, IMoPA (UMR7365), F54000 Nancy, France
| | - Lea-Marie Vogt
- Institute of Pharmaceutical and Biomedical Science, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Antonia Grober
- Institute of Medical Microbiology and Hygiene, Technische Universität Dresden, 01307 Dresden, Germany
| | - Isabel Freund
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Ruprecht-Karls University Heidelberg, 69117 Heidelberg, Germany
| | - Lilia Ayadi
- Université de Lorraine, CNRS, IMoPA (UMR7365), F54000 Nancy, France
- Université de Lorraine, CNRS, INSERM, IBSLor (UMS2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
| | - Valerie Bourguignon-Igel
- Université de Lorraine, CNRS, IMoPA (UMR7365), F54000 Nancy, France
- Université de Lorraine, CNRS, INSERM, IBSLor (UMS2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
| | - Larissa Bessler
- Institute of Pharmaceutical and Biomedical Science, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Dominik Jacob
- Institute of Pharmaceutical and Biomedical Science, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Tatjana Eigenbrod
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Ruprecht-Karls University Heidelberg, 69117 Heidelberg, Germany
| | - Virginie Marchand
- Université de Lorraine, CNRS, INSERM, IBSLor (UMS2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
| | - Alexander Dalpke
- Institute of Medical Microbiology and Hygiene, Technische Universität Dresden, 01307 Dresden, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Science, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Yuri Motorin
- Université de Lorraine, CNRS, IMoPA (UMR7365), F54000 Nancy, France
- Université de Lorraine, CNRS, INSERM, IBSLor (UMS2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
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Abstract
Host-associated microbial communities have an important role in shaping the health and fitness of plants and animals. Most studies have focused on the bacterial, fungal or viral communities, but often the archaeal component has been neglected. The archaeal community, the so-called archaeome, is now increasingly recognized as an important component of host-associated microbiomes. It is composed of various lineages, including mainly Methanobacteriales and Methanomassiliicoccales (Euryarchaeota), as well as representatives of the Thaumarchaeota. Host-archaeome interactions have mostly been delineated from methanogenic archaea in the gastrointestinal tract, where they contribute to substantial methane production and are potentially also involved in disease-relevant processes. In this Review, we discuss the diversity and potential roles of the archaea associated with protists, plants and animals. We also present the current understanding of the archaeome in humans, the specific adaptations involved in interaction with the resident microbial community as well as with the host, and the roles of the archaeome in both health and disease.
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Dauros-Singorenko P, Hong J, Swift S, Phillips A, Blenkiron C. Effect of the Extracellular Vesicle RNA Cargo From Uropathogenic Escherichia coli on Bladder Cells. Front Mol Biosci 2020; 7:580913. [PMID: 33102527 PMCID: PMC7546368 DOI: 10.3389/fmolb.2020.580913] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/03/2020] [Indexed: 12/14/2022] Open
Abstract
Iron restriction in mammals, part of innate antimicrobial defense, may be sensed as a signal by an infecting pathogen. Iron-dependent regulators not only activate the pathogen’s specific iron acquisition and storage mechanisms needed for survival but also influence a number of other processes. Bacterial extracellular vesicles (EVs) are a conserved communication mechanism, which can have roles in host colonization, transfer of antimicrobial resistance, modulation of the host’s immune response, and biofilm formation. Here we analyze the iron-responsive effect of RNA cargo from Escherichia coli EVs in bladder cells. No differences were found in total RNA quantified from EVs released from representative pathogenic and probiotic strains grown in different iron conditions; nevertheless, lipopolysaccharide (LPS) associated with purified RNA was 10 times greater from EVs derived from the pathogenic strain. The pathogen and probiotic EV-RNA have no substantial toxic effect on the viability of cultured bladder cells, regardless of the iron concentration during bacterial culture. Transcriptomic analysis of bladder cells treated with pathogen EV-RNA delivered in artificial liposomes revealed a gene expression profile with a strong similarity to that of cells treated with liposomes containing LPS alone, with the majority being immune response pathways. EV-RNA from the probiotic strain gave no significant perturbation of gene expression in bladder cells. Cytokine profiling showed that EV-LPS has a role modulating the immune response when internalized by bladder cells, highlighting a key factor that must be considered when evaluating functional studies of bacterial RNA.
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Affiliation(s)
- Priscila Dauros-Singorenko
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.,Department of Surgery, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Jiwon Hong
- Department of Surgery, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.,School of Biological Sciences, Faculty of Science, The University of Auckland, Auckland, New Zealand.,Surgical and Translational Research Centre, The University of Auckland, Auckland, New Zealand
| | - Simon Swift
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Anthony Phillips
- Department of Surgery, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.,School of Biological Sciences, Faculty of Science, The University of Auckland, Auckland, New Zealand.,Surgical and Translational Research Centre, The University of Auckland, Auckland, New Zealand
| | - Cherie Blenkiron
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.,Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
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Archaea, specific genetic traits, and development of improved bacterial live biotherapeutic products: another face of next-generation probiotics. Appl Microbiol Biotechnol 2020; 104:4705-4716. [PMID: 32281023 DOI: 10.1007/s00253-020-10599-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/25/2020] [Accepted: 03/31/2020] [Indexed: 02/07/2023]
Abstract
Trimethylamine (TMA) and its oxide TMAO are important biomolecules involved in disease-associated processes in humans (e.g., trimethylaminuria and cardiovascular diseases). TMAO in plasma (pTMAO) stems from intestinal TMA, which is formed from various components of the diet in a complex interplay between diet, gut microbiota, and the human host. Most approaches to prevent the occurrence of such deleterious molecules focus on actions to interfere with gut microbiota metabolism to limit the synthesis of TMA. Some human gut archaea however use TMA as terminal electron acceptor for producing methane, thus indicating that intestinal TMA does not accumulate in some human subjects. Therefore, a rational alternative approach is to eliminate neo-synthesized intestinal TMA. This can be achieved through bioremediation of TMA by these peculiar methanogenic archaea, either by stimulating or providing them, leading to a novel kind of next-generation probiotics referred to as archaebiotics. Finally, specific components which are involved in this archaeal metabolism could also be used as intestinal TMA sequesters, facilitating TMA excretion along with stool. Referring to a standard pharmacological approach, these TMA traps could be synthesized ex vivo and then delivered into the human gut. Another approach is the engineering of known probiotic strain in order to metabolize TMA, i.e., live engineered biotherapeutic products. These alternatives would require, however, to take into account the necessity of synthesizing the 22nd amino acid pyrrolysine, i.e., some specificities of the genetics of TMA-consuming archaea. Here, we present an overview of these different strategies and recent advances in the field that will sustain such biotechnological developments. KEY POINTS: • Some autochthonous human archaea can use TMA for their essential metabolism, a methyl-dependent hydrogenotrophic methanogenesis. • They could therefore be used as next-generation probiotics for preventing some human diseases, especially cardiovascular diseases and trimethylaminuria. • Their genetic capacities can also be used to design live recombinant biotherapeutic products. • Encoding of the 22nd amino acid pyrrolysine is necessary for such alternative developments.
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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: 17] [Impact Index Per Article: 4.3] [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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RNA Sensing of Mycobacterium tuberculosis and Its Impact on TB Vaccination Strategies. Vaccines (Basel) 2020; 8:vaccines8010067. [PMID: 32033104 PMCID: PMC7158685 DOI: 10.3390/vaccines8010067] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/01/2020] [Accepted: 02/01/2020] [Indexed: 02/07/2023] Open
Abstract
Tuberculosis (TB) is still an important global threat and although the causing organism has been discovered long ago, effective prevention strategies are lacking. Mycobacterium tuberculosis (MTB) is a unique pathogen with a complex host interaction. Understanding the immune responses upon infection with MTB is crucial for the development of new vaccination strategies and therapeutic targets for TB. Recently, it has been proposed that sensing bacterial nucleic acid in antigen-presenting cells via intracellular pattern recognition receptors (PRRs) is a central mechanism for initiating an effective host immune response. Here, we summarize key findings of the impact of mycobacterial RNA sensing for innate and adaptive host immunity after MTB infection, with emphasis on endosomal toll-like receptors (TLRs) and cytosolic sensors such as NLRP3 and RLRs, modulating T-cell differentiation through IL-12, IL-21, and type I interferons. Ultimately, these immunological pathways may impact immune memory and TB vaccine efficacy. The novel findings described here may change our current understanding of the host response to MTB and potentially impact clinical research, as well as future vaccination design. In this review, the current state of the art is summarized, and an outlook is given on how progress can be made.
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Neutrophil extracellular trap-associated RNA and LL37 enable self-amplifying inflammation in psoriasis. Nat Commun 2020; 11:105. [PMID: 31913271 PMCID: PMC6949246 DOI: 10.1038/s41467-019-13756-4] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/13/2019] [Indexed: 12/21/2022] Open
Abstract
Psoriasis is an inflammatory skin disease with strong neutrophil (PMN) infiltration and high levels of the antimicrobial peptide, LL37. LL37 in complex with DNA and RNA is thought to initiate disease exacerbation via plasmacytoid dendritic cells. However, the source of nucleic acids supposed to start this initial inflammatory event remains unknown. We show here that primary murine and human PMNs mount a fulminant and self-propagating neutrophil extracellular trap (NET) and cytokine response, but independently of the canonical NET component, DNA. Unexpectedly, RNA, which is abundant in NETs and psoriatic but not healthy skin, in complex with LL37 triggered TLR8/TLR13-mediated cytokine and NET release by PMNs in vitro and in vivo. Transfer of NETs to naive human PMNs prompts additional NET release, promoting further inflammation. Our study thus uncovers a self-propagating vicious cycle contributing to chronic inflammation in psoriasis, and NET-associated RNA (naRNA) as a physiologically relevant NET component.
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Budden KF, Shukla SD, Rehman SF, Bowerman KL, Keely S, Hugenholtz P, Armstrong-James DPH, Adcock IM, Chotirmall SH, Chung KF, Hansbro PM. Functional effects of the microbiota in chronic respiratory disease. THE LANCET. RESPIRATORY MEDICINE 2019; 7:907-920. [PMID: 30975495 DOI: 10.1016/s2213-2600(18)30510-1] [Citation(s) in RCA: 230] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 11/29/2018] [Accepted: 11/29/2018] [Indexed: 01/19/2023]
Abstract
The composition of the lung microbiome is increasingly well characterised, with changes in microbial diversity or abundance observed in association with several chronic respiratory diseases such as asthma, cystic fibrosis, bronchiectasis, and chronic obstructive pulmonary disease. However, the precise effects of the microbiome on pulmonary health and the functional mechanisms by which it regulates host immunity are only now beginning to be elucidated. Bacteria, viruses, and fungi from both the upper and lower respiratory tract produce structural ligands and metabolites that interact with the host and alter the development and progression of chronic respiratory diseases. Here, we review recent advances in our understanding of the composition of the lung microbiome, including the virome and mycobiome, the mechanisms by which these microbes interact with host immunity, and their functional effects on the pathogenesis, exacerbations, and comorbidities of chronic respiratory diseases. We also describe the present understanding of how respiratory microbiota can influence the efficacy of common therapies for chronic respiratory disease, and the potential of manipulation of the microbiome as a therapeutic strategy. Finally, we highlight some of the limitations in the field and propose how these could be addressed in future research.
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Affiliation(s)
- Kurtis F Budden
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and The University of Newcastle, Newcastle, NSW, Australia
| | - Shakti D Shukla
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and The University of Newcastle, Newcastle, NSW, Australia
| | - Saima Firdous Rehman
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and The University of Newcastle, Newcastle, NSW, Australia
| | - Kate L Bowerman
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biology, The University of Queensland, QLD, Australia
| | - Simon Keely
- Priority Research Centre for Digestive Health and Neurogastroenterology, Hunter Medical Research Institute and The University of Newcastle, Newcastle, NSW, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biology, The University of Queensland, QLD, Australia
| | | | - Ian M Adcock
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Kian Fan Chung
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Philip M Hansbro
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and The University of Newcastle, Newcastle, NSW, Australia; Centre for Inflammation, Centenary Institute, and University of Technology Sydney, NSW, Australia.
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46
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Rühlemann M, Franke A. Editorial: gut microbial profile associated with primary sclerosing cholangitis-what is new and how do we progress from here? Authors' reply. Aliment Pharmacol Ther 2019; 50:606-607. [PMID: 31414547 PMCID: PMC6899696 DOI: 10.1111/apt.15434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
LINKED CONTENT This article is linked to Rühlemann et al and Quraishi and Shaheen papers. To view these articles, visit https://doi.org/10.1111/apt.15375 and https://doi.org/10.1111/apt.15424.
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Affiliation(s)
- Malte Rühlemann
- Institute of Clinical Molecular BiologyChristian‐Albrechts‐University of KielKielGermany
| | - Andre Franke
- Institute of Clinical Molecular BiologyChristian‐Albrechts‐University of KielKielGermany
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47
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Freund I, Buhl DK, Boutin S, Kotter A, Pichot F, Marchand V, Vierbuchen T, Heine H, Motorin Y, Helm M, Dalpke AH, Eigenbrod T. 2'- O-methylation within prokaryotic and eukaryotic tRNA inhibits innate immune activation by endosomal Toll-like receptors but does not affect recognition of whole organisms. RNA (NEW YORK, N.Y.) 2019; 25:869-880. [PMID: 31019095 PMCID: PMC6573781 DOI: 10.1261/rna.070243.118] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 04/20/2019] [Indexed: 05/10/2023]
Abstract
Bacterial RNA has emerged as an important activator of innate immune responses by stimulating Toll-like receptors TLR7 and TLR8 in humans. Guanosine 2'-O-methylation at position 18 (Gm18) in bacterial tRNA was shown to antagonize tRNA-induced TLR7/8 activation, suggesting a potential role of Gm18 as an immune escape mechanism. This modification also occurs in eukaryotic tRNA, yet a physiological immune function remained to be tested. We therefore set out to investigate the immune modulatory role of Gm18 in both prokaryotic and eukaryotic microorganisms, Escherichia coli and Saccharomyces cerevisiae, and in human cells. Using RiboMethSeq analysis we show that mutation of trmH in E. coli, trm3 in S. cereviase, and CRISPR/Cas9-induced knockout of TARBP1 in H. sapiens results in loss of Gm18 within tRNA. Lack of Gm18 across the kingdoms resulted in increased immunostimulation of peripheral blood mononuclear cells when activated by tRNA preparations. In E. coli, lack of 2'-O-methyltransferase trmH also enhanced immune stimulatory properties by whole cellular RNA. In contrast, lack of Gm18 in yeasts and human cells did not affect immunostimulation by whole RNA preparations. When using live E. coli bacteria, lack of trmH did not affect overall immune stimulation although we detected a defined TLR8/RNA-dependent gene expression signature upon E. coli infection. Together, these results demonstrate that Gm18 is a global immune inhibitory tRNA modification across the kingdoms and contributes to tRNA recognition by innate immune cells, but as an individual modification has insufficient potency to modulate recognition of the investigated microorganisms.
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Affiliation(s)
- Isabel Freund
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Daniel K Buhl
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Sébastien Boutin
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Annika Kotter
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Florian Pichot
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
- IMoPA UMR7365 CNRS-Lorraine University, BioPole Lorraine University, 54500 Vandoeuvre-les-Nancy, France
| | - Virginie Marchand
- UMS2008 IBSLor, CNRS-Lorraine University-INSERM, BioPole Lorraine University, 54500 Vandoeuvre-les-Nancy, France
| | - Tim Vierbuchen
- Division of Innate Immunity, Research Center Borstel, 23845 Borstel, Germany
| | - Holger Heine
- Division of Innate Immunity, Research Center Borstel, 23845 Borstel, Germany
| | - Yuri Motorin
- IMoPA UMR7365 CNRS-Lorraine University, BioPole Lorraine University, 54500 Vandoeuvre-les-Nancy, France
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Alexander H Dalpke
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, 69120 Heidelberg, Germany
- Institute of Medical Microbiology and Hygiene, Technical University Dresden, 01307 Dresden, Germany
| | - Tatjana Eigenbrod
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, 69120 Heidelberg, Germany
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48
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Moen SH, Ehrnström B, Kojen JF, Yurchenko M, Beckwith KS, Afset JE, Damås JK, Hu Z, Yin H, Espevik T, Stenvik J. Human Toll-like Receptor 8 (TLR8) Is an Important Sensor of Pyogenic Bacteria, and Is Attenuated by Cell Surface TLR Signaling. Front Immunol 2019; 10:1209. [PMID: 31214180 PMCID: PMC6554558 DOI: 10.3389/fimmu.2019.01209] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/13/2019] [Indexed: 11/15/2022] Open
Abstract
TLR8 is an endosomal sensor of RNA degradation products in human phagocytes, and is involved in the recognition of viral and bacterial pathogens. We previously showed that in human primary monocytes and monocyte derived macrophages, TLR8 senses entire Staphylococcus aureus and Streptococcus agalactiae (group B streptococcus, GBS), resulting in the activation of IRF5 and production of IFNβ, IL-12p70, and TNF. However, the quantitative and qualitative impact of TLR8 for the sensing of bacteria have remained unclear because selective inhibitors have been unavailable. Moreover, while we have shown that TLR2 activation attenuates TLR8-IRF5 signaling, the molecular mechanism of this crosstalk is unknown. We here used a recently developed chemical antagonist of TLR8 to determine its role in human primary monocytes challenged with S. aureus, GBS, Streptococcus pneumonia, Pseudomonas aeruginosa, and E. coli. The inhibitor completely blocked cytokine production in monocytes stimulated with TLR8-agonists, but not TLR2-, and TLR4-agonists. Upon challenge with S. aureus, GBS, and S. pneumonia, the TLR8 inhibitor almost eliminated the production of IL-1β and IL-12p70, and it strongly reduced the release of IL-6, TNF, and IL-10. With P. aeruginosa infection, the TLR8 inhibitor impaired the production of IL-12p70 and IL-1β, while with E. coli infection the inhibitor had less effect that varied depending on the strain and conditions. Signaling via TLR2, TLR4, or TLR5, but not TLR8, rapidly eliminated IRAK-1 detection by immunoblotting due to IRAK-1 modifications during activation. Silencing of IRAK-1 reduced the induction of IFNβ and TNF by TLR8 activation, suggesting that IRAK-1 is required for TLR8-IRF5 signaling. The TLR-induced modifications of IRAK-1 also correlated closely with attenuation of TLR8-IRF5 activation, suggesting that sequestration and/or modification of Myddosome components by cell surface TLRs limit the function of TLR8. Accordingly, inhibition of CD14- and TLR4-activation during E. coli challenge increased the activation of IRF5 and the production of IL-1β and IL-12p70. We conclude that TLR8 is a dominating sensor of several species of pyogenic bacteria in human monocytes, while some bacteria attenuate TLR8-signaling via cell surface TLR- activation. Taken together, TLR8 appears as a more important sensor in the antibacterial defense system than previously known.
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Affiliation(s)
- Siv H Moen
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Birgitta Ehrnström
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Infectious Diseases, Clinic of Medicine, St. Olavs Hospital HF, Trondheim University Hospital, Trondheim, Norway
| | - June F Kojen
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Mariia Yurchenko
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Kai S Beckwith
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jan E Afset
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital HF, Trondheim University Hospital, Trondheim, Norway
| | - Jan K Damås
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Infectious Diseases, Clinic of Medicine, St. Olavs Hospital HF, Trondheim University Hospital, Trondheim, Norway
| | - Zhenyi Hu
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, United States
| | - Hang Yin
- School of Pharmaceutical Sciences, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
| | - Terje Espevik
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jørgen Stenvik
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Infectious Diseases, Clinic of Medicine, St. Olavs Hospital HF, Trondheim University Hospital, Trondheim, Norway
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49
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Zwirzitz B, Pinior B, Metzler-Zebeli B, Handler M, Gense K, Knecht C, Ladinig A, Dzieciol M, Wetzels SU, Wagner M, Schmitz-Esser S, Mann E. Microbiota of the Gut-Lymph Node Axis: Depletion of Mucosa-Associated Segmented Filamentous Bacteria and Enrichment of Methanobrevibacter by Colistin Sulfate and Linco-Spectin in Pigs. Front Microbiol 2019; 10:599. [PMID: 31031713 PMCID: PMC6470194 DOI: 10.3389/fmicb.2019.00599] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 03/08/2019] [Indexed: 12/11/2022] Open
Abstract
Microorganisms are translocated from the gut to lymphatic tissues via immune cells, thereby challenging and training the mammalian immune system. Antibiotics alter the gut microbiome and consecutively might also affect the corresponding translocation processes, resulting in an imbalanced state between the intestinal microbiota and the host. Hence, understanding the variant effects of antibiotics on the microbiome of gut-associated tissues is of vital importance for maintaining metabolic homeostasis and animal health. In the present study, we analyzed the microbiome of (i) pig feces, ileum, and ileocecal lymph nodes under the influence of antibiotics (Linco-Spectin and Colistin sulfate) using 16S rRNA gene sequencing for high-resolution community profiling and (ii) ileocecal lymph nodes in more detail with two additional methodological approaches, i.e., cultivation of ileocecal lymph node samples and (iii) metatranscriptome sequencing of a single lymph node sample. Supplementation of medicated feed showed a local effect on feces and ileal mucosa-associated microbiomes. Pigs that received antibiotics harbored significantly reduced amounts of segmented filamentous bacteria (SFB) along the ileal mucosa (p = 0.048; 199.17-fold change) and increased amounts of Methanobrevibacter, a methanogenic Euryarchaeote in fecal samples (p = 0.005; 20.17-fold change) compared to the control group. Analysis of the porcine ileocecal lymph node microbiome exposed large differences between the viable and the dead fraction of microorganisms and the microbiome was altered to a lesser extent by antibiotics compared with feces and ileum. The core microbiome of lymph nodes was constituted mainly of Proteobacteria. RNA-sequencing of a single lymph node sample unveiled transcripts responsible for amino acid and carbohydrate metabolism as well as protein turnover, DNA replication and signal transduction. The study presented here is the first comparative study of microbial communities in feces, ileum, and its associated ileocecal lymph nodes. In each analyzed site, we identified specific phylotypes susceptible to antibiotic treatment that can have profound impacts on the host physiological and immunological state, or even on global biogeochemical cycles. Our results indicate that pathogenic bacteria, e.g., enteropathogenic Escherichia coli, could escape antibiotic treatment by translocating to lymph nodes. In general ileocecal lymph nodes harbor a more diverse and active community of microorganisms than previously assumed.
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Affiliation(s)
- Benjamin Zwirzitz
- Institute of Milk Hygiene, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria
| | - Beate Pinior
- Institute for Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Barbara Metzler-Zebeli
- University Clinic for Swine, University of Veterinary Medicine, Vienna, Austria.,Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, Vienna, Austria
| | - Monika Handler
- Institute of Milk Hygiene, University of Veterinary Medicine, Vienna, Austria
| | - Kristina Gense
- Institute of Milk Hygiene, University of Veterinary Medicine, Vienna, Austria
| | - Christian Knecht
- University Clinic for Swine, University of Veterinary Medicine, Vienna, Austria
| | - Andrea Ladinig
- University Clinic for Swine, University of Veterinary Medicine, Vienna, Austria
| | - Monika Dzieciol
- Institute of Milk Hygiene, University of Veterinary Medicine, Vienna, Austria
| | - Stefanie U Wetzels
- Institute of Milk Hygiene, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria
| | - Martin Wagner
- Institute of Milk Hygiene, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria
| | | | - Evelyne Mann
- Institute of Milk Hygiene, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria
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50
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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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