1
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Aghighi F, Salami M. What we need to know about the germ-free animal models. AIMS Microbiol 2024; 10:107-147. [PMID: 38525038 PMCID: PMC10955174 DOI: 10.3934/microbiol.2024007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 03/26/2024] Open
Abstract
The gut microbiota (GM), as a forgotten organ, refers to the microbial community that resides in the gastrointestinal tract and plays a critical role in a variety of physiological activities in different body organs. The GM affects its targets through neurological, metabolic, immune, and endocrine pathways. The GM is a dynamic system for which exogenous and endogenous factors have negative or positive effects on its density and composition. Since the mid-twentieth century, laboratory animals are known as the major tools for preclinical research; however, each model has its own limitations. So far, two main models have been used to explore the effects of the GM under normal and abnormal conditions: the isolated germ-free and antibiotic-treated models. Both methods have strengths and weaknesses. In many fields of host-microbe interactions, research on these animal models are known as appropriate experimental subjects that enable investigators to directly assess the role of the microbiota on all features of physiology. These animal models present biological model systems to either study outcomes of the absence of microbes, or to verify the effects of colonization with specific and known microbial species. This paper reviews these current approaches and gives advantages and disadvantages of both models.
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Affiliation(s)
| | - Mahmoud Salami
- Physiology Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, I. R. Iran
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2
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Lin Q, Kuypers M, Liu Z, Copeland JK, Chan D, Robertson SJ, Kontogiannis J, Guttman DS, Banks EK, Philpott DJ, Mallevaey T. Invariant natural killer T cells minimally influence gut microbiota composition in mice. Gut Microbes 2022; 14:2104087. [PMID: 35912530 PMCID: PMC9348128 DOI: 10.1080/19490976.2022.2104087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Invariant Natural Killer T (iNKT) cells are unconventional T cells that respond to glycolipid antigens found in microbes in a CD1d-dependent manner. iNKT cells exert innate-like functions and produce copious amounts of cytokines, chemokines and cytotoxic molecules within only minutes of activation. As such, iNKT cells can fuel or dampen inflammation in a context-dependent manner. In addition, iNKT cells provide potent immunity against bacteria, viruses, parasites and fungi. Although microbiota-iNKT cell interactions are not well-characterized, mounting evidence suggests that microbiota colonization early in life impacts iNKT cell homeostasis and functions in disease. In this study, we showed that CD1d-/- and Vα14 Tg mice, which lack and have increased numbers of iNKT cells, respectively, had no significant alterations in gut microbiota composition compared to their littermate controls. Furthermore, specific iNKT cell activation by glycolipid antigens only resulted in a transient and minimal shift in microbiota composition when compared to the natural drift found in our colony. Our findings demonstrate that iNKT cells have little to no influence in regulating commensal bacteria at steady state.Abbreviations: iNKT: invariant Natural Killer T cell; αGC: α-galactosylceramide.
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Affiliation(s)
- Qiaochu Lin
- Department of Immunology, University of Toronto, Toronto, ON, Canada,CONTACT Thierry Mallevaey University of Toronto, Department of Immunology, Medical Sciences Building, Room 7334,1 King’s College Circle, Toronto, OntarioM5S 1A8, Canada
| | - Meggie Kuypers
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Zhewei Liu
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Julia K Copeland
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada
| | - Donny Chan
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada
| | - Susan J Robertson
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Jean Kontogiannis
- Division of Comparative Medicine, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - David S Guttman
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - E. Kate Banks
- Division of Comparative Medicine, Faculty of Medicine, University of Toronto, Toronto, ON, Canada,Department of Physiology, University of Toronto, Toronto, ON, Canada
| | - Dana J Philpott
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Thierry Mallevaey
- Department of Immunology, University of Toronto, Toronto, ON, Canada,Institute of Biomaterials & Biomedical Engineering, University of Toronto, Toronto, ON, Canada
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3
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Abstract
Despite identification of numerous associations between microbiomes and diseases, the complexity of the human microbiome has hindered identification of individual species and strains that are causative in host phenotype or disease. Uncovering causative microbes is vital to fully understand disease processes and to harness the potential therapeutic benefits of microbiota manipulation. Developments in sequencing technology, animal models, and bacterial culturing have facilitated the discovery of specific microbes that impact the host and are beginning to advance the characterization of host-microbiome interaction mechanisms. We summarize the historical and contemporary experimental approaches taken to uncover microbes from the microbiota that affect host biology and describe examples of commensals that have specific effects on the immune system, inflammation, and metabolism. There is still much to learn, and we lay out challenges faced by the field and suggest potential remedies for common pitfalls encountered in the hunt for causative commensal microbes. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Graham J Britton
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; .,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jeremiah J Faith
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; .,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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4
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Pearson JA, Wong FS, Wen L. Inflammasomes and Type 1 Diabetes. Front Immunol 2021; 12:686956. [PMID: 34177937 PMCID: PMC8219953 DOI: 10.3389/fimmu.2021.686956] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 05/17/2021] [Indexed: 01/10/2023] Open
Abstract
Microbiota have been identified as an important modulator of susceptibility in the development of Type 1 diabetes in both animal models and humans. Collectively these studies highlight the association of the microbiota composition with genetic risk, islet autoantibody development and modulation of the immune responses. However, the signaling pathways involved in mediating these changes are less well investigated, particularly in humans. Importantly, understanding the activation of signaling pathways in response to microbial stimulation is vital to enable further development of immunotherapeutics, which may enable enhanced tolerance to the microbiota or prevent the initiation of the autoimmune process. One such signaling pathway that has been poorly studied in the context of Type 1 diabetes is the role of the inflammasomes, which are multiprotein complexes that can initiate immune responses following detection of their microbial ligands. In this review, we discuss the roles of the inflammasomes in modulating Type 1 diabetes susceptibility, from genetic associations to the priming and activation of the inflammasomes. In addition, we also summarize the available inhibitors for therapeutically targeting the inflammasomes, which may be of future use in Type 1 diabetes.
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Affiliation(s)
- James Alexander Pearson
- Diabetes Research Group, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - F Susan Wong
- Diabetes Research Group, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Li Wen
- Section of Endocrinology, Internal Medicine, School of Medicine, Yale University, New Haven, CT, United States
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5
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Kuypers M, Despot T, Mallevaey T. Dirty mice join the immunologist's toolkit. Microbes Infect 2021; 23:104817. [PMID: 33785421 DOI: 10.1016/j.micinf.2021.104817] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/10/2021] [Accepted: 03/22/2021] [Indexed: 02/08/2023]
Abstract
The microbiota is a driving force that influences host physiological functions. In this review, we discuss some of the methods that have been used in the pursuit of relevant host-microbiota interactions that control immune fitness and disease susceptibility, with a focus on dirty mice which have been recently incorporated in the immunologist's toolkit.
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Affiliation(s)
- Meggie Kuypers
- Department of Immunology, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Tijana Despot
- Department of Immunology, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Thierry Mallevaey
- Department of Immunology, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada; Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada.
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6
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Guo H, Gibson SA, Ting JPY. Gut microbiota, NLR proteins, and intestinal homeostasis. J Exp Med 2021; 217:152098. [PMID: 32941596 PMCID: PMC7537383 DOI: 10.1084/jem.20181832] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/10/2020] [Accepted: 08/14/2020] [Indexed: 12/21/2022] Open
Abstract
The gastrointestinal tract harbors a highly complex microbial community, which is referred to as gut microbiota. With increasing evidence suggesting that the imbalance of gut microbiota plays a significant role in the pathogenesis of multiple diseases, interactions between the host immune system and the gut microbiota are now attracting emerging interest. Nucleotide-binding and leucine-rich repeat–containing receptors (NLRs) encompass a large number of innate immune sensors and receptors, which mediate the activation of Caspase-1 and the subsequent release of mature interleukin-1β and interleukin-18. Several family members have been found to restrain rather than activate inflammatory cytokines and immune signaling. NLR family members are central regulators of pathogen recognition, host immunity, and inflammation with utmost importance in human diseases. In this review, we focus on the potential roles played by NLRs in controlling and shaping the microbiota community and discuss how the functional axes interconnecting gut microbiota with NLRs impact the modulation of colitis, inflammatory bowel diseases, and colorectal cancer.
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Affiliation(s)
- Hao Guo
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Sara A Gibson
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jenny P Y Ting
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC.,Department of Microbiology-Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC
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7
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Lin Q, Kuypers M, Philpott DJ, Mallevaey T. The dialogue between unconventional T cells and the microbiota. Mucosal Immunol 2020; 13:867-876. [PMID: 32704035 DOI: 10.1038/s41385-020-0326-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 06/19/2020] [Accepted: 06/19/2020] [Indexed: 02/04/2023]
Abstract
The mammalian immune system is equipped with unconventional T cells that respond to microbial molecules such as glycolipids and small-molecule metabolites, which are invisible to conventional CD4 and CD8 T cells. Unconventional T cells include invariant natural killer T (iNKT) cells and mucosa-associated invariant T (MAIT) cells, which are involved in a wide range of infectious and non-infectious diseases, such as cancer and autoimmunity. In addition, their high conservation across mammals, their restriction by non-polymorphic antigen-presenting molecules, and their immediate and robust responses make these 'innate' T cells appealing targets for the development of one-size-fits-all immunotherapies. In this review, we discuss how iNKT and MAIT cells directly and indirectly detect the presence of and respond to pathogenic and commensal microbes. We also explore the current understanding of the bidirectional relationship between the microbiota and innate T cells, and how this crosstalk shapes the immune response in disease.
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Affiliation(s)
- Qiaochu Lin
- Department of Immunology, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Meggie Kuypers
- Department of Immunology, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Dana J Philpott
- Department of Immunology, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Thierry Mallevaey
- Department of Immunology, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada. .,Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada.
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8
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Fattinger SA, Sellin ME, Hardt WD. Epithelial inflammasomes in the defense against Salmonella gut infection. Curr Opin Microbiol 2020; 59:86-94. [PMID: 33128958 DOI: 10.1016/j.mib.2020.09.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/15/2020] [Accepted: 09/22/2020] [Indexed: 02/06/2023]
Abstract
The gut epithelium prevents bacterial access to the host's tissues and coordinates a number of mucosal defenses. Here, we review the function of epithelial inflammasomes in the infected host and focus on their role in defense against Salmonella Typhimurium. This pathogen employs flagella to swim towards the epithelium and a type III secretion system (TTSS) to dock and invade intestinal epithelial cells. Flagella and TTSS components are recognized by the canonical NAIP/NLRC4 inflammasome, while LPS activates the non-canonical Caspase-4/11 inflammasome. The relative contributions of these inflammasomes, the activated cell death pathways and the elicited mucosal defenses are subject to environmental control and appear to change along the infection trajectory. It will be an important future task to explain how this may enable defense against the challenges imposed by diverse bacterial enteropathogens.
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Affiliation(s)
- Stefan A Fattinger
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland; Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Mikael E Sellin
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Wolf-Dietrich Hardt
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland.
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9
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Grasset EK, Chorny A, Casas-Recasens S, Gutzeit C, Bongers G, Thomsen I, Chen L, He Z, Matthews DB, Oropallo MA, Veeramreddy P, Uzzan M, Mortha A, Carrillo J, Reis BS, Ramanujam M, Sintes J, Magri G, Maglione PJ, Cunningham-Rundles C, Bram RJ, Faith J, Mehandru S, Pabst O, Cerutti A. Gut T cell-independent IgA responses to commensal bacteria require engagement of the TACI receptor on B cells. Sci Immunol 2020; 5:eaat7117. [PMID: 32737068 PMCID: PMC8349226 DOI: 10.1126/sciimmunol.aat7117] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 07/09/2020] [Indexed: 12/29/2022]
Abstract
The gut mounts secretory immunoglobulin A (SIgA) responses to commensal bacteria through nonredundant T cell-dependent (TD) and T cell-independent (TI) pathways that promote the establishment of mutualistic host-microbiota interactions. SIgAs from the TD pathway target penetrant bacteria, and their induction requires engagement of CD40 on B cells by CD40 ligand on T follicular helper cells. In contrast, SIgAs from the TI pathway bind a larger spectrum of bacteria, but the mechanism underpinning their production remains elusive. Here, we show that the intestinal TI pathway required CD40-independent B cell-activating signals from TACI, a receptor for the innate CD40 ligand-like factors BAFF and APRIL. TACI-induced SIgA responses targeted a fraction of the gut microbiota without shaping its overall composition. Of note, TACI was dispensable for TD induction of IgA in gut-associated lymphoid organs. Thus, BAFF/APRIL signals acting on TACI orchestrate commensal bacteria-specific SIgA responses through an intestinal TI program.
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Affiliation(s)
- E K Grasset
- Department of Medicine, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
- Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, SE-171 77 Stockholm, Sweden
| | - A Chorny
- Department of Medicine, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - S Casas-Recasens
- Department of Medicine, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - C Gutzeit
- Department of Medicine, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - I Thomsen
- Institute of Molecular Medicine, Aachen University, Aachen D-52074, Germany
| | - L Chen
- Department of Medicine, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Z He
- Department of Medicine, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - D B Matthews
- Department of Medicine, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - M A Oropallo
- Department of Medicine, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - P Veeramreddy
- Department of Medicine, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - M Uzzan
- Department of Medicine, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - A Mortha
- Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - J Carrillo
- Department of Medicine, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- IrsiCaixa, Hospital Germans Trias i Pujol, Badalona 08916, Spain
| | - B S Reis
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY 10065, USA
| | - M Ramanujam
- Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT 06877, USA
| | - J Sintes
- Program for Inflammatory and Cardiovascular Disorders, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona 08003, Spain
| | - G Magri
- Program for Inflammatory and Cardiovascular Disorders, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona 08003, Spain
| | - P J Maglione
- Department of Medicine, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - C Cunningham-Rundles
- Department of Medicine, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - R J Bram
- Departments of Pediatrics and Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - J Faith
- Department of Medicine, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - S Mehandru
- Department of Medicine, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - O Pabst
- Institute of Molecular Medicine, Aachen University, Aachen D-52074, Germany
| | - A Cerutti
- Department of Medicine, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
- Program for Inflammatory and Cardiovascular Disorders, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona 08003, Spain
- Catalan Institute for Research and Advanced Studies (ICREA), Barcelona 08003, Spain
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10
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Eberl C, Ring D, Münch PC, Beutler M, Basic M, Slack EC, Schwarzer M, Srutkova D, Lange A, Frick JS, Bleich A, Stecher B. Reproducible Colonization of Germ-Free Mice With the Oligo-Mouse-Microbiota in Different Animal Facilities. Front Microbiol 2020; 10:2999. [PMID: 31998276 PMCID: PMC6965490 DOI: 10.3389/fmicb.2019.02999] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 12/11/2019] [Indexed: 12/26/2022] Open
Abstract
The Oligo-Mouse-Microbiota (OMM12) is a recently developed synthetic bacterial community for functional microbiome research in mouse models (Brugiroux et al., 2016). To date, the OMM12 model has been established in several germ-free mouse facilities world-wide and is employed to address a growing variety of research questions related to infection biology, mucosal immunology, microbial ecology and host-microbiome metabolic cross-talk. The OMM12 consists of 12 sequenced and publically available strains isolated from mice, representing five bacterial phyla that are naturally abundant in the murine gastrointestinal tract (Lagkouvardos et al., 2016). Under germ-free conditions, the OMM12 colonizes mice stably over multiple generations. Here, we investigated whether stably colonized OMM12 mouse lines could be reproducibly established in different animal facilities. Germ-free C57Bl/6J mice were inoculated with a frozen mixture of the OMM12 strains. Within 2 weeks after application, the OMM12 community reached the same stable composition in all facilities, as determined by fecal microbiome analysis. We show that a second application of the OMM12 strains after 72 h leads to a more stable community composition than a single application. The availability of such protocols for reliable de novo generation of gnotobiotic rodents will certainly contribute to increasing experimental reproducibility in biomedical research.
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Affiliation(s)
- Claudia Eberl
- Max von Pettenkofer-Institute, LMU Munich, Munich, Germany
| | - Diana Ring
- Max von Pettenkofer-Institute, LMU Munich, Munich, Germany.,German Center for Infection Research (DZIF), LMU Munich, Munich, Germany
| | - Philipp C Münch
- Max von Pettenkofer-Institute, LMU Munich, Munich, Germany.,Department for Computational Biology of Infection Research, Helmholtz Center for Infection Research, Brunswick, Germany
| | - Markus Beutler
- Max von Pettenkofer-Institute, LMU Munich, Munich, Germany
| | - Marijana Basic
- Institute for Laboratory Animal Science and Central Animal Facility, Hannover Medical School, Hanover, Germany
| | | | - Martin Schwarzer
- Institute of Microbiology of the Czech Academy of Sciences, Nový Hrádek, Czechia
| | - Dagmar Srutkova
- Institute of Microbiology of the Czech Academy of Sciences, Nový Hrádek, Czechia
| | - Anna Lange
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany.,German Center for Infection Research (DZIF), Tübingen, Germany
| | - Julia S Frick
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany.,German Center for Infection Research (DZIF), Tübingen, Germany
| | - André Bleich
- Institute for Laboratory Animal Science and Central Animal Facility, Hannover Medical School, Hanover, Germany
| | - Bärbel Stecher
- Max von Pettenkofer-Institute, LMU Munich, Munich, Germany.,German Center for Infection Research (DZIF), LMU Munich, Munich, Germany
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11
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Ahern PP, Maloy KJ. Understanding immune-microbiota interactions in the intestine. Immunology 2020; 159:4-14. [PMID: 31777071 PMCID: PMC6904641 DOI: 10.1111/imm.13150] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/01/2019] [Accepted: 10/07/2019] [Indexed: 12/13/2022] Open
Abstract
The past two decades have seen an explosion in research that aims to understand how the dynamic interplay with the gut microbiota impacts host health and disease, establishing a role for the gut microbiota in a plethora of pathologies. Understanding how health-promoting microbiota are established and how beneficial host-microbiota interactions are maintained is of immense biomedical importance. Despite the enormous progress that has been made, our knowledge of the specific microbiota members that mediate these effects and the mechanisms underlying these interactions is rudimentary. The dearth of information regarding the nature of advantageous host-microbiota interactions, and the factors that cause these relationships to go awry, has hampered our ability to realize the therapeutic potential of the microbiota. Here we discuss key issues that limit current knowledge and describe a path forwards to improving our understanding of the contributions of the microbiota to host health.
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Affiliation(s)
- Philip P. Ahern
- Department of Cardiovascular and Metabolic SciencesCleveland Clinic Lerner Research InstituteClevelandOHUSA
| | - Kevin J. Maloy
- Institute of Infection, Immunity and InflammationCollege of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
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12
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Intestinal epithelial NAIP/NLRC4 restricts systemic dissemination of the adapted pathogen Salmonella Typhimurium due to site-specific bacterial PAMP expression. Mucosal Immunol 2020; 13:530-544. [PMID: 31953493 PMCID: PMC7181392 DOI: 10.1038/s41385-019-0247-0] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 11/18/2019] [Accepted: 12/10/2019] [Indexed: 02/07/2023]
Abstract
Inflammasomes can prevent systemic dissemination of enteropathogenic bacteria. As adapted pathogens including Salmonella Typhimurium (S. Tm) have evolved evasion strategies, it has remained unclear when and where inflammasomes restrict their dissemination. Bacterial population dynamics establish that the NAIP/NLRC4 inflammasome specifically restricts S. Tm migration from the gut to draining lymph nodes. This is solely attributable to NAIP/NLRC4 within intestinal epithelial cells (IECs), while S. Tm evades restriction by phagocyte NAIP/NLRC4. NLRP3 and Caspase-11 also fail to restrict S. Tm mucosa traversal, migration to lymph nodes, and systemic pathogen growth. The ability of IECs (not phagocytes) to mount a NAIP/NLRC4 defense in vivo is explained by particularly high NAIP/NLRC4 expression in IECs and the necessity for epithelium-invading S. Tm to express the NAIP1-6 ligands-flagella and type-III-secretion-system-1. Imaging reveals both ligands to be promptly downregulated following IEC-traversal. These results highlight the importance of intestinal epithelial NAIP/NLRC4 in blocking bacterial dissemination in vivo, and explain why this constitutes a uniquely evasion-proof defense against the adapted enteropathogen S. Tm.
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13
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Damjanovic K, Menéndez P, Blackall LL, Oppen MJH. Mixed‐mode bacterial transmission in the common brooding coral
Pocillopora acuta. Environ Microbiol 2019; 22:397-412. [DOI: 10.1111/1462-2920.14856] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 10/14/2019] [Accepted: 11/07/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Katarina Damjanovic
- School of BioSciences, The University of Melbourne Parkville Vic 3010 Australia
- Australian Institute of Marine Science PMB No 3, Townsville, MC 4810 Qld Australia
| | - Patricia Menéndez
- Australian Institute of Marine Science PMB No 3, Townsville, MC 4810 Qld Australia
- Department of Econometrics and Business Statistics Monash University Vic 3800 Australia
| | - Linda L. Blackall
- School of BioSciences, The University of Melbourne Parkville Vic 3010 Australia
| | - Madeleine J. H. Oppen
- School of BioSciences, The University of Melbourne Parkville Vic 3010 Australia
- Australian Institute of Marine Science PMB No 3, Townsville, MC 4810 Qld Australia
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14
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Khan AA, Yurkovetskiy L, O'Grady K, Pickard JM, de Pooter R, Antonopoulos DA, Golovkina T, Chervonsky A. Polymorphic Immune Mechanisms Regulate Commensal Repertoire. Cell Rep 2019; 29:541-550.e4. [PMID: 31618625 PMCID: PMC6904226 DOI: 10.1016/j.celrep.2019.09.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 07/28/2019] [Accepted: 09/04/2019] [Indexed: 12/18/2022] Open
Abstract
Environmental influences (infections and diet) strongly affect a host's microbiota. However, host genetics may influence commensal communities, as suggested by the greater similarity between the microbiomes of identical twins compared to non-identical twins. Variability of human genomes and microbiomes complicates the understanding of polymorphic mechanisms regulating the commensal communities. Whereas animal studies allow genetic modifications, they are sensitive to influences known as "cage" or "legacy" effects. Here, we analyze ex-germ-free mice of various genetic backgrounds, including immunodeficient and major histocompatibility complex (MHC) congenic strains, receiving identical input microbiota. The host's polymorphic mechanisms affect the gut microbiome, and both innate (anti-microbial peptides, complement, pentraxins, and enzymes affecting microbial survival) and adaptive (MHC-dependent and MHC-independent) pathways influence the microbiota. In our experiments, polymorphic mechanisms regulate only a limited number of microbial lineages (independently of their abundance). Our comparative analyses suggest that some microbes may benefit from the specific immune responses that they elicit.
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Affiliation(s)
- Aly A Khan
- Toyota Technological Institute at Chicago, Chicago, IL 60637, USA; Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Leonid Yurkovetskiy
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA; Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA
| | - Kelly O'Grady
- Department of Microbiology, University of Chicago, Chicago, IL 60637, USA
| | - Joseph M Pickard
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA; Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Renée de Pooter
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Dionysios A Antonopoulos
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Biosciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Tatyana Golovkina
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA; Department of Microbiology, University of Chicago, Chicago, IL 60637, USA; Committee on Immunology, University of Chicago, Chicago, IL 60637, USA.
| | - Alexander Chervonsky
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA; Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA; Committee on Immunology, University of Chicago, Chicago, IL 60637, USA.
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15
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Iannone LF, Preda A, Blottière HM, Clarke G, Albani D, Belcastro V, Carotenuto M, Cattaneo A, Citraro R, Ferraris C, Ronchi F, Luongo G, Santocchi E, Guiducci L, Baldelli P, Iannetti P, Pedersen S, Petretto A, Provasi S, Selmer K, Spalice A, Tagliabue A, Verrotti A, Segata N, Zimmermann J, Minetti C, Mainardi P, Giordano C, Sisodiya S, Zara F, Russo E, Striano P. Microbiota-gut brain axis involvement in neuropsychiatric disorders. Expert Rev Neurother 2019; 19:1037-1050. [PMID: 31260640 DOI: 10.1080/14737175.2019.1638763] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Introduction: The microbiota-gut brain (MGB) axis is the bidirectional communication between the intestinal microbiota and the brain. An increasing body of preclinical and clinical evidence has revealed that the gut microbial ecosystem can affect neuropsychiatric health. However, there is still a need of further studies to elucidate the complex gene-environment interactions and the role of the MGB axis in neuropsychiatric diseases, with the aim of identifying biomarkers and new therapeutic targets, to allow early diagnosis and improving treatments. Areas covered: To review the role of MGB axis in neuropsychiatric disorders, prediction and prevention of disease through exploitation, integration, and combination of data from existing gut microbiome/microbiota projects and appropriate other International '-Omics' studies. The authors also evaluated the new technological advances to investigate and modulate, through nutritional and other interventions, the gut microbiota. Expert opinion: The clinical studies have documented an association between alterations in gut microbiota composition and/or function, whereas the preclinical studies support a role for the gut microbiota in impacting behaviors which are of relevance to psychiatry and other central nervous system (CNS) disorders. Targeting MGB axis could be an additional approach for treating CNS disorders and all conditions in which alterations of the gut microbiota are involved.
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Affiliation(s)
- Luigi Francesco Iannone
- Science of Health Department, School of Medicine, University of Catanzaro , Catanzaro , Italy
| | - Alberto Preda
- Paediatric Neurology and Muscular Diseases Unit, Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, "G. Gaslini" Institute , Genova , Italy
| | - Hervé M Blottière
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, JouyenJosas&MetaGenoPolis, INRA, Université Paris-Saclay , Jouyen Josas , France
| | - Gerard Clarke
- Department of Psychiatry and Neurobehavioural Science, School of Medicine, College of Medicine & Health, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork , Cork , Ireland
| | - Diego Albani
- Department of Neuroscience, IRCCS - Istituto di Ricerche Farmacologiche Mario Negri , Milan , Italy
| | | | - Marco Carotenuto
- Clinic of Child and Adolescent Neuropsychiatry, Department of Mental Health, Physical and Preventive Medicine, Università degli Studi della Campania 'Luigi Vanvitelli' , Napoli , Italy
| | - Annamaria Cattaneo
- Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli , Brescia , Italy.,Stress, Psychiatry and Immunology Laboratory, Department of Psychological Medicine, Institute of Psychiatry , King's College , London
| | - Rita Citraro
- Science of Health Department, School of Medicine, University of Catanzaro , Catanzaro , Italy
| | - Cinzia Ferraris
- Human Nutrition and Eating Disorder Research Center, Department of Public Health, Experimental and Forensic Medicine University of Pavia , Pavia , Italy
| | - Francesca Ronchi
- Department forBiomedical Research, University of Bern , Bern , Switzerland
| | - Gaia Luongo
- Ordine dei Tecnologi Alimentari Campania e Lazio , Napoli , Italy
| | | | - Letizia Guiducci
- National Research Council, Institute of Clinical Physiology , Pisa , Italy
| | - Pietro Baldelli
- Department of Experimental Medicine, Section of Physiology, University of Genova , Genova , Italy
| | - Paola Iannetti
- Department of Pediatrics`, "Sapienza" University of Rome , Rome , Italy
| | - Sigrid Pedersen
- Department of Refractory Epilepsy, Division of Clinical Neuroscience, Oslo University Hospital , Oslo , Norway
| | - Andrea Petretto
- Laboratory of Mass Spectrometry - Core Facilities, Istituto Giannina Gaslini , Genova , Italy
| | - Stefania Provasi
- Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli , Brescia , Italy
| | - Kaja Selmer
- Department of Research and Development, Division of Clinical Neuroscience, Oslo University Hospital, Osla, Norway and Department of Refractory Epilepsy, Division of Clinical Neuroscience, Oslo University Hospital , Osla , Norway
| | - Alberto Spalice
- Department of Experimental Medicine, Section of Physiology, University of Genova , Genova , Italy
| | - Anna Tagliabue
- Stress, Psychiatry and Immunology Laboratory, Department of Psychological Medicine, Institute of Psychiatry , King's College , London
| | - Alberto Verrotti
- Department of Pediatrics, University of L'Aquila , L'Aquila , Italy
| | - Nicola Segata
- Centre for Integrative Biology, University of Trento , Trento , Italy
| | - Jakob Zimmermann
- Human Nutrition and Eating Disorder Research Center, Department of Public Health, Experimental and Forensic Medicine University of Pavia , Pavia , Italy
| | - Carlo Minetti
- Paediatric Neurology and Muscular Diseases Unit, Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, "G. Gaslini" Institute , Genova , Italy
| | | | - Carmen Giordano
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano , Milano , Italy
| | - Sanjay Sisodiya
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology , Queen Square, London , UK
| | - Federico Zara
- Laboratory of Neurogenetics, Istituto Giannina Gaslini , Genova , Italy
| | - Emilio Russo
- Science of Health Department, School of Medicine, University of Catanzaro , Catanzaro , Italy
| | - Pasquale Striano
- Paediatric Neurology and Muscular Diseases Unit, Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, "G. Gaslini" Institute , Genova , Italy
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16
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Glasl B, Smith CE, Bourne DG, Webster NS. Disentangling the effect of host-genotype and environment on the microbiome of the coral Acropora tenuis. PeerJ 2019; 7:e6377. [PMID: 30740275 PMCID: PMC6368029 DOI: 10.7717/peerj.6377] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 12/30/2018] [Indexed: 12/31/2022] Open
Abstract
Genotype-specific contributions to the environmental tolerance and disease susceptibility of corals are widely accepted. Yet our understanding of how host genotype influences the composition and stability of the coral microbiome subjected to environmental fluctuations is limited. To gain insight into the community dynamics and environmental stability of microbiomes associated with distinct coral genotypes, we assessed the microbial community associated with Acropora tenuis under single and cumulative pressure experiments. Experimental treatments comprised either a single pulse of reduced salinity (minimum of 28 psu) or exposure to the cumulative pressures of reduced salinity (minimum of 28 psu), elevated seawater temperature (+2 °C), elevated pCO2 (900 ppm), and the presence of macroalgae. Analysis of 16S rRNA gene amplicon sequence data revealed that A. tenuis microbiomes were highly host-genotype specific and maintained high compositional stability irrespective of experimental treatment. On average, 48% of the A. tenuis microbiome was dominated by Endozoicomonas. Amplicon sequence variants (ASVs) belonging to this genus were significantly different between host individuals. Although no signs of stress were evident in the coral holobiont and the vast majority of ASVs remained stable across treatments, a microbial indicator approach identified 26 ASVs belonging to Vibrionaceae, Rhodobacteraceae, Hahellaceae, Planctomycetes, Phylobacteriaceae, Flavobacteriaceae, and Cryomorphaceae that were significantly enriched in corals exposed to single and cumulative stressors. While several recent studies have highlighted the efficacy of microbial indicators as sensitive markers for environmental disturbance, the high host-genotype specificity of coral microbiomes may limit their utility and we therefore recommend meticulous control of host-genotype effects in coral microbiome research.
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Affiliation(s)
- Bettina Glasl
- Australian Institute of Marine Science, Townsville, QLD, Australia.,College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,AIMS@JCU, Townsville, QLD, Australia
| | - Caitlin E Smith
- Australian Institute of Marine Science, Townsville, QLD, Australia.,College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,AIMS@JCU, Townsville, QLD, Australia
| | - David G Bourne
- Australian Institute of Marine Science, Townsville, QLD, Australia.,College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,AIMS@JCU, Townsville, QLD, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, QLD, Australia.,AIMS@JCU, Townsville, QLD, Australia.,Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, Australia
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