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Hill JH, Round JL. Intestinal fungal-host interactions in promoting and maintaining health. Cell Host Microbe 2024; 32:1668-1680. [PMID: 39389031 DOI: 10.1016/j.chom.2024.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Revised: 09/05/2024] [Accepted: 09/14/2024] [Indexed: 10/12/2024]
Abstract
The resident microbiota are a key component of a healthy organism. The vast majority of microbiome studies have focused on bacterial members, which constitute a significant portion of resident microbial biomass. Recent studies have demonstrated how the fungal component of the microbiota, or the mycobiome, influences mammalian biology despite its low abundance compared to other microbes. Fungi are known for their pathogenic potential, yet fungi are also prominent colonizers in healthy states, highlighting their duality. We summarize the characteristics that define the gut mycobiome across life, the factors that can impact its composition, and studies that identify mechanisms of how fungi confer health benefits. The goal of this review is to synthesize our knowledge regarding the composition and function of a healthy mycobiome with a view to inspiring future therapeutic advances.
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Affiliation(s)
- Jennifer H Hill
- University of Colorado Boulder, BioFrontiers Institute, Department of Molecular, Cellular & Developmental Biology, Boulder, CO 80303, USA.
| | - June L Round
- University of Utah, School of Medicine, Department of Pathology, Huntsman Cancer Institute, Salt Lake City, UT 84112, USA.
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2
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Henry LP, Fernandez M, Wolf S, Abhyankar V, Ayroles JF. Wolbachia impacts microbiome diversity and fitness-associated traits for Drosophila melanogaster in a seasonally fluctuating environment. Ecol Evol 2024; 14:e70004. [PMID: 39041013 PMCID: PMC11262851 DOI: 10.1002/ece3.70004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 06/21/2024] [Accepted: 06/28/2024] [Indexed: 07/24/2024] Open
Abstract
The microbiome contributes to many different host traits, but its role in host adaptation remains enigmatic. The fitness benefits of the microbiome often depend on ecological conditions, but theory suggests that fluctuations in both the microbiome and environment modulate these fitness benefits. Moreover, vertically transmitted bacteria might constrain the ability of both the microbiome and host to respond to changing environments. Drosophila melanogaster provides an excellent system to investigate the impacts of interactions between the microbiome and the environment. To address this question, we created field mesocosms of D. melanogaster undergoing seasonal environmental change with and without the vertically transmitted bacteria, Wolbachia pipientis. Sampling temporal patterns in the microbiome revealed that Wolbachia constrained microbial diversity. Furthermore, Wolbachia and a dominant member of the microbiome, Commensalibacter, were associated with differences in two higher-order fitness traits, starvation resistance and lifespan. Our work here suggests that the interplay between the abiotic context and microbe-microbe interactions may shape key host phenotypes that underlie adaptation to changing environments. We conclude by exploring the consequences of complex interactions between Wolbachia and the microbiome for our understanding of eco-evolutionary processes that shape host-microbiome interactions.
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Affiliation(s)
- Lucas P. Henry
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew JerseyUSA
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonNew JerseyUSA
- Department of Biology, Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Michael Fernandez
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew JerseyUSA
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonNew JerseyUSA
| | - Scott Wolf
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew JerseyUSA
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonNew JerseyUSA
| | - Varada Abhyankar
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew JerseyUSA
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonNew JerseyUSA
| | - Julien F. Ayroles
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew JerseyUSA
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonNew JerseyUSA
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3
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Genetics determines how environmental change alters immune phenotypes. Nat Immunol 2024; 25:1138-1139. [PMID: 38898158 DOI: 10.1038/s41590-024-01879-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
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4
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Oyesola O, Downie AE, Howard N, Barre RS, Kiwanuka K, Zaldana K, Chen YH, Menezes A, Lee SC, Devlin J, Mondragón-Palomino O, Souza COS, Herrmann C, Koralov SB, Cadwell K, Graham AL, Loke P. Genetic and environmental interactions contribute to immune variation in rewilded mice. Nat Immunol 2024; 25:1270-1282. [PMID: 38877178 PMCID: PMC11224019 DOI: 10.1038/s41590-024-01862-5] [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: 05/02/2023] [Accepted: 05/02/2024] [Indexed: 06/16/2024]
Abstract
The relative and synergistic contributions of genetics and environment to interindividual immune response variation remain unclear, despite implications in evolutionary biology and medicine. Here we quantify interactive effects of genotype and environment on immune traits by investigating C57BL/6, 129S1 and PWK/PhJ inbred mice, rewilded in an outdoor enclosure and infected with the parasite Trichuris muris. Whereas cellular composition was shaped by interactions between genotype and environment, cytokine response heterogeneity including IFNγ concentrations was primarily driven by genotype with consequence on worm burden. In addition, we show that other traits, such as expression of CD44, were explained mostly by genetics on T cells, whereas expression of CD44 on B cells was explained more by environment across all strains. Notably, genetic differences under laboratory conditions were decreased following rewilding. These results indicate that nonheritable influences interact with genetic factors to shape immune variation and parasite burden.
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Affiliation(s)
- Oyebola Oyesola
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Alexander E Downie
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Nina Howard
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ramya S Barre
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of Texas Health Sciences Center at San Antonio, San Antonio, TX, USA
| | - Kasalina Kiwanuka
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kimberly Zaldana
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Pathology, New York University, Grossman School of Medicine, New York, NY, USA
| | - Ying-Han Chen
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University, Grossman School of Medicine, New York, NY, USA
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Arthur Menezes
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Soo Ching Lee
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Joseph Devlin
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University, Grossman School of Medicine, New York, NY, USA
| | - Octavio Mondragón-Palomino
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Camila Oliveira Silva Souza
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Christin Herrmann
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University, Grossman School of Medicine, New York, NY, USA
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sergei B Koralov
- Department of Pathology, New York University, Grossman School of Medicine, New York, NY, USA
| | - Ken Cadwell
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA
| | - Andrea L Graham
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
- Santa Fe Institute, Santa Fe, NM, USA.
| | - P'ng Loke
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA.
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5
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Nie X, Li Q, Chen X, Onyango S, Xie J, Nie S. Bacterial extracellular vesicles: Vital contributors to physiology from bacteria to host. Microbiol Res 2024; 284:127733. [PMID: 38678680 DOI: 10.1016/j.micres.2024.127733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 05/01/2024]
Abstract
Bacterial extracellular vesicles (bEVs) represent spherical particles with diameters ranging from 20 to 400 nm filled with multiple parental bacteria-derived components, including proteins, nucleic acids, lipids, and other biomolecules. The production of bEVs facilitates bacteria interacting with their environment and exerting biological functions. It is increasingly evident that the bEVs play integral roles in both bacterial and host physiology, contributing to environmental adaptations to functioning as health promoters for their hosts. This review highlights the current state of knowledge on the composition, biogenesis, and diversity of bEVs and the mechanisms by which different bEVs elicit effects on bacterial physiology and host health. We posit that an in-depth exploration of the mechanistic aspects of bEVs activity is essential to elucidate their health-promoting effects on the host and may facilitate the translation of bEVs into applications as novel natural biological nanomaterials.
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Affiliation(s)
- Xinke Nie
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
| | - Qiqiong Li
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
| | - Xinyang Chen
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
| | | | - Junhua Xie
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China.
| | - Shaoping Nie
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China.
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Downie AE, Barre RS, Robinson A, Yang J, Chen YH, Lin JD, Oyesola O, Yeung F, Cadwell K, Loke P, Graham AL. Assessing immune phenotypes using simple proxy measures: promise and limitations. DISCOVERY IMMUNOLOGY 2024; 3:kyae010. [PMID: 39045514 PMCID: PMC11264049 DOI: 10.1093/discim/kyae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 05/25/2024] [Accepted: 06/27/2024] [Indexed: 07/25/2024]
Abstract
The study of immune phenotypes in wild animals is beset by numerous methodological challenges, with assessment of detailed aspects of phenotype difficult to impossible. This constrains the ability of disease ecologists and ecoimmunologists to describe immune variation and evaluate hypotheses explaining said variation. The development of simple approaches that allow characterization of immune variation across many populations and species would be a significant advance. Here we explore whether serum protein concentrations and coarse-grained white blood cell profiles, immune quantities that can easily be assayed in many species, can predict, and therefore serve as proxies for, lymphocyte composition properties. We do this in rewilded laboratory mice, which combine the benefits of immune phenotyping of lab mice with the natural context and immune variation found in the wild. We find that easily assayed immune quantities are largely ineffective as predictors of lymphocyte composition, either on their own or with other covariates. Immunoglobulin G (IgG) concentration and neutrophil-lymphocyte ratio show the most promise as indicators of other immune traits, but their explanatory power is limited. Our results prescribe caution in inferring immune phenotypes beyond what is directly measured, but they do also highlight some potential paths forward for the development of proxy measures employable by ecoimmunologists.
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Affiliation(s)
- Alexander E Downie
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Ramya S Barre
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of Texas Health Sciences Center at San Antonio; San Antonio, TX, USA
| | - Annie Robinson
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Jennie Yang
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Ying-Han Chen
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine; New York, NY, USA
- Department of Microbiology, New York University Grossman School of Medicine; New York, NY, USA
- Institute of Biomedical Sciences, Academia Sinica, Taipei City, Taiwan
| | - Jian-Da Lin
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei City, Taiwan
- Center for Computational and Systems Biology, National Taiwan University, Taipei City, Taiwan
| | - Oyebola Oyesola
- Laboratory of Parasitic Diseases, National Institute for Allergy and Infectious Diseases, National Institutes of Health; Bethesda, MD, USA
| | - Frank Yeung
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine; New York, NY, USA
| | - Ken Cadwell
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine; New York, NY, USA
- Department of Microbiology, New York University Grossman School of Medicine; New York, NY, USA
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - P’ng Loke
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine; New York, NY, USA
- Department of Microbiology, New York University Grossman School of Medicine; New York, NY, USA
- Laboratory of Parasitic Diseases, National Institute for Allergy and Infectious Diseases, National Institutes of Health; Bethesda, MD, USA
| | - Andrea L Graham
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Santa Fe Institute; Santa Fe, NM, USA
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7
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Sekeresova Kralova J, Donic C, Dassa B, Livyatan I, Jansen PM, Ben-Dor S, Fidel L, Trzebanski S, Narunsky-Haziza L, Asraf O, Brenner O, Dafni H, Jona G, Boura-Halfon S, Stettner N, Segal E, Brunke S, Pilpel Y, Straussman R, Zeevi D, Bacher P, Hube B, Shlezinger N, Jung S. Competitive fungal commensalism mitigates candidiasis pathology. J Exp Med 2024; 221:e20231686. [PMID: 38497819 PMCID: PMC10949073 DOI: 10.1084/jem.20231686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 01/17/2024] [Accepted: 02/14/2024] [Indexed: 03/19/2024] Open
Abstract
The mycobiota are a critical part of the gut microbiome, but host-fungal interactions and specific functional contributions of commensal fungi to host fitness remain incompletely understood. Here, we report the identification of a new fungal commensal, Kazachstania heterogenica var. weizmannii, isolated from murine intestines. K. weizmannii exposure prevented Candida albicans colonization and significantly reduced the commensal C. albicans burden in colonized animals. Following immunosuppression of C. albicans colonized mice, competitive fungal commensalism thereby mitigated fatal candidiasis. Metagenome analysis revealed K. heterogenica or K. weizmannii presence among human commensals. Our results reveal competitive fungal commensalism within the intestinal microbiota, independent of bacteria and immune responses, that could bear potential therapeutic value for the management of C. albicans-mediated diseases.
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Affiliation(s)
| | - Catalina Donic
- Departments of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Bareket Dassa
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Ilana Livyatan
- Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Paul Mathias Jansen
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knoell Institute Jena (HKI), Jena, Germany
| | - Shifra Ben-Dor
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Lena Fidel
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Sébastien Trzebanski
- Departments of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Omer Asraf
- Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ori Brenner
- Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Hagit Dafni
- Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Ghil Jona
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Sigalit Boura-Halfon
- Departments of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Stettner
- Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Segal
- Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sascha Brunke
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knoell Institute Jena (HKI), Jena, Germany
| | - Yitzhak Pilpel
- Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ravid Straussman
- Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - David Zeevi
- Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Petra Bacher
- Institute of Immunology, Christian-Albrecht-University of Kiel, Kiel, Germany
- Institute of Clinical Molecular Biology, Christian-Albrecht-University of Kiel, Kiel, Germany
| | - Bernhard Hube
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knoell Institute Jena (HKI), Jena, Germany
- Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Neta Shlezinger
- The Robert H. Smith Faculty of Agriculture, Food and Environment The Hebrew University of Jerusalem, Rehovot, Israel
| | - Steffen Jung
- Departments of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
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8
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McCumber AW, Kim YJ, Granek J, Tighe RM, Gunsch CK. Soil exposure modulates the immune response to an influenza challenge in a mouse model. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 922:170865. [PMID: 38340827 DOI: 10.1016/j.scitotenv.2024.170865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
There is increasing evidence that early life microbial exposure aids in immune system maturation, more recently known as the "old friends" hypothesis. To test this hypothesis, 4-week-old mice were exposed to soils of increasing microbial diversity for four weeks followed by an intranasal challenge with either live or heat inactivated influenza A virus and monitored for 7 additional days. Perturbations of the gut and lung microbiomes were explored through 16S rRNA amplicon sequencing. RNA-sequencing was used to examine the host response in the lung tissue through differential gene expression. We determined that compared to the gut microbiome, the lung microbiome is more susceptible to changes in beta diversity following soil exposure with Lachnospiraceae ASVs accounting for most of the differences between groups. While several immune system genes were found to be significantly differentially expressed in lung tissue due to soil exposures, there were no differences in viral load or weight loss. This study shows that exposure to diverse microbial communities through soil exposure alters the gut and lung microbiomes resulting in differential expression of specific immune system related genes within the lung following an influenza challenge.
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Affiliation(s)
- Alexander W McCumber
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Yeon Ji Kim
- Civil and Environmental Engineering Department, Duke University, Durham, NC, USA
| | - Joshua Granek
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Robert M Tighe
- Department of Medicine, Duke University, Durham, NC, USA
| | - Claudia K Gunsch
- Civil and Environmental Engineering Department, Duke University, Durham, NC, USA.
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9
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Bornbusch SL, Power ML, Schulkin J, Drea CM, Maslanka MT, Muletz-Wolz CR. Integrating microbiome science and evolutionary medicine into animal health and conservation. Biol Rev Camb Philos Soc 2024; 99:458-477. [PMID: 37956701 DOI: 10.1111/brv.13030] [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: 04/03/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023]
Abstract
Microbiome science has provided groundbreaking insights into human and animal health. Similarly, evolutionary medicine - the incorporation of eco-evolutionary concepts into primarily human medical theory and practice - is increasingly recognised for its novel perspectives on modern diseases. Studies of host-microbe relationships have been expanded beyond humans to include a wide range of animal taxa, adding new facets to our understanding of animal ecology, evolution, behaviour, and health. In this review, we propose that a broader application of evolutionary medicine, combined with microbiome science, can provide valuable and innovative perspectives on animal care and conservation. First, we draw on classic ecological principles, such as alternative stable states, to propose an eco-evolutionary framework for understanding variation in animal microbiomes and their role in animal health and wellbeing. With a focus on mammalian gut microbiomes, we apply this framework to populations of animals under human care, with particular relevance to the many animal species that suffer diseases linked to gut microbial dysfunction (e.g. gut distress and infection, autoimmune disorders, obesity). We discuss diet and microbial landscapes (i.e. the microbes in the animal's external environment), as two factors that are (i) proposed to represent evolutionary mismatches for captive animals, (ii) linked to gut microbiome structure and function, and (iii) potentially best understood from an evolutionary medicine perspective. Keeping within our evolutionary framework, we highlight the potential benefits - and pitfalls - of modern microbial therapies, such as pre- and probiotics, faecal microbiota transplants, and microbial rewilding. We discuss the limited, yet growing, empirical evidence for the use of microbial therapies to modulate animal gut microbiomes beneficially. Interspersed throughout, we propose 12 actionable steps, grounded in evolutionary medicine, that can be applied to practical animal care and management. We encourage that these actionable steps be paired with integration of eco-evolutionary perspectives into our definitions of appropriate animal care standards. The evolutionary perspectives proposed herein may be best appreciated when applied to the broad diversity of species under human care, rather than when solely focused on humans. We urge animal care professionals, veterinarians, nutritionists, scientists, and others to collaborate on these efforts, allowing for simultaneous care of animal patients and the generation of valuable empirical data.
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Affiliation(s)
- Sally L Bornbusch
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Ave. NW, Washington, DC, 20008, USA
- Department of Nutrition Science, Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Ave. NW, Washington, DC, 20008, USA
| | - Michael L Power
- Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Washington, 3001 Connecticut Ave. NW, Washington, DC, 20008, USA
| | - Jay Schulkin
- Department of Obstetrics & Gynecology, University of Washington School of Medicine, 1959 NE Pacific St., Box 356460, Seattle, WA, 98195, USA
| | - Christine M Drea
- Department of Evolutionary Anthropology, Duke University, 104 Biological Sciences, Campus Box 90383, Durham, NC, 27708, USA
| | - Michael T Maslanka
- Department of Nutrition Science, Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Ave. NW, Washington, DC, 20008, USA
| | - Carly R Muletz-Wolz
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, 3001 Connecticut Ave. NW, Washington, DC, 20008, USA
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10
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Vogt CC, Zipple MN, Sprockett DD, Miller CH, Hardy SX, Arthur MK, Greenstein AM, Colvin MS, Michel LM, Moeller AH, Sheehan MJ. Female behavior drives the formation of distinct social structures in C57BL/6J versus wild-derived outbred mice in field enclosures. BMC Biol 2024; 22:35. [PMID: 38355587 PMCID: PMC10865716 DOI: 10.1186/s12915-024-01809-0] [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: 11/09/2023] [Accepted: 01/02/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Social behavior and social organization have major influences on individual health and fitness. Yet, biomedical research focuses on studying a few genotypes under impoverished social conditions. Understanding how lab conditions have modified social organizations of model organisms, such as lab mice, relative to natural populations is a missing link between socioecology and biomedical science. RESULTS Using a common garden design, we describe the formation of social structure in the well-studied laboratory mouse strain, C57BL/6J, in replicated mixed-sex populations over 10-day trials compared to control trials with wild-derived outbred house mice in outdoor field enclosures. We focus on three key features of mouse social systems: (i) territory establishment in males, (ii) female social relationships, and (iii) the social networks formed by the populations. Male territorial behaviors were similar but muted in C57 compared to wild-derived mice. Female C57 sharply differed from wild-derived females, showing little social bias toward cage mates and exploring substantially more of the enclosures compared to all other groups. Female behavior consistently generated denser social networks in C57 than in wild-derived mice. CONCLUSIONS C57 and wild-derived mice individually vary in their social and spatial behaviors which scale to shape overall social organization. The repeatable societies formed under field conditions highlights opportunities to experimentally study the interplay between society and individual biology using model organisms.
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Affiliation(s)
- Caleb C Vogt
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA.
| | - Matthew N Zipple
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Daniel D Sprockett
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Caitlin H Miller
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Summer X Hardy
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Matthew K Arthur
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Adam M Greenstein
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Melanie S Colvin
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Lucie M Michel
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA
| | - Andrew H Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Michael J Sheehan
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, USA.
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11
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Yeh YW, Xiang Z. Mouse hygiene status-A tale of two environments for mast cells and allergy. Allergol Int 2024; 73:58-64. [PMID: 37673735 DOI: 10.1016/j.alit.2023.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 09/08/2023] Open
Abstract
Animal models, including those employing the use of house mice (Mus musculus), are crucial in elucidating mechanisms in human pathophysiology. However, it is evident that the impreciseness of using laboratory mice maintained in super-hygienic barrier facilities to mirror relevant aspects of human physiology and pathology exists, which is a major limitation in translating mouse findings to inferring human medicine. Interestingly, free-living wild mice are found to be substantially different from laboratory-bred, specific pathogen-free mice with respect to various immune system compartments. Wild mice have an immune system that better reflects human immunity. In this review article, we discuss recent experimental findings that address the so-called "wild immunology", which reveals the contrasting immune features between laboratory-raised mice and their wild companions as well as laboratory mice that have been exposed to a natural rodent habitat. A particular focus will be given to the development of pulmonary mast cells and its possible impact on the use of "naturalized" or "rewilded" laboratory mice as experimental asthma models.
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Affiliation(s)
- Yu-Wen Yeh
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong, China
| | - Zou Xiang
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong, China.
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12
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Downie AE, Oyesola O, Barre RS, Caudron Q, Chen YH, Dennis EJ, Garnier R, Kiwanuka K, Menezes A, Navarrete DJ, Mondragón-Palomino O, Saunders JB, Tokita CK, Zaldana K, Cadwell K, Loke P, Graham AL. Spatiotemporal-social association predicts immunological similarity in rewilded mice. SCIENCE ADVANCES 2023; 9:eadh8310. [PMID: 38134275 PMCID: PMC10745690 DOI: 10.1126/sciadv.adh8310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023]
Abstract
Environmental influences on immune phenotypes are well-documented, but our understanding of which elements of the environment affect immune systems, and how, remains vague. Behaviors, including socializing with others, are central to an individual's interaction with its environment. We therefore tracked behavior of rewilded laboratory mice of three inbred strains in outdoor enclosures and examined contributions of behavior, including associations measured from spatiotemporal co-occurrences, to immune phenotypes. We found extensive variation in individual and social behavior among and within mouse strains upon rewilding. In addition, we found that the more associated two individuals were, the more similar their immune phenotypes were. Spatiotemporal association was particularly predictive of similar memory T and B cell profiles and was more influential than sibling relationships or shared infection status. These results highlight the importance of shared spatiotemporal activity patterns and/or social networks for immune phenotype and suggest potential immunological correlates of social life.
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Affiliation(s)
- Alexander E. Downie
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Oyebola Oyesola
- Laboratory of Parasitic Diseases, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ramya S. Barre
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of Texas Health Sciences Center at San Antonio, San Antonio, TX 78229, USA
| | - Quentin Caudron
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Ying-Han Chen
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Emily J. Dennis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Romain Garnier
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Kasalina Kiwanuka
- Laboratory of Parasitic Diseases, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Arthur Menezes
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Daniel J. Navarrete
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Octavio Mondragón-Palomino
- Laboratory of Parasitic Diseases, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jesse B. Saunders
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Christopher K. Tokita
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Kimberly Zaldana
- Laboratory of Parasitic Diseases, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Ken Cadwell
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - P’ng Loke
- Laboratory of Parasitic Diseases, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrea L. Graham
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
- Santa Fe Institute, Santa Fe, NM 87501, USA
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13
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Han SJ, Stacy A, Corral D, Link VM, De Siqueira MK, Chi L, Teijeiro A, Yong DS, Perez-Chaparro PJ, Bouladoux N, Lim AI, Enamorado M, Belkaid Y, Collins N. Microbiota configuration determines nutritional immune optimization. Proc Natl Acad Sci U S A 2023; 120:e2304905120. [PMID: 38011570 PMCID: PMC10710091 DOI: 10.1073/pnas.2304905120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 09/25/2023] [Indexed: 11/29/2023] Open
Abstract
Mild or transient dietary restriction (DR) improves many aspects of health and aging. Emerging evidence from us and others has demonstrated that DR also optimizes the development and quality of immune responses. However, the factors and mechanisms involved remain to be elucidated. Here, we propose that DR-induced optimization of immunological memory requires a complex cascade of events involving memory T cells, the intestinal microbiota, and myeloid cells. Our findings suggest that DR enhances the ability of memory T cells to recruit and activate myeloid cells in the context of a secondary infection. Concomitantly, DR promotes the expansion of commensal Bifidobacteria within the large intestine, which produce the short-chain fatty acid acetate. Acetate conditioning of the myeloid compartment during DR enhances the capacity of these cells to kill pathogens. Enhanced host protection during DR is compromised when Bifidobacteria expansion is prevented, indicating that microbiota configuration and function play an important role in determining immune responsiveness to this dietary intervention. Altogether, our study supports the idea that DR induces both memory T cells and the gut microbiota to produce distinct factors that converge on myeloid cells to promote optimal pathogen control. These findings suggest that nutritional cues can promote adaptation and co-operation between multiple immune cells and the gut microbiota, which synergize to optimize immunity and protect the collective metaorganism.
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Affiliation(s)
- Seong-Ji Han
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Apollo Stacy
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Dan Corral
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Verena M. Link
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | | | - Liang Chi
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Ana Teijeiro
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Daniel S. Yong
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - P. Juliana Perez-Chaparro
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Nicolas Bouladoux
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Ai Ing Lim
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Michel Enamorado
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
| | - Nicholas Collins
- Metaorganism Immunity Section, Laboratory of Host Immunity and the Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD20892
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14
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Wan T, Wang Y, He K, Zhu S. Microbial sensing in the intestine. Protein Cell 2023; 14:824-860. [PMID: 37191444 PMCID: PMC10636641 DOI: 10.1093/procel/pwad028] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/04/2023] [Indexed: 05/17/2023] Open
Abstract
The gut microbiota plays a key role in host health and disease, particularly through their interactions with the immune system. Intestinal homeostasis is dependent on the symbiotic relationships between the host and the diverse gut microbiota, which is influenced by the highly co-evolved immune-microbiota interactions. The first step of the interaction between the host and the gut microbiota is the sensing of the gut microbes by the host immune system. In this review, we describe the cells of the host immune system and the proteins that sense the components and metabolites of the gut microbes. We further highlight the essential roles of pattern recognition receptors (PRRs), the G protein-coupled receptors (GPCRs), aryl hydrocarbon receptor (AHR) and the nuclear receptors expressed in the intestinal epithelial cells (IECs) and the intestine-resident immune cells. We also discuss the mechanisms by which the disruption of microbial sensing because of genetic or environmental factors causes human diseases such as the inflammatory bowel disease (IBD).
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Affiliation(s)
- Tingting Wan
- Division of Life Sciences and Medicine, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Institute of Immunology, School of Basic Medical Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Yalong Wang
- Division of Life Sciences and Medicine, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Institute of Immunology, School of Basic Medical Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Kaixin He
- Division of Life Sciences and Medicine, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Institute of Immunology, School of Basic Medical Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Shu Zhu
- Division of Life Sciences and Medicine, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Institute of Immunology, School of Basic Medical Sciences, University of Science and Technology of China, Hefei 230027, China
- Department of Digestive Disease, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei 230001, China
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei 230601, China
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15
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Li J, Ji Y, Chen N, Dai L, Deng H. Colitis-associated carcinogenesis: crosstalk between tumors, immune cells and gut microbiota. Cell Biosci 2023; 13:194. [PMID: 37875976 PMCID: PMC10594787 DOI: 10.1186/s13578-023-01139-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 09/21/2023] [Indexed: 10/26/2023] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer worldwide. One of the main causes of colorectal cancer is inflammatory bowel disease (IBD), which includes ulcerative colitis (UC) and Crohn's disease (CD). Intestinal epithelial cells (IECs), intestinal mesenchymal cells (IMCs), immune cells, and gut microbiota construct the main body of the colon and maintain colon homeostasis. In the development of colitis and colitis-associated carcinogenesis, the damage, disorder or excessive recruitment of different cells such as IECs, IMCs, immune cells and intestinal microbiota play different roles during these processes. This review aims to discuss the various roles of different cells and the crosstalk of these cells in transforming intestinal inflammation to cancer, which provides new therapeutic methods for chemotherapy, targeted therapy, immunotherapy and microbial therapy.
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Affiliation(s)
- Junshu Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Ke Yuan Road 4, No. 1 Gao Peng Street, Chengdu, 610041, China
| | - Yanhong Ji
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Ke Yuan Road 4, No. 1 Gao Peng Street, Chengdu, 610041, China
| | - Na Chen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Ke Yuan Road 4, No. 1 Gao Peng Street, Chengdu, 610041, China
| | - Lei Dai
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Ke Yuan Road 4, No. 1 Gao Peng Street, Chengdu, 610041, China.
| | - Hongxin Deng
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Ke Yuan Road 4, No. 1 Gao Peng Street, Chengdu, 610041, China.
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16
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Huang KY, Liang BS, Zhang XY, Chen H, Ma N, Lan JL, Li DY, Zhou ZW, Yang M. Molecular characterization of Clostridium perfringens isolates from a tertiary children's hospital in Guangzhou, China, establishing an association between bacterial colonization and food allergies in infants. Gut Pathog 2023; 15:47. [PMID: 37807056 PMCID: PMC10561448 DOI: 10.1186/s13099-023-00572-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 09/14/2023] [Indexed: 10/10/2023] Open
Abstract
BACKGROUND Cow's milk protein allergy (CMPA) is one of the most common types of food allergy in infants. Faecal pathogen cultures showed that the positive rate of Clostridium perfringens was more than 30%, which was significantly higher than that for other bacteria. Therefore, it is speculated that Clostridium perfringens colonization may be one of the pathogenetic factors for CMPA in infants. We conducted a real-world evidence study. Infants aged 0-6 months with diarrhoea and mucoid and/or bloody stools were recruited from a large tertiary hospital in China. Faecal pathogen cultures for the detection of Clostridium perfringens were confirmed by flight mass spectrometry, and potential toxin genes were identified using PCR. After 12 months of follow-up, the diagnoses of CMPA and food allergy were recorded. The correlation was assessed by Pearson correlation analysis. RESULTS In this study, 358 infants aged 0-6 months with gastrointestinal symptoms and faecal pathogen cultures were recruited. A total of 270 (44.07% girls; mean age, 2.78 ± 2.84 months) infants were followed up for 12 months. Overall, the rate of positivity for Clostridium perfringens in faecal pathogen cultures was 35.75% (128/358) in infants aged ≤ 6 months. The earliest Clostridium perfringens colonization was detected within 2 days after birth. The majority of Clostridium perfringens isolates were classified as type C in 85 stool samples. In the Clostridium perfringens-positive group, 48.21% (54/112) of infants were clinically diagnosed with food allergies after 12 months, including 37.5% (42/112) with CMPA, which was significantly higher than that of the negative group, with 7.59% (12/158) exhibiting food allergies and 5.06% (8/158) presenting CMPA (P < 0.0001). Faecal Clostridium perfringens positivity was significantly correlated with CMPA, food allergy, faecal occult blood, faecal white blood cells, antibiotic use, increased peripheral blood platelet counts, and decreased haemoglobin levels (P < 0.0001). CONCLUSIONS This study demonstrates that intestinal colonization by Clostridium perfringens is common in infants. The majority of Clostridium perfringens isolates are classified as type C. Colonization of the intestine by Clostridium perfringens is associated with the development of CMPA and food allergy in infants.
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Affiliation(s)
- Kun-Yi Huang
- Department of Gastroenterology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
- Department of Pediatrics, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Bing-Shao Liang
- Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xiao-Yan Zhang
- Department of Pediatrics, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Huan Chen
- Department of Gastroenterology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Ni Ma
- Department of Pediatrics, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Jiao-Li Lan
- Department of Pediatrics, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Ding-You Li
- Division of Gastroenterology, Children's Mercy Hospital, University of Missouri Kansas City School of Medicine, Kansas City, USA
| | - Zhen-Wen Zhou
- Clinical Laboratory, Longgang Maternity and Child Institute of Shantou University Medical College (Longgang District Maternity & Child Healthcare Hospital of Shenzhen City), Shenzhen, China.
| | - Min Yang
- Department of Gastroenterology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.
- Department of Pediatrics, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China.
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17
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Ma J, Urgard E, Runge S, Classon CH, Mathä L, Stark JM, Cheng L, Álvarez JA, von Zedtwitz S, Baleviciute A, Martinez Hoyer S, Li M, Gernand AM, Osbelt L, Bielecka AA, Lesker TR, Huang HJ, Vrtala S, Boon L, Beyaert R, Adner M, Martinez Gonzalez I, Strowig T, Du J, Nylén S, Rosshart SP, Coquet JM. Laboratory mice with a wild microbiota generate strong allergic immune responses. Sci Immunol 2023; 8:eadf7702. [PMID: 37774008 DOI: 10.1126/sciimmunol.adf7702] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 08/30/2023] [Indexed: 10/01/2023]
Abstract
Allergic disorders are caused by a combination of hereditary and environmental factors. The hygiene hypothesis postulates that early-life microbial exposures impede the development of subsequent allergic disease. Recently developed "wildling" mice are genetically identical to standard laboratory specific pathogen-free (SPF) mice but are housed under seminatural conditions and have rich microbial exposures from birth. Thus, by comparing conventional SPF mice with wildlings, we can uncouple the impact of lifelong microbial exposures from genetic factors on the allergic immune response. We found that wildlings developed larger populations of antigen-experienced T cells than conventional SPF mice, which included interleukin-10-producing CD4 T cells specific for commensal Lactobacilli strains and allergy-promoting T helper 2 (TH2) cells. In models of airway exposure to house dust mite (HDM), recombinant interleukin-33, or Alternaria alternata, wildlings developed strong allergic inflammation, characterized by eosinophil recruitment, goblet cell metaplasia, and antigen-specific immunoglobulin G1 (IgG1) and IgE responses. Wildlings developed robust de novo TH2 cell responses to incoming allergens, whereas preexisting TH2 cells could also be recruited into the allergic immune response in a cytokine-driven and TCR-independent fashion. Thus, wildling mice, which experience diverse and lifelong microbial exposures, were not protected from developing pathological allergic immune responses. Instead, wildlings mounted robust allergic responses to incoming allergens, shedding new light on the hygiene hypothesis.
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Affiliation(s)
- Junjie Ma
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Egon Urgard
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
- Leo Foundation Skin Immunology Research Centre, Department of Immunology and Microbiology, University of Copenhagen, Denmark
| | - Solveig Runge
- Department of Microbiome Research, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Cajsa H Classon
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Laura Mathä
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Julian M Stark
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Liqin Cheng
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Javiera A Álvarez
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Silvia von Zedtwitz
- Department of Medicine II, Medical Center-University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Austeja Baleviciute
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Sergio Martinez Hoyer
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Muzhen Li
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Anne Marleen Gernand
- Department of Medicine II, Medical Center-University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Lisa Osbelt
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Agata Anna Bielecka
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Till R Lesker
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Huey-Jy Huang
- Division of Immunopathology, Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology, and Immunology, Medical University of Vienna, Vienna, Austria
| | - Susanne Vrtala
- Division of Immunopathology, Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology, and Immunology, Medical University of Vienna, Vienna, Austria
| | | | - Rudi Beyaert
- VIB Centre for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Mikael Adner
- Institute of Environmental Medicine and Centre for Allergy Research, Karolinska Institutet, Stockholm, Sweden
| | - Itziar Martinez Gonzalez
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
- Center for Individualized Infection Medicine (CiiM), a joint venture between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Juan Du
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Susanne Nylén
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Stephan P Rosshart
- Department of Microbiome Research, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
- Department of Medicine II, Medical Center-University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Jonathan M Coquet
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
- Leo Foundation Skin Immunology Research Centre, Department of Immunology and Microbiology, University of Copenhagen, Denmark
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18
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Lanzer KG, Cookenham T, Lehrmann E, Zhang Y, Duso D, Xie Q, Reiley WW, Becker KG, Blackman MA. Sequential Early-Life Infections Alter Peripheral Blood Transcriptomics in Aging Female Mice but Not the Response to De Novo Infection with Influenza Virus or M. tuberculosis. Immunohorizons 2023; 7:562-576. [PMID: 37555847 PMCID: PMC10587504 DOI: 10.4049/immunohorizons.2200066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 07/07/2023] [Indexed: 08/10/2023] Open
Abstract
To determine the impact of accumulating Ag exposure on immunity in the aging mouse, and to develop a model more relevant to humans who are exposed to multiple pathogens during life, we sequentially infected young female mice with four distinct pathogens at 8-wk intervals: murine γ-herpesvirus 68, Sendai virus, murine CMV, and Heligmosomoides polygyrus. Mock-infected mice received PBS. After aging the sequentially infected and mock-infected mice to 18-25 mo under specific pathogen-free conditions, we analyzed multiple immune parameters. We assessed transcriptional activity in peripheral blood, T cell phenotype, the diversity of influenza epitopes recognized by CD8 T cells, and the response of the animals to infection with influenza virus and Mycobacterium tuberculosis. Our data show enhanced transcriptional activation in sequentially infected aged mice, with changes in some CD8 T cell subsets. However, there was no measurable difference in the response of mock-infected and sequentially infected aged mice to de novo infection with either influenza virus or M. tuberculosis at 18-21 mo. Unexpectedly, a single experiment in which 25-mo-old female mice were challenged with influenza virus revealed a significantly higher survival rate for sequentially infected (80%) versus mock-infected (20%) mice. These data suggest that although exposure to a variety of pathogen challenges in the mouse model does not overtly impact cellular markers of immunity in aged female mice following de novo respiratory infection, subtle changes may emerge in other compartments or with increasing age.
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Affiliation(s)
| | | | - Elin Lehrmann
- Computational Biology and Genomics Core, Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD
| | - Yongqing Zhang
- Computational Biology and Genomics Core, Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD
| | | | | | | | - Kevin G. Becker
- Computational Biology and Genomics Core, Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD
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19
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Chen YH, Yeung F, Lacey KA, Zaldana K, Lin JD, Bee GCW, McCauley C, Barre RS, Liang SH, Hansen CB, Downie AE, Tio K, Weiser JN, Torres VJ, Bennett RJ, Loke P, Graham AL, Cadwell K. Rewilding of laboratory mice enhances granulopoiesis and immunity through intestinal fungal colonization. Sci Immunol 2023; 8:eadd6910. [PMID: 37352372 PMCID: PMC10350741 DOI: 10.1126/sciimmunol.add6910] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 05/31/2023] [Indexed: 06/25/2023]
Abstract
The paucity of blood granulocyte populations such as neutrophils in laboratory mice is a notable difference between this model organism and humans, but the cause of this species-specific difference is unclear. We previously demonstrated that laboratory mice released into a seminatural environment, referred to as rewilding, display an increase in blood granulocytes that is associated with expansion of fungi in the gut microbiota. Here, we find that tonic signals from fungal colonization induce sustained granulopoiesis through a mechanism distinct from emergency granulopoiesis, leading to a prolonged expansion of circulating neutrophils that promotes immunity. Fungal colonization after either rewilding or oral inoculation of laboratory mice with Candida albicans induced persistent expansion of myeloid progenitors in the bone marrow. This increase in granulopoiesis conferred greater long-term protection from bloodstream infection by gram-positive bacteria than by the trained immune response evoked by transient exposure to the fungal cell wall component β-glucan. Consequently, introducing fungi into laboratory mice may restore aspects of leukocyte development and provide a better model for humans and free-living mammals that are constantly exposed to environmental fungi.
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Affiliation(s)
- Ying-Han Chen
- Kimmel Center for Biology and Medicine at the Skirball Institute
| | - Frank Yeung
- Kimmel Center for Biology and Medicine at the Skirball Institute
| | - Keenan A. Lacey
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Kimberly Zaldana
- Kimmel Center for Biology and Medicine at the Skirball Institute
| | - Jian-Da Lin
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei City, Taiwan
| | - Gavyn Chern Wei Bee
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Caroline McCauley
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Ramya S. Barre
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Shen-Huan Liang
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| | - Christina B. Hansen
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Alexander E Downie
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Kyle Tio
- Kimmel Center for Biology and Medicine at the Skirball Institute
| | - Jeffrey N. Weiser
- Antimicrobial-Resistant Pathogens Program
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Victor J Torres
- Antimicrobial-Resistant Pathogens Program
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Richard J. Bennett
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| | - P’ng Loke
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrea L. Graham
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Ken Cadwell
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
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20
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Oyesola O, Downie AE, Howard N, Barre RS, Kiwanuka K, Zaldana K, Chen YH, Menezes A, Lee SC, Devlin J, Mondragón-Palomino O, Souza COS, Herrmann C, Koralov S, Cadwell K, Graham AL, Loke P. Genetic and Environmental interactions contribute to immune variation in rewilded mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.533121. [PMID: 36993484 PMCID: PMC10055251 DOI: 10.1101/2023.03.17.533121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
The relative and synergistic contributions of genetics and environment to inter-individual immune response variation remain unclear, despite its implications for understanding both evolutionary biology and medicine. Here, we quantify interactive effects of genotype and environment on immune traits by investigating three inbred mouse strains rewilded in an outdoor enclosure and infected with the parasite, Trichuris muris. Whereas cytokine response heterogeneity was primarily driven by genotype, cellular composition heterogeneity was shaped by interactions between genotype and environment. Notably, genetic differences under laboratory conditions can be decreased following rewilding, and variation in T cell markers are more driven by genetics, whereas B cell markers are driven more by environment. Importantly, variation in worm burden is associated with measures of immune variation, as well as genetics and environment. These results indicate that nonheritable influences interact with genetic factors to shape immune variation, with synergistic impacts on the deployment and evolution of defense mechanisms.
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Affiliation(s)
- Oyebola Oyesola
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institute of Health; Bethesda, MD, USA
| | - Alexander E. Downie
- Department of Ecology and Evolutionary Biology, Princeton University; Princeton, NJ, USA
| | - Nina Howard
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institute of Health; Bethesda, MD, USA
| | - Ramya S. Barre
- Department of Ecology and Evolutionary Biology, Princeton University; Princeton, NJ, USA
| | - Kasalina Kiwanuka
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institute of Health; Bethesda, MD, USA
| | - Kimberly Zaldana
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institute of Health; Bethesda, MD, USA
| | - Ying-Han Chen
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University, Grossman School of Medicine; New York, NY, USA
| | - Arthur Menezes
- Department of Ecology and Evolutionary Biology, Princeton University; Princeton, NJ, USA
| | - Soo Ching Lee
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institute of Health; Bethesda, MD, USA
| | - Joseph Devlin
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University, Grossman School of Medicine; New York, NY, USA
| | - Octavio Mondragón-Palomino
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institute of Health; Bethesda, MD, USA
| | - Camila Oliveira Silva Souza
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institute of Health; Bethesda, MD, USA
| | - Christin Herrmann
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University, Grossman School of Medicine; New York, NY, USA
| | - Sergei Koralov
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University, Grossman School of Medicine; New York, NY, USA
| | - Ken Cadwell
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University, Grossman School of Medicine; New York, NY, USA
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Andrea L. Graham
- Department of Ecology and Evolutionary Biology, Princeton University; Princeton, NJ, USA
- Santa Fe Institute, Santa Fe, NM, USA
| | - P’ng Loke
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institute of Health; Bethesda, MD, USA
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21
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Abstract
Immunity to infection has been extensively studied in humans and mice bearing naturally occurring or experimentally introduced germline mutations. Mouse studies are sometimes neglected by human immunologists, on the basis that mice are not humans and the infections studied are experimental and not natural. Conversely, human studies are sometimes neglected by mouse immunologists, on the basis of the uncontrolled conditions of study and small numbers of patients. However, both sides would agree that the infectious phenotypes of patients with inborn errors of immunity often differ from those of the corresponding mutant mice. Why is that? We argue that this important question is best addressed by revisiting and reinterpreting the findings of both mouse and human studies from a genetic perspective. Greater caution is required for reverse-genetics studies than for forward-genetics studies, but genetic analysis is sufficiently strong to define the studies likely to stand the test of time. Genetically robust mouse and human studies can provide invaluable complementary insights into the mechanisms of immunity to infection common and specific to these two species.
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Affiliation(s)
- Philippe Gros
- McGill University Research Center on Complex Traits, Department of Biochemistry, and Department of Human Genetics, McGill University, Montréal, Québec, Canada;
| | - Jean-Laurent Casanova
- Howard Hughes Medical Institute and St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA;
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, and University of Paris Cité, Imagine Institute and Necker Hospital for Sick Children, Paris, France
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22
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Downie AE, Oyesola O, Barre RS, Caudron Q, Chen YH, Dennis EJ, Garnier R, Kiwanuka K, Menezes A, Navarrete DJ, Mondragón-Palomino O, Saunders JB, Tokita CK, Zaldana K, Cadwell K, Loke P, Graham AL. Social association predicts immunological similarity in rewilded mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.15.532825. [PMID: 36993264 PMCID: PMC10055139 DOI: 10.1101/2023.03.15.532825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Environmental influences on immune phenotypes are well-documented, but our understanding of which elements of the environment affect immune systems, and how, remains vague. Behaviors, including socializing with others, are central to an individual's interaction with its environment. We tracked behavior of rewilded laboratory mice of three inbred strains in outdoor enclosures and examined contributions of behavior, including social associations, to immune phenotypes. We found that the more associated two individuals were, the more similar their immune phenotypes were. Social association was particularly predictive of similar memory T and B cell profiles and was more influential than sibling relationships or worm infection status. These results highlight the importance of social networks for immune phenotype and reveal important immunological correlates of social life.
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Affiliation(s)
- A. E. Downie
- Department of Ecology and Evolutionary Biology, Princeton University; Princeton, NJ 08544, USA
| | - O. Oyesola
- Laboratory of Parasitic Diseases, National Institute for Allergy and Infectious Diseases, National Institutes of Health; Bethesda, MD 20892, USA
| | - R. S. Barre
- Department of Ecology and Evolutionary Biology, Princeton University; Princeton, NJ 08544, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of Texas Health Sciences Center at San Antonio; San Antonio, TX 78229, USA
| | - Q. Caudron
- Department of Ecology and Evolutionary Biology, Princeton University; Princeton, NJ 08544, USA
| | - Y.-H. Chen
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine; New York, NY 10016, USA
| | - E. J. Dennis
- Janelia Research Campus, Howard Hughes Medical Institute; Ashburn, VA 20147, USA
| | - R. Garnier
- Department of Ecology and Evolutionary Biology, Princeton University; Princeton, NJ 08544, USA
| | - K. Kiwanuka
- Laboratory of Parasitic Diseases, National Institute for Allergy and Infectious Diseases, National Institutes of Health; Bethesda, MD 20892, USA
| | - A. Menezes
- Department of Ecology and Evolutionary Biology, Princeton University; Princeton, NJ 08544, USA
| | - D. J. Navarrete
- Department of Ecology and Evolutionary Biology, Princeton University; Princeton, NJ 08544, USA
- Department of Microbiology and Immunology, School of Medicine, Stanford University; Stanford, CA 94305, USA
| | - O. Mondragón-Palomino
- Laboratory of Parasitic Diseases, National Institute for Allergy and Infectious Diseases, National Institutes of Health; Bethesda, MD 20892, USA
| | - J. B. Saunders
- Department of Ecology and Evolutionary Biology, Princeton University; Princeton, NJ 08544, USA
| | - C. K. Tokita
- Department of Ecology and Evolutionary Biology, Princeton University; Princeton, NJ 08544, USA
| | - K. Zaldana
- Laboratory of Parasitic Diseases, National Institute for Allergy and Infectious Diseases, National Institutes of Health; Bethesda, MD 20892, USA
- Department of Microbiology, New York University Grossman School of Medicine; New York, NY 10016, USA
| | - K. Cadwell
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine; New York, NY 10016, USA
- Department of Microbiology, New York University Grossman School of Medicine; New York, NY 10016, USA
- Division of Gastroenterology and Hepatology, Department of Medicine, New York University Grossman School of Medicine; New York, NY 10016, USA
| | - P. Loke
- Laboratory of Parasitic Diseases, National Institute for Allergy and Infectious Diseases, National Institutes of Health; Bethesda, MD 20892, USA
| | - A. L. Graham
- Department of Ecology and Evolutionary Biology, Princeton University; Princeton, NJ 08544, USA
- Santa Fe Institute; Santa Fe, NM 87501, USA
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23
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Shim JA, Ryu JH, Jo Y, Hong C. The role of gut microbiota in T cell immunity and immune mediated disorders. Int J Biol Sci 2023; 19:1178-1191. [PMID: 36923929 PMCID: PMC10008692 DOI: 10.7150/ijbs.79430] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/23/2023] [Indexed: 03/14/2023] Open
Abstract
Gut microbiota was only considered as a commensal organism that aids in digestion, but recent studies revealed that the microbiome play a critical role in both physiological and pathological immune system. The gut microbiome composition is altered by environmental factors such as diet and hygiene, and the alteration affects immune cells, especially T cells. Advanced genomic techniques in microbiome research defined that specific microbes regulate T cell responses and the pathogenesis of immune-mediated disorders. Here, we review features of specific microbes-T cell crosstalk and relationship between the microbes and immunopathogenesis of diseases including in cancers, autoimmune disorders and allergic inflammations. We also discuss the limitations of current experimental animal models, cutting-edge developments and current challenges to overcome in the field, and the possibility of considering gut microbiome in the development of new drug.
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Affiliation(s)
- Ju A Shim
- Department of Anatomy, Pusan National University School of Medicine, Yangsan 50612, Republic of Korea
| | - Jeong Ha Ryu
- Department of Anatomy, Pusan National University School of Medicine, Yangsan 50612, Republic of Korea.,PNU GRAND Convergence Medical Science Education Research Center, Pusan National University School of Medicine, Yangsan 50612, Republic of Korea
| | - Yuna Jo
- Department of Anatomy, Pusan National University School of Medicine, Yangsan 50612, Republic of Korea
| | - Changwan Hong
- Department of Anatomy, Pusan National University School of Medicine, Yangsan 50612, Republic of Korea.,PNU GRAND Convergence Medical Science Education Research Center, Pusan National University School of Medicine, Yangsan 50612, Republic of Korea
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24
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Li P, Ma X, Liu D, Wei Y, Li P, Hou H, Yao J, Chen A, Liang Y, Zhou Z, Wang P. A microbiome abundant environment remodels the intestinal microbiota and improves resistance to obesity induced by chlorpyrifos in mice. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 315:120415. [PMID: 36257564 DOI: 10.1016/j.envpol.2022.120415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/23/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
There is a growing consensus that the appropriate microbiome abundant environment actuates microbiota changes to influence human health. Whether living environment reacts on the threat of contaminants and the underlying mechanism remain largely unknown. Therefore, we constructed microbiome abundant environment models, focusing on their regulatory effects on the obesity induced by the exogenous chemical chlorpyrifos (CPF) and the related mechanisms. The results uncovered that the constructed farm and woodland microbiome abundant environment could protect mice against CPF-induced obesity effectively. The microbiome abundant environment regulated CPF-induced microbiota imbalance, characterized by an increase in Lactobacillus abundance. These altered microbiotas modified the intestinal immune system by increasing the expression of Foxp3 and IL-10, and mitigated intestinal barrier injury by upregulating the expression of IL-22 and intestinal tight junction proteins. Fecal microbiota transplantation could receive similar phenotypes on alleviating CPF-induced obesity development. Our results demonstrate that the microbiome abundant environment attenuates exogenous chemical-induced health risks by remodeling the intestinal microbiota, improving the intestinal ecosystem, and preventing intestinal epithelial leakage.
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Affiliation(s)
- Peize Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Science, China Agricultural University, No. 2, West Yuanmingyuan Road, Beijing, 100193, China
| | - Xiaoran Ma
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Science, China Agricultural University, No. 2, West Yuanmingyuan Road, Beijing, 100193, China
| | - Donghui Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Science, China Agricultural University, No. 2, West Yuanmingyuan Road, Beijing, 100193, China
| | - Yimu Wei
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Science, China Agricultural University, No. 2, West Yuanmingyuan Road, Beijing, 100193, China
| | - Pengxi Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Science, China Agricultural University, No. 2, West Yuanmingyuan Road, Beijing, 100193, China
| | - Haonan Hou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Science, China Agricultural University, No. 2, West Yuanmingyuan Road, Beijing, 100193, China
| | - Jianing Yao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Science, China Agricultural University, No. 2, West Yuanmingyuan Road, Beijing, 100193, China
| | - Aisong Chen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Science, China Agricultural University, No. 2, West Yuanmingyuan Road, Beijing, 100193, China
| | - Yiran Liang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Science, China Agricultural University, No. 2, West Yuanmingyuan Road, Beijing, 100193, China
| | - Zhiqiang Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Science, China Agricultural University, No. 2, West Yuanmingyuan Road, Beijing, 100193, China
| | - Peng Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Science, China Agricultural University, No. 2, West Yuanmingyuan Road, Beijing, 100193, China.
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25
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Into the wild: How exposure to wild or domesticated fungi shapes immune responses in mice. PLoS Pathog 2022; 18:e1010841. [PMID: 36227856 PMCID: PMC9562158 DOI: 10.1371/journal.ppat.1010841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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26
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Olatunde AC, Cornwall DH, Roedel M, Lamb TJ. Mouse Models for Unravelling Immunology of Blood Stage Malaria. Vaccines (Basel) 2022; 10:1525. [PMID: 36146602 PMCID: PMC9501382 DOI: 10.3390/vaccines10091525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 11/16/2022] Open
Abstract
Malaria comprises a spectrum of disease syndromes and the immune system is a major participant in malarial disease. This is particularly true in relation to the immune responses elicited against blood stages of Plasmodium-parasites that are responsible for the pathogenesis of infection. Mouse models of malaria are commonly used to dissect the immune mechanisms underlying disease. While no single mouse model of Plasmodium infection completely recapitulates all the features of malaria in humans, collectively the existing models are invaluable for defining the events that lead to the immunopathogenesis of malaria. Here we review the different mouse models of Plasmodium infection that are available, and highlight some of the main contributions these models have made with regards to identifying immune mechanisms of parasite control and the immunopathogenesis of malaria.
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Affiliation(s)
| | | | | | - Tracey J. Lamb
- Department of Pathology, University of Utah, Emma Eccles Jones Medical Research Building, 15 N Medical Drive E, Room 1420A, Salt Lake City, UT 84112, USA
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27
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Berton RR, Jensen IJ, Harty JT, Griffith TS, Badovinac VP. Inflammation Controls Susceptibility of Immune-Experienced Mice to Sepsis. Immunohorizons 2022; 6:528-542. [PMID: 35878936 PMCID: PMC9650784 DOI: 10.4049/immunohorizons.2200050] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 06/30/2022] [Indexed: 11/19/2022] Open
Abstract
Sepsis, an amplified immune response to systemic infection that leads to life-threatening organ dysfunction, affects >125,000 people/day worldwide with 20% mortality. Modest therapeutic progress for sepsis has been made, in part because of the lack of therapeutic translatability between mouse-based experimental models and humans. One potential reason for this difference stems from the extensive use of immunologically naive specific pathogen-free mice in preclinical research. To address this issue, we used sequential infections with well-defined BSL-2 pathogens to establish a novel immune-experienced mouse model (specific pathogen experienced [SPexp]) to determine the extent to which immunological experience and/or inflammation influences the host capacity to respond to subsequent infections, including sepsis. Consistent with their immunological experience, SPexp inbred or outbred mice had significant changes in the composition and activation status of multiple leukocyte populations known to influence the severity of cecal ligation and puncture-induced sepsis. Importantly, by varying the timing of sepsis induction, we found the level of basal inflammation controls sepsis-induced morbidity and mortality in SPexp mice. In addition, although a beneficial role of NK cells in sepsis was recently demonstrated in specific pathogen-free mice, NK cell depletion before cecal ligation and puncture induction in SPexp mice lead to diminished mortality, suggesting NK cells may have beneficial or detrimental roles in the response to septic insult dependent on host immune status. Thus, data highlight the importance of utilizing immune-experienced models for preclinical studies to interrogate the cellular/molecular mechanism(s) that could be therapeutically exploited during severe and dysregulated infection-induced inflammatory responses, such as sepsis.
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Affiliation(s)
- Roger R Berton
- Department of Pathology, University of Iowa, Iowa City, IA.,Interdisciplinary Program in Immunology, University of Iowa, Iowa City, IA
| | - Isaac J Jensen
- Department of Pathology, University of Iowa, Iowa City, IA.,Interdisciplinary Program in Immunology, University of Iowa, Iowa City, IA.,Department of Microbiology and Immunology, Columbia University, New York, NY
| | - John T Harty
- Department of Pathology, University of Iowa, Iowa City, IA.,Interdisciplinary Program in Immunology, University of Iowa, Iowa City, IA
| | - Thomas S Griffith
- Department of Urology, University of Minnesota, Minneapolis, MN; and.,Minneapolis VA Health Care System, Minneapolis, MN
| | - Vladimir P Badovinac
- Department of Pathology, University of Iowa, Iowa City, IA; .,Interdisciplinary Program in Immunology, University of Iowa, Iowa City, IA
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28
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Abstract
Animal models are a critical tool in modern biology. To increase reproducibility and to reduce confounding variables modern animal models exclude many microbes, including key natural commensals and pathogens. Here we discuss recent strategies to incorporate a natural microbiota to laboratory mouse models and the impacts the microbiota has on immune responses, with a focus on viruses.
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Affiliation(s)
- Jessica K Fiege
- Department of Microbiology and Immunology and the Center for Immunology, University of Minnesota, Minneapolis, USA
| | - Ryan A Langlois
- Department of Microbiology and Immunology and the Center for Immunology, University of Minnesota, Minneapolis, USA
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29
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Loke P, Lee SC, Oyesola OO. Effects of helminths on the human immune response and the microbiome. Mucosal Immunol 2022; 15:1224-1233. [PMID: 35732819 DOI: 10.1038/s41385-022-00532-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/17/2022] [Accepted: 05/22/2022] [Indexed: 02/04/2023]
Abstract
Helminths have evolved sophisticated immune regulating mechanisms to prevent rejection by their mammalian host. Our understanding of how the human immune system responds to these parasites remains poor compared to mouse models of infection and this limits our ability to develop vaccines as well as harness their unique properties as therapeutic strategies against inflammatory disorders. Here, we review how recent studies on human challenge infections, self-infected individuals, travelers, and endemic populations have improved our understanding of human type 2 immunity and its effects on the microbiome. The heterogeneity of responses between individuals and the limited access to tissue samples beyond the peripheral blood are challenges that limit human studies on helminths, but also provide opportunities to transform our understanding of human immunology. Organoids and single-cell sequencing are exciting new tools for immunological analysis that may aid this pursuit. Learning about the genetic and immunological basis of resistance, tolerance, and pathogenesis to helminth infections may thus uncover mechanisms that can be utilized for therapeutic purposes.
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Affiliation(s)
- P'ng Loke
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Soo Ching Lee
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Oyebola O Oyesola
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
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30
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Shao TY, Kakade P, Witchley JN, Frazer C, Murray KL, Ene IV, Haslam DB, Hagan T, Noble SM, Bennett RJ, Way SS. Candida albicans oscillating UME6 expression during intestinal colonization primes systemic Th17 protective immunity. Cell Rep 2022; 39:110837. [PMID: 35584674 PMCID: PMC9196946 DOI: 10.1016/j.celrep.2022.110837] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 03/23/2022] [Accepted: 04/27/2022] [Indexed: 01/09/2023] Open
Abstract
Systemic immunity is stringently regulated by commensal intestinal microbes, including the pathobiont Candida albicans. This fungus utilizes various transcriptional and morphological programs for host adaptation, but how this heterogeneity affects immunogenicity remains uncertain. We show that UME6, a transcriptional regulator of filamentation, is essential for intestinal C. albicans-primed systemic Th17 immunity. UME6 deletion and constitutive overexpression strains are non-immunogenic during commensal colonization, whereas immunogenicity is restored by C. albicans undergoing oscillating UME6 expression linked with β-glucan and mannan production. In turn, intestinal reconstitution with these fungal cell wall components restores protective Th17 immunity to mice colonized with UME6-locked variants. These fungal cell wall ligands and commensal C. albicans stimulate Th17 immunity through multiple host pattern recognition receptors, including Toll-like receptor 2 (TLR2), TLR4, Dectin-1, and Dectin-2, which work synergistically for colonization-induced protection. Thus, dynamic gene expression fluctuations by C. albicans during symbiotic colonization are essential for priming host immunity against disseminated infection.
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Affiliation(s)
- Tzu-Yu Shao
- Division of Infectious Diseases, Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Immunobiology Graduate Program, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Pallavi Kakade
- Molecular Microbiology and Immunology Department, Brown University, Providence, RI 02912, USA
| | - Jessica N Witchley
- Department of Microbiology and Immunology, University of California, San Francisco School of Medicine, San Francisco, CA 94143, USA
| | - Corey Frazer
- Molecular Microbiology and Immunology Department, Brown University, Providence, RI 02912, USA
| | - Kathryn L Murray
- Division of Infectious Diseases, Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Iuliana V Ene
- Fungal Heterogeneity Lab, Institut Pasteur, Université Paris Cité, 75015 Paris, France
| | - David B Haslam
- Division of Infectious Diseases, Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Thomas Hagan
- Division of Infectious Diseases, Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Suzanne M Noble
- Department of Microbiology and Immunology, University of California, San Francisco School of Medicine, San Francisco, CA 94143, USA
| | - Richard J Bennett
- Molecular Microbiology and Immunology Department, Brown University, Providence, RI 02912, USA
| | - Sing Sing Way
- Division of Infectious Diseases, Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.
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Friend virus severity is associated with male mouse social status and environmental temperature. Anim Behav 2022; 187:221-231. [PMID: 35602411 PMCID: PMC9119425 DOI: 10.1016/j.anbehav.2022.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Pathogen virulence is highly variable within populations, and although many factors contributing to virulence differences are known, there is still much variation left unexplained. Identifying and characterizing environmental conditions associated with different virulence levels is therefore an important undertaking in infectious disease research. One factor considered to be a major determinant of overall health and susceptibility to disease in social animals is social status. Health differences associated with social status are thought to be caused by different levels of chronic stress in higher- versus lower-status individuals. There is considerable evidence that these effects extend to the standing immune profile and that social status directly influences susceptibility to pathogens. Here we examined the association between dominance status in male wild-derived house mice, Mus musculus, and susceptibility to Friend virus complex in the context of seminatural populations with intense male-male competition and no predation. Due to an interruption in our facility's heating system, we were unexpectedly presented with the opportunity to assess how reduced ambient temperature influences the association of host social status and pathogen virulence. Environmental temperature has been implicated as a contributor to pathogen virulence, giving us a unique chance to examine its role in a previously unexamined pathogen system, while the added context of social status can expand our understanding of how the interaction of different environmental conditions affects virulence. We found that pathogen virulence and replication were lower in socially dominant hosts compared to nondominant hosts. When temperature was reduced, cool enclosure-housed dominant males were more susceptible to infection than their warm enclosure-housed counterparts. The mechanistic underpinnings that link infectious disease and social status remain difficult to disentangle from their associated factors, but this study opens the door for future experiments using a novel approach in the most well-studied mammalian model available.
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Oyesola OO, Souza COS, Loke P. The Influence of Genetic and Environmental Factors and Their Interactions on Immune Response to Helminth Infections. Front Immunol 2022; 13:869163. [PMID: 35572520 PMCID: PMC9103684 DOI: 10.3389/fimmu.2022.869163] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 04/04/2022] [Indexed: 12/20/2022] Open
Abstract
Helminth infection currently affect over 2 billion people worldwide, with those with the most pathologies and morbidities, living in regions with unequal and disproportionate access to effective healthcare solutions. Host genetics and environmental factors play critical roles in modulating and regulating immune responses following exposure to various pathogens and insults. However, the interplay of environment and genetic factors in influencing who gets infected and the establishment, persistence, and clearance of helminth parasites remains unclear. Inbred strains of mice have long been used to investigate the role of host genetic factors on pathogenesis and resistance to helminth infection in a laboratory setting. This review will discuss the use of ecological and environmental mouse models to study helminth infections and how this could be used in combination with host genetic variation to explore the relative contribution of these factors in influencing immune response to helminth infections. Improved understanding of interactions between genetics and the environment to helminth immune responses would be important for efforts to identify and develop new prophylactic and therapeutic options for the management of helminth infections and their pathogenesis.
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Affiliation(s)
- Oyebola O. Oyesola
- Laboratory of Parasitic Disease, National Institute of Allergy and Infectious Disease (NIAID), National Institute of Health, Bethesda, MD, United States
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33
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Regulation of tissue-resident memory T cells by the Microbiota. Mucosal Immunol 2022; 15:408-417. [PMID: 35194180 PMCID: PMC9063729 DOI: 10.1038/s41385-022-00491-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 02/04/2023]
Abstract
Resident memory T cells (Trms) predominantly reside within tissue and are critical for providing rapid protection against invasive viruses, fungi and bacteria. Given that tissues are heavily impacted and shaped by the microbiota, it stands to reason that Trms are also influenced by the microbiota that inhabits barrier sites. The influence of the microbiota is largely mediated by microbial production of metabolites which are crucial to the immune response to both viral infection and cancerous tumors. In addition to the effects of metabolites, antigens derived from the microbiota can activate T cell responses. While microbiota-specific T cells may assist in tissue repair, control of infection and anti-tumor immunity, the actual 'memory' potential of these cells remains unclear. Here, we hypothesize that memory responses to antigens from the microbiota must be 'licensed' by inflammatory signals activated by invasion of the host by microorganisms.
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34
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Herrmann C, Cadwell K. Playing dirty with virus transmission. J Exp Med 2022; 219:e20212358. [PMID: 34962567 PMCID: PMC8717928 DOI: 10.1084/jem.20212358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In this issue of JEM, Fay et al. (2021. J. Exp. Med.https://doi.org/10.1084/jem.20211220) cohouse dirty pet store mice and rats with clean laboratory mice to gain insights into infection dynamics, discover new viruses, and identify relationships between viruses and the microbiome.
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Affiliation(s)
- Christin Herrmann
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman University School of Medicine, New York, NY
| | - Ken Cadwell
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman University School of Medicine, New York, NY
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY
- Division of Gastroenterology and Hepatology, Department of Medicine, New York University Grossman School of Medicine, New York, NY
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35
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Chiang E, Deblois CL, Carey HV, Suen G. Characterization of captive and wild 13-lined ground squirrel cecal microbiotas using Illumina-based sequencing. Anim Microbiome 2022; 4:1. [PMID: 34980290 PMCID: PMC8722175 DOI: 10.1186/s42523-021-00154-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/12/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Hibernating animals experience extreme changes in diet that make them useful systems for understanding host-microbial symbioses. However, most of our current knowledge about the hibernator gut microbiota is derived from studies using captive animals. Given that there are substantial differences between captive and wild environments, conclusions drawn from studies with captive hibernators may not reflect the gut microbiota's role in the physiology of wild animals. To address this, we used Illumina-based sequencing of the 16S rRNA gene to compare the bacterial cecal microbiotas of captive and wild 13-lined ground squirrels (TLGS) in the summer. As the first study to use Illumina-based technology to compare the microbiotas of an obligate rodent hibernator across the year, we also reported changes in captive TLGS microbiotas in summer, winter, and spring. RESULTS Wild TLGS microbiotas had greater richness and phylogenetic diversity with less variation in beta diversity when compared to captive microbiotas. Taxa identified as core operational taxonomic units (OTUs) and found to significantly contribute to differences in beta diversity were primarily in the families Lachnospiraceae and Ruminococcaceae. Captive TLGS microbiotas shared phyla and core OTUs across the year, but active season (summer and spring) microbiotas had different alpha and beta diversities than winter season microbiotas. CONCLUSIONS This is the first study to compare the microbiotas of captive and wild rodent hibernators. Our findings suggest that data from captive and wild ground squirrels should be interpreted separately due to their distinct microbiotas. Additionally, as the first study to compare seasonal microbiotas of obligate rodent hibernators using Illumina-based 16S rRNA sequencing, we reported changes in captive TLGS microbiotas that are consistent with previous work. Taken together, this study provides foundational information for improving the reproducibility and experimental design of future hibernation microbiota studies.
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Affiliation(s)
- Edna Chiang
- Microbiology Doctoral Training Program, Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Courtney L. Deblois
- Microbiology Doctoral Training Program, Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Hannah V. Carey
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Garret Suen
- Present Address: Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
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36
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Wahida A, Müller M, Hiergeist A, Popper B, Steiger K, Branca C, Tschurtschenthaler M, Engleitner T, Donakonda S, De Coninck J, Öllinger R, Pfautsch MK, Müller N, Silva M, Usluer S, Thiele Orberg E, Böttcher JP, Pfarr N, Anton M, Slotta-Huspenina JB, Nerlich AG, Madl T, Basic M, Bleich A, Berx G, Ruland J, Knolle PA, Rad R, Adolph TE, Vandenabeele P, Kanegane H, Gessner A, Jost PJ, Yabal M. XIAP restrains TNF-driven intestinal inflammation and dysbiosis by promoting innate immune responses of Paneth and dendritic cells. Sci Immunol 2021; 6:eabf7235. [PMID: 34739338 DOI: 10.1126/sciimmunol.abf7235] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Deficiency in X-linked inhibitor of apoptosis protein (XIAP) is the cause for X-linked lymphoproliferative syndrome 2 (XLP2). About one-third of these patients suffer from severe and therapy-refractory inflammatory bowel disease (IBD), but the exact cause of this pathogenesis remains undefined. Here, we used XIAP-deficient mice to characterize the mechanisms underlying intestinal inflammation. In Xiap−/− mice, we observed spontaneous terminal ileitis and microbial dysbiosis characterized by a reduction of Clostridia species. We showed that in inflamed mice, both TNF receptor 1 and 2 (TNFR1/2) cooperated in promoting ileitis by targeting TLR5-expressing Paneth cells (PCs) or dendritic cells (DCs). Using intestinal organoids and in vivo modeling, we demonstrated that TLR5 signaling triggered TNF production, which induced PC dysfunction mediated by TNFR1. TNFR2 acted upon lamina propria immune cells. scRNA-seq identified a DC population expressing TLR5, in which Tnfr2 expression was also elevated. Thus, the combined activity of TLR5 and TNFR2 signaling may be responsible for DC loss in lamina propria of Xiap−/− mice. Consequently, both Tnfr1−/−Xiap−/− and Tnfr2−/−Xiap−/− mice were rescued from dysbiosis and intestinal inflammation. Furthermore, RNA-seq of ileal crypts revealed that in inflamed Xiap−/− mice, TLR5 signaling was abrogated, linking aberrant TNF responses with the development of a dysbiosis. Evidence for TNFR2 signaling driving intestinal inflammation was detected in XLP2 patient samples. Together, these data point toward a key role of XIAP in mediating resilience of TLR5-expressing PCs and intestinal DCs, allowing them to maintain tissue integrity and microbiota homeostasis.
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MESH Headings
- Animals
- Dendritic Cells/immunology
- Dysbiosis/immunology
- Humans
- Immunity, Innate/immunology
- Inflammation/immunology
- Intestines/immunology
- Mice
- Mice, Knockout
- Paneth Cells/immunology
- Receptors, Tumor Necrosis Factor, Type I/deficiency
- Receptors, Tumor Necrosis Factor, Type I/immunology
- Receptors, Tumor Necrosis Factor, Type II/deficiency
- Receptors, Tumor Necrosis Factor, Type II/immunology
- Toll-Like Receptor 5/immunology
- X-Linked Inhibitor of Apoptosis Protein/deficiency
- X-Linked Inhibitor of Apoptosis Protein/immunology
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Affiliation(s)
- Adam Wahida
- Medical Department III for Hematology and Oncology, TUM School of Medicine, Technical University of Munich, Munich, Germany
- TranslaTUM, Center for Translational Cancer Research, Munich, Germany
| | - Madeleine Müller
- Institute of Molecular Immunology and Experimental Oncology, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Andreas Hiergeist
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Bastian Popper
- Biomedical Center, Core Facility Animal Models, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
| | - Katja Steiger
- Institute of Pathology and Pathological Anatomy, Technical University of Munich, Munich, Germany
- Comparative Experimental Pathology and Digital Pathology, Institute for Pathology and Pathological Anatomy, Technical University of Munich, Munich, Germany
| | - Caterina Branca
- Medical Department III for Hematology and Oncology, TUM School of Medicine, Technical University of Munich, Munich, Germany
- TranslaTUM, Center for Translational Cancer Research, Munich, Germany
| | - Markus Tschurtschenthaler
- TranslaTUM, Center for Translational Cancer Research, Munich, Germany
- Institute of Translational Cancer Research and Experimental Cancer Therapy, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Thomas Engleitner
- TranslaTUM, Center for Translational Cancer Research, Munich, Germany
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Sainitin Donakonda
- Institute of Molecular Immunology and Experimental Oncology, TUM School of Medicine, Technical University of Munich, Munich, Germany
- German Center for Infection Research (DZIF), Munich, Germany
| | - Jordy De Coninck
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Rupert Öllinger
- TranslaTUM, Center for Translational Cancer Research, Munich, Germany
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Marie K Pfautsch
- Institute of Molecular Immunology and Experimental Oncology, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Nicole Müller
- Medical Department III for Hematology and Oncology, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Miguel Silva
- TranslaTUM, Center for Translational Cancer Research, Munich, Germany
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Sinem Usluer
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
| | - Erik Thiele Orberg
- Medical Department III for Hematology and Oncology, TUM School of Medicine, Technical University of Munich, Munich, Germany
- TranslaTUM, Center for Translational Cancer Research, Munich, Germany
| | - Jan P Böttcher
- Institute of Molecular Immunology and Experimental Oncology, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Nicole Pfarr
- Institute of Pathology and Pathological Anatomy, Technical University of Munich, Munich, Germany
| | - Martina Anton
- Institute of Molecular Immunology and Experimental Oncology, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Julia B Slotta-Huspenina
- Institute of Pathology and Pathological Anatomy, Technical University of Munich, Munich, Germany
| | - Andreas G Nerlich
- Institute of Pathology, Academic Clinic Munich-Bogenhausen, Munich, Germany
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
| | - Marijana Basic
- Institute for Laboratory Animal Science and Central Animal Facility, Hannover Medical School, Hannover, Germany
| | - André Bleich
- Institute for Laboratory Animal Science and Central Animal Facility, Hannover Medical School, Hannover, Germany
| | - Geert Berx
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Jürgen Ruland
- TranslaTUM, Center for Translational Cancer Research, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Percy A Knolle
- Institute of Molecular Immunology and Experimental Oncology, TUM School of Medicine, Technical University of Munich, Munich, Germany
- German Center for Infection Research (DZIF), Munich, Germany
| | - Roland Rad
- TranslaTUM, Center for Translational Cancer Research, Munich, Germany
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Timon E Adolph
- Department of Internal Medicine I for Gastroenterology, Hepatology, and Endocrinology, Medical University of Innsbruck, Innsbruck, Austria
| | - Peter Vandenabeele
- Cell Death and Inflammation Unit, VIB-Center for Inflammation Research (IRC), VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, Belgium
| | - Hirokazu Kanegane
- Department of Child Health and Development, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - André Gessner
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Philipp J Jost
- Medical Department III for Hematology and Oncology, TUM School of Medicine, Technical University of Munich, Munich, Germany
- Division of Clinical Oncology, Department of Medicine, Medical University of Graz, Graz, Austria
| | - Monica Yabal
- Institute of Molecular Immunology and Experimental Oncology, TUM School of Medicine, Technical University of Munich, Munich, Germany
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37
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Fiege JK, Block KE, Pierson MJ, Nanda H, Shepherd FK, Mickelson CK, Stolley JM, Matchett WE, Wijeyesinghe S, Meyerholz DK, Vezys V, Shen SS, Hamilton SE, Masopust D, Langlois RA. Mice with diverse microbial exposure histories as a model for preclinical vaccine testing. Cell Host Microbe 2021; 29:1815-1827.e6. [PMID: 34731647 DOI: 10.1016/j.chom.2021.10.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 08/30/2021] [Accepted: 10/08/2021] [Indexed: 12/13/2022]
Abstract
Laboratory mice comprise an expeditious model for preclinical vaccine testing; however, vaccine immunogenicity in these models often inadequately translates to humans. Reconstituting physiologic microbial experience to specific pathogen-free (SPF) mice induces durable immunological changes that better recapitulate human immunity. We examined whether mice with diverse microbial experience better model human responses post vaccination. We co-housed laboratory mice with pet-store mice, which have varied microbial exposures, and then assessed immune responses to influenza vaccines. Human transcriptional responses to influenza vaccination are better recapitulated in co-housed mice. Although SPF and co-housed mice were comparably susceptible to acute influenza infection, vaccine-induced humoral responses were dampened in co-housed mice, resulting in poor control upon challenge. Additionally, protective heterosubtypic T cell immunity was compromised in co-housed mice. Because SPF mice exaggerated humoral and T cell protection upon influenza vaccination, reconstituting microbial experience in laboratory mice through co-housing may better inform preclinical vaccine testing.
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Affiliation(s)
- Jessica K Fiege
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA; Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Katharine E Block
- Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA; Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mark J Pierson
- Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA; Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Hezkiel Nanda
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Frances K Shepherd
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA; Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Clayton K Mickelson
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA; Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - J Michael Stolley
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA; Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - William E Matchett
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA; Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sathi Wijeyesinghe
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA; Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - David K Meyerholz
- Department of Pathology, University of Iowa, Iowa City, IA 52242, USA
| | - Vaiva Vezys
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA; Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Steven S Shen
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sara E Hamilton
- Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA; Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA.
| | - David Masopust
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA; Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Ryan A Langlois
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA; Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA.
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38
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Oh JH, Rehermann B. Natural versus Laboratory World: Incorporating Wild-Derived Microbiota into Preclinical Rodent Models. THE JOURNAL OF IMMUNOLOGY 2021; 207:1703-1709. [PMID: 34544812 DOI: 10.4049/jimmunol.2100426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/28/2021] [Indexed: 01/12/2023]
Abstract
Advances in data collection (high-throughput shotgun metagenomics, transcriptomics, and metabolomics) and analysis (bioinformatics and multiomics) led to the realization that all mammals are metaorganisms, shaped not only by their own genome but also by the genomes of the microbes that colonize them. To date, most studies have focused on the bacterial microbiome, whereas curated databases for viruses, fungi, and protozoa are still evolving. Studies on the interdependency of microbial kingdoms and their combined effects on host physiology are just starting. Although it is clear that past and present exposure to commensals and pathogens profoundly affect human physiology, such exposure is lacking in standard preclinical models such as laboratory mice. Laboratory mouse colonies are repeatedly rederived in germ-free status and subjected to restrictive, pathogen-free housing conditions. This review summarizes efforts to bring the wild microbiome into the laboratory setting to improve preclinical models and their translational research value.
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Affiliation(s)
- Ji Hoon Oh
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, MD
| | - Barbara Rehermann
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, MD
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39
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Glowacki RWP, Engelhart MJ, Ahern PP. Controlled Complexity: Optimized Systems to Study the Role of the Gut Microbiome in Host Physiology. Front Microbiol 2021; 12:735562. [PMID: 34646255 PMCID: PMC8503645 DOI: 10.3389/fmicb.2021.735562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/24/2021] [Indexed: 12/26/2022] Open
Abstract
The profound impact of the gut microbiome on host health has led to a revolution in biomedical research, motivating researchers from disparate fields to define the specific molecular mechanisms that mediate host-beneficial effects. The advent of genomic technologies allied to the use of model microbiomes in gnotobiotic mouse models has transformed our understanding of intestinal microbial ecology and the impact of the microbiome on the host. However, despite incredible advances, our understanding of the host-microbiome dialogue that shapes host physiology is still in its infancy. Progress has been limited by challenges associated with developing model systems that are both tractable enough to provide key mechanistic insights while also reflecting the enormous complexity of the gut ecosystem. Simplified model microbiomes have facilitated detailed interrogation of transcriptional and metabolic functions of the microbiome but do not recapitulate the interactions seen in complex communities. Conversely, intact complex communities from mice or humans provide a more physiologically relevant community type, but can limit our ability to uncover high-resolution insights into microbiome function. Moreover, complex microbiomes from lab-derived mice or humans often do not readily imprint human-like phenotypes. Therefore, improved model microbiomes that are highly defined and tractable, but that more accurately recapitulate human microbiome-induced phenotypic variation are required to improve understanding of fundamental processes governing host-microbiome mutualism. This improved understanding will enhance the translational relevance of studies that address how the microbiome promotes host health and influences disease states. Microbial exposures in wild mice, both symbiotic and infectious in nature, have recently been established to more readily recapitulate human-like phenotypes. The development of synthetic model communities from such "wild mice" therefore represents an attractive strategy to overcome the limitations of current approaches. Advances in microbial culturing approaches that allow for the generation of large and diverse libraries of isolates, coupled to ever more affordable large-scale genomic sequencing, mean that we are now ideally positioned to develop such systems. Furthermore, the development of sophisticated in vitro systems is allowing for detailed insights into host-microbiome interactions to be obtained. Here we discuss the need to leverage such approaches and highlight key challenges that remain to be addressed.
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Affiliation(s)
- Robert W. P. Glowacki
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Morgan J. Engelhart
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Philip P. Ahern
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH, United States
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40
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Lin JD, Loke P. Helminth infections and cardiovascular diseases: A role for the microbiota and Mϕs? J Leukoc Biol 2021; 110:1269-1276. [PMID: 34467547 DOI: 10.1002/jlb.5mr0721-786r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 07/18/2021] [Accepted: 07/27/2021] [Indexed: 12/14/2022] Open
Abstract
Cardiovascular diseases are rising in developing countries with increasing urbanization and lifestyle changes and remains a major cause of death in the developed world. In this mini review, we discuss the possibility that the effect of helminth infections on the immune system and the microbiota may affect risk factors in cardiovascular diseases such as atherosclerosis, as part of the hygiene hypothesis. The effects of Type 2 immune responses induced by helminths and helminth derived molecules on regulating metabolism and Mϕ function could be a mechanistic link for further investigation. We emphasize the complexity and difficulties in determining indirect or direct and causal relationships between helminth infection status and cardiovascular diseases. New experimental models, such as rewilding laboratory mice, whereby different aspects of the environment and host genetics can be carefully dissected may provide further mechanistic insights and therapeutic strategies for treating cardiovascular diseases.
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Affiliation(s)
- Jian-Da Lin
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei City, Taiwan
| | - P'ng Loke
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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41
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Abstract
Laboratory mice have long been an invaluable tool in biomedical science and have made significant contributions in research into life-threatening diseases. However, the translation of research results from mice to humans often proves difficult due to the incomplete nature of laboratory animal-based research. Hence, there is increasing demand for complementary methods or alternatives to laboratory mice that can better mimic human physiological traits and potentially bridge the translational research gap. Under these circumstances, the natural/naturalized mice including “wild”, “dirty”, “wildling”, and “wilded” systems have been found to better reflect some aspects of human pathophysiology. Here, we discuss the pros and cons of the laboratory mouse system and contemplate how wild mice and wild microbiota are able to help in refining such systems to better mimic the real-world situation and contribute to more productive translational research.
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Affiliation(s)
- Ho-Keun Kwon
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases and Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Korea
| | - Je Kyung Seong
- Laboratory of Developmental Biology and Genomics, Research Institute for Veterinary Science, and BK 21 PLUS Program for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul, 08826, South Korea.
- Interdisciplinary Program for Bioinformatics, Program for Cancer Biology and BIO-MAX/N-Bio Institute, Seoul National University, Seoul, 08826, South Korea.
- Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, 08826, South Korea.
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42
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Runge S, Rosshart SP. The Mammalian Metaorganism: A Holistic View on How Microbes of All Kingdoms and Niches Shape Local and Systemic Immunity. Front Immunol 2021; 12:702378. [PMID: 34276696 PMCID: PMC8278200 DOI: 10.3389/fimmu.2021.702378] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/17/2021] [Indexed: 12/12/2022] Open
Abstract
The field of microbiome research has developed rapidly over the past decades and has become a topic of major interest to basic, preclinical, and clinical research, the pharmaceutical industry as well as the general public. The microbiome is a complex and diverse ecosystem and defined as the collection of all host-associated microorganisms and their genes. It is acquired through vertical transmission and environmental exposure and includes microbes of all kingdoms: bacteria, archaea, prokaryotic and eukaryotic viruses, fungi, protozoa, and the meiofauna. These microorganisms co-evolved with their respective hosts over millions of years, thereby establishing a mutually beneficial, symbiotic relationship on all epithelial barriers. Thus, the microbiome plays a pivotal role in virtually every aspect of mammalian physiology, particularly in the development, homeostasis, and function of the immune system. Consequently, the combination of the host genome and the microbial genome, together referred to as the metagenome, largely drives the mammalian phenotype. So far, the majority of studies have unilaterally focused on the gastrointestinal bacterial microbiota. However, recent work illustrating the impact of viruses, fungi, and protozoa on host immunity urges us towards a holistic view of the mammalian microbiome and the appreciation for its non-bacterial kingdoms. In addition, the importance of microbiota on epithelial barriers other than the gut as well as their systemic effects via microbially-derived biologically active compounds is increasingly recognized. Here, we want to provide a brief but comprehensive overview of the most important findings and the current knowledge on how microbes of all kingdoms and microbial niches shape local and systemic immunity in health and disease.
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Affiliation(s)
- Solveig Runge
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
- Faculty of Biology, University of Freiburg, Freiburg im Breisgau, Germany
| | - Stephan Patrick Rosshart
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
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43
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The intestinal microbiota: from health to disease, and back. Microbes Infect 2021; 23:104849. [PMID: 34146716 DOI: 10.1016/j.micinf.2021.104849] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/06/2021] [Indexed: 01/08/2023]
Abstract
Our understanding of the composition and the function of the intestinal microbiota has significantly increased over the past few years. In a series of reviews focusing on the role of the intestinal microbiota in health and disease, we explore recent conceptual and technological advances in this rapidly evolving research arena.
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Abstract
Laboratory strains of mice are typically housed in specific pathogen-free facilities to minimize exposure to microbes. This method encourages uniformity in responses to experimentally induced parameters and reduces loss of animals, allowing for the survival and study of immunodeficient mice. However, the restrictions also limit physiologic relevance to humans, who are exposed to numerous microbes from birth. Recent evidence from several groups has demonstrated that exposure of laboratory mice to commensal and pathogenic microbes normally found in wild or pet store mice can dramatically impact the cellular makeup and function of the immune system. This article outlines procedures for exposing laboratory strains of mice to the diverse array of microbes typically found in pet store mice. Suggested methods for characterization of the immune system following this exposure are also described. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Cohousing laboratory strains of mice with pet store mice Support Protocol: Antibody staining of circulating immune cells and analysis by flow cytometry Basic Protocol 2: Exposure of laboratory strains of mice to fomite bedding.
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Affiliation(s)
- Mark Pierson
- Department of Laboratory Medicine and Pathology, Center for Immunology, University of Minnesota, Minneapolis, Minnesota
| | - Anne Merley
- Research Animal Resources, University of Minnesota, Minneapolis, Minnesota
| | - Sara E Hamilton
- Department of Laboratory Medicine and Pathology, Center for Immunology, University of Minnesota, Minneapolis, Minnesota
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45
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Intestinal Inflammation and Altered Gut Microbiota Associated with Inflammatory Bowel Disease Render Mice Susceptible to Clostridioides difficile Colonization and Infection. mBio 2021; 12:e0273320. [PMID: 34126769 PMCID: PMC8262858 DOI: 10.1128/mbio.02733-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Clostridioides difficile is a noteworthy pathogen in patients with inflammatory bowel disease (IBD). Patients with IBD who develop concurrent C. difficile infection (CDI) experience increased morbidity and mortality. IBD is associated with intestinal inflammation and alterations of the gut microbiota, both of which can diminish colonization resistance to C. difficile. Here, we describe the development of a mouse model to explore the role that IBD-induced changes of the gut microbiome play in susceptibility to C. difficile. Helicobacter hepaticus, a normal member of the mouse gut microbiota, triggers pathological inflammation in the distal intestine akin to human IBD in mice that lack intact interleukin 10 (IL-10) signaling. We demonstrate that mice with H. hepaticus-induced IBD were susceptible to C. difficile colonization in the absence of other perturbations, such as antibiotic treatment. Concomitant IBD and CDI were associated with significantly worse disease than observed in animals with colitis alone. Development of IBD resulted in a distinct intestinal microbiota community compared to that of non-IBD controls. Inflammation played a critical role in the susceptibility of animals with IBD to C. difficile colonization, as mice colonized with an isogenic mutant of H. hepaticus that triggers an attenuated intestinal inflammation maintained full colonization resistance. These studies with a novel mouse model of IBD and CDI emphasize the importance of host responses and alterations of the gut microbiota in susceptibility to C. difficile colonization and infection in the setting of IBD.
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46
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Dallari S, Heaney T, Rosas-Villegas A, Neil JA, Wong SY, Brown JJ, Urbanek K, Herrmann C, Depledge DP, Dermody TS, Cadwell K. Enteric viruses evoke broad host immune responses resembling those elicited by the bacterial microbiome. Cell Host Microbe 2021; 29:1014-1029.e8. [PMID: 33894129 PMCID: PMC8192460 DOI: 10.1016/j.chom.2021.03.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/04/2021] [Accepted: 03/23/2021] [Indexed: 02/08/2023]
Abstract
The contributions of the viral component of the microbiome-the virome-to the development of innate and adaptive immunity are largely unknown. Here, we systematically defined the host response in mice to a panel of eukaryotic enteric viruses representing six different families. Infections with most of these viruses were asymptomatic in the mice, the magnitude and duration of which was dependent on the microbiota. Flow cytometric and transcriptional profiling of mice mono-associated with these viruses unveiled general adaptations by the host, such as lymphocyte differentiation and IL-22 signatures in the intestine, as well as numerous viral-strain-specific responses that persisted. Comparison with a dataset derived from analogous bacterial mono-association in mice identified bacterial species that evoke an immune response comparable with the viruses we examined. These results expand an understanding of the immune space occupied by the enteric virome and underscore the importance of viral exposure events.
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Affiliation(s)
- Simone Dallari
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Thomas Heaney
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Adriana Rosas-Villegas
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Jessica A Neil
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Serre-Yu Wong
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY, USA; Department of Medicine, Henry D. Janowitz Division of Gastroenterology, Susan and Leonard Feinstein Inflammatory Bowel Disease Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judy J Brown
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Biology, Trevecca Nazarene University, Nashville, TN, USA
| | - Kelly Urbanek
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Christin Herrmann
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Daniel P Depledge
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Terence S Dermody
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA
| | - Ken Cadwell
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA; Division of Gastroenterology and Hepatology, Department of Medicine, New York University Langone Health, New York, NY, USA.
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Bergelson J, Kreitman M, Petrov DA, Sanchez A, Tikhonov M. Functional biology in its natural context: A search for emergent simplicity. eLife 2021; 10:e67646. [PMID: 34096867 PMCID: PMC8184206 DOI: 10.7554/elife.67646] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/28/2021] [Indexed: 01/03/2023] Open
Abstract
The immeasurable complexity at every level of biological organization creates a daunting task for understanding biological function. Here, we highlight the risks of stripping it away at the outset and discuss a possible path toward arriving at emergent simplicity of understanding while still embracing the ever-changing complexity of biotic interactions that we see in nature.
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Affiliation(s)
- Joy Bergelson
- Department of Ecology & Evolution, University of ChicagoChicagoUnited States
| | - Martin Kreitman
- Department of Ecology & Evolution, University of ChicagoChicagoUnited States
| | - Dmitri A Petrov
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Alvaro Sanchez
- Department of Ecology & Evolutionary Biology, Yale UniversityNew HavenUnited States
| | - Mikhail Tikhonov
- Department of Physics, Washington University in St LouisSt. LouisUnited States
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48
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Wale N, Duffy MA. The Use and Underuse of Model Systems in Infectious Disease Ecology and Evolutionary Biology. Am Nat 2021; 198:69-92. [PMID: 34143716 DOI: 10.1086/714595] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
AbstractEver since biologists began studying the ecology and evolution of infectious diseases (EEID), laboratory-based model systems have been important for developing and testing theory. Yet what EEID researchers mean by the term "model systems" and what they want from them is unclear. This uncertainty hinders our ability to maximally exploit these systems, identify knowledge gaps, and establish effective new model systems. Here, we borrow a definition of model systems from the biomolecular sciences to assess how EEID researchers are (and are not) using 10 key model systems. According to this definition, model systems in EEID are not being used to their fullest and, in fact, cannot even be considered model systems. Research using these systems consistently addresses only two of the three fundamental processes that underlie disease dynamics-transmission and disease, but not recovery. Furthermore, studies tend to focus on only a few scales of biological organization that matter for disease ecology and evolution. Moreover, the field lacks an infrastructure to perform comparative analyses. We aim to begin a discussion of what we want from model systems, which would further progress toward a thorough, holistic understanding of EEID.
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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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50
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Iliev ID, Cadwell K. Effects of Intestinal Fungi and Viruses on Immune Responses and Inflammatory Bowel Diseases. Gastroenterology 2021; 160:1050-1066. [PMID: 33347881 PMCID: PMC7956156 DOI: 10.1053/j.gastro.2020.06.100] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/23/2020] [Accepted: 06/23/2020] [Indexed: 12/26/2022]
Abstract
The intestinal microbiota comprises diverse fungal and viral components, in addition to bacteria. These microbes interact with the immune system and affect human physiology. Advances in metagenomics have associated inflammatory and autoimmune diseases with alterations in fungal and viral species in the gut. Studies of animal models have found that commensal fungi and viruses can activate host-protective immune pathways related to epithelial barrier integrity, but can also induce reactions that contribute to events associated with inflammatory bowel disease. Changes in our environment associated with modernization and the COVID-19 pandemic have exposed humans to new fungi and viruses, with unknown consequences. We review the lessons learned from studies of animal viruses and fungi commonly detected in the human gut and how these might affect health and intestinal disease.
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Affiliation(s)
- Iliyan D Iliev
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, New York; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, New York.
| | - Ken Cadwell
- Kimmel Center for Biology and Medicine, Skirball Institute, New York University Grossman School of Medicine, New York, New York; Department of Microbiology, New York University Grossman School of Medicine, New York, New York; Division of Gastroenterology and Hepatology, Department of Medicine, New York University Langone Health, New York, New York.
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