Virus-induced perturbations in the mouse microbiome are impacted by microbial experience
ABSTRACT The bacterial microbiome has a major impact on health and can shape metabolism, host tolerance, immune responses, and the outcome of future infections. The bacterial microbiome is highly variable between individuals. Specific pathogen-free animals have reduced microbiome diversity, making i...
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2025-03-01
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| Series: | mSphere |
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| Online Access: | https://journals.asm.org/doi/10.1128/msphere.00563-24 |
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| author | Shanley N. Roach Wendy Phillips Lauren M. Pross Autumn E. Sanders Mark J. Pierson Ryan C. Hunter Ryan A. Langlois |
| author_facet | Shanley N. Roach Wendy Phillips Lauren M. Pross Autumn E. Sanders Mark J. Pierson Ryan C. Hunter Ryan A. Langlois |
| author_sort | Shanley N. Roach |
| collection | DOAJ |
| description | ABSTRACT The bacterial microbiome has a major impact on health and can shape metabolism, host tolerance, immune responses, and the outcome of future infections. The bacterial microbiome is highly variable between individuals. Specific pathogen-free animals have reduced microbiome diversity, making it difficult to evaluate the impact of infection-induced microbiome disruption that would be observed in free-living animals, including people. Mice are commonly used as a preclinical model but unfortunately often fail to predict translation success or failure, particularly for immune and infectious disease-targeting therapies. Here, we utilize pet store mouse cohoused “dirty” mice with diverse microbial experience to explore how host variability and infection may be interacting to drive unique microbiome changes. We found that cohoused animals had significantly increased bacterial diversity in the small intestine and cecum but not in the large intestine. There were differentially abundant taxa between clean and dirty animals in all three tissues. After infection with influenza A virus, samples clustered by both housing condition and infection status in the cecum and large intestine, while small intestine samples clustered predominantly by infection. Altogether, these results highlight the differential impact of housing, infection, and interaction between the two in dictating community composition across the gastrointestinal microbiome.IMPORTANCETraditionally housed pathogen-free mouse models do not fully capture the natural variability observed among human microbiomes, which may underlie their poor translationally predictive value. Understanding the difference between pathogen-induced shifts in the bacterial microbiome and natural microbiome variance is a major hurdle to determining bacterial biomarkers of disease. It is also critical to understand how diverse baseline microbiomes may be differentially impacted by infection and contribute to disease. Pet store cohoused “dirty” mice have diverse microbial experiences and microbiomes, allowing us to evaluate how baseline variation, infection, and interaction between the two impact the microbiome. |
| format | Article |
| id | doaj-art-061cc4bf5d7744e9bcf3cc4660f0dab6 |
| institution | DOAJ |
| issn | 2379-5042 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mSphere |
| spelling | doaj-art-061cc4bf5d7744e9bcf3cc4660f0dab62025-08-20T02:40:33ZengAmerican Society for MicrobiologymSphere2379-50422025-03-0110310.1128/msphere.00563-24Virus-induced perturbations in the mouse microbiome are impacted by microbial experienceShanley N. Roach0Wendy Phillips1Lauren M. Pross2Autumn E. Sanders3Mark J. Pierson4Ryan C. Hunter5Ryan A. Langlois6Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USAMinnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota, USADepartment of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USADepartment of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USADepartment of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USADepartment of Microbiology and Immunology, University at Buffalo, Getzville, New York, USADepartment of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USAABSTRACT The bacterial microbiome has a major impact on health and can shape metabolism, host tolerance, immune responses, and the outcome of future infections. The bacterial microbiome is highly variable between individuals. Specific pathogen-free animals have reduced microbiome diversity, making it difficult to evaluate the impact of infection-induced microbiome disruption that would be observed in free-living animals, including people. Mice are commonly used as a preclinical model but unfortunately often fail to predict translation success or failure, particularly for immune and infectious disease-targeting therapies. Here, we utilize pet store mouse cohoused “dirty” mice with diverse microbial experience to explore how host variability and infection may be interacting to drive unique microbiome changes. We found that cohoused animals had significantly increased bacterial diversity in the small intestine and cecum but not in the large intestine. There were differentially abundant taxa between clean and dirty animals in all three tissues. After infection with influenza A virus, samples clustered by both housing condition and infection status in the cecum and large intestine, while small intestine samples clustered predominantly by infection. Altogether, these results highlight the differential impact of housing, infection, and interaction between the two in dictating community composition across the gastrointestinal microbiome.IMPORTANCETraditionally housed pathogen-free mouse models do not fully capture the natural variability observed among human microbiomes, which may underlie their poor translationally predictive value. Understanding the difference between pathogen-induced shifts in the bacterial microbiome and natural microbiome variance is a major hurdle to determining bacterial biomarkers of disease. It is also critical to understand how diverse baseline microbiomes may be differentially impacted by infection and contribute to disease. Pet store cohoused “dirty” mice have diverse microbial experiences and microbiomes, allowing us to evaluate how baseline variation, infection, and interaction between the two impact the microbiome.https://journals.asm.org/doi/10.1128/msphere.00563-24microbiomeinfluenza virusdysbiosisdirty mice |
| spellingShingle | Shanley N. Roach Wendy Phillips Lauren M. Pross Autumn E. Sanders Mark J. Pierson Ryan C. Hunter Ryan A. Langlois Virus-induced perturbations in the mouse microbiome are impacted by microbial experience mSphere microbiome influenza virus dysbiosis dirty mice |
| title | Virus-induced perturbations in the mouse microbiome are impacted by microbial experience |
| title_full | Virus-induced perturbations in the mouse microbiome are impacted by microbial experience |
| title_fullStr | Virus-induced perturbations in the mouse microbiome are impacted by microbial experience |
| title_full_unstemmed | Virus-induced perturbations in the mouse microbiome are impacted by microbial experience |
| title_short | Virus-induced perturbations in the mouse microbiome are impacted by microbial experience |
| title_sort | virus induced perturbations in the mouse microbiome are impacted by microbial experience |
| topic | microbiome influenza virus dysbiosis dirty mice |
| url | https://journals.asm.org/doi/10.1128/msphere.00563-24 |
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