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Updated: Feb 22, 2026

Operating and Biocontainment Procedures of a Facility for Laboratory Mice with a Natural Microbiome: Immunophenotyping Procedure
Published on: December 13, 2024
Modeling a Superorganism - Considerations Regarding the Use of "Dirty" Mice in Biomedical Research
Aaron C Ericsson1,2,3,4, Daniel R Montonye4, Cierra R Smith4
1University of Missouri Metagenomics Center (MUMC), Columbia, MO.
Abstract:
An ever-expanding body of evidence in both humans and animal models demonstrates the influence of the resident gut microbiota on host health and disease susceptibility. However, as unwanted bacterial, viral, protozoal, and parasitic agents have gradually been eliminated from colonies of purpose-bred laboratory mice, the resident microbiota has lost richness and complexity. Recent studies have shown that the ultra-hygienic environment of traditional laboratory mice and lack of antigenic exposure during development results in mice with an immune system more akin to that of a neonate than an adult human. In contrast, wild mice or mice purchased from pet stores are exposed to much greater antigen burdens and their immune system reflects this with significantly greater numbers of memory T cells and more robust vaccine responses. The current review explores the use of alternative sources for research rodents, with an emphasis on the differences in resident gut microbiota and pathogen burden between wild mice, pet store-origin mice, and traditional laboratory mice. Specifically, the literature is compared and contrasted to our own data reflecting the endogenous gut microbiota and pathogen load of wild and pet store mice, as well as the changes in both during and after procedures intended to eliminate certain zoonotic agents present in pet store mice. These data demonstrate that, while alternative sources of research rodents will likely provide models that are more translatable to the human condition, there are also several real-world considerations for scientists including contamination of research facilities and human health risks such as zoonotic diseases.
Insights
Research rodents from wild or pet store sources have richer gut microbiota and more developed immune systems than traditional lab mice. This offers more translatable models but requires careful management of contamination and zoonotic risks.
Area of Science:
- Microbiology
- Immunology
- Comparative Medicine
Background:
- The gut microbiota significantly impacts host health and disease susceptibility.
- Traditional laboratory mice, due to sterile environments, possess a simplified microbiota and underdeveloped immune systems.
- Wild and pet store mice exhibit greater microbial diversity and more mature immune responses due to higher antigen exposure.
Purpose of the Study:
- To explore alternative sources of research rodents, focusing on gut microbiota and pathogen burden.
- To compare traditional lab mice with wild and pet store mice regarding their resident microbiota and immune status.
- To assess the implications of using alternative rodent sources for research translatability and safety.
Main Methods:
- Literature review comparing gut microbiota and pathogen load across different mouse sources.
- Analysis of endogenous gut microbiota and pathogen load in wild and pet store mice.
- Evaluation of changes in microbiota and pathogen load after decontamination procedures.
Main Results:
- Alternative rodent sources (wild, pet store) possess more complex gut microbiota and enhanced immune profiles compared to conventional lab mice.
- These alternative models show greater similarity to human immune responses.
- Decontamination procedures can alter the microbiota of pet store mice.
Conclusions:
- Alternative rodent sources offer more translatable research models due to their more robust immune systems and diverse gut microbiota.
- Considerations for using these models include potential contamination of research facilities.
- Human health risks, such as zoonotic diseases, must be carefully managed when working with alternative rodent sources.

