Laboratory mice born to wild mice have natural microbiota and model human immune responses

Abstract

Born to be a wildling Inbred laboratory mouse strains are used extensively in basic and translational immunology research. However, the commensal and pathogenic repertoire of resident microbes encountered in the wild is not replicated in a lab setting. This can substantially distort how the immune system develops and functions, leading to false assumptions of how our own “wild” immune system works. Rosshart et al. circumvented this dilemma by implanting lab-strain embryos into wild mice (see the Perspective by Nobs and Elinav). The resultant “wildlings” had a systemic immune phenotype and a bacterial, viral, and fungal microbiome much closer to those of their wild counterparts. In two preclinical experiments, where lab mice had previously failed to predict the human response to drug treatments, wildlings accurately phenocopied patient outcomes. Science, this issue p. eaaw4361; see also p. 444 The wildling model fuses lab mouse strains with naturally occurring microorganisms for increased translational research value. INTRODUCTION Laboratory mice are a mainstay of biomedical research and have been instrumental for many important discoveries in the field of immunology. However, there are also major limitations, including conflicting results rooted in divergent microbiota among research facilities and the limited ability to predict the complex immune responses of humans. Recent studies have shown that conventional laboratory mice are too far removed from natural environmental conditions to faithfully mirror the physiology of free-living mammals such as humans. Mammals and their immune systems evolved to survive and thrive in a microbial world and behave differently in a sanitized environment. RATIONALE To generate a mouse model that more closely resembles the natural mammalian metaorganism with coevolved microbes and pathogens, we transferred C57BL/6 embryos into wild mice. This resulted in a colony of C57BL/6 mice, which we call “wildlings.” RESULTS Wildlings resembled wild mice and differed substantially from conventional laboratory mice with regard to their bacterial microbiome at important epithelial barrier sites (gut, skin, and vagina), their gut mycobiome and virome, and their level of pathogen exposure. The natural microbiota of wildlings were stable over multiple generations and resilient against antibiotic, dietary, and microbial challenges. Next, we delineated the immune landscape of wildlings, wild mice, and laboratory mice at immunologically important barrier sites (gut, skin, and vagina), a central nonlymphoid organ (liver), and a central lymphoid organ (spleen) by mass cytometry. Additionally, we characterized the blood immune cell profile by RNA sequencing. The differential contribution of microbial and host genomes in shaping the immune phenotype varied among tissues. Wildlings closely mirrored the wild mouse immune phenotype in the spleen and blood. Finally, we tested the translational research value of wildlings in a retrospective bench-to-bedside approach. This required well-documented, rodent-based studies that had failed upon transitioning to clinical trials in humans. We chose the CD28-superagonist (CD28SA) trial as representative for treatments targeting adaptive immune responses. Although CD28SA expanded anti-inflammatory regulatory T cells (Tregs) in laboratory mice and showed therapeutic effects in multiple models of autoimmune and inflammatory diseases, the first phase 1 clinical trial resulted in life-threatening activation of inflammatory T cells and cytokine storms. Similarly, the CD28SA treatment of wildlings, but not laboratory mice, resulted in an inflammatory cytokine response and lack of Treg expansion. As a representative for trials targeting innate immune responses, we chose anti–tumor necrosis factor–alpha (TNF-α) treatment (anti-TNF-α or TNF-receptor:Fc fusion protein) during septic shock, which was successful in animal models, but failed in humans. Anti–TNF-α treatment during lethal endotoxemia rescued laboratory mice, but not wildlings. Thus, wildlings better phenocopied human immune responses than did conventional laboratory mice in the two models studied. CONCLUSION The wildling model combines resilient natural microbiota and pathogens at all body sites and the tractable genetics of C57BL/6. Given the wide-ranging effects of microbiota on host physiology, natural microbiota-based models may benefit different research fields (e.g., metabolism and neurodegenerative diseases) and may also be applicable to other animals. Such models may enhance the validity and reproducibility of biomedical studies among research institutes, facilitate the discovery of disease mechanisms and treatments that cannot be studied in regular laboratory mice, and increase the translatability of immunological results to humans. Harnessing natural microbiota and pathogens to address shortcomings of current mouse models. To restore the natural microbiome while preserving the research benefits of tractable genetics, we transferred C57BL/6 embryos into wild mice and created a colony of C57BL/6 mice, which we call “wildlings.” Their microbiome was stable over time and resilient to environmental challenges. Wildlings also exhibited an increased translational research value in immunological studies. Laboratory mouse studies are paramount for understanding basic biological phenomena but also have limitations. These include conflicting results caused by divergent microbiota and limited translational research value. To address both shortcomings, we transferred C57BL/6 embryos into wild mice, creating “wildlings.” These mice have a natural microbiota and pathogens at all body sites and the tractable genetics of C57BL/6 mice. The bacterial microbiome, mycobiome, and virome of wildlings affect the immune landscape of multiple organs. Their gut microbiota outcompete laboratory microbiota and demonstrate resilience to environmental challenges. Wildlings, but not conventional laboratory mice, phenocopied human immune responses in two preclinical studies. A combined natural microbiota- and pathogen-based model may enhance the reproducibility of biomedical studies and increase the bench-to-bedside safety and success of immunological studies.