In the confines of the animal room, lab mice reared for research encounter few microbes. While this safeguards against random infections and improves experimental reproducibility, the artificially sterile environment on its own may have effects on the mice. Now, scientists led by Barbara Rehermann of the National Institute of Diabetes and Digestive and Kidney Diseases in Bethesda, Maryland, report in the October 19 Cell online that transplanting intestinal flora from wild mice into the guts of their lab cousins bolsters the latter’s response to viral infection and cancer. The results suggest that rounding out the microbiomes of lab mice could make them more resilient. It could also make disease models scientists use to study neurodegenerative diseases more representative of real-world conditions.

  • Intestinal bacteria from wild mice fight disease in lab mice.
  • Treated mice resisted influenza infection, colon cancer.
  • Treated mice had fewer pro-, more anti-inflammatory cytokines.

“Recent years have seen the increasing realization that gut microbiota can influence a wide range of host immune and homeostatic processes,” wrote Malu Tansey, Madelyn Houser, and Andrew Neish at Emory University in Atlanta (see full comment below). Laboratory mice are kept in sterile environments, and mice with minimal gut microbiota, or even germ-free mice, increasingly have been touted as necessary controls, they noted. “However, this work by [first author Stephan] Rosshart and colleagues vividly illustrates a limitation of this trend,” they added.

Robert Friedland, University of Louisville School of Medicine in Kentucky, said the present study could have implications for neurodegenerative disease. “Researchers of Alzheimer’s and related disorders who use animal models should consider the possible role gut bacteria play in their animal systems,” he told Alzforum. “The nature of these bacteria is critical for the development, maturation, and education of the immune system, which is involved in diseases such as cancer, Alzheimer’s, Parkinson’s, and ALS.”

Putting Reins on Cancer.

Mutagen-induced tumors (green) invade the colon of a germ-free lab mouse engrafted with the microbiota of a littermate (left). Microbiota from a wild mouse protected against tumors (right). [Cell, Rosshart et al.]

Rehermann, along with Rosshart and colleagues, suspected that since lab mice lack a complete set of symbiotic microbes, they miss out on the immune-boosting and inflammation-reducing capabilities of mice in the wild (Feng and Olson, 2011). To explore this hypothesis, Rosshart and colleagues transplanted the gut microbiota of wild mice into lab-dwelling cousins and observed the response to infection and cancer. 

The scientists went into horse barns in Maryland, trapped 100 house mice, and determined that they were close genetic relatives of the inbred C57BL/6 lab strain. They analyzed the wild mouse gut microbiomes, which, while similar among the wild mice, were more diverse than the microbiome of C57BL/6. Next, the scientists engrafted bacteria from three of these wild mice into C57BL/6 mice specifically raised to be germ-free; these mice have no microbiome. The researchers examined how the wild microbiome recipients (WildR) responded to intranasal infection with the influenza virus, and compared them to germ-free C57BL/6 controls that received the microbiome of a lab littermate (LabR).

Seventeen percent of LabR mice survived 11 days after viral infection, whereas 92 percent of the WildR mice did. The latter had 10-fold fewer viruses in their lungs, as well as less bronchitis and cell death. Their lungs harbored fewer inflammatory cells and pro-inflammatory cytokines, but their anti-inflammatory cytokines were elevated compared to LabR mice. Likewise, if the researchers induced colorectal cancer by injecting a mutagen and encouraging an inflammatory response, the wild microbiome led to fewer tumors, which spread more slowly than in mice that received the lab animal microbiome (see image above).

Together, the results suggest wild gut microbiota protects lab mice against flu, cancer, and inflammation. Previous studies suggested that intestinal flora was important in these responses, because depleting the already limited microbiome of lab animals makes them more susceptible to infections and cancer (Abt et al., 2012; Zackular et al., 2016). 

The authors hypothesize that microbes, which co-evolved with their hosts, help fight against pathogens and mutagens in the environment. Perhaps introducing a complete microbiome in the gastrointestinal tract, lung, skin, and vagina could improve responses and make more representative disease models, they suggested.

Other research suggests that microglia need a healthy microbiome to function optimally in the brain, that the microbiome changes with ongoing neurodegenerative disease, and that it may exacerbate pathology in animal models (Jun 2015 newsApr 2017 news; Dec 2016 news; Feb 2017 news). Given our growing appreciation for the role of neuroinflammation in different neurodegenerative diseases, it will be essential to understand both the mechanisms that are common and those that are specific to each, noted Mike Sasner, The Jackson Laboratory, Bar Harbor, Maine.

Sasner cautioned that improved fitness due to a more natural microbiota could be beneficial or detrimental. “The typical lab mouse model of colitis-induced tumorigenesis may be more useful for some experimental applications than the wild-mouse microbiome-reconstituted model that gets far fewer tumors,” he wrote (see full comment below). Nonetheless, Sasner thinks more attention should be paid to the choice and health status of experimental models. “We need to work toward using multiple complementary model systems that take into account not only disease-related genetic variants but also genetic and epigenetic context and environmental and health/microbiome status.”—Gwyneth Dickey Zakaib


  1. Our understanding of complex disorders has been immeasurably advanced with the use of model organisms such as mice. The use of inbred strains maintained under highly controlled conditions necessarily limits potential variables that typically confound in vivo experimentation. In addition, recent years have seen the increasing realization that the gut microbiota can influence a wide range of host immune and homeostatic processes, and variations in microbiota community structure can have profound effects on experimental outcomes. Thus, laborious efforts, such as mice maintained in isolator facilities in a germ-free state or with a minimal defined (gnotobiotic) microbiota, have been touted as necessary controls to standardize and reduce the complexity of the murine microbiota in an effort to reduce this variable. However, this work by Rosshart et al. vividly illustrates a limitation of this trend.

    The authors evaluated 101 wild-caught mice (Mus musculus domesticus) trapped from locations in the District of Columbia and Maryland. They took a comprehensive approach in comparing microbiota of numerous wild-type mice separated geographically and temporally and lab mice from different suppliers. They found that the microbiota compositions of different populations of wild-type mice were surprisingly similar and also distinct from those of lab mice. Specifically, taxonomic 16s analysis of ileocecal microbiota from the animals revealed distinct grouping of the wild microbiomes relative to the microbiota of standard laboratory animals. Then they reconstituted pregnant germ-free laboratory mice with wild-mouse microbiota so that pups would experience microbe-mediated effects before birth as well as vertical transmission of the microbiota. This design helps alleviate concerns about abnormal immune development that arise when adult germ-free mice are colonized and then evaluated in experiments. Importantly, transfer of the wild murine microbiota into germ-free mice was shown to be stable across generations, retaining specific operational taxonomic units (OTUs) characteristic of wild or laboratory mice. This is intriguing given that the environmental conditions in which wild-mouse microbiomes developed were not recapitulated in the lab. Remarkably, these “wild-mouse microbiome-reconstituted” animals show markedly increased resistance to challenge with a mouse-adapted influenza virus as well as reduced-inflammation-associated neoplasia development (DSS-AOM model). The protective effects of wild-mouse microbiota were associated with abrogation of hyperinflammatory responses and immune-mediated damage, suggesting that the wild microbiota stimulates the effective activation of mechanisms which regulate the resolution of inflammatory responses and epithelial homeostasis.

    In addition, it has been shown that pathogen exposure can alter immune activity in laboratory mice to more closely resemble that found in adult humans (Beura et al., 2016; Abolins et al., 2017; Reese et al., 2016), but a novel feature of this study was their use of wild-mouse microbiota that met typical specific pathogen-free facility standards. This specific pathogen-free wild microbiota clearly altered immune responses in recipient mice compared to a standard laboratory mouse microbiota. This wild-microbiota mouse model should be tested to see if its responses to such interventions as vaccinations or drugs recapitulate human responses more accurately than in typical laboratory mice, as has been shown for pathogen-exposed mice. If so, then this would present the exciting possibility that laboratory mouse models could be rendered more representative with immune responses that more closely resemble those in humans without the logistical challenges and experimental confounds associated with pathogen infections.

    The implication of these observations is that a naturally occurring microbiota community structure (i.e., not selected for experimental convenience or rigor) has intrinsic benefits for the host, presumably as a result of longstanding mutual co-evolution. Additionally, these data suggest the search for beneficial members of the microbiota may find a productive source in previously understudied natural populations.

    With regard to human populations, the data are consistent with current notions of the “hygiene hypothesis,” wherein many disorders of the modern human condition may result from divergence of our microbiota from that of people in traditional societies, whose diet and proximity to domestic animals supports a more ancestral and “wild like” microbiota.  


    . Normalizing the environment recapitulates adult human immune traits in laboratory mice. Nature. 2016 Apr 28;532(7600):512-6. Epub 2016 Apr 20 PubMed.

    . The comparative immunology of wild and laboratory mice, Mus musculus domesticus. Nat Commun. 2017 May 3;8:14811. PubMed.

    . Sequential Infection with Common Pathogens Promotes Human-like Immune Gene Expression and Altered Vaccine Response. Cell Host Microbe. 2016 May 11;19(5):713-9. Epub 2016 Apr 20 PubMed.

  2. Rosshart et al. have made a great contribution to our understanding of the role of gut microbiome in determining disease phenotypes in mouse models.

    This work highlights the importance of reporting experimental details, and raises an issue that the field will need to address—if we want to simulate more natural microbiota in animal models, how can we standardize the bacterial gut microbiome so that work can be replicated?

    Improved fitness due to a more natural microbiota could be either beneficial or detrimental, as a useful experimental disease model may lose its utility in a more “fit” model. For example, the typical lab mouse model of colitis-induced tumorogenesis in Figure 7B-D may be more useful for some experimental applications than the wild-mouse microbiome-reconstituted model that gets far fewer tumors.

    In terms of models of neurodegeneration of interest to the Alzforum audience, there already have been a few papers showing a role for microbiome in altering disease-like phenotypes (e.g. Sampson et al., 2016), and I expect we will see many more soon. Given our growing appreciation for the role of neuroinflammation in neurodegenerative diseases, it will be essential to understand both the mechanisms that are common and those that are specific to each.

    In all cases we need to pay more attention to the choice and health status of our experimental models, ideally be able to both replicate results in more than one distinct model and in a single model at more than one experimental site, and be careful not to generalize our interpretation of results too broadly. We need to work toward using multiple complementary model systems that take into account not only disease-related genetic variants but also genetic and epigenetic context and environmental and health/microbiome status. There is also a lot of work to be done to understand how genetic context interacts with environment to alter the microbiome. Of course, these are all logistically complex and make projects more costly, so funding agencies need to appreciate the importance of supporting these efforts.


    . Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson's Disease. Cell. 2016 Dec 1;167(6):1469-1480.e12. PubMed.

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News Citations

  1. To Be Hale and Hearty, Brain Microglia Need a Healthy Gut
  2. Rumblings of Parkinson’s: Gut Microbiome Shifts in Early Stage of Disease
  3. Do Microbes in the Gut Trigger Parkinson’s Disease?
  4. Microbes in the Gut Egg on Aβ Pathology in Mice

Paper Citations

  1. . Adaptive immunity in the host-microbiota dialog. Mucosal Immunol. 2011 Jan;4(1):15-21. Epub 2010 Oct 13 PubMed.
  2. . Commensal bacteria calibrate the activation threshold of innate antiviral immunity. Immunity. 2012 Jul 27;37(1):158-70. Epub 2012 Jun 14 PubMed.
  3. . Manipulation of the Gut Microbiota Reveals Role in Colon Tumorigenesis. mSphere. 2016 Jan-Feb;1(1) Epub 2015 Nov 4 PubMed.

Further Reading


  1. . Regulation of inflammation by microbiota interactions with the host. Nat Immunol. 2017 Jul 19;18(8):851-860. PubMed.
  2. . The gut microbiome in human neurological disease: A review. Ann Neurol. 2017 Mar;81(3):369-382. Epub 2017 Mar 20 PubMed.

Primary Papers

  1. . Wild Mouse Gut Microbiota Promotes Host Fitness and Improves Disease Resistance. Cell. 2017 Oct 17; PubMed.