Scientists have been using mouse models in biomedical research since the 17th century for a number of good reasons. Mice are easy to maintain and breed in the laboratory and they are quite similar to humans, both physiologically and genetically (their genome is 85% similar to the human genome). Besides these obvious advantages, there are also some problems with using mouse models. For example, variability in the composition of their intestinal microbiota may result in unwanted variations between experiments in animal facilities. The intestinal microbiota may be influenced by many factors including breeding conditions, diet, and genetics. Scientists have been trying to design stable and easy to manipulate mouse models by reducing their gut microbial diversity to make them as uniform as possible for over 80 years. One of the reasons that makes this task rather complicated is the fact that gut microbiota is highly diverse and is usually represented by around 300 bacterial genera. The specific pathogen-free (SPF) hygienic status of mouse husbandries and specific (and opportunistic) pathogen-free (SOPF) inbred lines represent first attempts at creating a new standard for experimental mouse breeding and are currently widely used (Lane-Petter 1962; FELASA working group, 2014). However, scientists continue to use a so-called facility specific cocktail of bacteria, because a common SPF standard cocktail still doesn’t exist. This leads to the fact that a certain degree of variability in the microbial composition of the gut persists. Since microbes are very susceptible to the influence of diet and environment, it is impossible to maintain the exact same microbiota across multiple facilities. To further standardize preclinical studies, a group of scientists created a simplified model of mouse gut microbiota that is “representative of SOPF microbiota at the functional level”. This means that even though this model has fewer microbial species, it is as functionally capable as other models with more microbes. This new mouse model is the topic of today’s post at Pretty Light Science.
In a recently published article a collaborative research team led by a group of French researchers reported the development of a new mouse model, called GM15 that has some significant advantages over existing models (Darnaud et al., 2021). More specifically, the newly designed model has a very minimal selection of gut microorganisms that provides “a superior functional potential” as compared to previously developed models including Oligo-MM12 and ASF models (Brugiroux et al., 2016; Wymore Brand et al., 2015). GM15’s microbial consortium consists of only 15 strains from 7 of the 20 most prevalent bacterial families. How did the researchers manage to create such a streamlined model and make it stable and functionally capable?
First, they identified the most prevalent bacterial families in the mouse gut. They did this by analyzing the bacterial composition of fecal pellets from four mice (two females and two males housed in different cages) via whole-genome sequencing (WGS). Then they compared the cleaned and classified sequences to a publicly available genome database and identified 20 dominant families that are consistently present in all mice. The identified bacterial composition was comparable across four mice, meaning that all four mice had a similar selection of bacteria in their gut. After this step the researchers did what most scientists do after analyzing data on the computer, they went back to the lab. They used different isolation strategies to obtain in pure culture the maximum number of bacterial strains from these 20 dominant groups of microorganisms. Out of a 400 species collection of bacterial strains created at this step, they selected 11 strains representing 7 of the most prevalent bacterial families of the intestinal microbiota and obtained four additional strains from the DSMZ miBC collection. These fifteen strains formed a base for the new mouse model named GM15.
The researchers then looked into the functional potential of this microbial consortium by annotating all protein sequences. They discovered that the functional potential of this group of microorganisms covers almost a half (44%) of all protein-coding sequences. This means that this highly reduced community of microorganisms has the genetic potential to perform almost half of all known enzymatic activities. Next, they compared functionalities of the 15 selected strains to a list of known enzymatic activities in the gut and discovered that different bacterial strains may be capable of performing the same enzymatic activity. This crucial bacterial feature called “functional/enzymatic redundancy” allows for the generation of minimal bacterial consortiums that consist of just a small number of species but cover a wide range of enzymatic functions.
Additional laboratory analyses allowed researchers to conclude that the GM15 community was sufficiently stable under a variety of conditions. The GM15 consortium could consistently colonize the mouse intestine over several generations, it could be transmitted by fecal microbiota transplantation, and it demonstrated significant resistance in response to dietary changes. This allows scientists to set up more consistent experiments and obtain more reproducible results.
Take Home message
The main take home message is that this new mouse model with a well defined and highly specialized intestinal microbial community has the potential to increase reproducibility and robustness of preclinical studies. This is important because “reproducibility is imperative to preclinical research” since it allows scientists to have exactly the same conditions for their experiments at different research institutions and even different countries, and it also gives them the opportunity to repeat their experiments multiple times to verify the results. This model provides researchers and clinicians with a significant advantage of being able to manage short-term and long-term microbial dynamics. This is possible thanks to a number of features of the GM15 model including:
Reduced microbial complexity;
Efficacy of transfer to germ-free mice;
Stability across different breeding facilities;
Precise control over members of the microbiota
These specific features may provide significant advantages in preclinical research studies focused on host-microbe and microbe-microbe interactions and on how intestinal microbes are connected to disease progression and drug efficacy.
References:
Darnaud, M., De Vadder, F., Bogeat, P. et al. A standardized gnotobiotic mouse model harboring a minimal 15-member mouse gut microbiota recapitulates SOPF/SPF phenotypes. Nat Commun 12, 6686 (2021). https://doi.org/10.1038/s41467-021-26963-9
Why Mouse Matters. https://www.genome.gov/10001345/importance-of-mouse-genome
Lane-Petter, W. Provision of pathogen-free animals. Proc. R. Soc. Med. 55, 253–256 (1962).
FELASA Working Group on Revision of Guidelines for Health Monitoring of Rodents and Rabbits, M. Mähler, M. Berard, R. Feinstein, A. Gallagher, B. Illgen-Wilcke, K. Pritchett-Corning, and M. Raspa. "FELASA recommendations for the health monitoring of mouse, rat, hamster, guinea pig and rabbit colonies in breeding and experimental units." Laboratory animals 48, no. 3 (2014). https://doi.org/10.1177/0023677213516312
Brugiroux, S., Beutler, M., Pfann, C. et al. Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium. Nat Microbiol 2, 16215 (2017). https://doi.org/10.1038/nmicrobiol.2016.215
Wymore Brand, M., Wannemuehler, M. J., Phillips, G. J., Proctor, A., Overstreet, A. M., Jergens, A. E., Orcutt, R. P., & Fox, J. G. (2015). The Altered Schaedler Flora: Continued Applications of a Defined Murine Microbial Community. ILAR journal, 56(2), 169–178. (2015). https://doi.org/10.1093/ilar/ilv012
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