The production of genetically modified mice that serve as models of inherited diseases or as tools to dissect biological mechanisms has proven essential to the progress of biomedical science. Mice, like humans, are heavily colonized by microrganisms that can be pathogenic, innocuous or beneficial commensals. In humans and mice, the microflora roughly represents 90% of the cells that compose an individual. Therefore, the phenotype associated with a specific mouse genome modification may result from disruption of the interactions between the host and its microflora. Commonly, mice are raised in the now standard Specific Pathogen Free conditions, which do not significantly modify the extreme diversity and number of colonizing micro-organisms. The techniques of gnotobiology allow for the generation and maintenance of animals in a germ-free or axenic environment and by extension with the possibility to restore specific components of the microflora. The comparative analysis of a given mouse line raised in SPF and in germ-free condition, reveals the contribution of the microflora to the phenotype associated with a specific mouse genotype. This approach has been essential, for instance, to discriminate between autoimmunity and inflammatory immunopathologies in various mouse models. Germ-free animals may also help us to understand the host-commensal interactions during tissue regeneration, for instance of the intestinal epithelium. Even more classically, metabolic disorders are now clearly associated with the microbiota composition. Finally, the notion that the microbiota could also influence behavior is being developed.

Over the last 10 years, gnotobiology has experienced a comeback, likely because of the development of high-throughput analyses of the microbiome as well as the expansion of organism centered biology and attempts at developing empirical system biology. Interestingly, while differences in phenotype severity, penetrance or incidence for the same mouse genotype have been long noted between institutions and largely understood as an influence of the micro-environment, the effort to define SPF conditions - by exclusion criteria - at an international level did not fully solve the discrepancies. As an example, the identification of Helicobacter Hepaticus as an opportunist pathogen that affects much biological parameters and its subsequent inclusion in the SPF list, clarified much discrepancies in the field of intestinal inflammation. More recently, the identification of Segmented Filamentous Bacteria (SFB) in the Taconic but not the Jackson C57BL/6 colonies has finally elucidated most intriguing phenotypic variations across institutions, in WT and in specific mutant mice, unwillingly cross-colonized. These two examples highlight that only a radical approach, such as axenization and colonization with a defined flora will ensure both reproducibility of investigations and proper assessment of the host genotype contribution to a given phenotype. It is worth noting that a minimal commensal flora is already defined and routinely used in some mouse production centers. Yet, it is also clear that even this restricted commensal flora (5-8 species) modify their host biology. In essence, it is becoming more common and there is indeed a requirement to assess the contribution of the microbiome to specific phenotypes.

Recent advances in disentangling mouse genotype and microbiota contribution to bio-medical phenotypes have been published in the literature.

EMMA offers as a service the generation of germ-free (axenic) mice via the Germ-Free Oeiras Service (GFOS). Please have a look at the details about this service.

The axenic service is funded by the INFRAFRONTIER-I3 project, a four year Integrated Infrastructure Initiative (I3) project that started in January 2013. INFRAFRONTIER-I3 is funded by the EC's FP7 Capacities Specific Programme.


For general enquiries on EMMA germ-free service
Dr. Michael Hagn
The European Mouse Mutant Archive
Helmholtz Zentrum München
Institute of Experimental Genetics
Ingolstädter Landstraße 1
85764 Neuherberg Germany
Phone: +49 89 31873628
FAX: +49 89 31873500


For scientific enquiries
EMMA Portugal
Instituto Gulbenkian de Ciência
Rua da Quinta Grande 6, Apartado 14
2781-901 Oeiras, Portugal
Phone: +351 21 440 79 08
FAX : + 351 21 440 79 70