In addition to providing single bacterial strains from the mouse intestine, this resource gives access to cryostocks of the Oligo‐Mouse Microbiota (OMM) synthetic communities to perform colonisation studies in gnotobiotic mice.

OMM12 and OMM19.1 are curated synthetic communities of known bacterial strains originating from miBC. All strains within these communities are taxonomically and functionally described, and precisely chosen to encompass a broad phylogenetic diversity, as well as cover a large array of essential microbial functions from the mouse gut.
The original OMM12 community (Brugiroux et al., 2016) contains bacteria that emulate many functions of a complex microbiota. When supplemented with three facultative anaerobic species, it provided colonisation resistance to Salmonella enterica serovar Typhimurium infection in mice. The reproducibility of colonisation in different animal facilities has been shown previously (Eberl et al., 2020).
OMM19.1 builds upon OMM12 using additional strains from miBC. These strains cover a greater taxonomic range, and with it an expanded spectrum of functions, including secondary bile acid producers and fibre degraders. The phenotype of OMM19.1 colonised mice is shown to be more similar to specified-pathogen-free mice both physiologically, and immunologically.
Colonisation reproducibility of OMM19.1 has also been assured over generations and across multiple animal facilities. However, some variability is observed due to differences in detection methods and the protocol used for colonisation. To reduce variability, standardised cryostocks (as provided here by the DSMZ) should be used for colonisation. Please follow this link to access our recommendations.
The OMM cryostocks are provided as 1mL aliquots of cell suspension containing ca. 14%‐glycerol. They are stored at ‐80 °C in air‐tight, glass vials that were prepared under anaerobic conditions. Two stocks of each the OMM‐basis and one of the extension mixtures (to generate either the OMM12 or OMM19.1 community) are required for colonisation of one cage of mice (hosting up to six mice depending on cage specifications).
To order cryostocks, please contact pathogen(at)


SpeciesDSM number
Akkermansia muciniphila26127
Bacteroides caecimuris26085T
Blautia coccoides26115
Enterocloster clostridioformis26114
Clostridium innocuum26113
Enterococcus faecalis32036
Flavonifractor plautii26117
Limosilactobacillus reuteri32035
Muribaculum intestinale28989T
Turicimonas muris26109T



SpeciesDSM number
Acutalibacter muris26090T
Bifidobacterium animalis26074T



SpeciesDSM number
Clostridium ramosum29357
Adlercreutzia mucosicola19490T
Escherichia coli28618
Extibacter muris28560T
Flintibacter butyricus27579T
Ligilactobacillus murinus28683
Mucispirillum schaedleri104751
Parabacteroides goldsteinii29187
Prevotella sp.105243