The mouse gut microbiome could affect the result of the experiment, which uses the mouse as the mammalian model organism. For example, the C57BL/6 mouse obtained from Jackson Laboratory and Taconic farms showed different resistances against the melanoma tumor, which resulted from the gut microbiome differences (Sivan et al., 2015). Given that the mouse gut microbiome could affect the physiology of the mouse, researchers should be fully aware of their mouse gut microbiome background.
The Murine Microbiome Database (MMDB) contains microbiome taxonomic profiles (MTPs) of the healthy mouse gut with manually curated metadata. MTP is a unit of data that has the taxonomic profile of a bacterial microbiome sample, and it can be generated from the sample using the bacterial 16S ribosomal RNA gene (Yoon et al., 2017). In this database, each metagenome sequence was analyzed with EzBioCloud 16S database version PKSSU4.0 after trimming V4 region, and only samples containing >10,000 valid reads were parsed and inserted into the database.
This database provides researchers with information about not only which bacterial species are predominant in the specific mouse condition, including types of sampling locations, genotypes or vendors but also which mouse environment harbors high levels of the specific bacteria.
In this section, researchers can check the projects in the MMDB. It provides search services that show filtered entries based on the words typed in the search box. Each project page contains more specific metadata about the project and information about samples included in the project.
In this section, researchers can check the samples in the MMDB. It provides search services that show filtered entries based on the words typed in the search box. Each sample page contains more specific metadata about the sample, diversity indices, and the bacterial composition visualized using Krona (Ondov et al., 2011). In addition, researchers can obtain the specific bacterial composition rates of samples in the descending order with the “Search for species or other taxa” service providing them with information about which mouse environment harbors the high level of the specific bacteria.
Sivan, Ayelet, et al. "Commensal Bifidobacterium promotes antitumor immunity and facilitates anti–PD-L1 efficacy." Science 350.6264 (2015): 1084-1089.
Yoon, Seok-Hwan, et al. "Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies." International journal of systematic and evolutionary microbiology 67.5 (2017): 1613.
Ondov BD, Bergman NH, and Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics. 2011 Sep 30; 12(1):385.
1Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 00826, Republic of Korea
2Institute of Molecular Biology and Genetics, Seoul National University, Seoul 00826, Republic of Korea
3School of Biological Sciences, Seoul National University, Seoul 00826, Republic of Korea