Murine Microbiome Database

Search for species or other taxa

The number of projects
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The number of samples
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Notable bacterial taxa

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Muribaculaceae This family was a major bacterial component of mouse gastrointestinal tract, and previously known as S24-7 group (Lagkouvardos et al., 2019).
Arthromitus This Candidatus genus is a key regulator of mouse T cells and previously known as Segmented Filamentous Bacteria (SFB). SFB can interact closely with villous epithelium in the terminal ileum forming long filaments and cross-talk intimately with the host immune system. They were present only in mice with Th17 cell-inducing microbiota, such as C57BL/6 mice from Taconic Farms, however, not detected in mice without Th17 cell-inducing microbiota, including C57BL/6 mice from Jackson Laboratory (Ivanov, 2010).
Lactobacillus reuteri group This group contains Lactobacillus reuteri that was reported to ameliorate autism model in mouse (Sgritta et al., 2019).
Bacteroides acidifaciens group This group contains Bacteroides acidifaciens that was reported to gain less weight and fat mass than the control so that it can be a therapeutic candidate for obesity (Yang et al., 2017).
Turicibacter This genus was reported as characteristic of mice when comparing shotgun metagenomic datasets of human and mouse feces (Nguyen et al., 2015).

Overall relationships among the samples (PCoA plot of Bray-Curtis distances)


Data Projects

  • Shin, Jongoh, et al. "Analysis of the mouse gut microbiome using full-length 16S rRNA amplicon sequencing." Scientific reports 6.1 (2016): 1-10.
  • Suez, Jotham, et al. "Post-antibiotic gut mucosal microbiome reconstitution is impaired by probiotics and improved by autologous FMT." Cell 174.6 (2018): 1406-1423.
  • Campbell, James H., et al. "Host genetic and environmental effects on mouse intestinal microbiota." The ISME journal 6.11 (2012): 2033-2044.
  • Ericsson, Aaron C., et al. "Effects of vendor and genetic background on the composition of the fecal microbiota of inbred mice." PloS one 10.2 (2015): e0116704.
  • Sivan, Ayelet, et al. "Commensal Bifidobacterium promotes antitumor immunity and facilitates anti–PD-L1 efficacy." Science 350.6264 (2015): 1084-1089.
  • Ju, Tingting, et al. "Initial gut microbial composition as a key factor driving host response to antibiotic treatment, as exemplified by the presence or absence of commensal Escherichia coli." Applied and environmental microbiology 83.17 (2017).
  • Feng, Zhou, et al. "A human stool-derived Bilophila wadsworthia strain caused systemic inflammation in specific-pathogen-free mice." Gut pathogens 9.1 (2017): 1-10.
  • Casero, David, et al. "Space-type radiation induces multimodal responses in the mouse gut microbiome and metabolome." Microbiome 5.1 (2017): 1-18.
  • Caparrós-Martín, Jose A., et al. "Statin therapy causes gut dysbiosis in mice through a PXR-dependent mechanism." Microbiome 5.1 (2017): 1-15.
  • Lai, Zi-Lun, et al. "Fecal microbiota transplantation confers beneficial metabolic effects of diet and exercise on diet-induced obese mice." Scientific reports 8.1 (2018): 1-11.
  • Yildiz, Soner, et al. "Influenza A virus infection impacts systemic microbiota dynamics and causes quantitative enteric dysbiosis." Microbiome 6.1 (2018): 1-17.
  • Kok, Dieuwertje EG, et al. "Lifelong calorie restriction affects indicators of colonic health in aging C57Bl/6J mice." The Journal of nutritional biochemistry 56 (2018): 152-164.
  • Fabbiano, Salvatore, et al. "Functional gut microbiota remodeling contributes to the caloric restriction-induced metabolic improvements." Cell metabolism 28.6 (2018): 907-921.
  • Denis, Marie-Claude, et al. "Apple peel polyphenols: a key player in the prevention and treatment of experimental inflammatory bowel disease." Clinical Science 130.23 (2016): 2217-2237.
  • Rosshart, Stephan P., et al. "Wild mouse gut microbiota promotes host fitness and improves disease resistance." Cell 171.5 (2017): 1015-1028.
  • Rosshart, Stephan P., et al. "Laboratory mice born to wild mice have natural microbiota and model human immune responses." Science 365.6452 (2019).
  • Tam, Anthony, et al. "Effects of sex and chronic cigarette smoke exposure on the mouse cecal microbiome." PloS one 15.4 (2020): e0230932.

Data Analysis

  • 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.
  • Bolyen, Evan et al. "Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2". Nature Biotechnology 37. 8(2019): 852-857.
  • Vázquez-Baeza, Yoshiki et al. "EMPeror: a tool for visualizing high-throughput microbial community data". Gigascience 2. 1(2013): 16.
  • Vázquez-Baeza, Yoshiki et al. "Bringing the dynamic microbiome to life with animations". Cell host & microbe 21. 1(2017): 7–10.
  • Sørensen, Thorvald. "A method of establishing groups of equal amplitude in plant sociology based on similarity of species and its application to analyses of the vegetation on Danish commons". Biol. Skr. 5. (1948): 1–34.
  • McDonald, Daniel et al. "The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome". GigaScience 1. 1(2012): 7.
  • McDonald, Daniel et al. "The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome". GigaScience 1. 1(2012): 7.
  • Weiss, Sophie et al. "Normalization and microbial differential abundance strategies depend upon data characteristics". Microbiome 5. 1(2017): 27.
  • Legendre, Pierre, and Louis Legendre. Numerical ecology. Elsevier, 2012.
  • Halko, Nathan et al. "An algorithm for the principal component analysis of large data sets". arXiv e-prints. (2010).
  • McDonald, Daniel et al. "The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome". GigaScience 1. 1(2012): 7.