miBC: The mouse intestinal Bacterial Collection
This collection includes bacterial strains isolated from the intestine of mice. They have been taxonomically described and are all publicly available. This well-curated resource was built to increase our knowledge of cultured diversity within the mouse gut microbiota and to support scientists with their own research by providing multiple strains representing a broad phylogenetic diversity to be used for functional experiments.
miBC is an initiative from the RTWH Aachen (Prof. Thomas Clavel) and the Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures. It is supported by Collaborative Research Centre (CRC) 1371 and CRC1382 and by the German Federal Ministry of Science and Education through the German Center of Infection Research (DZIF).
The list below gives the identity of all strains currently included into the collection (strain-specific information is accessible via links through the DSM No.). The original version of the collection published in 2016 (the publication can be accessed here) was doubled by the addition of 112 strains, representing a total of 141 species across 6 phyla for the entire collection. The work has been published and can be accessed here. Note that, due to ongoing curation work, the list below is not yet complete and is being amended regularly.
In addition to providing single strains (see list below), this resource also gives access to cryo-stocks of OMM (Oligo-Mouse Microbiota) synthetic communities to perform colonization studies in gnotobiotic mice.
The original OMM12 model (see publication) can be generated by combining the basis set with extension 1. The new OMM19.1 model (see publication) is obtained by combining the basis and extension set 2.
Synthetic community designation | ID |
---|---|
Basis OMM set (10 strains) | OMM-basis |
Extension set 1 (2 strains) | OMM-ext-1.2 |
Extension set 2 (9 strains) | OMM-ext-2.9 |
miBC: The mouse intestinal Bacterial Collection
Species | DSM No. |
---|---|
Acetatifactor aquisgranensis | |
Acetatifactor muris Pfeiffer et al. 2013 | |
Actinomyces bowdenii Pascual et al. 1999 | |
Acutalibacter muris Lagkouvardos et al. 2016 | |
Adlercreutzia agrestimuris | |
Adlercreutzia aquisgranensis | |
Adlercreutzia caecicola (Clavel et al. 2013) Nouioui et al. 2018 | |
Adlercreutzia caecimuris (Clavel et al. 2010) Nouioui et al. 2018 | |
Adlercreutzia mucosicola (Clavel et al. 2009) Nouioui et al. 2018 | |
"Adlercreutzia murintestinalis" | |
Adlercreutzia muris (Lagkouvardos et al. 2016) Nouioui et al. 2018 | |
Adlercreutzia muris (Lagkouvardos et al. 2016) Nouioui et al. 2018 | |
Adlercreutzia muris (Lagkouvardos et al. 2016) Nouioui et al. 2018 | |
Akkermansia muciniphila Derrien et al. 2004 emend. Hahnke et al. 2016 | |
"Alistipes muris" | |
Alistipes timonensis Lagier et al. 2014 | |
Anaerofustis stercorihominis Finegold et al. 2004 | |
Anaerosalibacter massiliensis Dione et al. 2016 | |
Anaerotruncus colihominis Lawson et al. 2004 | |
Bacillus cereus Frankland and Frankland 1887 | |
Bacillus licheniformis (Weigmann 1898) Chester 1901 | |
Bacillus licheniformis (Weigmann 1898) Chester 1901 | |
Bacillus subtilis (Ehrenberg 1835) Cohn 1872 | |
Bacillus thermoamylovorans Combet-Blanc et al. 1995 emend. Coorevits et al. 2011 | |
Bacteroides acidifaciens Miyamoto and Itoh 2000 | |
Bacteroides acidifaciens Miyamoto and Itoh 2000 | |
Bacteroides acidifaciens Miyamoto and Itoh 2000 | |
Bacteroides caecimuris Lagkouvardos et al. 2016 | |
Bacteroides faecichinchillae Kitahara et al. 2012 | |
Bacteroides muris | |
Bacteroides muris | |
Bacteroides uniformis Eggerth and Gagnon 1933 emend. Hahnke et al. 2016 | |
Bacteroides xylanisolvens Chassard et al. 2008 | |
Bacteroides xylanisolvens Chassard et al. 2008 | |
Bifidobacterium animalis (Mitsuoka 1969) Scardovi and Trovatelli 1974 emend. Masco et al. 2004 | |
Bifidobacterium animalis (Mitsuoka 1969) Scardovi and Trovatelli 1974 emend. Masco et al. 2004 | |
Bifidobacterium pseudolongum Mitsuoka 1969 emend. Nouioui et al. 2018 | |
Blautia caecimuris Lagkouvardos et al. 2016 | |
Blautia coccoides (Kaneuchi et al. 1976) Liu et al. 2008 | |
Blautia pseudococcoides | |
Blautia pseudococcoides | |
Caniella muris | |
Caniella muris | |
Caniella muris | |
Caniella muris | |
Cellulosimicrobium cellulans (Metcalfe and Brown 1957) Schumann et al. 2001 | |
Clostridioides mangenotii (Prévot and Zimmès-Chaverou 1947) Lawson et al. 2016 | |
Clostridium butyricum Prazmowski 1880 | |
Clostridium chromiireducens Inglett et al. 2011 | |
Clostridium cochlearium (Douglas et al. 1919) Bergey et al. 1923 | |
Clostridium innocuum Smith and King 1962 | |
Clostridium innocuum Smith and King 1962 | |
"Clostridium mucosae" | |
Clostridium perfringens (Veillon and Zuber 1898) Hauduroy et al. 1937 | |
Clostridium sporogenes (Metchnikoff 1908) Bergey et al. 1923 | |
Clostridium symbiosum (Stevens 1956) Kaneuchi et al. 1976 | |
Clostridium tepidum Dobritsa et al. 2017 | |
Cuneatibacter caecimuris Lagkouvardos et al. 2016 | |
Dubosiella muris | |
Duncaniella muris Lagkouvardos et al. 2019 | |
Enterocloster bolteae (Song et al. 2003) Haas and Blanchard 2020 | |
Enterocloster clostridioformis (Burri and Ankersmit 1906) Haas and Blanchard 2020 | |
Enterococcus avium (ex Nowlan and Deibel 1967) Collins et al. 1984 | |
Enterococcus faecalis (Andrewes and Horder 1906) Schleifer and Kilpper-Bälz 1984 | |
Enterococcus faecalis (Andrewes and Horder 1906) Schleifer and Kilpper-Bälz 1984 | |
Enterococcus faecalis (Andrewes and Horder 1906) Schleifer and Kilpper-Bälz 1984 | |
Enterococcus faecalis (Andrewes and Horder 1906) Schleifer and Kilpper-Bälz 1984 | |
Enterococcus faecalis (Andrewes and Horder 1906) Schleifer and Kilpper-Bälz 1984 | |
Enterococcus gallinarum (Bridge and Sneath 1982) Collins et al. 1984 | |
Enterococcus gallinarum (Bridge and Sneath 1982) Collins et al. 1984 | |
Enterococcus gallinarum (Bridge and Sneath 1982) Collins et al. 1984 | |
Enterococcus gallinarum (Bridge and Sneath 1982) Collins et al. 1984 | |
Enterococcus gallinarum (Bridge and Sneath 1982) Collins et al. 1984 | |
Enterococcus hirae Farrow and Collins 1985 | |
Escherichia coli (Migula 1895) Castellani and Chalmers 1919 | |
Escherichia coli (Migula 1895) Castellani and Chalmers 1919 | |
Escherichia coli (Migula 1895) Castellani and Chalmers 1919 | |
Escherichia coli (Migula 1895) Castellani and Chalmers 1919 | |
Escherichia coli (Migula 1895) Castellani and Chalmers 1919 | |
Escherichia coli (Migula 1895) Castellani and Chalmers 1919 | |
Escherichia coli (Migula 1895) Castellani and Chalmers 1919 | |
Escherichia coli (Migula 1895) Castellani and Chalmers 1919 | |
Escherichia coli (Migula 1895) Castellani and Chalmers 1919 | |
Escherichia coli (Migula 1895) Castellani and Chalmers 1919 | |
Escherichia coli (Migula 1895) Castellani and Chalmers 1919 | |
Escherichia coli (Migula 1895) Castellani and Chalmers 1919 | |
Escherichia coli (Migula 1895) Castellani and Chalmers 1919 | |
Escherichia coli (Migula 1895) Castellani and Chalmers 1919 | |
Escherichia coli (Migula 1895) Castellani and Chalmers 1919 | |
Escherichia coli (Migula 1895) Castellani and Chalmers 1919 | |
Escherichia coli (Migula 1895) Castellani and Chalmers 1919 | |
Escherichia coli (Migula 1895) Castellani and Chalmers 1919 | |
Escherichia coli (Migula 1895) Castellani and Chalmers 1919 | |
Escherichia coli (Migula 1895) Castellani and Chalmers 1919 | |
Escherichia coli (Migula 1895) Castellani and Chalmers 1919 | 112128 |
Extibacter muris Lagkouvardos et al. 2017 | |
Extibacter muris Lagkouvardos et al. 2017 | |
Faecalibaculum rodentium Chang et al. 2016 emend. Cox et al. 2017 | |
Flavonifractor plautii (Séguin 1928) Carlier et al. 2010 | |
Flavonifractor plautii (Séguin 1928) Carlier et al. 2010 | |
Flavonifractor plautii (Séguin 1928) Carlier et al. 2010 | |
Flintibacter butyricus corrig. Lagkouvardos et al. 2016 | |
Flintibacter muris | |
Frisingicoccus caecimuris Lagkouvardos et al. 2016 | |
"Hominisplanchenecus murintestinalis" | |
"Hominisplanchenecus murintestinalis" | |
Hungatella effluvii Kaur et al. 2014 | |
Intestinimonas butyriciproducens Kläring et al. 2013 | |
Irregularibacter muris Lagkouvardos et al. 2016 | |
Kosakonia cowanii (Inoue et al. 2001) Brady et al. 2013 | |
Lactobacillus agrestimuris | |
Lactobacillus intestinalis (ex Hemme 1974) Fujisawa et al. 1990 | |
Lactobacillus johnsonii Fujisawa et al. 1992 | |
Lactobacillus paracasei Collins et al. 1989 | |
Lactobacillus rodentium Killer et al. 2014 | |
Lactobacillus taiwanensis Wang et al. 2009 | |
Lactobacillus taiwanensis Wang et al. 2009 | |
Lactococcus ileimucosae | |
Lactococcus lactis (Lister 1873) Schleifer et al. 1986 | |
Lactococcus muris | |
Lactococcus petauri Goodman et al. 2017 | |
Lepagella muris | |
Ligilactobacillus apodemi (Osawa et al. 2006) Zheng et al. 2020 | |
Ligilactobacillus murinus (Hemme et al. 1982) Zheng et al. 2020 | |
Ligilactobacillus murinus (Hemme et al. 1982) Zheng et al. 2020 | |
Ligilactobacillus murinus (Hemme et al. 1982) Zheng et al. 2020 | |
Ligilactobacillus murinus (Hemme et al. 1982) Zheng et al. 2020 | |
Limosilactobacillus agrestimuris | |
Limosilactobacillus antri (Roos et al. 2005) Zheng et al. 2020 | |
Limosilactobacillus antri (Roos et al. 2005) Zheng et al. 2020 | |
Limosilactobacillus caecicola | |
Limosilactobacillus reuteri (Kandler et al. 1982) Zheng et al. 2020 | |
Limosilactobacillus reuteri (Kandler et al. 1982) Zheng et al. 2020 | |
Limosilactobacillus reuteri (Kandler et al. 1982) Zheng et al. 2020 | |
Limosilactobacillus reuteri (Kandler et al. 1982) Zheng et al. 2020 | |
Limosilactobacillus urinaemulieris Ksiezarek et al. 2021 | |
Longibaculum muris Lagkouvardos et al. 2017 | |
Longicatena caecimuris Lagkouvardos et al. 2016 | |
Longicatena caecimuris Lagkouvardos et al. 2016 | |
Mammaliicoccus lentus (Kloos et al. 1976) Madhaiyan et al. 2020 | |
"Mediterraneibacter agrestimuris" | |
Mucispirillum schaedleri Robertson et al. 2005 | |
Muribaculum caecicola | |
Muribaculum gordoncarteri Miyake et al. 2020 | |
Muribaculum intestinale Lagkouvardos et al. 2016 | |
Muribaculum intestinale Lagkouvardos et al. 2016 | |
Muribaculum intestinale Lagkouvardos et al. 2016 | |
Muricaecibacterium torontonense | |
Muricomes intestini Lagkouvardos et al. 2016 | |
Murimonas intestini Kläring et al. 2015 | |
Murimonas intestini Kläring et al. 2015 | |
Murimonas intestini Kläring et al. 2015 | |
Neobacillus muris | |
Oceanobacillus caeni Nam et al. 2008 | |
Odoribacter lunatus | |
Otoolea muris | |
Paenibacillus lactis Scheldeman et al. 2004 | |
Paeniclostridium sordellii (Hall and Scott 1927) Sasi Jyothsna et al. 2016 | |
Palleniella intestinalis | |
Palleniella muris | |
Parabacteroides distasonis (Eggerth and Gagnon 1933) Sakamoto and Benno 2006 emend. Hahnke et al. 2016 | |
Parabacteroides distasonis (Eggerth and Gagnon 1933) Sakamoto and Benno 2006 emend. Hahnke et al. 2016 | |
Parabacteroides goldsteinii (Song et al. 2006) Sakamoto and Benno 2006 | |
Parabacteroides goldsteinii (Song et al. 2006) Sakamoto and Benno 2006 | |
Paraclostridium bifermentans (Weinberg and Séguin 1918) Sasi Jyothsna et al. 2016 emend. Kutsuna et al. 2018 | |
Paramuribaculum intestinale Lagkouvardos et al. 2019 | |
Paramuribaculum intestinale Lagkouvardos et al. 2019 | |
"Parasutterella muris" | |
"Parasutterella muris" | |
"Parasutterella sp." | |
Pasteurella caecimuris Lagkouvardos et al. 2016 | |
Pasteurella caecimuris Lagkouvardos et al. 2016 | |
Pediococcus pentosaceus Mees 1934 | |
"Petralouisia muris" | |
Phocaeicola sartorii (Clavel et al. 2010) García-López et al. 2020 | |
Phocaeicola sartorii (Clavel et al. 2010) García-López et al. 2020 | |
Phocaeicola vulgatus (Eggerth and Gagnon 1933) García-López et al. 2020 | |
Proteus mirabilis Hauser 1885 | |
Pseudomonas oleovorans Lee and Chandler 1941 emend. Saha et al. 2010 | |
"Senimuribacter intestinalis" | |
"Senimuribacter intestinalis" | |
Sphingomonas olei Chaudhary and Kim 2017 | |
Sporofaciens musculi Rasmussen et al. 2021 | |
Staphylococcus warneri Kloos and Schleifer 1975 | |
Staphylococcus xylosus Schleifer and Kloos 1975 | |
"Stenotrophomonas muris" | |
Streptococcus acidominimus Ayers and Mudge 1922 | |
Streptococcus caecimuris | |
Streptococcus danieliae Clavel et al. 2013 | |
Streptococcus thoraltensis Devriese et al. 1997 | |
"Taurinivorans muris" | |
"Terrisporobacter sp." | |
Thomasclavelia cocleata | |
Thomasclavelia ramosa | |
Thomasclavelia ramosa | |
Turicimonas muris Lagkouvardos et al. 2017 | |
Veillonella agrestimuris | |
Veillonella intestinalis | |
Veillonella intestinalis | |
"Vermiculatibacterium agrestimuris" | |
Weizmannia agrestimuris | |
"Xylanibacter caecicola" | |
Xylanibacter muris | |
Xylanibacter rodentium | |
Xylanibacter rodentium | |
Xylanibacter rodentium | 105244 |
Yersinia enterocolitica (Schleifstein and Coleman 1939) Frederiksen 1964 |