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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 weekly.

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 here) can be generated by combining the basis set with extension 1. The new OMM19.1 model (see preprint here) is obtained by combining the basis and extension set 2.

Synthetic community designationID
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"

110981

Acetatifactor  muris Pfeiffer et al. 2013

23669

Actinomyces  bowdenii Pascual et al. 1999

28589

Acutalibacter  muris Lagkouvardos et al. 2016

26090

"Adlercreutzia  agrestimuris"

109821

"Adlercreutzia  aquisgranensis"

108611

Adlercreutzia  caecicola (Clavel et al. 2013) Nouioui et al. 2018

22242

Adlercreutzia  caecimuris (Clavel et al. 2010) Nouioui et al. 2018

21839

Adlercreutzia  mucosicola (Clavel et al. 2009) Nouioui et al. 2018

19490

"Adlercreutzia  murintestinalis"

112345

Adlercreutzia  muris (Lagkouvardos et al. 2016) Nouioui et al. 2018

29508

Adlercreutzia  muris (Lagkouvardos et al. 2016) Nouioui et al. 2018

110078

Adlercreutzia  muris (Lagkouvardos et al. 2016) Nouioui et al. 2018

110158

Akkermansia  muciniphila Derrien et al. 2004 emend. Hahnke et al. 2016

26127

"Alistipes  muris"

112343

Alistipes  timonensis Lagier et al. 2014

27924

Anaerofustis  stercorihominis Finegold et al. 2004

28733

Anaerosalibacter  massiliensis Dione et al. 2016

29482

Anaerotruncus  colihominis Lawson et al. 2004

28734

Bacillus  cereus Frankland and Frankland 1887

28590

Bacillus  licheniformis (Weigmann 1898) Chester 1901

28591

Bacillus  licheniformis (Weigmann 1898) Chester 1901

111625

Bacillus  subtilis (Ehrenberg 1835) Cohn 1872

28592

Bacillus  thermoamylovorans Combet-Blanc et al. 1995 emend. Coorevits et al. 2011

28625

Bacteroides  acidifaciens Miyamoto and Itoh 2000

100502

Bacteroides  caecimuris Lagkouvardos et al. 2016

26085

Bacteroides  faecichinchillae Kitahara et al. 2012

110161

"Bacteroides  muris"

110164

"Bacteroides  muris"

114231

Bacteroides  uniformis Eggerth and Gagnon 1933 emend. Hahnke et al. 2016

110080

Bacteroides  xylanisolvens Chassard et al. 2008

100015

Bacteroides  xylanisolvens Chassard et al. 2008

110079

Bifidobacterium  animalis (Mitsuoka 1969) Scardovi and Trovatelli 1974 emend. Masco et al. 2004

28736

Bifidobacterium  animalis (Mitsuoka 1969) Scardovi and Trovatelli 1974 emend. Masco et al. 2004

26074

Bifidobacterium  globosum (ex Scardovi et al. 1969) Biavati et al. 1982 emend. Nouioui et al. 2018

105315

Blautia  caecimuris Lagkouvardos et al. 2016

29492

Blautia  coccoides (Kaneuchi et al. 1976) Liu et al. 2008

29138

Blautia  pseudococcoides

28737

Blautia  pseudococcoides

26115

"Caniella  muris"

105314

"Caniella  muris"

110323

"Caniella  muris"

110563

"Caniella  muris"

110983

Cellulosimicrobium  cellulans (Metcalfe and Brown 1957) Schumann et al. 2001

29131

Clostridioides  mangenotii (Prévot and Zimmès-Chaverou 1947) Lawson et al. 2016

29133

Clostridium  butyricum Prazmowski 1880

107392

Clostridium  chromiireducens Inglett et al. 2011

110167

Clostridium  cochlearium (Douglas et al. 1919) Bergey et al. 1923

29358

Clostridium  cocleatum Kaneuchi et al. 1979

1551

Clostridium  innocuum Smith and King 1962

29132

Clostridium  innocuum Smith and King 1962

26113

"Clostridium  mucosae"

100503

Clostridium  perfringens (Veillon and Zuber 1898) Hauduroy et al. 1937

29991

Clostridium  ramosum (Veillon and Zuber 1898) Holdeman et al. 1971

29355

Clostridium  ramosum (Veillon and Zuber 1898) Holdeman et al. 1971

29357

Clostridium  sporogenes (Metchnikoff 1908) Bergey et al. 1923

29422

Clostridium  symbiosum (Stevens 1956) Kaneuchi et al. 1976

29356

Clostridium  tepidum Dobritsa et al. 2017

29420

Cuneatibacter  caecimuris Lagkouvardos et al. 2016

29486

"Dubosiella  muris"

110160

Duncaniella  muris Lagkouvardos et al. 2019

103720

Clostridium  bolteae Song et al. 2003

29485

Enterocloster  clostridioformis (Burri and Ankersmit 1906) Haas and Blanchard 2020

26114

Enterococcus  avium (ex Nowlan and Deibel 1967) Collins et al. 1984

106040

Enterococcus  faecalis (Andrewes and Horder 1906) Schleifer and Kilpper-Bälz 1984

29488

Enterococcus  faecalis (Andrewes and Horder 1906) Schleifer and Kilpper-Bälz 1984

32036

Enterococcus  faecalis (Andrewes and Horder 1906) Schleifer and Kilpper-Bälz 1984

106192

Enterococcus  faecalis (Andrewes and Horder 1906) Schleifer and Kilpper-Bälz 1984

110077

Enterococcus  gallinarum (Bridge and Sneath 1982) Collins et al. 1984

28564

Enterococcus  gallinarum (Bridge and Sneath 1982) Collins et al. 1984

28565

Enterococcus  gallinarum (Bridge and Sneath 1982) Collins et al. 1984

100110

Enterococcus  gallinarum (Bridge and Sneath 1982) Collins et al. 1984

106191

Enterococcus  gallinarum (Bridge and Sneath 1982) Collins et al. 1984

111134

Enterococcus  hirae Farrow and Collins 1985

28619

Escherichia  coli (Migula 1895) Castellani and Chalmers 1919

28618

Escherichia  coli (Migula 1895) Castellani and Chalmers 1919

112109

Escherichia  coli (Migula 1895) Castellani and Chalmers 1919

112110

Escherichia  coli (Migula 1895) Castellani and Chalmers 1919

112111

Escherichia  coli (Migula 1895) Castellani and Chalmers 1919

112112

Escherichia  coli (Migula 1895) Castellani and Chalmers 1919

112113

Escherichia  coli (Migula 1895) Castellani and Chalmers 1919

112114

Escherichia  coli (Migula 1895) Castellani and Chalmers 1919

112115

Escherichia  coli (Migula 1895) Castellani and Chalmers 1919

112116

Escherichia  coli (Migula 1895) Castellani and Chalmers 1919

112117

Escherichia  coli (Migula 1895) Castellani and Chalmers 1919

112118

Escherichia  coli (Migula 1895) Castellani and Chalmers 1919

112119

Escherichia  coli (Migula 1895) Castellani and Chalmers 1919

112120

Escherichia  coli (Migula 1895) Castellani and Chalmers 1919

112121

Escherichia  coli (Migula 1895) Castellani and Chalmers 1919

112122

Escherichia  coli (Migula 1895) Castellani and Chalmers 1919

112123

Escherichia  coli (Migula 1895) Castellani and Chalmers 1919

112124

Escherichia  coli (Migula 1895) Castellani and Chalmers 1919

112125

Escherichia  coli (Migula 1895) Castellani and Chalmers 1919

112126

Escherichia  coli (Migula 1895) Castellani and Chalmers 1919

112127

Escherichia  coli (Migula 1895) Castellani and Chalmers 1919

112128

Extibacter  muris Lagkouvardos et al. 2017

28560

Extibacter  muris Lagkouvardos et al. 2017

28561

Faecalibaculum  rodentium Chang et al. 2016 emend. Cox et al. 2017

110083

Flavonifractor  plautii (Séguin 1928) Carlier et al. 2010

29136

Flavonifractor  plautii (Séguin 1928) Carlier et al. 2010

29137

Flavonifractor  plautii (Séguin 1928) Carlier et al. 2010

26117

Flintibacter  butyricus corrig. Lagkouvardos et al. 2016

27579

"Flintibacter  muris"

110149

Frisingicoccus  caecimuris Lagkouvardos et al. 2016

28559

"Hominisplanchenecus  murintestinalis"

110165

Hungatella  effluvii Kaur et al. 2014

107394

Intestinimonas  butyriciproducens Kläring et al. 2013

26588

Irregularibacter  muris Lagkouvardos et al. 2016

28593

Kosakonia  cowanii (Inoue et al. 2001) Brady et al. 2013

111930

"Lachnospiraceae  bacterium"

111138

"Lactobacillus  agrestimuris"

110155

Lactobacillus  intestinalis (ex Hemme 1974) Fujisawa et al. 1990

107393

Lactobacillus  johnsonii Fujisawa et al. 1992

100219

Lactobacillus  paracasei Collins et al. 1989

28675

Lactobacillus  rodentium Killer et al. 2014

24759

Lactobacillus  taiwanensis Wang et al. 2009

28674

Lactobacillus  taiwanensis Wang et al. 2009

100220

"Lactococcus  ileimucosae"

107391

Lactococcus  lactis (Lister 1873) Schleifer et al. 1986

110082

"Lactococcus  muris"

109779

Lactococcus  petauri Goodman et al. 2017

109777

"Lepagella  muris"

110157

Ligilactobacillus  apodemi (Osawa et al. 2006) Zheng et al. 2020

16748

Ligilactobacillus  murinus (Hemme et al. 1982) Zheng et al. 2020

28690

Ligilactobacillus  murinus (Hemme et al. 1982) Zheng et al. 2020

28683

Ligilactobacillus  murinus (Hemme et al. 1982) Zheng et al. 2020

100193

Ligilactobacillus  murinus (Hemme et al. 1982) Zheng et al. 2020

100194

Limosilactobacillus  antri (Roos et al. 2005) Zheng et al. 2020

106038

Limosilactobacillus  antri (Roos et al. 2005) Zheng et al. 2020

110087

"Limosilactobacillus  caecicola"

110982

Limosilactobacillus  reuteri (Kandler et al. 1982) Zheng et al. 2020

28673

Limosilactobacillus  reuteri (Kandler et al. 1982) Zheng et al. 2020

100191

Limosilactobacillus  reuteri (Kandler et al. 1982) Zheng et al. 2020

100192

Limosilactobacillus  reuteri (Kandler et al. 1982) Zheng et al. 2020

32035

Limosilactobacillus  urinaemulieris Ksiezarek et al. 2021

106190

Longibaculum  muris Lagkouvardos et al. 2017

29487

Longicatena  caecimuris Lagkouvardos et al. 2016

29481

Longicatena  caecimuris Lagkouvardos et al. 2016

29490

Mammaliicoccus  lentus (Kloos et al. 1976) Madhaiyan et al. 2020

100111

"Mediterraneibacter  agrestimuris"

111629

Mucispirillum  schaedleri Robertson et al. 2005

104751

"Muribaculum  caecicola"

110169

Muribaculum  gordoncarteri Miyake et al. 2020

110163

Muribaculum  intestinale Lagkouvardos et al. 2016

100739

Muribaculum  intestinale Lagkouvardos et al. 2016

100746

Muribaculum  intestinale Lagkouvardos et al. 2016

28989

"Muricaecibacterium  torontonense"

110159

Muricomes  intestini Lagkouvardos et al. 2016

29489

Murimonas  intestini Kläring et al. 2015

26524

Murimonas  intestini Kläring et al. 2015

27577

Murimonas  intestini Kläring et al. 2015

27578

"Neobacillus  muris"

110989

Oceanobacillus  caeni Nam et al. 2008

28620

"Odoribacter  lunatus"

112344

Paenibacillus  lactis Scheldeman et al. 2004

28626

Paeniclostridium  sordellii (Hall and Scott 1927) Sasi Jyothsna et al. 2016

29974

"Palleniella  intestinalis"

103738

"Palleniella  muris"

110166

Parabacteroides  distasonis (Eggerth and Gagnon 1933) Sakamoto and Benno 2006 emend. Hahnke et al. 2016

29491

Parabacteroides  distasonis (Eggerth and Gagnon 1933) Sakamoto and Benno 2006 emend. Hahnke et al. 2016

111137

Parabacteroides  goldsteinii (Song et al. 2006) Sakamoto and Benno 2006

29187

Parabacteroides  goldsteinii (Song et al. 2006) Sakamoto and Benno 2006

111136

Paraclostridium  bifermentans (Weinberg and Séguin 1918) Sasi Jyothsna et al. 2016 emend. Kutsuna et al. 2018

29423

Paramuribaculum  intestinale Lagkouvardos et al. 2019

100749

Paramuribaculum  intestinale Lagkouvardos et al. 2019

100764

Parasutterella  excrementihominis Nagai et al. 2009

111000

"Parasutterella  muris"

108034

"Parasutterella  muris"

110635

Pasteurella  caecimuris Lagkouvardos et al. 2016

28627

Pasteurella  caecimuris Lagkouvardos et al. 2016

100775

Pediococcus  pentosaceus Mees 1934

28628

"Petralouisia  muris"

110156

Phocaeicola  sartorii (Clavel et al. 2010) García-López et al. 2020

21941

Phocaeicola  sartorii (Clavel et al. 2010) García-López et al. 2020

110081

Phocaeicola  vulgatus (Eggerth and Gagnon 1933) García-López et al. 2020

28735

Proteus  mirabilis Hauser 1885

28629

Pseudomonas  oleovorans Lee and Chandler 1941 emend. Saha et al. 2010

28630

"Senimuribacter  intestinalis"

106208

"Senimuribacter  intestinalis"

109599

Sphingomonas  olei Chaudhary and Kim 2017

110168

Sporofaciens  musculi Rasmussen et al. 2021

106039

Staphylococcus  warneri Kloos and Schleifer 1975

28567

Staphylococcus  xylosus Schleifer and Kloos 1975

28566

"Stenotrophomonas  muris"

28631

Streptococcus  acidominimus Ayers and Mudge 1922

108490

"Streptococcus  caecimuris"

110150

Streptococcus  danieliae Clavel et al. 2013

22233

Streptococcus  thoraltensis Devriese et al. 1997

110086

"Taurinivorans  muris"

111569

Terrisporobacter  sp.

29186

Turicimonas  muris Lagkouvardos et al. 2017

26109

"Veillonella  agrestimuris"

110088

"Veillonella  intestinalis"

105313

"Veillonella  intestinalis"

110113

"Vermiculatibacterium  agrestimuris"

112226

"Weizmannia  agrestimuris"

106041

"Xylanibacter  caecicola"

105245

"Xylanibacter  muris"

103722

"Xylanibacter  rodentium"

103721

"Xylanibacter  rodentium"

105243

"Xylanibacter  rodentium"

105244

Yersinia  enterocolitica (Schleifstein and Coleman 1939) Frederiksen 1964

110076