Strain identifier

BacDive ID: 24772

Type strain: Yes

Species: Intestinimonas butyriciproducens

Strain Designation: SRB-521-5-l

Strain history: <- DSM <- T Clavel, TU Munich, Freising-Weihenstephan, Germany, SRB-521-5-l <- K Klaring(2012)

NCBI tax ID(s): 1297617 (species)

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General

@ref: 21298

BacDive-ID: 24772

DSM-Number: 26588

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, Gram-positive, rod-shaped

description: Intestinimonas butyriciproducens SRB-521-5-l is an anaerobe, spore-forming, mesophilic bacterium that was isolated from caecal content of a 17-week-old female heterozygous TNF deltaARE mouse.

NCBI tax id

  • NCBI tax id: 1297617
  • Matching level: species

strain history

@refhistory
21298<- T. Clavel, TU Munich, Freising-Weihenstephan, Germany; SRB-521-5-l <- K. Kläring {2012}
67770CCUG 63529 <-- T. Clavel; Tech. Univ. of Munich, Germany; SRB-521-5-I.
67771<- DSM <- T Clavel, TU Munich, Freising-Weihenstephan, Germany, SRB-521-5-l <- K Klaring(2012)

doi: 10.13145/bacdive24772.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Oscillospiraceae
  • genus: Intestinimonas
  • species: Intestinimonas butyriciproducens
  • full scientific name: Intestinimonas butyriciproducens Kläring et al. 2013

@ref: 21298

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridia, not assigned to order

family: Oscillospiraceae

genus: Intestinimonas

species: Intestinimonas butyriciproducens

full scientific name: Intestinimonas butyriciproducens Kläring et al. 2013

strain designation: SRB-521-5-l

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31076positive3.5 µm0.5 µmrod-shapedno
67771rod-shapedno
67771positive

colony morphology

  • @ref: 62991
  • incubation period: 2 days

pigmentation

  • @ref: 31076
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 21298
  • name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/339
  • composition: Name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water

culture temp

@refgrowthtypetemperature
21298positivegrowth37
31076positivegrowth25-45
62991positivegrowth37
67770positivegrowth37
67771positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
21298anaerobe
31076anaerobe
62991anaerobe
67771anaerobe
125439anaerobe98.1

spore formation

@refspore formationtype of spore
31076yes
67771yesspore

compound production

  • @ref: 21298
  • compound: butyrate

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3107623652dextrin+carbon source
3107628260galactose+carbon source
3107617234glucose+carbon source
3107617596inosine+carbon source
3107624996lactate+carbon source
31076506227N-acetylglucosamine+carbon source
3107615361pyruvate+carbon source
3107651850methyl pyruvate+carbon source
3107617822serine+carbon source
3107630911sorbitol+carbon source
3107626986threonine+carbon source
3107617748thymidine+carbon source
3107616704uridine+carbon source

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic location
21298caecal content of a 17-week-old female heterozygous TNF deltaARE mouseGermanyDEUEurope
62991Mouse caecumGermanyDEUEurope2012-08-01Weihenstephan,Freising
67770Cecal content of a TNFdeltaARE mouse
67771From caecal content of a 17-week-old female heterozygous TNF deltaARE mouseGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Muridae (Mouse/Rat)
#Host Body-Site#Gastrointestinal tract#Large intestine
#Host Body Product#Gastrointestinal tract#Caecal content

taxonmaps

  • @ref: 69479
  • File name: preview.99_984.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_91;96_569;97_661;98_767;99_984&stattab=map
  • Last taxonomy: Intestinimonas butyriciproducens subclade
  • 16S sequence: KC311367
  • Sequence Identity:
  • Total samples: 73691
  • soil counts: 249
  • aquatic counts: 463
  • animal counts: 72859
  • plant counts: 120

Safety information

risk assessment

  • @ref: 21298
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21298
  • description: Intestinimonas butyriciproducens strain SRB-521-5-I 16S ribosomal RNA gene, partial sequence
  • accession: KC311367
  • length: 1475
  • database: nuccore
  • NCBI tax ID: 1297617

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Intestinimonas butyriciproducens DSM 26588GCA_003096335scaffoldncbi1297617
66792Intestinimonas butyriciproducens strain DSM 265881297617.27wgspatric1297617
66792Intestinimonas butyriciproducens strain SRB-521-5-I1297617.82completepatric1297617
66792Intestinimonas butyriciproducens DSM 265882756170247draftimg1297617
66792Intestinimonas butyriciproducens DSM 26588GCA_024622565contigncbi1297617

GC content

@refGC-contentmethod
2129858.4high performance liquid chromatography (HPLC)
3107658.4

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes64.984yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes89.606no
125438spore-formingspore-formingAbility to form endo- or exosporesno53.152no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no93.864yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno89.378no
125438motile2+flagellatedAbility to perform flagellated movementno82.208yes
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes50.5
125439BacteriaNetmotilityAbility to perform movementyes56.5
125439BacteriaNetgram_stainReaction to gram-stainingpositive66.2
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthanaerobe98.1

External links

@ref: 21298

culture collection no.: DSM 26588, CCUG 63529, KCTC 15744, JCM 32124

straininfo link

  • @ref: 88598
  • straininfo: 404444

literature

  • topic: Phylogeny
  • Pubmed-ID: 23918795
  • title: Intestinimonas butyriciproducens gen. nov., sp. nov., a butyrate-producing bacterium from the mouse intestine.
  • authors: Klaring K, Hanske L, Bui N, Charrier C, Blaut M, Haller D, Plugge CM, Clavel T
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.051441-0
  • year: 2013
  • mesh: Animals, Bacteria, Anaerobic/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Butyrates/*metabolism, DNA, Bacterial/genetics, Female, Gram-Positive Endospore-Forming Rods/*classification/genetics/isolation & purification, Intestines/*microbiology, Mice, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Enzymology

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmedjournal
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
21298Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-26588Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26588)
31076Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172740528776041
62991Curators of the CCUGhttps://www.ccug.se/strain?id=63529Culture Collection University of Gothenburg (CCUG) (CCUG 63529)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
88598Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID404444.1
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG