Strain identifier

BacDive ID: 23017

Type strain: Yes

Species: Coprobacillus cateniformis

Strain Designation: RCA1-24

Strain history: CIP <- 2000, JCM <- Y. Benno: strain RCA1-24

NCBI tax ID(s): 1297794 (strain), 100884 (species)

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General

@ref: 18807

BacDive-ID: 23017

DSM-Number: 15921

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, Gram-positive

description: Coprobacillus cateniformis RCA1-24 is an anaerobe, Gram-positive bacterium that was isolated from human feces.

NCBI tax id

NCBI tax idMatching level
100884species
1297794strain

strain history

@refhistory
18807<- JCM <- Y. Benno; RCA1-24
67770Y. Benno RCA1-24.
117215CIP <- 2000, JCM <- Y. Benno: strain RCA1-24

doi: 10.13145/bacdive23017.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Erysipelotrichia
  • order: Erysipelotrichales
  • family: Coprobacillaceae
  • genus: Coprobacillus
  • species: Coprobacillus cateniformis
  • full scientific name: Coprobacillus cateniformis corrig. Kageyama and Benno 2000

  • synonyms

    • @ref: 20215
    • synonym: Coprobacillus catenaformis

@ref: 18807

domain: Bacteria

phylum: Firmicutes

class: Erysipelotrichia

order: Erysipelotrichales

family: Coprobacillaceae

genus: Coprobacillus

species: Coprobacillus cateniformis

full scientific name: Coprobacillus cateniformis Kageyama and Benno 2000

strain designation: RCA1-24

type strain: yes

Morphology

cell morphology

  • @ref: 117215
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refincubation periodhemolysis ability
567462-3 days
1172151

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
18807CHOPPED MEAT MEDIUM (DSMZ Medium 78)yeshttps://mediadive.dsmz.de/medium/78Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water
34755MEDIUM 433 - for Atopobium, Clostridium scindens, C. hylemonae, Corpobacillus cateniformis, Catenibacterium mitsuokai, Solobacterium mooreiyesDistilled water make up to (950.000 ml);Agar (15.000 g);Glucose (1.500 g);Yeast extract (5.000 g);Horse blood (50.000 ml);Starch maize (0.500 g);Beef extract(2.400 g);Proteose Peptone N°3 (10.000 g);Di Sodium hydrogen phosphate (4.000 g);L-Cysteine (0.500
117215CIP Medium 433yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=433

culture temp

@refgrowthtypetemperature
18807positivegrowth37
34755positivegrowth37
56746positivegrowth37
67770positivegrowth37
117215positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
18807anaerobe
56746anaerobe
117215anaerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11721517108D-arabinose-degradation
11721515824D-fructose+/-degradation
11721517634D-glucose+/-degradation
11721516024D-mannose-degradation
11721565327D-xylose-degradation
11721517057cellobiose+degradation
11721517716lactose+/-degradation
11721517306maltose+/-degradation
11721517814salicin+degradation
11721517992sucrose+/-degradation
1172154853esculin+hydrolysis
11721517632nitrate-reduction
11721516301nitrite-reduction
11721517632nitrate+respiration
6838016199urea-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
11721535581indoleno
6838035581indoleno

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase+3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase-3.2.1.20
68380beta-Galactosidase 6-phosphate+
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380urease-3.5.1.5
117215oxidase-
117215beta-galactosidase-3.2.1.23
117215gelatinase-
117215amylase+
117215DNase-
117215caseinase-3.4.21.50
117215catalase+1.11.1.6
117215tween esterase+
117215lecithinase-
117215lipase-
117215protease-
117215urease-3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase-3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
117215--++------++---+----

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
18807-+/---+-----------------+------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
18807human fecesJapanJPNAsia
56746Human fecesJapanJPNAsia
67770Human feces
117215Human, FecesJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3499.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_209;96_1820;97_2184;98_2681;99_3499&stattab=map
  • Last taxonomy: Coprobacillus cateniformis subclade
  • 16S sequence: AB030219
  • Sequence Identity:
  • Total samples: 14310
  • soil counts: 89
  • aquatic counts: 235
  • animal counts: 13962
  • plant counts: 24

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
188071Risk group (German classification)
1172151Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Coprobacillus catenaformis gene for 16S rRNA, strain: JCM 10604
  • accession: AB030219
  • length: 1485
  • database: nuccore
  • NCBI tax ID: 1297794

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Coprobacillus cateniformis RCA1-24GCA_009767585scaffoldncbi100884
66792Coprobacillus cateniformis JCM 10604GCA_001312445contigncbi1297794
66792Coprobacillus cateniformis JCM 106041297794.4wgspatric1297794
66792Coprobacillus cateniformis strain RCA1-24 strain not collected100884.13wgspatric100884
66792Coprobacillus cateniformis JCM 106042734481901draftimg1297794

GC content

  • @ref: 67770
  • GC-content: 33.1
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingyes76.272no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes87.671no
69480spore-formingspore-formingAbility to form endo- or exosporesno60.458no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no96.236yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno93.696yes
69480flagellatedmotile2+Ability to perform flagellated movementno87.759no

External links

@ref: 18807

culture collection no.: CCUG 45368, CIP 106690, DSM 15921, JCM 10604

straininfo link

  • @ref: 87257
  • straininfo: 88228

literature

  • topic: Phylogeny
  • Pubmed-ID: 10711596
  • title: Coprobacillus catenaformis gen. nov., sp. nov., a new genus and species isolated from human feces.
  • authors: Kageyama A, Benno Y
  • journal: Microbiol Immunol
  • DOI: 10.1111/j.1348-0421.2000.tb01242.x
  • year: 2000
  • mesh: Base Composition, DNA Primers, DNA, Bacterial/analysis/genetics, DNA, Ribosomal/analysis/genetics, Feces/*microbiology, Gram-Positive Asporogenous Rods/*classification/genetics/physiology, Humans, Molecular Sequence Data, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
18807Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15921)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15921
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
34755Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18848
56746Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 45368)https://www.ccug.se/strain?id=45368
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68380Automatically annotated from API rID32A
68382Automatically annotated from API zym
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
87257Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID88228.1StrainInfo: A central database for resolving microbial strain identifiers
117215Curators of the CIPCollection of Institut Pasteur (CIP 106690)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106690