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, mesophilic, Gram-positive, rod-shaped

description: Coprobacillus cateniformis RCA1-24 is an anaerobe, mesophilic, 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/bacdive23017.20230509.8.1

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

@refgrowthtypetemperaturerange
18807positivegrowth37mesophilic
34755positivegrowth37mesophilic
56746positivegrowth37mesophilic
67770positivegrowth37mesophilic
117215positivegrowth37mesophilic

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: ena
  • 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

traitpredictionconfidencetraining_data
motileno93.269no
gram-positiveyes95.298no
anaerobicyes97.515yes
aerobicno98.492yes
halophileno70.67no
spore-formingno77.489no
thermophileno98.017no
glucose-utilyes82.489no
flagellatedno97.349no
glucose-fermentyes70.535no

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
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