Strain identifier

BacDive ID: 13529

Type strain: Yes

Species: Rarobacter faecitabidus

Strain Designation: YLM-1

Strain history: CIP <- 1989, JCM <- 1986, S. Sato, Japan: strain YLM-1

NCBI tax ID(s): 13243 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 1838

BacDive-ID: 13529

DSM-Number: 4813

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Rarobacter faecitabidus YLM-1 is a mesophilic bacterium that was isolated from waste water treatment system.

NCBI tax id

  • NCBI tax id: 13243
  • Matching level: species

strain history

@refhistory
1838<- JCM <- S. Sato, YLM-1
67770S. Sato YLM-1.
119223CIP <- 1989, JCM <- 1986, S. Sato, Japan: strain YLM-1

doi: 10.13145/bacdive13529.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Rarobacteraceae
  • genus: Rarobacter
  • species: Rarobacter faecitabidus
  • full scientific name: Rarobacter faecitabidus Yamamoto et al. 1988

@ref: 1838

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Rarobacteraceae

genus: Rarobacter

species: Rarobacter faecitabidus

full scientific name: Rarobacter faecitabidus Yamamoto et al. 1988

strain designation: YLM-1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no95.114
69480100positive

colony morphology

@refcolony colorincubation periodmedium used
19721Lemon yellow10-14 days5006
1972110-14 daysISP 2
1972110-14 daysISP 4
1972110-14 daysISP 5
1972110-14 daysISP 6
1972110-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19721noISP 2
19721noISP 3
19721noISP 4
19721noISP 5
19721noISP 6
19721noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1838YM-CATALASE MEDIUM (DSMZ Medium 469)yeshttps://mediadive.dsmz.de/medium/469Name: YM-CATALASE MEDIUM (DSMZ Medium 469) Composition: K2HPO4 5.7 g/l Malt extract 5.0 g/l Yeast extract 5.0 g/l NH4H2PO4 1.2 g/l MgSO4 x 7 H2O 0.2 g/l Catalase 0.06 g/l Distilled water
197215006yesMedium: 5006 Name: Composition (g/l) Sucrose 3,0 Dextrin 15,0 Meat extract 1,0 Yeast extract 2,0 Tryptone soy broth (Oxoid) 5,0 NaCl 0,5 K2HPO4 0,5 MgSO4 x 7 H2O 0,5 FeSO4 x 7 H2O 0,01 Agar 20,0 Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7,3 Usage: Maintenance Organisms: All Actinomycetes
19721ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19721ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19721ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19721ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19721ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
34256MEDIUM 67 - for Rarobacter faecitabidusyesDistilled water make up to (1000.000 ml);Brain heart infusion (37.000 g);Hemin solution - M00149 (1.000 ml)
119223CIP Medium 67yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=67

culture temp

@refgrowthtypetemperaturerange
1838positivegrowth30mesophilic
34256positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.994

halophily

  • @ref: 19721
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

murein

  • @ref: 1838
  • murein short key: A21.12
  • type: A4ß L-Orn-D-Ser-D-Glu

observation

  • @ref: 67770
  • observation: quinones: MK-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
6837917632nitrate-reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase-3.5.1.B15
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19721--++-++-+----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19721+---+-+--++---+----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19721---------+-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
1838waste water treatment systemJapanJPNAsia
67770Activated sludge from a wastewater treatment system of an alcoholic beverage factory
119223Other, Activated sludge in an alcoholic beverageJapanJPNAsia1983

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste#Wastewater
#Engineered#Waste#Water treatment plant

taxonmaps

  • @ref: 69479
  • File name: preview.99_80705.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_33890;97_42977;98_56165;99_80705&stattab=map
  • Last taxonomy: Rarobacter faecitabidus subclade
  • 16S sequence: Y17870
  • Sequence Identity:
  • Total samples: 1102
  • soil counts: 315
  • aquatic counts: 227
  • animal counts: 505
  • plant counts: 55

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
18381Risk group (German classification)
197211Hazard group
1192231Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Rarobacter faecitabidus 16S rRNA gene, partialY178701464ena13243
20218Rarobacter faecitabidus gene for 16S rRNA, partial sequence, strain:IFO 14760AB0561271503ena13243

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rarobacter faecitabidus strain DSM 481313243.3wgspatric13243
66792Rarobacter faecitabidus DSM 48132814123535draftimg13243
67770Rarobacter faecitabidus DSM 4813GCA_006716265contigncbi13243

GC content

  • @ref: 1838
  • GC-content: 66.1
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.332no
gram-positiveyes92.844no
anaerobicno91.94no
halophileno76.915no
spore-formingno90.293no
glucose-utilyes77.845no
aerobicno54.386no
flagellatedno97.905no
thermophileno98.585yes
glucose-fermentno79.021yes

External links

@ref: 1838

culture collection no.: DSM 4813, ATCC 49628, DSM 46362, IFO 14760, JCM 6097, NBRC 14760, CIP 103380, NCIMB 12724

straininfo link

  • @ref: 82720
  • straininfo: 42589

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1838Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4813)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4813
19721Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM4813.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
34256Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15171
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/
68368Automatically annotated from API 20E
68379Automatically annotated from API Coryne
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
82720Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42589.1StrainInfo: A central database for resolving microbial strain identifiers
119223Curators of the CIPCollection of Institut Pasteur (CIP 103380)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103380