Strain identifier

BacDive ID: 131134

Type strain: Yes

Species: Paracraurococcus ruber

Strain Designation: N89, NS89

Strain history: CIP <- 1998, Y. Nishimura, Tokyo Univ., Tokyo, Japan: strain NS89

NCBI tax ID(s): 77675 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.1 (current version):
version 9:
version 8.1:
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 9.1 (current version)

General

@ref: 22426

BacDive-ID: 131134

DSM-Number: 15382

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, Gram-negative, coccus-shaped

description: Paracraurococcus ruber N89 is an obligate aerobe, Gram-negative, coccus-shaped bacterium that was isolated from Soil.

NCBI tax id

  • NCBI tax id: 77675
  • Matching level: species

strain history

@refhistory
22426<- JCM; JCM 9931 <- Y. Nishimura, Dept. Applied Biological Sci., Tokyo Univ. Sci., Noda, Japan; N89
393421998, Y. Nishimura, Sci. Univ. Tokyo, Japan: strain NS89
67770Y. Nishimura NS89.
122272CIP <- 1998, Y. Nishimura, Tokyo Univ., Tokyo, Japan: strain NS89

doi: 10.13145/bacdive131134.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodospirillales
  • family: Acetobacteraceae
  • genus: Paracraurococcus
  • species: Paracraurococcus ruber
  • full scientific name: Paracraurococcus ruber Saitoh et al. 1998

@ref: 22426

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Acetobacteraceae

genus: Paracraurococcus

species: Paracraurococcus ruber

full scientific name: Paracraurococcus ruber Saitoh et al. 1998

strain designation: N89, NS89

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
122272negativecoccus-shapedno
69480negative96.702

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
22426NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
39342MEDIUM 293 - for Craurococcus roseusyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (2.500g);Beef extract (1.500 g);Potato dextrose broth (24.000 g)
122272CIP Medium 293yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=293

culture temp

@refgrowthtypetemperature
22426positivegrowth28
39342positivegrowth30
67770positivegrowth30
122272positivegrowth15-41
122272nogrowth10
122272nogrowth45

Physiology and metabolism

oxygen tolerance

  • @ref: 122272
  • oxygen tolerance: obligate aerobe

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose+builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose+builds acid from65328
68371D-xylose+builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose+builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
122272nitrate+reduction17632
122272nitrite-reduction16301

metabolite production

  • @ref: 122272
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 122272
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
122272beta-galactosidase-3.2.1.23
122272alcohol dehydrogenase-1.1.1.1
122272gelatinase-
122272amylase-
122272DNase-
122272caseinase-3.4.21.50
122272catalase+1.11.1.6
122272tween esterase-
122272gamma-glutamyltransferase+2.3.2.2
122272lecithinase-
122272lipase-
122272lysine decarboxylase-4.1.1.18
122272ornithine decarboxylase-4.1.1.17
122272phenylalanine ammonia-lyase-4.3.1.24
122272protease-
122272urease+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
122272-+++-+----+---------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122272--+-+++---------------------------------+--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122272-----------------------------------------------++--------------------------+---+-++-----+----------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
22426SoilNodaJapanJPNAsia
67770Soil
122272Environment, SoilNodaJapanJPNAsia1992

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_78366.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_266;96_8951;97_41907;98_54706;99_78366&stattab=map
  • Last taxonomy: Paracraurococcus ruber subclade
  • 16S sequence: LC055640
  • Sequence Identity:
  • Total samples: 1648
  • soil counts: 928
  • aquatic counts: 211
  • animal counts: 323
  • plant counts: 186

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
224261Risk group (German classification)
1222721Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
22426Paracraurococcus ruber gene for 16S ribosomal RNA, partial sequence, strain: JCM 9931LC0556401409nuccore77675
22426Paracraurococcus ruber gene for 16S rRNA, partial sequence, strain: NS89D858271439nuccore77675

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paracraurococcus ruber DSM 15382GCA_016584045scaffoldncbi77675
66792Paracraurococcus ruber strain DSM 1538277675.7wgspatric77675
66792Paracraurococcus ruber strain JCM993177675.4wgspatric77675
66792Paracraurococcus ruber JCM99312887745528draftimg77675
67770Paracraurococcus ruber JCM9931GCA_004353985contigncbi77675

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno68no
69480gram-positivegram-positivePositive reaction to Gram-stainingno96.702no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no89.999no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes79.901yes
69480spore-formingspore-formingAbility to form endo- or exosporesno82.939no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno96.353yes
69480flagellatedmotile2+Ability to perform flagellated movementyes69.561no

External links

@ref: 22426

culture collection no.: DSM 15382, JCM 9931, CIP 105708

straininfo link

  • @ref: 89588
  • straininfo: 60929

literature

  • topic: Phylogeny
  • Pubmed-ID: 9734062
  • title: Proposal of Craurococcus roseus gen. nov., sp. nov. and Paracraurococcus ruber gen. nov., sp. nov., novel aerobic bacteriochlorophyll a-containing bacteria from soil.
  • authors: Saitoh S, Suzuki T, Nishimura Y
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-48-3-1043
  • year: 1998
  • mesh: Bacteriochlorophylls/*analysis, Base Sequence, Gram-Negative Aerobic Bacteria/*classification, Molecular Sequence Data, *Soil Microbiology
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogue
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
22426Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-15382Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15382)
39342Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17758
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
89588Reimer, 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-ID60929.1
122272Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105708Collection of Institut Pasteur (CIP 105708)