Strain identifier

BacDive ID: 17428

Type strain: Yes

Species: Xanthobacter flavus

Strain Designation: 301

Strain history: CIP <- 1998, JCM <- DSM <- J.R. Postgate <- Kalininskaya: strain 301

NCBI tax ID(s): 281 (species)

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General

@ref: 79

BacDive-ID: 17428

DSM-Number: 338

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, rod-shaped

description: Xanthobacter flavus 301 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from turf podsol soil.

NCBI tax id

  • NCBI tax id: 281
  • Matching level: species

strain history

@refhistory
79<- J.R. Postgate <- Kalininskaya; 301 (Mycobacterium flavum)
67770DSM 338 <-- J. R. Postgate <-- T. A. Kalininskaya 301.
119390CIP <- 1998, JCM <- DSM <- J.R. Postgate <- Kalininskaya: strain 301

doi: 10.13145/bacdive17428.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Xanthobacteraceae
  • genus: Xanthobacter
  • species: Xanthobacter flavus
  • full scientific name: Xanthobacter flavus Malik and Claus 1979 (Approved Lists 1980)

@ref: 79

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Xanthobacteraceae

genus: Xanthobacter

species: Xanthobacter flavus

full scientific name: Xanthobacter flavus Malik and Claus 1979 emend. Reding et al. 1992

strain designation: 301

type strain: yes

Morphology

cell morphology

  • @ref: 119390
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 119390

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
79HETEROTROPHIC MEDIUM H3P (DSMZ Medium 428)yeshttps://mediadive.dsmz.de/medium/428Name: HETEROTROPHIC MEDIUM H3P (DSMZ Medium 428) Composition: Agar 19.802 g/l Na2HPO4 x 2 H2O 2.87129 g/l KH2PO4 2.27723 g/l D-Glucose 1.9802 g/l Na-lactate 0.990099 g/l Na-pyruvate 0.990099 g/l D-Mannitol 0.990099 g/l DL-Malate 0.990098 g/l Na-acetate 0.990098 g/l Yeast extract 0.990098 g/l NH4Cl 0.990098 g/l Disodium succinate 0.990098 g/l MgSO4 x 7 H2O 0.495049 g/l Ferric ammonium citrate 0.049505 g/l CaCl2 x 2 H2O 0.00990098 g/l NaVO3 x H2O 0.00495049 g/l Thiamine-HCl x 2 H2O 0.00247525 g/l Nicotinic acid 0.00247525 g/l Pyridoxine hydrochloride 0.00247525 g/l Calcium pantothenate 0.00247525 g/l H3BO3 0.00148515 g/l CoCl2 x 6 H2O 0.000990099 g/l Riboflavin 0.00049505 g/l ZnSO4 x 7 H2O 0.00049505 g/l MnCl2 x 4 H2O 0.000148515 g/l Na2MoO4 x 2 H2O 0.000148515 g/l NiCl2 x 6 H2O 9.90099e-05 g/l CuCl2 x 2 H2O 4.95049e-05 g/l Vitamin B12 4.95049e-05 g/l Folic acid 9.90099e-06 g/l Biotin 4.9505e-06 g/l Distilled water
79MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81)yeshttps://mediadive.dsmz.de/medium/81Name: MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81) Composition: Agar 20.1005 g/l Na2HPO4 x 2 H2O 2.91457 g/l KH2PO4 2.31156 g/l NH4Cl 1.00503 g/l MgSO4 x 7 H2O 0.502512 g/l Ferric ammonium citrate 0.0502513 g/l CaCl2 x 2 H2O 0.0100503 g/l NaVO3 x H2O 0.00502512 g/l Calcium pantothenate 0.00251256 g/l Pyridoxine hydrochloride 0.00251256 g/l Nicotinic acid 0.00251256 g/l Thiamine-HCl x 2 H2O 0.00251256 g/l H3BO3 0.00150754 g/l CoCl2 x 6 H2O 0.00100503 g/l Riboflavin 0.000502513 g/l ZnSO4 x 7 H2O 0.000502513 g/l MnCl2 x 4 H2O 0.000150754 g/l Na2MoO4 x 2 H2O 0.000150754 g/l NiCl2 x 6 H2O 0.000100503 g/l CuCl2 x 2 H2O 5.02513e-05 g/l Vitamin B12 5.02513e-05 g/l Folic acid 1.00503e-05 g/l Biotin 5.02513e-06 g/l Distilled water
79NUTRIENT 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
40143MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
119390CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
79positivegrowth30mesophilic
40143positivegrowth30mesophilic
67770positivegrowth30mesophilic
119390positivegrowth25-30mesophilic
119390nogrowth5psychrophilic
119390nogrowth10psychrophilic
119390nogrowth37mesophilic
119390nogrowth41thermophilic
119390nogrowth45thermophilic

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
119390NaClpositivegrowth0-2 %
119390NaClnogrowth4 %
119390NaClnogrowth6 %
119390NaClnogrowth8 %
119390NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: Q-10

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
119390citrate-carbon source16947
119390esculin-hydrolysis4853
119390hippurate+hydrolysis606565
119390nitrate+reduction17632
119390nitrite-reduction16301
119390nitrate-respiration17632

antibiotic resistance

  • @ref: 119390
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 119390
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
119390oxidase-
119390beta-galactosidase-3.2.1.23
119390alcohol dehydrogenase-1.1.1.1
119390gelatinase-
119390amylase-
119390DNase-
119390caseinase-3.4.21.50
119390catalase+1.11.1.6
119390tween esterase-
119390gamma-glutamyltransferase-2.3.2.2
119390lecithinase-
119390lipase-
119390lysine decarboxylase-4.1.1.18
119390ornithine decarboxylase-4.1.1.17
119390phenylalanine ammonia-lyase-4.3.1.24
119390protease-
119390tryptophan deaminase-
119390urease+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
119390--++-+--+-+---------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119390-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119390-------------------------------------------------+-----++---+--------------+--+++-+-----+------++-+

Isolation, sampling and environmental information

isolation

@refsample typecountrycontinentorigin.country
79turf podsol soilUSSRAsia
67770Turf podsol soilRussiaRUS
119390Environment, Turf podsol soilUSSR

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3372.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_355;96_1529;97_1825;98_2585;99_3372&stattab=map
  • Last taxonomy: Xanthobacter
  • 16S sequence: X94199
  • Sequence Identity:
  • Total samples: 957
  • soil counts: 198
  • aquatic counts: 561
  • animal counts: 148
  • plant counts: 50

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
791Risk group (German classification)
1193901Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218X.flavus 16S ribosomal RNA (strain 301)X941991412ena281
20218Xanthobacter flavus strain BCRC 12271 16S-23S ribosomal RNA intergenic spacer, complete sequenceAY684797604ena281
20218Xanthobacter flavus gene for 16S rRNA, partial sequence, strain: NBRC 14759AB6806561410ena281

Genome sequences

  • @ref: 66792
  • description: Xanthobacter flavus DSM 338
  • accession: 2829740473
  • assembly level: draft
  • database: img
  • NCBI tax ID: 281

GC content

@refGC-contentmethod
7969.0
7968.1
6777069thermal denaturation, midpoint method (Tm)

External links

@ref: 79

culture collection no.: DSM 338, ATCC 35867, IFO 14759, NBRC 14759, NCIB 10071, JCM 1204, BCRC 12271, CCM 4469, CIP 105434, LMG 7045, NCAIM B.01946, NCIMB 10071, NRRL B-14838, VKM B-2106, CCRC 12271

straininfo link

  • @ref: 86424
  • straininfo: 5138

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
79Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 338)https://www.dsmz.de/collection/catalogue/details/culture/DSM-338
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
40143Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17453
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)
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
86424Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID5138.1StrainInfo: A central database for resolving microbial strain identifiers
119390Curators of the CIPCollection of Institut Pasteur (CIP 105434)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105434