Strain identifier

BacDive ID: 17420

Type strain: Yes

Species: Xanthobacter autotrophicus

Strain Designation: 7C

Strain history: CIP <- 1998, JCM <- DSM <- IMG <- D. Siebert: strain 7C, Corynebacterium autotrophicum

NCBI tax ID(s): 280 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 201

BacDive-ID: 17420

DSM-Number: 432

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

description: Xanthobacter autotrophicus 7C is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from black pool sludge.

NCBI tax id

  • NCBI tax id: 280
  • Matching level: species

strain history

@refhistory
201<- IMG (Corynebacterium autotrophicum) <- D. Siebert, 7C
67770DSM 432 <-- IMG <-- D. Siebert 7C.
116654CIP <- 1998, JCM <- DSM <- IMG <- D. Siebert: strain 7C, Corynebacterium autotrophicum

doi: 10.13145/bacdive17420.20230509.8.1

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 autotrophicus
  • full scientific name: Xanthobacter autotrophicus (Baumgarten et al. 1974) Wiegel et al. 1978 (Approved Lists 1980)
  • synonyms

    • @ref: 20215
    • synonym: Corynebacterium autotrophicum

@ref: 201

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Xanthobacteraceae

genus: Xanthobacter

species: Xanthobacter autotrophicus

full scientific name: Xanthobacter autotrophicus (Baumgarten et al. 1974) Wiegel et al. 1978

strain designation: 7C

type strain: yes

Morphology

cell morphology

  • @ref: 116654
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 116654

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
201HETEROTROPHIC 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
201NUTRIENT 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
40407MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
116654CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
201positivegrowth30mesophilic
40407positivegrowth30mesophilic
67770positivegrowth30mesophilic
116654positivegrowth25-37mesophilic
116654nogrowth5psychrophilic
116654nogrowth10psychrophilic
116654nogrowth41thermophilic
116654nogrowth45thermophilic

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
116654NaClpositivegrowth0 %
116654NaClnogrowth2 %
116654NaClnogrowth4 %
116654NaClnogrowth6 %
116654NaClnogrowth8 %
116654NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11665416947citrate+carbon source
1166544853esculin-hydrolysis
116654606565hippurate+hydrolysis
11665417632nitrate+reduction
11665416301nitrite-reduction
11665417632nitrate-respiration

metabolite production

  • @ref: 116654
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11665415688acetoin-
11665417234glucose-

enzymes

@refvalueactivityec
116654oxidase+
116654beta-galactosidase+3.2.1.23
116654alcohol dehydrogenase-1.1.1.1
116654gelatinase-
116654amylase-
116654DNase-
116654caseinase-3.4.21.50
116654catalase+1.11.1.6
116654tween esterase-
116654gamma-glutamyltransferase-2.3.2.2
116654lecithinase-
116654lipase-
116654lysine decarboxylase-4.1.1.18
116654ornithine decarboxylase-4.1.1.17
116654phenylalanine ammonia-lyase-4.3.1.24
116654tryptophan deaminase-
116654urease-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
116654--+--+--+-++--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116654-+---------------------------------------------+-+---+------+-+----------------++-+-----+---------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
201black pool sludgeGöttingenGermanyDEUEurope
67770Black pool sludge
116654Environment, Black pool sludge

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment#Water reservoir (Aquarium/pool)
#Engineered#Waste#Activated sludge

taxonmaps

  • @ref: 69479
  • File name: preview.99_4714.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_355;96_1529;97_2844;98_3536;99_4714&stattab=map
  • Last taxonomy: Xanthobacter
  • 16S sequence: X94201
  • Sequence Identity:
  • Total samples: 208
  • soil counts: 34
  • aquatic counts: 110
  • animal counts: 32
  • plant counts: 32

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
2011Risk group (German classification)
1166541Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218X.autotrophicus 16S ribosomal RNA (strain 7c)X942011412ena280
20218Xanthobacter autotrophicus gene for 16S rRNA, partial sequence, strain: NBRC 102463AB6818051410ena280

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Xanthobacter autotrophicus DSM 432GCA_005871085scaffoldncbi280
66792Xanthobacter autotrophicus strain DSM 432280.16wgspatric280
66792Xanthobacter autotrophicus DSM 4322596583657draftimg280

GC content

@refGC-contentmethod
20169.7
20167.3
6777069.7thermal denaturation, midpoint method (Tm)
6777067thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno76.406no
flagellatedno94.025no
gram-positiveno98.586no
anaerobicno97.126no
aerobicyes89.762no
halophileno85.949no
spore-formingno95.3no
thermophileno97.033yes
glucose-utilyes78.583no
glucose-fermentno91.109no

External links

@ref: 201

culture collection no.: DSM 432, ATCC 35674, JCM 1202, BCRC 12235, CIP 105431, IAM 12579, IAM 12636, LMG 7043, NBRC 102463, NCAIM B.01945, NCIMB 10809, NRRL B-14836, CCRC 12235

straininfo link

  • @ref: 86416
  • straininfo: 5136

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
201Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 432)https://www.dsmz.de/collection/catalogue/details/culture/DSM-432
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
40407Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17450
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/
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
86416Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID5136.1StrainInfo: A central database for resolving microbial strain identifiers
116654Curators of the CIPCollection of Institut Pasteur (CIP 105431)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105431