Strain identifier

BacDive ID: 11343

Type strain: Yes

Species: Oxalicibacterium flavum

Strain Designation: TA17

Strain history: CIP <- 2003, N. Sahin, Kötekli-Mugla, Turkey <- A.U. Tamer: strain TA17

NCBI tax ID(s): 179467 (species)

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General

@ref: 5966

BacDive-ID: 11343

DSM-Number: 15506

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

description: Oxalicibacterium flavum TA17 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil litter from close-to-ice-plant .

NCBI tax id

  • NCBI tax id: 179467
  • Matching level: species

strain history

@refhistory
5966<- A. Ü. Tamer; TA17
119384CIP <- 2003, N. Sahin, Kötekli-Mugla, Turkey <- A.U. Tamer: strain TA17

doi: 10.13145/bacdive11343.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Oxalobacteraceae
  • genus: Oxalicibacterium
  • species: Oxalicibacterium flavum
  • full scientific name: Oxalicibacterium flavum Tamer et al. 2003

@ref: 5966

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Oxalicibacterium

species: Oxalicibacterium flavum

full scientific name: Oxalicibacterium flavum Tamer et al. 2003

strain designation: TA17

type strain: yes

Morphology

cell morphology

  • @ref: 119384
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5966NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: Agar 15.0 g/l Glycerol 10.0 g/l Peptone 5.0 g/l Na-oxalate 4.0 g/l Meat extract 3.0 g/l Distilled water
33176MEDIUM 471 - for Oxalicibacterium flavumyesDistilled water make up to (1000.000 ml);Sodium chloride (5.000 g);Agar(15.000 g);Yeast extract (2.000 g);Peptone (5.000 g);Glycerol (10.000 ml);Beef extract(1.000 g);Potassium oxalate (4.000 g)
119384CIP Medium 471yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=471

culture temp

@refgrowthtypetemperaturerange
5966positivegrowth28mesophilic
33176positivegrowth30mesophilic
58160positivegrowth28-37mesophilic
119384positivegrowth25-37mesophilic
119384nogrowth5psychrophilic
119384nogrowth10psychrophilic
119384nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
58160aerobe
119384obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
119384NaClpositivegrowth0-2 %
119384NaClnogrowth4 %
119384NaClnogrowth6 %
119384NaClnogrowth8 %
119384NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
1193844853esculin-hydrolysis
11938417632nitrate-reduction
11938416301nitrite-reduction
11938417632nitrate-respiration

antibiotic resistance

  • @ref: 119384
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11938435581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
119384oxidase+
119384beta-galactosidase-3.2.1.23
119384alcohol dehydrogenase-1.1.1.1
119384gelatinase-
119384amylase-
119384DNase-
119384caseinase-3.4.21.50
119384catalase+1.11.1.6
119384tween esterase-
119384lecithinase-
119384lipase-
119384lysine decarboxylase-4.1.1.18
119384ornithine decarboxylase-4.1.1.17
119384protease-
119384tryptophan deaminase-
119384urease-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
119384--+--+-----+--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
5966-----------------+--+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119384-------------------------------------------------+-------------------------+------+---------++-----

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentsampling dateisolation date
5966soil litter from close-to-ice-plant (Mesembryanthemum sp.)MesembryanthemumIzmirTurkeyTURAsia
58160Soil litter close to Mesembryanthemum sp.IzmirTurkeyTURAsia1982
119384Environment, Soil, close to ice plantTurkeyTURAsia1982

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_72635.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_19273;97_39136;98_50892;99_72635&stattab=map
  • Last taxonomy: Oxalicibacterium
  • 16S sequence: AY061962
  • Sequence Identity:
  • Total samples: 211
  • soil counts: 135
  • aquatic counts: 27
  • animal counts: 13
  • plant counts: 36

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
59661Risk group (German classification)
1193841Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5966
  • description: Oxalicibacterium flavum strain TA17 16S ribosomal RNA gene, partial sequence
  • accession: AY061962
  • length: 1485
  • database: ena
  • NCBI tax ID: 179467

GC content

  • @ref: 5966
  • GC-content: 63

External links

@ref: 5966

culture collection no.: DSM 15506, LMG 21571, CCUG 48438, NEU 98, CIP 107889, RSKK 3004, CCM 7086, KUEN 1580

straininfo link

  • @ref: 80576
  • straininfo: 88866

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12583711Isolation and characterization of a new type of aerobic, oxalic acid utilizing bacteria, and proposal of Oxalicibacterium flavum gen. nov., sp. nov.Tamer AU, Aragno M, Sahin NSyst Appl Microbiol10.1078/072320202605176432002Bacteria, Aerobic/classification/growth & development/isolation & purification/metabolism, Base Composition, Betaproteobacteria/*classification/growth & development/isolation & purification/metabolism, Culture Media, Oxalates/metabolism, Oxalic Acid/*metabolism, Phenotype, Phylogeny, Pigments, Biological, Plants/microbiologyMetabolism
Metabolism16821716Identification of oxalotrophic bacteria by neural network analysis of numerical phenetic data.Sahin N, Aydin SFolia Microbiol (Praha)10.1007/BF029321612006Gram-Negative Aerobic Bacteria/*classification/metabolism, *Neural Networks, Computer, Oxalates/metabolismPhylogeny

Reference

@idauthorscataloguedoi/urltitle
5966Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15506)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15506
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
33176Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5449
58160Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 48438)https://www.ccug.se/strain?id=48438
68369Automatically annotated from API 20NE
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
80576Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID88866.1StrainInfo: A central database for resolving microbial strain identifiers
119384Curators of the CIPCollection of Institut Pasteur (CIP 107889)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107889