Strain identifier

BacDive ID: 14185

Type strain: No

Species: Sphingobium indicum

Strain Designation: UT26

Strain history: CIP <- 2005, CCM, Sphingobium japonicum <- 2005, R. Lal, Delhi Univ., Delhi, India <- Y. Nagata, Japan: strain UT26

NCBI tax ID(s): 332055 (species)

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General

@ref: 6439

BacDive-ID: 14185

DSM-Number: 16413

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

description: Sphingobium indicum UT26 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from nalidixic acid resistant mutant of strain SS86 isolated from upland experimental field.

NCBI tax id

  • NCBI tax id: 332055
  • Matching level: species

strain history

@refhistory
6439<- R. Lal, Zoology, Univ. New Delhi; UT26
120084CIP <- 2005, CCM, Sphingobium japonicum <- 2005, R. Lal, Delhi Univ., Delhi, India <- Y. Nagata, Japan: strain UT26

doi: 10.13145/bacdive14185.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Sphingobium
  • species: Sphingobium indicum
  • full scientific name: Sphingobium indicum Pal et al. 2005

  • synonyms

    @refsynonym
    20215Sphingobium chinhatense
    20215Sphingobium japonicum
    20215Sphingobium francense
    20215Sphingobium lucknowense

@ref: 6439

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingobium

species: Sphingobium indicum

full scientific name: Sphingobium indicum Pal et al. 2005

strain designation: UT26

type strain: no

Morphology

cell morphology

  • @ref: 120084
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 120084
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6439REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)yeshttps://mediadive.dsmz.de/medium/830cName: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c) Composition: Agar 15.0 g/l Yeast extract 0.5 g/l Proteose peptone 0.5 g/l Casamino acids 0.5 g/l Glucose 0.5 g/l Starch 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
6439REACTIVATION WITH TRYPTONE SOYA BROTH (DSMZ Medium 220a)yeshttps://mediadive.dsmz.de/medium/220aName: REACTIVATION WITH TRYPTONE SOYA BROTH (DSMZ Medium 220a) Composition: Casein peptone 17.0 g/l Agar 15.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
38371MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
6439TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
6439LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)yeshttps://mediadive.dsmz.de/medium/381Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water
6439NUTRIENT 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
120084CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6439positivegrowth28mesophilic
38371positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120084
  • oxygen tolerance: obligate aerobe

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
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
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371salicin-builds acid from17814
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
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-ribose-builds acid from16988
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
120084nitrate-reduction17632
120084nitrite-reduction16301

metabolite production

  • @ref: 120084
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
120084oxidase+
120084alcohol dehydrogenase-1.1.1.1
120084catalase+1.11.1.6
120084lysine decarboxylase-4.1.1.18
120084ornithine decarboxylase-4.1.1.17
120084urease-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
120084-++--++-+-++---++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120084---+/--+/----+/-+/------------+/-+/-+/--+/-----+/-------+/----------+/-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
6439nalidixic acid resistant mutant of strain SS86 isolated from upland experimental fieldJapanJPNAsia
120084Upland experimental fieldJapanJPNAsia

isolation source categories

Cat1Cat2
#Environmental#Terrestrial
#Host#Microbial

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
64391Risk group (German classification)
1200841Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6439
  • description: Sphingobium japonicum strain UT26 16S ribosomal RNA gene, partial sequence
  • accession: AF039168
  • length: 1450
  • database: ena
  • NCBI tax ID: 332055

External links

@ref: 6439

culture collection no.: DSM 16413, CCM 7287, MTCC 6362, CIP 108930

straininfo link

  • @ref: 83348
  • straininfo: 265630

literature

  • topic: Phylogeny
  • Pubmed-ID: 16166696
  • title: Hexachlorocyclohexane-degrading bacterial strains Sphingomonas paucimobilis B90A, UT26 and Sp+, having similar lin genes, represent three distinct species, Sphingobium indicum sp. nov., Sphingobium japonicum sp. nov. and Sphingobium francense sp. nov., and reclassification of [Sphingomonas] chungbukensis as Sphingobium chungbukense comb. nov.
  • authors: Pal R, Bala S, Dadhwal M, Kumar M, Dhingra G, Prakash O, Prabagaran SR, Shivaji S, Cullum J, Holliger C, Lal R
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63201-0
  • year: 2005
  • mesh: Bacterial Proteins/*genetics/metabolism, Bacterial Typing Techniques, Biodegradation, Environmental, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Hexachlorocyclohexane/*metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sphingomonadaceae/*classification/enzymology/genetics/physiology, Sphingomonas/*classification/enzymology/genetics/physiology
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitle
6439Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16413)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16413
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
38371Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6614
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
83348Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID265630.1StrainInfo: A central database for resolving microbial strain identifiers
120084Curators of the CIPCollection of Institut Pasteur (CIP 108930)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108930