Strain identifier

BacDive ID: 23269

Type strain: No

Species: Sphingobium indicum

Strain Designation: Sp+

Strain history: CIP <- 2005, CCM, Sphingobium francense <- 2005, R. Lal, Dehli Univ., Delhi, India: strain Sp+

NCBI tax ID(s): 332055 (species)

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General

@ref: 18919

BacDive-ID: 23269

DSM-Number: 26779

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

description: Sphingobium indicum Sp+ is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from soil contaminated with gamma-HCH .

NCBI tax id

  • NCBI tax id: 332055
  • Matching level: species

strain history

@refhistory
18919<- R. Lal, Department of Zoology, Univ. of Delhi; Sp+ <- T. Vogel, ?? France
120082CIP <- 2005, CCM, Sphingobium francense <- 2005, R. Lal, Dehli Univ., Delhi, India: strain Sp+

doi: 10.13145/bacdive23269.20230509.8.1

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: 18919

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: Sp+

type strain: no

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.999
120082negativerod-shapedyes

colony morphology

  • @ref: 120082

multimedia

  • @ref: 18919
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_26779.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
18919NUTRIENT 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
18919TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf
18919R2A MEDIUM (DSMZ Medium 830)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium830.pdf
34979MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120082CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328
120082CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
18919positivegrowth28mesophilic
34979positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120082
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.982

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
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
68371esculin-builds acid from4853
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-galactose-builds acid from12936
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
68369malate+assimilation25115
68369adipate-assimilation17128
68369decanoate-assimilation27689
68369gluconate-assimilation24265
68369maltose-assimilation17306
68369N-acetylglucosamine-assimilation59640
68369D-mannitol-assimilation16899
68369D-mannose-assimilation16024
68369L-arabinose+assimilation30849
68369D-glucose+assimilation17634
68369gelatin-hydrolysis5291
68369esculin+hydrolysis4853
68369urea-hydrolysis16199
68369arginine-hydrolysis29016
68369D-glucose-fermentation17634
68369tryptophan-energy source27897
68369nitrate-reduction17632
120082nitrate+reduction17632
120082nitrite-reduction16301

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12008235581indoleno

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
120082oxidase+
120082alcohol dehydrogenase-1.1.1.1
120082catalase+1.11.1.6
120082lysine decarboxylase-4.1.1.18
120082ornithine decarboxylase-4.1.1.17
120082urease-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
120082-++--++--+++---+----

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
18919-----+--++-------+--+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120082---+/--+/-----+/------------+/-+/---+/-----+/-------+/--+/---------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
18919soil contaminated with gamma-HCH (Lindane)FranceFRAEurope
60031Soil,gamma-HCH-contaminatedFranceFRAEurope
120082Environment, SoilFranceFRAEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_60.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_32;97_33;98_56;99_60&stattab=map
  • Last taxonomy: Sphingobium
  • 16S sequence: AY519130
  • Sequence Identity:
  • Total samples: 636
  • soil counts: 78
  • aquatic counts: 363
  • animal counts: 118
  • plant counts: 77

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
189191Risk group (German classification)
1200821Risk group (French classification)

Sequence information

16S sequences

  • @ref: 18919
  • description: Sphingobium francense strain Sp+ 16S ribosomal RNA gene, partial sequence
  • accession: AY519130
  • length: 1454
  • database: ena
  • NCBI tax ID: 332057

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingobium indicum DSM 26779GCA_013408165scaffoldncbi332055
66792Sphingobium indicum DSM 26779GCA_004152835contigncbi332055
66792Sphingobium francense strain DSM 26779332057.6wgspatric332055
66792Sphingobium francense strain DSM 26779332057.5wgspatric332055
66792Sphingobium francense DSM 267792828378008draftimg332057

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileyes55.821no
flagellatedno84.46no
gram-positiveno98.116no
anaerobicno99.367no
aerobicyes94.405no
halophileno97.409no
spore-formingno94.719no
glucose-utilyes88.622yes
thermophileno96.483no
glucose-fermentno93.269yes

External links

@ref: 18919

culture collection no.: DSM 26779, CCM 7288, MTCC 6363, CCUG 53833, CIP 108928

straininfo link

  • @ref: 87491
  • straininfo: 265628

Reference

@idauthorscataloguedoi/urltitle
18919Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26779)https://www.dsmz.de/collection/catalogue/details/culture/DSM-26779
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
34979Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6612
60031Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53833)https://www.ccug.se/strain?id=53833
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)
68369Automatically annotated from API 20NE
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
87491Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID265628.1StrainInfo: A central database for resolving microbial strain identifiers
120082Curators of the CIPCollection of Institut Pasteur (CIP 108928)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108928