Strain identifier

BacDive ID: 14176

Type strain: Yes

Species: Sphingobium herbicidovorans

Strain Designation: MH

Strain history: CIP <- 2000, LMG <- DSMZ <- H. Kohler <- F. Streichsbier, TU, Vienna, Flavobacterium sp.: strain MH

NCBI tax ID(s): 1219045 (strain), 76947 (species)

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General

@ref: 4161

BacDive-ID: 14176

DSM-Number: 11019

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

description: Sphingobium herbicidovorans MH is an aerobe, Gram-negative, motile bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
76947species
1219045strain

strain history

@refhistory
4161<- H-P.E. Kohler <- F. Streichsbier, TU Vienna (Flavobacterium sp. MH)
119881CIP <- 2000, LMG <- DSMZ <- H. Kohler <- F. Streichsbier, TU, Vienna, Flavobacterium sp.: strain MH

doi: 10.13145/bacdive14176.20240510.9

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 herbicidovorans
  • full scientific name: Sphingobium herbicidovorans (Zipper et al. 1997) Takeuchi et al. 2001

  • synonyms

    • @ref: 20215
    • synonym: Sphingomonas herbicidovorans

@ref: 4161

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingobium

species: Sphingobium herbicidovorans

full scientific name: Sphingobium herbicidovorans (Zipper et al. 1997) Takeuchi et al. 2001

strain designation: MH

type strain: yes

Morphology

cell morphology

  • @ref: 119881
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 119881
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4161CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
4161MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457)yeshttps://mediadive.dsmz.de/medium/457Name: MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457) Composition: Na2HPO4 2.44 g/l KH2PO4 1.52 g/l (NH4)2SO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l CaCl2 x 2 H2O 0.05 g/l EDTA 0.005 g/l FeSO4 x 7 H2O 0.002 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Distilled water
40601MEDIUM 356 - for Sphingomonas herbicidovoransyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (5.000g);Yeast extract (5.000 g);Peptone (5.000 g);Tryptone (5.000 g)
119881CIP Medium 356yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=356

culture temp

@refgrowthtypetemperature
4161positivegrowth28
40601positivegrowth30
60943positivegrowth30
119881positivegrowth25-37
119881nogrowth5
119881nogrowth10
119881nogrowth41

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
60943aerobe
119881obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
119881NaClpositivegrowth0-4 %
119881NaClnogrowth6 %
119881NaClnogrowth8 %
119881NaClnogrowth10 %

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
11988116947citrate-carbon source
1198814853esculin+hydrolysis
11988117632nitrate-reduction
11988116301nitrite-reduction
11988117632nitrate-respiration

antibiotic resistance

  • @ref: 119881
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11988135581indoleno

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
119881oxidase+
119881beta-galactosidase+3.2.1.23
119881alcohol dehydrogenase-1.1.1.1
119881gelatinase-
119881amylase-
119881DNase-
119881caseinase-3.4.21.50
119881catalase+1.11.1.6
119881tween esterase-
119881lecithinase-
119881lipase-
119881lysine decarboxylase-4.1.1.18
119881ornithine decarboxylase-4.1.1.17
119881protease-
119881tryptophan deaminase-
119881urease-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
119881-+---++++-++---++---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
4161-----+--+--------+--+
4161-----+--+--------+--+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119881+-+---------------+----+-------------------------+-------------------------+---++-+-----+-------+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
4161soilViennaAustriaAUTEurope
60943SoilAustriaAUTEurope
119881Environment, Soil

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_5198.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_32;97_33;98_3875;99_5198&stattab=map
  • Last taxonomy: Sphingobium herbicidovorans
  • 16S sequence: AB681063
  • Sequence Identity:
  • Total samples: 297
  • soil counts: 109
  • aquatic counts: 58
  • animal counts: 107
  • plant counts: 23

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
41611Risk group (German classification)
1198811Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Sphingobium herbicidovorans gene for 16S ribosomal RNA, partial sequenceAB0224281438nuccore76947
20218Sphingobium herbicidovorans gene for 16S rRNA, partial sequence, strain: NBRC 16415AB6810631412nuccore76947

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingobium herbicidovorans NBRC 16415GCA_001598535contigncbi1219045
66792Sphingobium herbicidovorans MHGCA_002080435completencbi76947
66792Sphingobium herbicidovorans NBRC 16415GCA_000632125contigncbi1219045
66792Sphingobium herbicidovorans NBRC 164151219045.4wgspatric1219045
66792Sphingobium herbicidovorans NBRC 164151219045.3wgspatric1219045
66792Sphingobium herbicidovorans NBRC 164152808606815completeimg1219045
66792Sphingobium herbicidovorans NBRC 164152574180318draftimg1219045
66792Sphingobium herbicidovorans NBRC 164152731957705draftimg1219045

External links

@ref: 4161

culture collection no.: DSM 11019, IFO 16415, LMG 18315, NBRC 16415, CCUG 56400, CIP 106705, ATCC 700291, KCTC 2939

straininfo link

  • @ref: 83339
  • straininfo: 11836

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16957112Description of Sphingobium fuliginis sp. nov., a phenanthrene-degrading bacterium from a fly ash dumping site, and reclassification of Sphingomonas cloacae as Sphingobium cloacae comb. nov.Prakash O, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.64080-02006Carbon, Coal Ash, DNA, Bacterial/*analysis, Molecular Sequence Data, Particulate Matter, Phenanthrenes/*metabolism, RNA, Ribosomal, 16S/*analysis/genetics, Soil Microbiology, Sphingomonadaceae/*classification/genetics, Terminology as TopicGenetics
Phylogeny19643879Sphingobium vermicomposti sp. nov., isolated from vermicompost.Vaz-Moreira I, Faria C, Lopes AR, Svensson L, Falsen E, Moore ER, Ferreira AC, Nunes OC, Manaia CMInt J Syst Evol Microbiol10.1099/ijs.0.006163-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Soil/analysis, *Soil Microbiology, Sphingomonadaceae/*classification/genetics/*isolation & purification/metabolismMetabolism
Phylogeny30565024Sphingobium pinisoli sp. nov., isolated from the rhizosphere soil of a Korean native pine tree.Lee JC, Song JS, Whang KSAntonie Van Leeuwenhoek10.1007/s10482-018-01215-x2018Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Phylogeny, Pinus/growth & development, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhizosphere, *Soil Microbiology, Sphingomonadaceae/classification/genetics/*isolation & purification/metabolismMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4161Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11019)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11019
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
40601Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18864
60943Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 56400)https://www.ccug.se/strain?id=56400
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
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
83339Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID11836.1StrainInfo: A central database for resolving microbial strain identifiers
119881Curators of the CIPCollection of Institut Pasteur (CIP 106705)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106705