Strain identifier

BacDive ID: 131402

Type strain: Yes

Species: Sphingomonas zeae

Strain Designation: JM-791

Strain history: CIP <- 2015, P. Kämpfer, Giessen Univ., Giessen, Germany: strain JM-791

NCBI tax ID(s): 1646122 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 22629

BacDive-ID: 131402

DSM-Number: 100049

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

description: Sphingomonas zeae JM-791 is a mesophilic, Gram-negative bacterium that was isolated from healthy internal stem tissue of a 4-week-old field-grown corn plant .

NCBI tax id

  • NCBI tax id: 1646122
  • Matching level: species

strain history

@refhistory
22629<- P. Kämpfer, Univ. Giessen, Germany; JM-791 <- J. McInroy
124029CIP <- 2015, P. Kämpfer, Giessen Univ., Giessen, Germany: strain JM-791

doi: 10.13145/bacdive131402.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Sphingomonas
  • species: Sphingomonas zeae
  • full scientific name: Sphingomonas zeae Kämpfer et al. 2015

@ref: 22629

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Pseudomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas zeae

full scientific name: Sphingomonas zeae Kämpfer et al. 2015

strain designation: JM-791

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.971
124029negativerod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
41950MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
22629TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yesName: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/535
124029CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

  • @ref: 22629
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no95
69480no99.989

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

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
22629-----+-++++-+--+----+

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
22629healthy internal stem tissue of a 4-week-old field-grown corn plant (Zea mays, cultivar ‘Sweet Belle’)Zea maysAlabama, Elmore county, Tallassee, Plant Breeding Unit of the E.V. Smith Research CenterUSAUSANorth America
124029Healthy internal stem tissue of corn, Zea mays, cultivar 'Sweet Belle'AlabamaUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Stem (Branch)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
226291Risk group (German classification)
1240291Risk group (French classification)

Sequence information

16S sequences

  • @ref: 22629
  • description: Sphingomonas zeae strain JM-791 16S ribosomal RNA gene, partial sequence
  • accession: KP999966
  • length: 1408
  • database: ena
  • NCBI tax ID: 1646122

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingomonas zeae DSM 100049GCA_014197135scaffoldncbi1646122
66792Sphingomonas zeae DSM 100049GCA_013359795contigncbi1646122
66792Sphingomonas zeae strain DSM 1000491646122.4wgspatric1646122
66792Sphingomonas zeae strain DSM 1000491646122.3wgspatric1646122
66792Sphingomonas zeae DSM 1000492830100248draftimg1646122

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno95no
flagellatedno89.603no
gram-positiveno96.653no
anaerobicno98.555no
aerobicyes94.672no
halophileno94.356no
spore-formingno93.654no
glucose-utilyes91.001yes
thermophileno98.931yes
motileyes73.267no
glucose-fermentno92.421yes

External links

@ref: 22629

culture collection no.: DSM 100049, CCM 8596, LMG 28739, CIP 110945, CIP 110899

straininfo link

  • @ref: 89835
  • straininfo: 403706

literature

  • topic: Phylogeny
  • Pubmed-ID: 25944808
  • title: Sphingomonas zeae sp. nov., isolated from the stem of Zea mays.
  • authors: Kampfer P, Busse HJ, McInroy JA, Glaeser SP
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.000298
  • year: 2015
  • mesh: Alabama, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, Plant Stems/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistry, Zea mays/*microbiology
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
22629Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100049Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100049)
41950Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/34493
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68369Automatically annotated from API 20NE
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
89835Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID403706.1
124029Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110945Collection of Institut Pasteur (CIP 110945)