Strain identifier

BacDive ID: 130661

Type strain: Yes

Species: Sphingobacterium yanglingense

Strain Designation: CCNWSP36-1

Strain history: S. Peng; Northwest A&F Univ., China; CCNWSP36-1.

NCBI tax ID(s): 1437280 (species)

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General

@ref: 21780

BacDive-ID: 130661

DSM-Number: 28353

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

description: Sphingobacterium yanglingense CCNWSP36-1 is a mesophilic, Gram-negative bacterium that was isolated from root nodule surface of soybean Merrill) cultivar Zhonghuang 13.

NCBI tax id

  • NCBI tax id: 1437280
  • Matching level: species

strain history

@refhistory
21780<- P. Shi, Northwest A&F Univ., Yangling, China; CCNWSP36-1
67770S. Peng; Northwest A&F Univ., China; CCNWSP36-1.

doi: 10.13145/bacdive130661.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Sphingobacteriia
  • order: Sphingobacteriales
  • family: Sphingobacteriaceae
  • genus: Sphingobacterium
  • species: Sphingobacterium yanglingense
  • full scientific name: Sphingobacterium yanglingense Peng et al. 2014

@ref: 21780

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Sphingobacterium

species: Sphingobacterium yanglingense

full scientific name: Sphingobacterium yanglingense Peng et al. 2014

strain designation: CCNWSP36-1

type strain: yes

Morphology

cell morphology

@refgram stainconfidencemotility
69480negative99.991
6948091.145no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
21780NUTRIENT AGAR (DSMZ Medium 1)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1.pdf
21780TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
21780positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.991

observation

  • @ref: 67770
  • observation: quinones: MK-7

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentlatitudelongitude
21780root nodule surface of soybean (Glycine max (L.) Merrill) cultivar Zhonghuang 13Glycine maxShaanxi Province, Yangling (34° 16' N 108° 4' E)ChinaCHNAsia34.2667108.067
67770Nodule surface of soybean [Glycine max (L.) Merrill]Glycine max

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root nodule

taxonmaps

  • @ref: 69479
  • File name: preview.99_50862.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15366;96_2384;97_28659;98_36534;99_50862&stattab=map
  • Last taxonomy: Sphingobacterium
  • 16S sequence: KF735812
  • Sequence Identity:
  • Total samples: 1945
  • soil counts: 648
  • aquatic counts: 257
  • animal counts: 951
  • plant counts: 89

Safety information

risk assessment

  • @ref: 21780
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21780
  • description: Sphingobacterium yanglingense strain CCNWSP36-1 16S ribosomal RNA gene, partial sequence
  • accession: KF735812
  • length: 1418
  • database: ena
  • NCBI tax ID: 1437280

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingobacterium yanglingense strain DSM 283531437280.3wgspatric1437280
66792Sphingobacterium yanglingense DSM 283532734482083draftimg1437280
67770Sphingobacterium yanglingense DSM 28353GCA_004363245scaffoldncbi1437280

GC content

  • @ref: 21780
  • GC-content: 41.1
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno89.648no
gram-positiveno97.627no
anaerobicno98.698no
halophileno91.452no
spore-formingno93.867no
thermophileno99.717yes
glucose-utilyes88.176no
aerobicyes88.249no
flagellatedno95.221no
glucose-fermentno86.257no

External links

@ref: 21780

culture collection no.: DSM 28353, ACCC 19328, JCM 30166

straininfo link

  • @ref: 89171
  • straininfo: 405434

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny25168614Sphingobacterium yanglingense sp. nov., isolated from the nodule surface of soybean.Peng S, Hong DD, Xin YB, Jun LM, Hong WGInt J Syst Evol Microbiol10.1099/ijs.0.068254-02014Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA, Soybeans/*microbiology, Sphingobacterium/*classification/genetics/isolation & purification, Vitamin K 2/chemistryGenetics
Phylogeny27498829Sphingobacterium jejuense sp. nov., with ginsenoside-converting activity, isolated from compost.Siddiqi MZ, Muhammad Shafi S, Choi KD, Im WT, Aslam ZInt J Syst Evol Microbiol10.1099/ijsem.0.0013702016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Ginsenosides/*metabolism, Panax/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Sphingobacterium/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

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
21780Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28353Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28353)
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
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
89171Reimer, 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-ID405434.1