Strain identifier

BacDive ID: 14132

Type strain: Yes

Species: Sphingobacterium nematocida

Strain Designation: M-SX103

Strain history: S.-K. Tang M-SX103.

NCBI tax ID(s): 1513896 (species)

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General

@ref: 17487

BacDive-ID: 14132

DSM-Number: 24091

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

description: Sphingobacterium nematocida M-SX103 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from leaf tissue of Nicotiana tabacum Linn. .

NCBI tax id

  • NCBI tax id: 1513896
  • Matching level: species

strain history

@refhistory
17487<- S.-K. Tang, Yunnan Univ., Yunnan Inst. Microbiol. (YIM), Kunming, China; M-SX103T <- J. Liu
67770S.-K. Tang M-SX103.

doi: 10.13145/bacdive14132.20230509.8.1

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 nematocida
  • full scientific name: Sphingobacterium nematocida Liu et al. 2012

@ref: 17487

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Sphingobacterium

species: Sphingobacterium nematocida

full scientific name: Sphingobacterium nematocida Liu et al. 2012

strain designation: M-SX103

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30333negative1.25 µm0.6 µmrod-shapedno
69480negative99.971

colony morphology

  • @ref: 17487
  • incubation period: 2-3 days

pigmentation

  • @ref: 30333
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17487
  • name: NA SPHINGOBACTERIUM MEDIUM (DSMZ Medium 1364)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1364
  • composition: Name: NA SPHINGOBACTERIUM MEDIUM (DSMZ Medium 1364) Composition: Agar 15.0 g/l Peptone 10.0 g/l NaCl 5.0 g/l Beef extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
17487positivegrowth28mesophilic
30333positivegrowth10-40
67770positivegrowth28mesophilic

culture pH

  • @ref: 30333
  • ability: positive
  • type: growth
  • pH: 06-09
  • PH range: alkaliphile

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.998

halophily

  • @ref: 30333
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-3 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3033330089acetate+carbon source
3033317057cellobiose+carbon source
3033323652dextrin+carbon source
3033328757fructose+carbon source
3033333984fucose+carbon source
3033328260galactose+carbon source
3033324175galacturonate+carbon source
3033324265gluconate+carbon source
3033317234glucose+carbon source
3033332323glucuronamide+carbon source
3033329987glutamate+carbon source
3033317754glycerol+carbon source
3033327570histidine+carbon source
3033317306maltose+carbon source
3033329864mannitol+carbon source
3033337684mannose+carbon source
3033328053melibiose+carbon source
30333506227N-acetylglucosamine+carbon source
3033326490quinate+carbon source
3033316634raffinose+carbon source
3033326546rhamnose+carbon source
3033317814salicin+carbon source
3033317822serine+carbon source
3033330911sorbitol+carbon source
3033317992sucrose+carbon source

enzymes

@refvalueactivityec
30333acid phosphatase+3.1.3.2
30333alkaline phosphatase+3.1.3.1
30333alpha-galactosidase+3.2.1.22
30333catalase+1.11.1.6
30333cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
17487leaf tissue of Nicotiana tabacum Linn. (HongHuaDaJinYuan variety)Nicotiana tabacumYunnan province, Yuxi CityChinaCHNAsia
67770Leaf tissue of Nicotiana tabacum Linn. (HongHuaDaJinYuan variety) from Yuxi CityNicotiana tabacumYunnan ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Leaf (Phyllosphere)

taxonmaps

  • @ref: 69479
  • File name: preview.99_34330.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15366;96_2384;97_20276;98_25355;99_34330&stattab=map
  • Last taxonomy: Sphingobacterium nematocida subclade
  • 16S sequence: JF731241
  • Sequence Identity:
  • Total samples: 4872
  • soil counts: 1308
  • aquatic counts: 667
  • animal counts: 2609
  • plant counts: 288

Safety information

risk assessment

  • @ref: 17487
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17487
  • description: Sphingobacterium nematocida strain M-SX103 16S ribosomal RNA gene, partial sequence
  • accession: JF731241
  • length: 1390
  • database: ena
  • NCBI tax ID: 1513896

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingobacterium nematocida strain DSM 240911513896.4wgspatric1513896
66792Sphingobacterium nematocida DSM 240912595698210draftimg1513896
67770Sphingobacterium nematocida DSM 24091GCA_900168125scaffoldncbi1513896

GC content

@refGC-contentmethod
1748740.6high performance liquid chromatography (HPLC)
3033340.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.344yes
gram-positiveno97.814no
anaerobicno98.845no
aerobicyes87.134no
halophileno93.13no
spore-formingno94.91no
thermophileno99.453yes
glucose-utilyes92.167yes
flagellatedno96.009no
glucose-fermentno87.58no

External links

@ref: 17487

culture collection no.: DSM 24091, CCTCC AB 2010390, JCM 17339

straininfo link

  • @ref: 83297
  • straininfo: 398400

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21984669Sphingobacterium nematocida sp. nov., a nematicidal endophytic bacterium isolated from tobacco.Liu J, Yang LL, Xu CK, Xi JQ, Yang FX, Zhou F, Zhou Y, Mo MH, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.033670-02011Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sphingobacterium/*classification/genetics/isolation & purification, Tobacco/*microbiologyGenetics
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
Phylogeny30159757Sphingobacterium praediipecoris sp. nov. isolated from effluent of a dairy manure treatment plant.Van Le V, Padakandla SR, Kim H, Chae JCArch Microbiol10.1007/s00203-018-1566-32018Base Composition, DNA, Bacterial/chemistry, Dairying, Fatty Acids/analysis, Manure, Phosphatidylethanolamines/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sphingobacterium/chemistry/*classification/genetics/isolation & purificationEnzymology
Phylogeny34165622Sphingobacterium rhinopitheci sp. Nov., isolated from the faeces of Rhinopithecus bieti in China.Han XL, Wang Q, Zhang CL, Fang ZQ, Shen JQ, Huang S, Lu TArch Microbiol10.1007/s00203-021-02450-z2021Animals, China, Fatty Acids/analysis, Feces/microbiology, Phylogeny, *Presbytini/microbiology, RNA, Ribosomal, 16S/genetics, Species Specificity, *Sphingobacterium/classification/genetics
Phylogeny34779758Sphingobacterium hungaricum sp. nov. a novel species on the borderline of the genus Sphingobacterium.Toth A, Mate R, Kutasi J, Toth E, Boka K, Tancsics A, Nagy I, Kovacs G, Kosztik J, Bata-Vidacs I, Kukolya JInt J Syst Evol Microbiol10.1099/ijsem.0.0051052021Agriculture, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Sphingobacterium/classification/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17487Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24091)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24091
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
30333Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2667428776041
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)
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.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
83297Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID398400.1StrainInfo: A central database for resolving microbial strain identifiers