Strain identifier

BacDive ID: 14296

Type strain: Yes

Species: Allosphingosinicella vermicomposti

Strain Designation: YC7378

Strain history: <- YR Chung, Kyeongsang Univ.

NCBI tax ID(s): 614671 (species)

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General

@ref: 15833

BacDive-ID: 14296

DSM-Number: 21593

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

description: Allosphingosinicella vermicomposti YC7378 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from vermicompost.

NCBI tax id

  • NCBI tax id: 614671
  • Matching level: species

strain history

@refhistory
15833<- Y. R. Chung, Gyeongsang Nat. Univ. (GSNU), Jinju, Korea; YC7378 <- M. Yasir
67771<- YR Chung, Kyeongsang Univ.

doi: 10.13145/bacdive14296.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Allosphingosinicella
  • species: Allosphingosinicella vermicomposti
  • full scientific name: Allosphingosinicella vermicomposti (Yasir et al. 2010) Hördt et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Sphingosinicella vermicomposti

@ref: 15833

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Allosphingosinicella

species: Allosphingosinicella vermicomposti

full scientific name: Allosphingosinicella vermicomposti (Yasir et al. 2010) Hördt et al. 2020

strain designation: YC7378

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapeconfidence
29315negative1.3 µm0.45 µmrod-shaped
67771negative
69480negative99.981

pigmentation

  • @ref: 29315
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 15833
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
15833positivegrowth28mesophilic
29315positivegrowth10-37
29315positiveoptimum30mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
29315positivegrowth06-11alkaliphile
29315positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29315aerobe
67771aerobe

spore formation

@refspore formationconfidence
29315no
69481no100
69480no99.994

halophily

  • @ref: 29315
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-1.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2931521217L-alaninamide+carbon source
2931516449alanine+carbon source
2931525115malate+carbon source
2931517306maltose+carbon source
293154853esculin+hydrolysis
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
29315acid phosphatase+3.1.3.2
29315alkaline phosphatase+3.1.3.1
29315cytochrome oxidase+1.9.3.1
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
15833-----+--------------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15833vermicompostMansan, farmRepublic of KoreaKORAsia
67771From vermicompostMasanRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Biodegradation
  • Cat3: #Composting

taxonmaps

  • @ref: 69479
  • File name: preview.99_66729.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_4605;97_36390;98_47078;99_66729&stattab=map
  • Last taxonomy: Allosphingosinicella vermicomposti subclade
  • 16S sequence: FJ442859
  • Sequence Identity:
  • Total samples: 11
  • soil counts: 2
  • aquatic counts: 8
  • animal counts: 1

Safety information

risk assessment

  • @ref: 15833
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15833
  • description: Sphingosinicella vermicomposti strain YC7378 16S ribosomal RNA gene, partial sequence
  • accession: FJ442859
  • length: 1315
  • database: ena
  • NCBI tax ID: 614671

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Allosphingosinicella vermicomposti KCTC 22446GCA_003012815contigncbi614671
66792Sphingosinicella vermicomposti strain KCTC 22446614671.3wgspatric614671
66792Allosphingosinicella vermicomposti KCTC 224462832661309draftimg614671

GC content

@refGC-contentmethod
1583359.4high performance liquid chromatography (HPLC)
2931559.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno97.19yes
anaerobicno97.823yes
halophileno92.567yes
spore-formingno94.265no
glucose-utilyes78.579no
thermophileno91.332yes
flagellatedno81.995no
aerobicyes87.389yes
motileyes81.285no
glucose-fermentno89.959yes

External links

@ref: 15833

culture collection no.: DSM 21593, KCTC 22446

straininfo link

  • @ref: 83449
  • straininfo: 398273

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19654337Sphingosinicella vermicomposti sp. nov., isolated from vermicompost, and emended description of the genus Sphingosinicella.Yasir M, Aslam Z, Song GC, Jeon CO, Chung YRInt J Syst Evol Microbiol10.1099/ijs.0.010777-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Sphingomonadaceae/*classification/genetics/*isolation & purification/metabolismMetabolism
Phylogeny22307515Sphingomonas indica sp. nov., isolated from hexachlorocyclohexane (HCH)-contaminated soil.Niharika N, Jindal S, Kaur J, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.033845-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Hexachlorocyclohexane/*analysis, India, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants/*analysis, Spermidine/analogs & derivatives/analysis, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/analogs & derivatives/analysisGenetics
Phylogeny26115991Sphingosinicella ginsenosidimutans sp. nov., with ginsenoside converting activity.Kim JK, Kang MS, Park SC, Kim KM, Choi K, Yoon MH, Im WTJ Microbiol10.1007/s12275-015-5087-32015Bacterial Typing Techniques, Base Composition/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry, Ginsenosides/*metabolism, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, *Soil Microbiology, Sphingomonadaceae/classification/genetics/*isolation & purification/*metabolism, Vitamin K 2/analysis, beta-Glucosidase/metabolismMetabolism
Phylogeny26315363Sphingosinicella cucumeris sp. nov., isolated from soil of a cucumber garden.Akter S, Du J, Won K, Yin CS, Kook M, Yi THAntonie Van Leeuwenhoek10.1007/s10482-015-0572-62015Base Composition, *Cucumis sativus/microbiology, DNA, Bacterial, Fatty Acids/chemistry, Lipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonadaceae/chemistry/*classification/isolation & purification/physiologyTranscriptome
Phylogeny27054358Sphingomonas faucium sp. nov., isolated from canyon soil.Liu D, Jin X, Sun X, Song Y, Feng L, Wang G, Li MInt J Syst Evol Microbiol10.1099/ijsem.0.0010642016Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/analogs & derivatives/chemistryTranscriptome
Phylogeny29116039Sphingomonas colocasiae sp. nov., isolated from taro (Colocasia esculanta).Lin SY, Hameed A, Hsu YH, Liu YC, Hung MH, Lai WA, Young CCInt J Syst Evol Microbiol10.1099/ijsem.0.0024712017Bacterial Typing Techniques, Base Composition, Colocasia/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Taiwan, Ubiquinone/chemistryTranscriptome
Phylogeny29872901Sphingomonas montis sp. nov., Isolated from Forest Soil of Low-Altitude Mountain.Chaudhary DK, Dahal RH, Kim JCurr Microbiol10.1007/s00284-018-1524-y2018*Altitude, DNA, Bacterial, Molecular Typing, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonas/chemistry/classification/genetics/*isolation & purificationTranscriptome
Phylogeny30543503Sphingomonas deserti sp. nov., isolated from Mu Us Sandy Land soil.Liu L, Hui N, Liang L, Zhang X, Sun Q, Li LInt J Syst Evol Microbiol10.1099/ijsem.0.0031682018Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, *Desert Climate, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonas/*classification/isolation & purification, Ubiquinone/analogs & derivatives/chemistryTranscriptome
Phylogeny30570478Sphingosinicella humi sp. nov., isolated from arsenic-contaminated farmland soil and emended description of the genus Sphingosinicella.Qiao Z, Cao M, Wang D, Liao S, Wang GInt J Syst Evol Microbiol10.1099/ijsem.0.0031862018*Arsenic, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Environmental Pollution, Farms, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants, Sphingomonadaceae/*classification/isolation & purification, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15833Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21593)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21593
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
29315Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2572828776041
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
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
83449Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID398273.1StrainInfo: A central database for resolving microbial strain identifiers