Strain identifier

BacDive ID: 14270

Type strain: Yes

Species: Sphingomonas formosensis

Strain Designation: CC-Nfb-2

Strain history: <- C. C. Young, Dept. Soil and Environmental Sci., Natl. Chung Hsing Univ., Taichung, Taiwan; CC-Nfb-2 <- S. Y. Lin

NCBI tax ID(s): 861534 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 17502

BacDive-ID: 14270

DSM-Number: 24164

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

description: Sphingomonas formosensis CC-Nfb-2 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from oil contaminated soil.

NCBI tax id

  • NCBI tax id: 861534
  • Matching level: species

strain history

  • @ref: 17502
  • history: <- C. C. Young, Dept. Soil and Environmental Sci., Natl. Chung Hsing Univ., Taichung, Taiwan; CC-Nfb-2 <- S. Y. Lin

doi: 10.13145/bacdive14270.20230509.8.1

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 formosensis
  • full scientific name: Sphingomonas formosensis Lin et al. 2012

@ref: 17502

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas formosensis

full scientific name: Sphingomonas formosensis Lin et al. 2012

strain designation: CC-Nfb-2

type strain: yes

Morphology

cell morphology

  • @ref: 30382
  • gram stain: negative
  • cell length: 1.4 µm
  • cell width: 0.4 µm
  • cell shape: rod-shaped

pigmentation

  • @ref: 30382
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17502
  • name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/535
  • composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
17502positivegrowth28mesophilic
30382positivegrowth25-37mesophilic
30382positiveoptimum30mesophilic

culture pH

@refabilitytypepHPH range
30382positivegrowth05-09alkaliphile
30382positiveoptimum7

Physiology and metabolism

halophily

  • @ref: 30382
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <3 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3038228260galactose+carbon source
3038217234glucose+carbon source
3038217992sucrose+carbon source
3038227082trehalose+carbon source

enzymes

@refvalueactivityec
30382alkaline phosphatase+3.1.3.1
30382catalase+1.11.1.6
30382cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 17502
  • sample type: oil contaminated soil
  • geographic location: Kaohsiung County
  • country: Taiwan
  • origin.country: TWN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination#Oil (Fuel)
#Environmental#Terrestrial#Soil

Safety information

risk assessment

  • @ref: 17502
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17502
  • description: Sphingomonas formosensis strain CC-Nfb-2 16S ribosomal RNA gene, partial sequence
  • accession: HM193517
  • length: 1478
  • database: ena
  • NCBI tax ID: 861534

Genome sequences

  • @ref: 66792
  • description: Sphingomonas formosensis CC-Nfb-2
  • accession: GCA_009755815
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 861534

GC content

@refGC-contentmethod
1750262.8high performance liquid chromatography (HPLC)
3038262.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno66.264no
flagellatedno96.51no
gram-positiveno96.733yes
anaerobicno99.075no
aerobicyes93.89no
halophileno97.489no
spore-formingno93.917no
glucose-utilyes84.553yes
thermophileno99.047yes
glucose-fermentno91.721no

External links

@ref: 17502

culture collection no.: DSM 24164, BCRC 80272

straininfo link

  • @ref: 83427
  • straininfo: 398242

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21873513Sphingomonas formosensis sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from agricultural soil.Lin SY, Shen FT, Lai WA, Zhu ZL, Chen WM, Chou JH, Lin ZY, Young CCInt J Syst Evol Microbiol10.1099/ijs.0.034728-02011Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, Polyamines/analysis, Polycyclic Aromatic Hydrocarbons/*metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Serine C-Palmitoyltransferase/metabolism, *Soil Microbiology, Sphingolipids/metabolism, Sphingomonas/*classification/genetics/*isolation & purification/metabolism, TaiwanMetabolism
Phylogeny25985831Sphingomonas morindae sp. nov., isolated from Noni (Morinda citrifolia L.) branch.Liu Y, Yao S, Lee YJ, Cao Y, Zhai L, Zhang X, Su J, Ge Y, Kim SG, Cheng CInt J Syst Evol Microbiol10.1099/ijs.0.0003402015Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Endophytes/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Molecular Sequence Data, Morinda/*microbiology, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistryEnzymology
Phylogeny27469025Sphingomonas prati sp. nov., isolated from alpine meadow soil.Manandhar P, Zhang G, Hu Y, Lama A, Gao F, Gu ZInt J Syst Evol Microbiol10.1099/ijsem.0.0013462016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Grassland, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonas/*classification/genetics/isolation & purification, Tibet, Ubiquinone/chemistryTranscriptome
Phylogeny28755311Sphingomonas montana sp. nov., isolated from a soil sample from the Tanggula Mountain in the Qinghai Tibetan Plateau.Manandhar P, Zhang G, Lama A, Liu F, Hu YAntonie Van Leeuwenhoek10.1007/s10482-017-0915-62017Computational Biology/methods, *Environment, Genome, Bacterial, Genomics/methods, Metabolomics/methods, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Sphingomonas/chemistry/*classification/*genetics/isolation & purification, Tibet, Whole Genome SequencingGenetics
Phylogeny28837005Sphingomonas crusticola sp. nov., isolated from biological soil crusts.Zhang K, Tang K, Feng F, Yuan B, Zhang X, Meng JInt J Syst Evol Microbiol10.1099/ijsem.0.0020742017Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistryTranscriptome
Phylogeny32496177Sphingomonas profundi sp. nov., isolated from deep-sea sediment of the Mariana Trench.Yang S, Li X, Xiao X, Zhuang G, Zhang YInt J Syst Evol Microbiol10.1099/ijsem.0.0042352020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/isolation & purification, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17502Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24164)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24164
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
30382Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2672128776041
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)
83427Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID398242.1StrainInfo: A central database for resolving microbial strain identifiers