Strain identifier
BacDive ID: 14270
Type strain:
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)
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
@ref | growth | type | temperature | range |
---|---|---|---|---|
17502 | positive | growth | 28 | mesophilic |
30382 | positive | growth | 25-37 | mesophilic |
30382 | positive | optimum | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
30382 | positive | growth | 05-09 | alkaliphile |
30382 | positive | optimum | 7 |
Physiology and metabolism
halophily
- @ref: 30382
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: <3 %
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30382 | 28260 | galactose | + | carbon source |
30382 | 17234 | glucose | + | carbon source |
30382 | 17992 | sucrose | + | carbon source |
30382 | 27082 | trehalose | + | carbon source |
enzymes
@ref | value | activity | ec |
---|---|---|---|
30382 | alkaline phosphatase | + | 3.1.3.1 |
30382 | catalase | + | 1.11.1.6 |
30382 | cytochrome 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
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | GC-content | method |
---|---|---|
17502 | 62.8 | high performance liquid chromatography (HPLC) |
30382 | 62.8 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 66.264 | no |
flagellated | no | 96.51 | no |
gram-positive | no | 96.733 | yes |
anaerobic | no | 99.075 | no |
aerobic | yes | 93.89 | no |
halophile | no | 97.489 | no |
spore-forming | no | 93.917 | no |
glucose-util | yes | 84.553 | yes |
thermophile | no | 99.047 | yes |
glucose-ferment | no | 91.721 | no |
External links
@ref: 17502
culture collection no.: DSM 24164, BCRC 80272
straininfo link
- @ref: 83427
- straininfo: 398242
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 21873513 | Sphingomonas 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 CC | Int J Syst Evol Microbiol | 10.1099/ijs.0.034728-0 | 2011 | Bacterial 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, Taiwan | Metabolism |
Phylogeny | 25985831 | Sphingomonas 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 C | Int J Syst Evol Microbiol | 10.1099/ijs.0.000340 | 2015 | Bacterial 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/chemistry | Enzymology |
Phylogeny | 27469025 | Sphingomonas prati sp. nov., isolated from alpine meadow soil. | Manandhar P, Zhang G, Hu Y, Lama A, Gao F, Gu Z | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001346 | 2016 | Bacterial 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/chemistry | Transcriptome |
Phylogeny | 28755311 | Sphingomonas 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 Y | Antonie Van Leeuwenhoek | 10.1007/s10482-017-0915-6 | 2017 | Computational 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 Sequencing | Genetics |
Phylogeny | 28837005 | Sphingomonas crusticola sp. nov., isolated from biological soil crusts. | Zhang K, Tang K, Feng F, Yuan B, Zhang X, Meng J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002074 | 2017 | Bacterial 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/chemistry | Transcriptome |
Phylogeny | 32496177 | Sphingomonas profundi sp. nov., isolated from deep-sea sediment of the Mariana Trench. | Yang S, Li X, Xiao X, Zhuang G, Zhang Y | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004235 | 2020 | Bacterial 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/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
17502 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24164) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24164 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
30382 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 26721 | 28776041 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
83427 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID398242.1 | StrainInfo: A central database for resolving microbial strain identifiers |