Strain identifier
BacDive ID: 154125
Type strain: 
Species: Sphingobacterium composti
Strain Designation: T5-12
Strain history: <- ST Lee, KAIST
NCBI tax ID(s): 363260 (species)
version 8.1 (current version)
General
@ref: 59558
BacDive-ID: 154125
keywords: genome sequence, 16S sequence, Bacteria, aerobe, rod-shaped
description: Sphingobacterium composti T5-12 is an aerobe, rod-shaped bacterium that was isolated from Soil,ginseng field.
NCBI tax id
- NCBI tax id: 363260
- Matching level: species
strain history
- @ref: 67771
- history: <- ST Lee, KAIST
doi: 10.13145/bacdive154125.20230509.8.1
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 composti
- full scientific name: Sphingobacterium composti Ten et al. 2007
@ref: 59558
domain: Bacteria
phylum: Bacteroidetes
class: Sphingobacteriia
order: Sphingobacteriales
family: Sphingobacteriaceae
genus: Sphingobacterium
species: Sphingobacterium composti
strain designation: T5-12
type strain: yes
Morphology
cell morphology
| @ref | cell shape | motility | gram stain | confidence |
|---|---|---|---|---|
| 67771 | rod-shaped | no | ||
| 67771 | negative | |||
| 69480 | no | 93.037 | ||
| 69480 | negative | 99.994 |
Culture and growth conditions
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 59558 | positive | growth | 30-42 | |
| 67771 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 59558 | aerobe |
| 67771 | aerobe |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 67771 | no | |
| 69480 | no | 99.997 |
| 69481 | no | 98 |
observation
- @ref: 67771
- observation: quinones: MK-7
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 59558 | Soil,ginseng field | Pocheon | Republic of Korea | KOR | Asia |
| 67771 | From compost composed of cow dung and rice straw | Daejeon | Republic of Korea | KOR | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Agriculture | #Field |
| #Environmental | #Terrestrial | #Soil |
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
taxonmaps
- @ref: 69479
- File name: preview.99_38905.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15366;96_3821;97_4714;98_28503;99_38905&stattab=map
- Last taxonomy: Sphingobacterium
- 16S sequence: AB244764
- Sequence Identity:
- Total samples: 265
- soil counts: 46
- aquatic counts: 26
- animal counts: 188
- plant counts: 5
Sequence information
16S sequences
- @ref: 67771
- description: Sphingobacterium composti Ten et al. 2007 non Yoo et al. 2007 gene for 16S rRNA, partial sequence
- accession: AB244764
- length: 1433
- database: ena
- NCBI tax ID: 363260
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Sphingobacterium composti Ten et al. 2007 non Yoo et al. 2007 KCTC 12578 | GCA_009829075 | scaffold | ncbi | 363260 |
| 66792 | Sphingobacterium composti Ten et al. 2007 non Yoo et al. 2007 strain KCTC 12578 | 363260.3 | wgs | patric | 363260 |
| 66792 | Sphingobacterium composti KCTC 12578 | 2898745591 | draft | img | 363260 |
GC content
- @ref: 67771
- GC-content: 36.0
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 98 | no |
| motile | no | 89.334 | yes |
| flagellated | no | 96.898 | no |
| gram-positive | no | 98.139 | yes |
| anaerobic | no | 99.091 | yes |
| aerobic | yes | 88.465 | no |
| halophile | no | 95.754 | no |
| spore-forming | no | 95.565 | yes |
| glucose-util | yes | 91.017 | no |
| thermophile | no | 99.486 | yes |
| glucose-ferment | no | 89.848 | no |
External links
@ref: 59558
culture collection no.: CCUG 52467, KCTC 12578, LMG 23401
straininfo link
- @ref: 107823
- straininfo: 289681
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 18768611 | Sphingobacterium anhuiense sp. nov., isolated from forest soil. | Wei W, Zhou Y, Wang X, Huang X, Lai R | Int J Syst Evol Microbiol | 10.1099/ijs.0.65864-0 | 2008 | Aerobiosis, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Sphingobacterium/*classification/genetics/*isolation & purification/physiology, Temperature, *Trees | Genetics |
| Phylogeny | 21984669 | Sphingobacterium 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 WJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.033670-0 | 2011 | Bacterial 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/*microbiology | Genetics |
| Phylogeny | 26303282 | Sphingobacterium rhinocerotis sp. nov., isolated from the faeces of Rhinoceros unicornis. | Li GD, Chen X, Li QY, Xu FJ, Qiu SM, Jiang Y, Jiang CL | Antonie Van Leeuwenhoek | 10.1007/s10482-015-0563-7 | 2015 | Animals, Feces/*microbiology, Lipid Metabolism, Perissodactyla/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sphingobacterium/*classification/genetics/isolation & purification/metabolism | Metabolism |
| Phylogeny | 29388539 | Sphingobacterium bovisgrunnientis sp. nov., isolated from yak milk. | Kaur M, Singh H, Sharma S, Mishra S, Tanuku NRS, Pinnaka AK | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002562 | 2018 | Animals, Bacterial Typing Techniques, Base Composition, Cattle/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, India, Milk/*microbiology, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sphingobacterium/*classification/genetics/isolation & purification | Transcriptome |
| Phylogeny | 32048984 | Sphingobacterium cavernae sp. nov., a novel bacterium isolated from soil sampled at Tiandong Cave. | Zhou XK, Huang Y, Li M, Zhang XF, Wei YQ, Cha QY, Zhang TK, Wang XJ, Liu JJ, Liu ZY, Qin SC, Mo MH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004044 | 2020 | Bacterial Typing Techniques, Base Composition, Caves/*microbiology, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingobacterium/*classification/isolation & purification, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
| Phylogeny | 34779758 | Sphingobacterium 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 J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005105 | 2021 | Agriculture, 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/chemistry | Transcriptome |
| Phylogeny | 35129696 | Sphingobacterium bovistauri sp. nov., Isolated from the Faeces of Bos Taurus. | Wang Q, Fang ZQ, Zhang CL, Shen JQ, Lai JD, Han XL, Lu T | Curr Microbiol | 10.1007/s00284-022-02763-2 | 2022 | Animals, Bacterial Typing Techniques, Cattle, China, DNA, Bacterial/genetics, Fatty Acids, Feces, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sphingobacterium/genetics, Vitamin K 2 | Transcriptome |
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |
| 59558 | Curators of the CCUG | https://www.ccug.se/strain?id=52467 | Culture Collection University of Gothenburg (CCUG) (CCUG 52467) | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||
| 69479 | João 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 beta | https://microbeatlas.org/ | |
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions 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 | |
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |
| 107823 | Reimer, 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 identifiers | 10.60712/SI-ID289681.1 |