Strain identifier
BacDive ID: 162007
Type strain: 
Species: Sphingobacterium spiritivorum
Strain history: NCTC 11388 <-- B. Holmes CL 48/80 <-- Univ. Leeds.
NCBI tax ID(s): 258 (species)
version 8.1 (current version)
General
@ref: 67770
BacDive-ID: 162007
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Sphingobacterium spiritivorum JCM 1732 is a mesophilic, Gram-negative bacterium that was isolated from Blood of an 11 year-old female.
NCBI tax id
- NCBI tax id: 258
- Matching level: species
strain history
- @ref: 67770
- history: NCTC 11388 <-- B. Holmes CL 48/80 <-- Univ. Leeds.
doi: 10.13145/bacdive162007.20230509.8.1
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 spiritivorum
- full scientific name: Sphingobacterium spiritivorum (Holmes et al. 1982) Yabuuchi et al. 1983
synonyms
@ref synonym 20215 Flavobacterium spiritivorum 20215 Flavobacterium yabuuchiae
@ref: 67770
domain: Bacteria
phylum: Bacteroidetes
class: Sphingobacteriia
order: Sphingobacteriales
family: Sphingobacteriaceae
genus: Sphingobacterium
species: Sphingobacterium spiritivorum
full scientific name: Sphingobacterium spiritivorum (Holmes et al. 1982) Yabuuchi et al. 1983
type strain: no
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.98
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69480 | no | 99.994 |
| 69481 | no | 100 |
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Blood of an 11 year-old female
taxonmaps
- @ref: 69479
- File name: preview.99_3331.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15366;96_1738;97_2079;98_2555;99_3331&stattab=map
- Last taxonomy: Sphingobacterium spiritivorum subclade
- 16S sequence: LC060920
- Sequence Identity:
- Total samples: 7762
- soil counts: 926
- aquatic counts: 1560
- animal counts: 4723
- plant counts: 553
Sequence information
16S sequences
- @ref: 67770
- description: Sphingobacterium spiritivorum gene for 16S ribosomal RNA, partial sequence, strain: JCM 1732
- accession: LC060920
- length: 1445
- database: ena
- NCBI tax ID: 258
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Sphingobacterium spiritivorum strain NCTC11388 | 258.4 | wgs | patric | 258 |
| 66792 | Sphingobacterium spiritivorum NCTC 11388 | 2808606755 | draft | img | 258 |
| 67770 | Sphingobacterium spiritivorum NCTC11388 | GCA_900457365 | contig | ncbi | 258 |
GC content
- @ref: 67770
- GC-content: 41.3
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 92.443 | no |
| gram-positive | no | 97.84 | no |
| anaerobic | no | 99.203 | no |
| aerobic | yes | 87.96 | no |
| halophile | no | 96.128 | no |
| spore-forming | no | 94.702 | no |
| glucose-util | yes | 91.326 | no |
| flagellated | no | 95.917 | no |
| thermophile | no | 99.021 | yes |
| glucose-ferment | no | 90.306 | no |
External links
@ref: 67770
culture collection no.: JCM 1732, ATCC 35004, NCTC 11388
straininfo link
- @ref: 113485
- straininfo: 40815
Reference
| @id | authors | title | doi/url |
|---|---|---|---|
| 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 |
| 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 |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |
| 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 |
| 113485 | 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-ID40815.1 |