Strain identifier
BacDive ID: 23284
Type strain:
Species: Sphingopyxis italica
Strain Designation: SC13E-971
Strain history: <- V. Jurado, Inst. de Recursos Naturales y Agrobiologia, CSIC, Sevilla, Spain; SC13E-971 <- L. Laiz, Inst. de Recursos Naturales y Agrobiologia, CSIC, Sevilla, Spain
NCBI tax ID(s): 1129133 (species)
General
@ref: 19367
BacDive-ID: 23284
DSM-Number: 25229
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Sphingopyxis italica SC13E-971 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from tuff from a catacomb wall.
NCBI tax id
- NCBI tax id: 1129133
- Matching level: species
strain history
- @ref: 19367
- history: <- V. Jurado, Inst. de Recursos Naturales y Agrobiologia, CSIC, Sevilla, Spain; SC13E-971 <- L. Laiz, Inst. de Recursos Naturales y Agrobiologia, CSIC, Sevilla, Spain
doi: 10.13145/bacdive23284.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Sphingomonadales
- family: Sphingomonadaceae
- genus: Sphingopyxis
- species: Sphingopyxis italica
- full scientific name: Sphingopyxis italica Alias-Villegas et al. 2013
@ref: 19367
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Sphingomonadales
family: Sphingomonadaceae
genus: Sphingopyxis
species: Sphingopyxis italica
full scientific name: Sphingopyxis italica Alias-Villegas et al. 2013
strain designation: SC13E-971
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
30877 | negative | 1.5 µm | 0.7 µm | rod-shaped | yes | |
69480 | negative | 99.975 |
pigmentation
- @ref: 30877
- production: yes
Culture and growth conditions
culture medium
- @ref: 19367
- 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 |
---|---|---|---|---|
19367 | positive | growth | 25 | mesophilic |
30877 | positive | growth | 10-30 | |
30877 | positive | optimum | 27.5 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
30877 | positive | growth | 4.5-8.5 | alkaliphile |
30877 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 30877
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
30877 | no | |
69481 | no | 100 |
69480 | no | 99.981 |
halophily
- @ref: 30877
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-2 %
observation
- @ref: 30877
- observation: aggregates in clumps
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30877 | 22599 | arabinose | + | carbon source |
30877 | 17234 | glucose | + | carbon source |
30877 | 25115 | malate | + | carbon source |
30877 | 17306 | maltose | + | carbon source |
30877 | 37684 | mannose | + | carbon source |
30877 | 506227 | N-acetylglucosamine | + | carbon source |
68369 | 25115 | malate | + | assimilation |
68369 | 17128 | adipate | - | assimilation |
68369 | 27689 | decanoate | - | assimilation |
68369 | 24265 | gluconate | - | assimilation |
68369 | 17306 | maltose | + | assimilation |
68369 | 59640 | N-acetylglucosamine | + | assimilation |
68369 | 16899 | D-mannitol | - | assimilation |
68369 | 16024 | D-mannose | + | assimilation |
68369 | 30849 | L-arabinose | + | assimilation |
68369 | 17634 | D-glucose | + | assimilation |
68369 | 5291 | gelatin | - | hydrolysis |
68369 | 4853 | esculin | + | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | - | reduction |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
30877 | alkaline phosphatase | + | 3.1.3.1 |
30877 | catalase | + | 1.11.1.6 |
30877 | cytochrome oxidase | + | 1.9.3.1 |
68369 | cytochrome oxidase | + | 1.9.3.1 |
68369 | gelatinase | - | |
68369 | beta-glucosidase | + | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19367 | - | - | - | - | - | + | - | + | + | + | + | - | + | + | - | - | - | + | - | - | + |
Isolation, sampling and environmental information
isolation
- @ref: 19367
- sample type: tuff (volcanic rock) from a catacomb wall
- geographic location: Rome, Roman catacombs of Saint Callixtus
- country: Italy
- origin.country: ITA
- continent: Europe
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Built environment | |
#Environmental | #Terrestrial | #Geologic |
#Environmental | #Terrestrial | #Volcanic |
Safety information
risk assessment
- @ref: 19367
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 19367
- description: Sphingopyxis italica partial 16S rRNA gene, type strain CS13E-S71T
- accession: HE648058
- length: 1411
- database: ena
- NCBI tax ID: 1129133
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Sphingopyxis italica DSM 25229 | GCA_011926545 | scaffold | ncbi | 1129133 |
66792 | Sphingopyxis italica strain DSM 25229 | 1129133.3 | wgs | patric | 1129133 |
66792 | Sphingopyxis italica DSM 25229 | 2828641578 | draft | img | 1129133 |
GC content
@ref | GC-content | method |
---|---|---|
19367 | 65.7 | high performance liquid chromatography (HPLC) |
30877 | 65.7 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 73.349 | no |
flagellated | no | 84.142 | no |
gram-positive | no | 96.624 | yes |
anaerobic | no | 99.559 | no |
aerobic | yes | 95.203 | no |
halophile | no | 93.827 | no |
spore-forming | no | 93.809 | no |
thermophile | no | 98.028 | no |
glucose-util | yes | 86.292 | yes |
glucose-ferment | no | 93.195 | yes |
External links
@ref: 19367
culture collection no.: DSM 25229, CECT 8016
straininfo link
- @ref: 87505
- straininfo: 390295
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 23264504 | Sphingopyxis italica sp. nov., isolated from Roman catacombs. | Alias-Villegas C, Jurado V, Laiz L, Saiz-Jimenez C | Int J Syst Evol Microbiol | 10.1099/ijs.0.046573-0 | 2012 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rome, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/analogs & derivatives/analysis | Genetics |
Phylogeny | 28613148 | Sphingopyxis solisilvae sp. nov., isolated from forest soil. | Chaudhary DK, Dahal RH, Kim J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001869 | 2017 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
19367 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25229) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25229 | |||
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 | |||
30877 | 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 | 27207 | 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) | |||
68369 | Automatically annotated from API 20NE | |||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
87505 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID390295.1 | StrainInfo: A central database for resolving microbial strain identifiers |