Strain identifier
BacDive ID: 24562
Type strain: 
Species: Sphingomonas yantingensis
Strain Designation: 1007
Strain history: J. Huang and X. Sheng 1007.
NCBI tax ID(s): 1241761 (species)
version 8.1 (current version)
General
@ref: 20819
BacDive-ID: 24562
DSM-Number: 27244
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Sphingomonas yantingensis 1007 is a mesophilic, Gram-negative bacterium that was isolated from purple paddy soil.
NCBI tax id
- NCBI tax id: 1241761
- Matching level: species
strain history
| @ref | history |
|---|---|
| 20819 | <- J. Huang, College of Life Sciences, Nanjing Agricultural University, China; 1007 |
| 67770 | J. Huang and X. Sheng 1007. |
doi: 10.13145/bacdive24562.20230509.8.1
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 yantingensis
- full scientific name: Sphingomonas yantingensis Huang et al. 2014
@ref: 20819
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Pseudomonadales
family: Sphingomonadaceae
genus: Sphingomonas
species: Sphingomonas yantingensis
full scientific name: Sphingomonas yantingensis Huang et al. 2014 emend. Feng et al. 2017
strain designation: 1007
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.988
multimedia
- @ref: 20819
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_27244.jpg
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
- @ref: 20819
- name: NUTRIENT AGAR (DSMZ Medium 1)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1
- composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 20819 | positive | growth | 28 | mesophilic |
| 67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.984 |
observation
- @ref: 67770
- observation: quinones: Q-10
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 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 |
|---|---|---|---|
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 20819 | - | - | - | - | - | + | - | + | + | + | + | - | + | + | - | - | - | + | - | - | - |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 20819 | purple paddy soil | Sichuan province, Yanting county, Linshan township (105° 27' E 31° 16' N, at an altitude of 420 m) | China | CHN | Asia | 31.2667 | 105.45 |
| 67770 | Purplish soil in Yanting | Sichuan | China | CHN | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_65904.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_348;97_35986;98_46517;99_65904&stattab=map
- Last taxonomy: Sphingomonas
- 16S sequence: JX566547
- Sequence Identity:
- Total samples: 723
- soil counts: 73
- aquatic counts: 254
- animal counts: 333
- plant counts: 63
Safety information
risk assessment
- @ref: 20819
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20819
- description: Sphingomonas yantingensis strain 1007 from China 16S ribosomal RNA gene, partial sequence
- accession: JX566547
- length: 1463
- database: ena
- NCBI tax ID: 1241761
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Sphingomonas yantingensis DSM 27244 | GCA_014199325 | contig | ncbi | 1241761 |
| 66792 | Sphingomonas yantingensis strain DSM 27244 | 1241761.3 | wgs | patric | 1241761 |
| 66792 | Sphingomonas yantingensis DSM 27244 | 2828398746 | draft | img | 1241761 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 20819 | 67 | high performance liquid chromatography (HPLC) |
| 67770 | 66.3-67.7 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 69.955 | no |
| gram-positive | no | 97.042 | no |
| anaerobic | no | 99.614 | no |
| aerobic | yes | 95.967 | no |
| halophile | no | 94.445 | no |
| spore-forming | no | 94.061 | no |
| glucose-util | yes | 90.686 | yes |
| flagellated | no | 88.774 | no |
| thermophile | no | 96.224 | yes |
| glucose-ferment | no | 92.865 | yes |
External links
@ref: 20819
culture collection no.: DSM 27244, CCTCC AB 2013146, JCM 19201
straininfo link
- @ref: 88416
- straininfo: 408184
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 24363294 | Sphingomonas yantingensis sp. nov., a mineral-weathering bacterium isolated from purplish paddy soil. | Huang J, Huang Z, Zhang ZD, He LY, Sheng XF | Int J Syst Evol Microbiol | 10.1099/ijs.0.055954-0 | 2013 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza/microbiology, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistry | Genetics |
| Phylogeny | 28691655 | Sphingomonas spermidinifaciens sp. nov., a novel bacterium containing spermidine as the major polyamine, isolated from an abandoned lead-zinc mine and emended descriptions of the genus Sphingomonas and the species Sphingomonas yantingensis and Sphingomonas japonica. | Feng GD, Yang SZ, Xiong X, Li HP, Zhu HH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001905 | 2017 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Mining, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistry, Zinc | 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 | |
| 20819 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-27244 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27244) | |
| 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/ | ||
| 68369 | Automatically annotated from API 20NE | |||
| 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 | |
| 88416 | 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-ID408184.1 |