Strain identifier
BacDive ID: 132295
Type strain:
Species: Pseudochelatococcus lubricantis
Strain Designation: LR4
Strain history: <- Jian-Dong Jiang, Nanjing Agricultural Univ.
NCBI tax ID(s): 1538102 (species)
General
@ref: 24084
BacDive-ID: 132295
DSM-Number: 103870
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic
description: Pseudochelatococcus lubricantis LR4 is an aerobe, mesophilic bacterium that was isolated from From polluted soil.
NCBI tax id
- NCBI tax id: 1538102
- Matching level: species
strain history
@ref | history |
---|---|
24084 | <- KCTC <- L. Zhang and J.-D. Jiang, Key Lab of Microbiological Engineering of Agricultural Environment, Nanjing Agricultural University, PR China |
67771 | <- Jian-Dong Jiang, Nanjing Agricultural Univ. |
doi: 10.13145/bacdive132295.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Beijerinckiaceae
- genus: Pseudochelatococcus
- species: Pseudochelatococcus lubricantis
- full scientific name: Pseudochelatococcus lubricantis Kämpfer et al. 2015
synonyms
- @ref: 20215
- synonym: Qingshengfania soli
@ref: 24084
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Beijerinckiaceae
genus: Pseudochelatococcus
species: Pseudochelatococcus lubricantis
full scientific name: Pseudochelatococcus lubricantis Kämpfer et al. 2015 emend. Kämpfer et al. 2018
strain designation: LR4
type strain: no
Culture and growth conditions
culture medium
- @ref: 24084
- 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 |
---|---|---|---|---|
24084 | positive | growth | 28 | mesophilic |
67771 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
24084 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | + | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent | geographic location |
---|---|---|---|---|---|
67771 | From polluted soil | China | CHN | Asia | |
24084 | soil of pesticide factory | China | CHN | Asia | Nanjing |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Industrial | #Plant (Factory) |
#Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_81422.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_19514;97_24213;98_56617;99_81422&stattab=map
- Last taxonomy: Pseudochelatococcus lubricantis subclade
- 16S sequence: KP973992
- Sequence Identity:
- Total samples: 143
- soil counts: 30
- aquatic counts: 66
- animal counts: 44
- plant counts: 3
Safety information
risk assessment
- @ref: 24084
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24084
- description: Qingshengfania soli strain LR4 16S ribosomal RNA gene, partial sequence
- accession: KP973992
- length: 1442
- database: ena
- NCBI tax ID: 1538102
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pseudochelatococcus lubricantis DSM 103870 | GCA_011762225 | scaffold | ncbi | 1538102 |
66792 | Pseudochelatococcus lubricantis strain DSM 103870 | 1538102.3 | wgs | patric | 1538102 |
66792 | Pseudochelatococcus lubricantis DSM 103870 | 2828467665 | draft | img | 1538102 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 72.365 | no |
flagellated | no | 68.827 | no |
gram-positive | no | 98.101 | no |
anaerobic | no | 96.737 | yes |
aerobic | yes | 87.296 | yes |
halophile | no | 94.909 | no |
spore-forming | no | 94.308 | no |
glucose-util | yes | 56.112 | yes |
thermophile | no | 96.892 | yes |
glucose-ferment | no | 90.183 | yes |
External links
@ref: 24084
culture collection no.: DSM 103870, CCTCC AB 2015036, KCTC 42463
straininfo link
- @ref: 90642
- straininfo: 403688
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 26382584 | Qingshengfania soli gen. nov., sp. nov., a member of the order Rhizobiales isolated from the soil of a pesticide factory. | Zhang L, Zhou QX, Song M, Chen XL, Xu XH, Chen K, Li SP, Jiang JD | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000620 | 2015 | Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis/chemistry, Molecular Sequence Data, *Pesticides, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry | Genetics |
Phylogeny | 29757129 | Qingshengfania soli Zhang et al. 2015 is a later heterotypic synonym of Pseudochelatococcus lubricantis Kampfer et al. 2015. | Kampfer P, Glaeser SP, Graber M, Rabenstein A, Kuever J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002817 | 2018 | Bacterial Typing Techniques, Base Composition, Beijerinckiaceae/*classification/genetics, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology | 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 | |
24084 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-103870 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103870) | |
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 | ||
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/ | |
90642 | 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-ID403688.1 |