Strain identifier
BacDive ID: 17442
Type strain:
Species: Pseudoxanthobacter soli
Strain Designation: CC-CC4, CC-4
Strain history: CIP <- 2007, P. Kämpfer, Giesssen Univ., Giessen, Germany: strain CC-4
NCBI tax ID(s): 1123029 (strain), 433840 (species)
General
@ref: 8202
BacDive-ID: 17442
DSM-Number: 19599
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Pseudoxanthobacter soli CC-CC4 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil sample collected at a regional agricultural research field station.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1123029 | strain |
433840 | species |
strain history
@ref | history |
---|---|
8202 | <- C.-C. Young, Dept. Soil and Environmental Sci., Natl. Chung Hsing Univ., Taichung, Taiwan; CC4 |
122663 | CIP <- 2007, P. Kämpfer, Giesssen Univ., Giessen, Germany: strain CC-4 |
doi: 10.13145/bacdive17442.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Pseudoxanthobacteraceae
- genus: Pseudoxanthobacter
- species: Pseudoxanthobacter soli
- full scientific name: Pseudoxanthobacter soli Arun et al. 2008
@ref: 8202
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Pseudoxanthobacteraceae
genus: Pseudoxanthobacter
species: Pseudoxanthobacter soli
full scientific name: Pseudoxanthobacter soli Arun et al. 2008
strain designation: CC-CC4, CC-4
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
32256 | negative | 2 µm | 0.2 µm | rod-shaped | yes | |
69480 | negative | 99.987 | ||||
122663 | negative | rod-shaped | yes |
colony morphology
- @ref: 60225
- incubation period: 1 day
multimedia
@ref | multimedia content | caption | intellectual property rights |
---|---|---|---|
66793 | EM_DSM_19599_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_19599_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_19599_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_19599_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_19599_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
8202 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | 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 |
37749 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
122663 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
8202 | positive | growth | 28 | mesophilic |
32256 | positive | growth | 10-37 | |
32256 | positive | optimum | 37 | mesophilic |
37749 | positive | growth | 30 | mesophilic |
60225 | positive | growth | 28-37 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
32256 | positive | growth | 5.5-10 | alkaliphile |
32256 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
32256 | aerobe |
60225 | aerobe |
122663 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
32256 | no | |
69481 | no | 100 |
69480 | no | 99.986 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32256 | 30089 | acetate | + | carbon source |
32256 | 15963 | ribitol | + | carbon source |
32256 | 21217 | L-alaninamide | + | carbon source |
32256 | 16449 | alanine | + | carbon source |
32256 | 22599 | arabinose | + | carbon source |
32256 | 18403 | L-arabitol | + | carbon source |
32256 | 22653 | asparagine | + | carbon source |
32256 | 15740 | formate | + | carbon source |
32256 | 28757 | fructose | + | carbon source |
32256 | 33984 | fucose | + | carbon source |
32256 | 28260 | galactose | + | carbon source |
32256 | 17234 | glucose | + | carbon source |
32256 | 29987 | glutamate | + | carbon source |
32256 | 17754 | glycerol | + | carbon source |
32256 | 24996 | lactate | + | carbon source |
32256 | 29864 | mannitol | + | carbon source |
32256 | 37684 | mannose | + | carbon source |
32256 | 17268 | myo-inositol | + | carbon source |
32256 | 26271 | proline | + | carbon source |
32256 | 26546 | rhamnose | + | carbon source |
32256 | 30911 | sorbitol | + | carbon source |
32256 | 30031 | succinate | + | carbon source |
32256 | 17151 | xylitol | + | carbon source |
122663 | 17632 | nitrate | - | reduction |
122663 | 16301 | nitrite | - | reduction |
metabolite production
- @ref: 122663
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
32256 | catalase | + | 1.11.1.6 |
32256 | cytochrome oxidase | + | 1.9.3.1 |
122663 | oxidase | + | |
122663 | catalase | + | 1.11.1.6 |
122663 | urease | + | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | + | |
68382 | cystine arylamidase | + | 3.4.11.3 |
68382 | trypsin | + | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
122663 | - | + | + | + | + | + | + | + | + | - | + | + | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | sampling date |
---|---|---|---|---|---|---|
8202 | soil sample collected at a regional agricultural research field station | Kaohsiung County | Taiwan | TWN | Asia | |
60225 | Soil | Chyai County | Taiwan | TWN | Asia | 2000 |
122663 | Environment, Soil | Chyai county | Taiwan | TWN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Agriculture | #Field |
#Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_90344.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_37398;97_47548;98_62331;99_90344&stattab=map
- Last taxonomy: Pseudoxanthobacter
- 16S sequence: EF465533
- Sequence Identity:
- Total samples: 296
- soil counts: 33
- aquatic counts: 152
- animal counts: 79
- plant counts: 32
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
8202 | 1 | Risk group (German classification) |
122663 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 8202
- description: Pseudoxanthobacter soli DSM 19599 16S ribosomal RNA gene, partial sequence
- accession: EF465533
- length: 1436
- database: ena
- NCBI tax ID: 1123029
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pseudoxanthobacter soli DSM 19599 | GCA_900148505 | scaffold | ncbi | 1123029 |
66792 | Pseudoxanthobacter soli DSM 19599 | 1123029.3 | wgs | patric | 1123029 |
66792 | Pseudoxanthobacter soli DSM 19599 | 2585428043 | draft | img | 1123029 |
66792 | Pseudoxanthobacter soli DSM 19599 MsE-30jul19-87 | GCA_945898215 | scaffold | ncbi | 1123029 |
66792 | Pseudoxanthobacter soli DSM 19599 strain MsE-30jul19-87 | 1123029.10 | wgs | patric | 1123029 |
GC content
@ref | GC-content |
---|---|
8202 | 68.0 |
32256 | 68 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 78.322 | no |
flagellated | no | 80.677 | no |
gram-positive | no | 97.499 | yes |
anaerobic | no | 98.078 | no |
aerobic | yes | 89.188 | yes |
halophile | no | 93.217 | no |
spore-forming | no | 95.639 | yes |
thermophile | no | 97.227 | yes |
glucose-util | yes | 92.296 | yes |
glucose-ferment | no | 89.986 | no |
External links
@ref: 8202
culture collection no.: DSM 19599, CIP 109513, CCUG 54547, CC 4
straininfo link
- @ref: 86438
- straininfo: 358831
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 18599697 | Pseudoxanthobacter soli gen. nov., sp. nov., a nitrogen-fixing alphaproteobacterium isolated from soil. | Arun AB, Schumann P, Chu HI, Tan CC, Chen WM, Lai WA, Kampfer P, Shen FT, Rekha PD, Hung MH, Chou JH, Young CC | Int J Syst Evol Microbiol | 10.1099/ijs.0.65206-0 | 2008 | Alphaproteobacteria/chemistry/*classification/genetics/growth & development, Lipids/chemistry, Molecular Sequence Data, Nitrogen Fixation/*physiology, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Species Specificity, Taiwan | Genetics |
Phylogeny | 25013230 | Pseudoxanthobacter liyangensis sp. nov., isolated from dichlorodiphenyltrichloroethane-contaminated soil. | Liu XM, Chen K, Meng C, Zhang L, Zhu JC, Huang X, Li SP, Jiang JD | Int J Syst Evol Microbiol | 10.1099/ijs.0.056507-0 | 2014 | Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DDT/*chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants/chemistry, Ubiquinone/chemistry | Genetics |
Phylogeny | 31800387 | Segnochrobactrum spirostomi gen. nov., sp. nov., isolated from the ciliate Spirostomum yagiui and description of a novel family, Segnochrobactraceae fam. nov. within the order Rhizobiales of the class Alphaproteobacteria. | Akter S, Shazib SUA, Shin MK | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003907 | 2020 | Alphaproteobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Ciliophora/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
8202 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19599) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19599 | ||||
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 | ||||
32256 | 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 | 28497 | 28776041 | ||
37749 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/7265 | |||||
60225 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 54547) | https://www.ccug.se/strain?id=54547 | ||||
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) | ||||
66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 28604660 | 35: 676-683 2017 | ||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
68382 | Automatically annotated from API zym | ||||||
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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | ||||
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 | ||||
86438 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID358831.1 | StrainInfo: A central database for resolving microbial strain identifiers | ||||
122663 | Curators of the CIP | Collection of Institut Pasteur (CIP 109513) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109513 |