Strain identifier
BacDive ID: 11877
Type strain:
Species: Pseudaminobacter salicylatoxidans
Strain Designation: BN12, BN12D
Strain history: CIP <- 2001, A. Stolz, Stuttgart Univ., Stuttgart, Germany: strain BN12 <- B. Nörtemann
NCBI tax ID(s): 93369 (species)
General
@ref: 2938
BacDive-ID: 11877
DSM-Number: 6986
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-negative
description: Pseudaminobacter salicylatoxidans BN12 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from river water.
NCBI tax id
- NCBI tax id: 93369
- Matching level: species
strain history
@ref | history |
---|---|
2938 | <- B. Nörtemann; BN12 |
122376 | CIP <- 2001, A. Stolz, Stuttgart Univ., Stuttgart, Germany: strain BN12 <- B. Nörtemann |
doi: 10.13145/bacdive11877.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Phyllobacteriaceae
- genus: Pseudaminobacter
- species: Pseudaminobacter salicylatoxidans
- full scientific name: Pseudaminobacter salicylatoxidans Kämpfer et al. 1999
@ref: 2938
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Phyllobacteriaceae
genus: Pseudaminobacter
species: Pseudaminobacter salicylatoxidans
full scientific name: Pseudaminobacter salicylatoxidans Kämpfer et al. 1999
strain designation: BN12, BN12D
type strain: yes
Morphology
cell morphology
@ref | gram stain | confidence | cell shape | motility |
---|---|---|---|---|
69480 | negative | 99.962 | ||
122376 | negative | rod-shaped | yes |
pigmentation
- @ref: 122376
- production: no
- name: Pyocyanin
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
2938 | CASO AGAR (MERCK 105458) (DSMZ Medium 220) | yes | https://mediadive.dsmz.de/medium/220 | Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water |
2938 | MINERAL MEDIUM PH 7.25 (DSMZ Medium 465) | yes | https://mediadive.dsmz.de/medium/465 | Name: MINERAL MEDIUM PH 7.25 (DSMZ Medium 465; with strain-specific modifications) Composition: Na2HPO4 x 2 H2O 3.5 g/l KH2PO4 1.0 g/l Naphthalene sulfonic acid 0.5 g/l (NH4)2SO4 0.5 g/l Yeast extract 0.1 g/l MgCl2 x 6 H2O 0.1 g/l Ca(NO3)2 x 4 H2O 0.05 g/l Na2-EDTA 0.0005 g/l H3BO3 0.0003 g/l FeSO4 x 7 H2O 0.0002 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Distilled water |
39625 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
122376 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
2938 | positive | growth | 28 | mesophilic |
39625 | positive | growth | 30 | mesophilic |
122376 | positive | growth | 25-41 | |
122376 | no | growth | 5 | psychrophilic |
122376 | no | growth | 10 | psychrophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 122376
- oxygen tolerance: obligate aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.996 |
halophily
- @ref: 122376
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-10 %
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
122376 | 16947 | citrate | - | carbon source |
122376 | 4853 | esculin | - | hydrolysis |
122376 | 17632 | nitrate | - | reduction |
122376 | 16301 | nitrite | - | reduction |
122376 | 17632 | nitrate | - | respiration |
antibiotic resistance
- @ref: 122376
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: no
- is resistant: yes
metabolite production
- @ref: 122376
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
122376 | oxidase | + | |
122376 | beta-galactosidase | - | 3.2.1.23 |
122376 | alcohol dehydrogenase | - | 1.1.1.1 |
122376 | gelatinase | - | |
122376 | amylase | - | |
122376 | DNase | - | |
122376 | caseinase | - | 3.4.21.50 |
122376 | catalase | + | 1.11.1.6 |
122376 | tween esterase | - | |
122376 | lecithinase | - | |
122376 | lipase | - | |
122376 | lysine decarboxylase | - | 4.1.1.18 |
122376 | ornithine decarboxylase | - | 4.1.1.17 |
122376 | protease | - | |
122376 | tryptophan deaminase | + | |
122376 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
122376 | - | + | + | - | - | + | - | - | + | - | + | + | - | - | - | - | - | - | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
122376 | + | + | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | + | - | - | + | - | + | - | - | - | - | + | - | + | - | - | + | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | - | - | + | + | - | + | - | - | - | - | - | + | - | + | - | + | - | - | + | - | - | + | - | + | - | - | + | - | + | + | + | + | + | + | - | + | + | + | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|
2938 | river water | Elbe river | Germany | DEU | Europe | |
122376 | Environment, Water, river | Germany | DEU | Europe | 1987 |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #River (Creek)
taxonmaps
- @ref: 69479
- File name: preview.99_50150.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_220;97_1977;98_36055;99_50150&stattab=map
- Last taxonomy: Mesorhizobium
- 16S sequence: AF072542
- Sequence Identity:
- Total samples: 456
- soil counts: 105
- aquatic counts: 135
- animal counts: 90
- plant counts: 126
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
2938 | 1 | Risk group (German classification) |
122376 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 20218
- description: Pseudaminobacter salicylatoxidans 16S ribosomal RNA, partial sequence
- accession: AF072542
- length: 1460
- database: ena
- NCBI tax ID: 93369
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pseudaminobacter salicylatoxidans DSM 6986 | GCA_003148475 | scaffold | ncbi | 93369 |
66792 | Pseudaminobacter salicylatoxidans strain DSM 6986 | 93369.5 | wgs | patric | 93369 |
66792 | Pseudaminobacter salicylatoxidans DSM 6986 | 2756170245 | draft | img | 93369 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | no | 79.031 | no |
gram-positive | no | 98.3 | no |
anaerobic | no | 98.429 | no |
halophile | no | 82.122 | no |
spore-forming | no | 96.06 | no |
glucose-util | yes | 90.741 | no |
aerobic | yes | 94.044 | no |
thermophile | no | 95.771 | yes |
motile | yes | 82.668 | no |
glucose-ferment | no | 91.543 | no |
External links
@ref: 2938
culture collection no.: DSM 6986, CIP 106963
straininfo link
- @ref: 81094
- straininfo: 48345
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 10319515 | Description of Pseudaminobacter gen. nov. with two new species, Pseudaminobacter salicylatoxidans sp. nov. and Pseudaminobacter defluvii sp. nov. | Kampfer P, Muller C, Mau M, Neef A, Auling G, Busse HJ, Osborn AM, Stolz A | Int J Syst Bacteriol | 10.1099/00207713-49-2-887 | 1999 | Bacterial Typing Techniques, Base Composition, Biodegradation, Environmental, DNA, Bacterial/analysis/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Gram-Negative Aerobic Bacteria/*classification/cytology/isolation & purification/metabolism, Molecular Sequence Data, Naphthalenesulfonates/*metabolism, Nucleic Acid Hybridization, RNA, Ribosomal, 16S/genetics, Sewage/microbiology, Water Microbiology | Metabolism |
Phylogeny | 28036252 | Pseudaminobacter manganicus sp. nov., isolated from sludge of a manganese mine. | Li J, Huang J, Liao S, Wang G | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001765 | 2017 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Manganese, *Mining, Nucleic Acid Hybridization, Phospholipids/chemistry, Phyllobacteriaceae/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Spermidine/analogs & derivatives/chemistry, Ubiquinone/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
2938 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6986) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-6986 | |||
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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
39625 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/19151 | ||||
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) | |||
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 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
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 | |||
81094 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID48345.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
122376 | Curators of the CIP | Collection of Institut Pasteur (CIP 106963) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106963 |