Strain identifier
BacDive ID: 135951
Type strain:
Species: Paracoccus thiocyanatus
Strain history: CIP <- 1999, IFO <- IAM <- Y. Fujimura & H. Kuraishi <- H. Murooka
NCBI tax ID(s): 34006 (species)
General
@ref: 35239
BacDive-ID: 135951
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic
description: Paracoccus thiocyanatus CIP 106060 is an obligate aerobe, mesophilic bacterium that was isolated from Activated sludge.
NCBI tax id
- NCBI tax id: 34006
- Matching level: species
strain history
@ref | history |
---|---|
67770 | IAM 12816 <-- Y. Katayama THI 011 <-- H. Murooka 1-8A. |
35239 | CIP <- 1999, IFO <- IAM <- Y. Fujimura & H. Kuraishi <- H. Murooka |
doi: 10.13145/bacdive135951.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Paracoccaceae
- genus: Paracoccus
- species: Paracoccus thiocyanatus
- full scientific name: Paracoccus thiocyanatus Katayama et al. 1996
@ref: 35239
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Paracoccus
species: Paracoccus thiocyanatus
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | no | 90.032 | ||
69480 | 99.998 | negative | ||
35239 | no | negative | rod-shaped |
Culture and growth conditions
culture medium
@ref | name | growth | composition | link |
---|---|---|---|---|
35239 | MEDIUM 127 - for Streptomyces scabiei and Thiobacillus novellus | yes | Distilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (0.100 g);Agar (15.000 g);Yeast extract (5.000 g);Potassium di-hydrogen phosphate (1.500 g);Ammonium chloride (0.300 g);Sodium thiosulphate pentahydrate (5.000 g);Di Sodium hydrogen | |
35239 | CIP Medium 127 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=127 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
35239 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
35239 | positive | growth | 25-37 | mesophilic |
35239 | no | growth | 5 | psychrophilic |
35239 | no | growth | 10 | psychrophilic |
35239 | no | growth | 41 | thermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 35239
- oxygen tolerance: obligate aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.985 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
35239 | NaCl | positive | growth | 0-4 % |
35239 | NaCl | no | growth | 6 % |
35239 | NaCl | no | growth | 8 % |
35239 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
35239 | 4853 | esculin | - | hydrolysis |
35239 | 17632 | nitrate | + | reduction |
35239 | 16301 | nitrite | + | reduction |
antibiotic resistance
- @ref: 35239
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: no
- is resistant: yes
metabolite production
- @ref: 35239
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
35239 | oxidase | + | |
35239 | beta-galactosidase | - | 3.2.1.23 |
35239 | alcohol dehydrogenase | - | 1.1.1.1 |
35239 | gelatinase | - | |
35239 | amylase | - | |
35239 | DNase | - | |
35239 | caseinase | - | 3.4.21.50 |
35239 | catalase | + | 1.11.1.6 |
35239 | tween esterase | - | |
35239 | lecithinase | - | |
35239 | lipase | - | |
35239 | lysine decarboxylase | - | 4.1.1.18 |
35239 | ornithine decarboxylase | - | 4.1.1.17 |
35239 | protease | - | |
35239 | tryptophan deaminase | - | |
35239 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
35239 | - | + | + | + | - | + | - | - | - | - | + | + | - | - | - | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
35239 | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | + | + | + | - | - | - | - | + | - | - | + | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | - | - | + | - | - | - | - | + | - | + | - | + | - | - | + | - | - | + | + | - | - | - | - | - | + | - | + | + | - | - | - | - | + | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
67770 | Activated sludge | Japan | JPN | Asia |
35239 | Environment, Activated sludge |
taxonmaps
- @ref: 69479
- File name: preview.99_62297.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_529;97_2307;98_44138;99_62297&stattab=map
- Last taxonomy: Paracoccus thiocyanatus subclade
- 16S sequence: D32242
- Sequence Identity:
- Total samples: 45
- soil counts: 5
- aquatic counts: 22
- animal counts: 9
- plant counts: 9
Safety information
risk assessment
- @ref: 35239
- biosafety level: 1
- biosafety level comment: Risk group (French classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
67770 | Paracoccus thiocyanatus gene for 16S rRNA, partial sequence, strain: NBRC 14569 | AB680635 | 1388 | ena | 34006 |
67770 | Paracoccus thiocyanatus gene for 16S rRNA, strain: THI 011 | D32242 | 1384 | ena | 34006 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Paracoccus thiocyanatus ATCC 700171 | GCA_900156255 | scaffold | ncbi | 34006 |
66792 | Paracoccus thiocyanatus strain ATCC 700171 | 34006.7 | wgs | patric | 34006 |
66792 | Paracoccus thiocyanatus ATCC 700171 | 2681812813 | draft | img | 34006 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 64.639 | no |
flagellated | no | 91.857 | no |
gram-positive | no | 98.619 | no |
anaerobic | no | 96.198 | no |
aerobic | yes | 86.651 | no |
halophile | no | 75.088 | no |
spore-forming | no | 96.437 | no |
thermophile | no | 82.81 | no |
glucose-util | yes | 83.273 | no |
glucose-ferment | no | 88.95 | no |
External links
@ref: 35239
culture collection no.: CIP 106060, IAM 12816, IFO 14569, JCM 20756, ATCC 700171, NBRC 14569, NCIMB 13627, VKM B-2162
straininfo link
- @ref: 93210
- straininfo: 46218
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Genetics | 11882723 | Characterization of the replicator region of megaplasmid pTAV3 of Paracoccus versutus and search for plasmid-encoded traits. | Bartosik D, Baj J, Bartosik AA, Wlodarczyk M | Microbiology (Reading) | 10.1099/00221287-148-3-871 | 2002 | Amino Acid Sequence, Base Sequence, Gene Deletion, Molecular Sequence Data, Paracoccus/*genetics/growth & development, Plasmids/*genetics, Replication Origin, Replicon/*genetics, Sequence Analysis, DNA | Transcriptome |
Metabolism | 32291967 | Involvement of membrane vesicles in long-chain-AHL delivery in Paracoccus species. | Morinaga K, Nagakubo T, Nomura N, Toyofuku M | Environ Microbiol Rep | 10.1111/1758-2229.12843 | 2020 | Acyl-Butyrolactones/*metabolism, Biological Transport, *Extracellular Vesicles, Microbial Interactions, Paracoccus/*metabolism, Paracoccus denitrificans/metabolism, *Quorum Sensing |
Reference
@id | authors | title | doi/url | catalogue | journal | pubmed |
---|---|---|---|---|---|---|
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 | |||
35239 | Curators of the CIP | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106060 | Collection of Institut Pasteur (CIP 106060) | |||
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 | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
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. | 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 | |||
93210 | 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-ID46218.1 |