Strain identifier
BacDive ID: 13713
Type strain:
Species: Paracoccus aminovorans
Strain Designation: DM-82
Strain history: CIP <- 1999, JCM <- T. Urakami: strain DM-82
NCBI tax ID(s): 34004 (species)
General
@ref: 3238
BacDive-ID: 13713
DSM-Number: 8537
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic
description: Paracoccus aminovorans DM-82 is an obligate aerobe, mesophilic bacterium that was isolated from soil Niigata Factory of Mitsubishi Gas Chemical Company.
NCBI tax id
- NCBI tax id: 34004
- Matching level: species
strain history
@ref | history |
---|---|
3238 | <- JCM <- T. Urakami, DM-82 |
67770 | T. Urakami DM-82. |
116338 | CIP <- 1999, JCM <- T. Urakami: strain DM-82 |
doi: 10.13145/bacdive13713.20230509.8.1
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 aminovorans
- full scientific name: Paracoccus aminovorans Urakami et al. 1990
@ref: 3238
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Paracoccus
species: Paracoccus aminovorans
full scientific name: Paracoccus aminovorans Urakami et al. 1990
strain designation: DM-82
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | no | 90.305 | ||
69480 | 99.997 | negative | ||
116338 | no | negative | rod-shaped |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
3238 | MEDIUM FOR PARACOCCUS AMINOPHILUS AND P. AMINOVORANS (DSMZ Medium 774) | yes | https://mediadive.dsmz.de/medium/774 | Name: MEDIUM FOR PARACOCCUS AMINOPHILUS AND P. AMINOVORANS (DSMZ Medium 774) Composition: Agar 20.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Peptone 5.0 g/l Distilled water |
40405 | MEDIUM 199 - for Clavibacter michiganense subsp. insidiosum | yes | Distilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (5.000g);Yeast extract (5.000 g);Peptone (5.000 g) | |
116338 | CIP Medium 364 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=364 | |
116338 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
3238 | positive | growth | 30 | mesophilic |
40405 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
116338 | positive | growth | 25-37 | mesophilic |
116338 | no | growth | 5 | psychrophilic |
116338 | no | growth | 10 | psychrophilic |
116338 | no | growth | 41 | thermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 116338
- oxygen tolerance: obligate aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 97 |
69480 | no | 99.995 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
116338 | NaCl | positive | growth | 0-6 % |
116338 | NaCl | no | growth | 8 % |
116338 | NaCl | no | growth | 10 % |
observation
- @ref: 67770
- observation: quinones: Q-10
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
116338 | 16947 | citrate | - | carbon source |
116338 | 4853 | esculin | + | hydrolysis |
116338 | 17632 | nitrate | + | reduction |
116338 | 16301 | nitrite | + | reduction |
116338 | 17632 | nitrate | + | respiration |
antibiotic resistance
- @ref: 116338
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: no
- is resistant: yes
metabolite production
- @ref: 116338
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
116338 | oxidase | + | |
116338 | beta-galactosidase | - | 3.2.1.23 |
116338 | gelatinase | - | |
116338 | amylase | - | |
116338 | DNase | - | |
116338 | caseinase | - | 3.4.21.50 |
116338 | catalase | + | 1.11.1.6 |
116338 | tween esterase | - | |
116338 | lecithinase | - | |
116338 | lipase | - | |
116338 | protease | - | |
116338 | tryptophan deaminase | - | |
116338 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116338 | - | + | + | + | - | + | - | + | - | - | + | + | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
3238 | soil Niigata Factory of Mitsubishi Gas Chemical Company | Japan | JPN | Asia |
67770 | Soil | |||
116338 | Environment, Soil | Japan | JPN | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_4614.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_529;97_2307;98_3463;99_4614&stattab=map
- Last taxonomy: Paracoccus
- 16S sequence: LN832559
- Sequence Identity:
- Total samples: 664
- soil counts: 38
- aquatic counts: 110
- animal counts: 513
- plant counts: 3
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
3238 | 1 | Risk group (German classification) |
116338 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
3238 | Paracoccus aminovorans gene for 16S rRNA, strain: JCM 7685 | D32240 | 1385 | ena | 34004 |
3238 | Paracoccus aminovorans gene for 16S rRNA, partial sequence, strain: NBRC 16711 | AB681112 | 1388 | ena | 34004 |
3238 | Paracoccus aminovorans isolate JCM7685 genome assembly, chromosome: I | LN832559 | 3108335 | ena | 34004 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Paracoccus aminovorans JCM7685 | GCA_900005615 | complete | ncbi | 34004 |
66792 | Paracoccus aminovorans DSM 8537 | GCA_900113565 | contig | ncbi | 34004 |
66792 | Paracoccus aminovorans strain DSM 8537 | 34004.15 | wgs | patric | 34004 |
66792 | Paracoccus aminovorans strain JCM7685 | 34004.11 | plasmid | patric | 34004 |
66792 | Paracoccus aminovorans strain JCM7685 | 34004.12 | plasmid | patric | 34004 |
66792 | Paracoccus aminovorans strain JCM7685 | 34004.10 | plasmid | patric | 34004 |
66792 | Paracoccus aminovorans strain JCM7685 | 34004.9 | complete | patric | 34004 |
66792 | Paracoccus aminovorans DSM 8537 | 2615840720 | draft | img | 34004 |
66792 | Paracoccus aminovorans JCM7685 | 2773857812 | complete | img | 34004 |
GC content
@ref | GC-content | method |
---|---|---|
3238 | 67.0 | high performance liquid chromatography (HPLC) |
67770 | 67 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 97 | no |
motile | no | 74.324 | no |
flagellated | no | 93.396 | no |
gram-positive | no | 98.248 | no |
anaerobic | no | 97.737 | no |
aerobic | yes | 91.643 | no |
halophile | no | 84.919 | no |
spore-forming | no | 94.649 | no |
glucose-ferment | no | 90.546 | no |
thermophile | no | 95.061 | yes |
glucose-util | yes | 89.465 | no |
External links
@ref: 3238
culture collection no.: DSM 8537, ATCC 49632, IAM 14244, JCM 7685, BCRC 80946, CIP 106076, IFO 16711, LMG 23829, NBRC 16711, VKM B-2140
straininfo link
- @ref: 82897
- straininfo: 42592
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 2397196 | Paracoccus aminophilus sp. nov. and Paracoccus aminovorans sp. nov., which utilize N,N-dimethylformamide. | Urakami T, Araki H, Oyanagi H, Suzuki K, Komagata K | Int J Syst Bacteriol | 10.1099/00207713-40-3-287 | 1990 | Base Composition, DNA, Bacterial/analysis, Dimethylformamide/*metabolism, Nucleic Acid Hybridization, Paracoccus/*classification/metabolism | Metabolism |
Phylogeny | 22753523 | Paracoccus huijuniae sp. nov., an amide pesticide-degrading bacterium isolated from activated sludge of a wastewater biotreatment system. | Sun LN, Zhang J, Kwon SW, He J, Zhou SG, Li SP | Int J Syst Evol Microbiol | 10.1099/ijs.0.044180-0 | 2012 | Amides/*metabolism, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Paracoccus/*classification/genetics/isolation & purification, Pesticides/*metabolism, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Ubiquinone/analysis, Waste Water/microbiology | Metabolism |
Phylogeny | 28809137 | Paracoccus mangrovi sp. nov., isolated from a mangrove. | Chen WM, Li YS, Young CC, Sheu SY | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001993 | 2017 | Avicennia/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hydroxybutyrates/metabolism, Nucleic Acid Hybridization, Paracoccus/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, Polyesters/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Taiwan, Ubiquinone/chemistry | Metabolism |
Metabolism | 28856785 | Lifestyle-determining extrachromosomal replicon pAMV1 and its contribution to the carbon metabolism of the methylotrophic bacterium Paracoccus aminovorans JCM 7685. | Czarnecki J, Dziewit L, Puzyna M, Prochwicz E, Tudek A, Wibberg D, Schluter A, Puhler A, Bartosik D | Environ Microbiol | 10.1111/1462-2920.13901 | 2017 | Carbon/*metabolism, Gene Expression Regulation, Bacterial/genetics, Gene Transfer, Horizontal/genetics, Genome, Bacterial/genetics, Paracoccus/*genetics/*metabolism, Plasmids/*genetics, Replicon/*genetics | Genetics |
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 | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
3238 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8537) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-8537 | |||
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 | |||
40405 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/18165 | ||||
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 | |
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. | 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 | |||
82897 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID42592.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
116338 | Curators of the CIP | Collection of Institut Pasteur (CIP 106076) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106076 |