Strain identifier

BacDive ID: 13714

Type strain: Yes

Species: Paracoccus aminophilus

Strain Designation: DM-15

Strain history: CIP <- 1999, JCM <- T. Urakami: strain DM-15

NCBI tax ID(s): 1367847 (strain), 34003 (species)

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General

@ref: 3239

BacDive-ID: 13714

DSM-Number: 8538

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, Gram-negative

description: Paracoccus aminophilus DM-15 is an obligate aerobe, Gram-negative bacterium that was isolated from soil Niigata Factory of Mitsubishi Gas Chemical Company.

NCBI tax id

NCBI tax idMatching level
1367847strain
34003species

strain history

@refhistory
3239<- JCM <- T. Urakami, DM-15
67770T. Urakami DM-15.
116332CIP <- 1999, JCM <- T. Urakami: strain DM-15

doi: 10.13145/bacdive13714.20240916.9.1

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 aminophilus
  • full scientific name: Paracoccus aminophilus Urakami et al. 1990

@ref: 3239

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Paracoccus

species: Paracoccus aminophilus

full scientific name: Paracoccus aminophilus Urakami et al. 1990

strain designation: DM-15

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
116332negativerod-shapedno
69480negative97.982

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3239MEDIUM FOR PARACOCCUS AMINOPHILUS AND P. AMINOVORANS (DSMZ Medium 774)yeshttps://mediadive.dsmz.de/medium/774Name: 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
34679MEDIUM 199 - for Clavibacter michiganense subsp. insidiosumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (5.000g);Yeast extract (5.000 g);Peptone (5.000 g)
116332CIP Medium 364yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=364

culture temp

@refgrowthtypetemperature
3239positivegrowth30
34679positivegrowth30
67770positivegrowth30
116332positivegrowth25-41
116332nogrowth5
116332nogrowth10

Physiology and metabolism

oxygen tolerance

  • @ref: 116332
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

halophily

@refsaltgrowthtested relationconcentration
116332NaClpositivegrowth0-8 %
116332NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11633216947citrate-carbon source
1163324853esculin-hydrolysis
11633217632nitrate-reduction
11633216301nitrite-reduction
11633217632nitrate-respiration

antibiotic resistance

  • @ref: 116332
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 116332
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
116332oxidase+
116332beta-galactosidase-3.2.1.23
116332alcohol dehydrogenase-1.1.1.1
116332gelatinase-
116332amylase-
116332DNase-
116332caseinase-3.4.21.50
116332catalase+1.11.1.6
116332tween esterase-
116332lecithinase-
116332lipase-
116332lysine decarboxylase-4.1.1.18
116332ornithine decarboxylase-4.1.1.17
116332tryptophan deaminase+
116332urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116332-+++-+----++--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116332--+----------------++----------------+--------------------+--+---------+---+--+---------+--+-+--+--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
3239soil Niigata Factory of Mitsubishi Gas Chemical CompanyJapanJPNAsia
67770Soil
116332Environment, SoilJapanJPNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_4190.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_529;97_2552;98_3162;99_4190&stattab=map
  • Last taxonomy: Paracoccus aminophilus subclade
  • 16S sequence: AB681111
  • Sequence Identity:
  • Total samples: 1434
  • soil counts: 221
  • aquatic counts: 910
  • animal counts: 266
  • plant counts: 37

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
32391Risk group (German classification)
1163321Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
3239Paracoccus aminophilus gene for 16S rRNA, partial sequence, strain: NBRC 16710AB6811111388nuccore34003
3239Paracoccus aminophilus gene for 16S rRNA, strain: JCM 7686D322391385nuccore34003
3239Paracoccus aminophilus 16S ribosomal RNA gene, partial sequenceAY0141761458nuccore34003

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paracoccus aminophilus JCM 7686GCA_000444995completencbi1367847
66792Paracoccus aminophilus JCM 76861367847.13plasmidpatric1367847
66792Paracoccus aminophilus JCM 76861367847.12plasmidpatric1367847
66792Paracoccus aminophilus JCM 76861367847.15plasmidpatric1367847
66792Paracoccus aminophilus JCM 76861367847.14plasmidpatric1367847
66792Paracoccus aminophilus JCM 76861367847.3completepatric1367847
66792Paracoccus aminophilus JCM 76861367847.11plasmidpatric1367847
66792Paracoccus aminophilus JCM 76862547132467completeimg1367847

GC content

  • @ref: 3239
  • GC-content: 62.6
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno97.982no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.725yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes84.102yes
69480spore-formingspore-formingAbility to form endo- or exosporesno89.664no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno98.25yes
69480flagellatedmotile2+Ability to perform flagellated movementyes61.225no

External links

@ref: 3239

culture collection no.: DSM 8538, ATCC 49673, IAM 14245, JCM 7686, CIP 106077, IFO 16710, LMG 23830, NBRC 16710, VKM B-2141

straininfo link

  • @ref: 82898
  • straininfo: 42612

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny2397196Paracoccus aminophilus sp. nov. and Paracoccus aminovorans sp. nov., which utilize N,N-dimethylformamide.Urakami T, Araki H, Oyanagi H, Suzuki K, Komagata KInt J Syst Bacteriol10.1099/00207713-40-3-2871990Base Composition, DNA, Bacterial/analysis, Dimethylformamide/*metabolism, Nucleic Acid Hybridization, Paracoccus/*classification/metabolismMetabolism
Phylogeny18218935Paracoccus marinus sp. nov., an adonixanthin diglucoside-producing bacterium isolated from coastal seawater in Tokyo Bay.Khan ST, Takaichi S, Harayama SInt J Syst Evol Microbiol10.1099/ijs.0.65103-02008Bacterial Typing Techniques, Carotenoids/*biosynthesis, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Glucosides/*biosynthesis, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Paracoccus/*classification/genetics/*isolation & purification/physiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Species SpecificityGenetics
Metabolism20118371Plasmid pAMI2 of Paracoccus aminophilus JCM 7686 carries N,N-dimethylformamide degradation-related genes whose expression is activated by a LuxR family regulator.Dziewit L, Dmowski M, Baj J, Bartosik DAppl Environ Microbiol10.1128/AEM.01926-092010Bacterial Proteins/genetics/*metabolism, DNA, Bacterial/chemistry/genetics, Dimethylformamide, Enzymes/genetics/*metabolism, Formamides/metabolism, *Gene Expression Regulation, Bacterial, Genes, Bacterial, Metabolic Networks and Pathways/genetics, Molecular Sequence Data, Multigene Family, Operon, Paracoccus/*enzymology/*genetics, *Plasmids, Sequence Analysis, DNA, Trans-Activators/genetics/*metabolismEnzymology
Enzymology21569803DIY series of genetic cassettes useful in construction of versatile vectors specific for Alphaproteobacteria.Dziewit L, Adamczuk M, Szuplewska M, Bartosik DJ Microbiol Methods10.1016/j.mimet.2011.04.0162011Alphaproteobacteria/*genetics, Cloning, Molecular/methods, Conjugation, Genetic, DNA Replication, Escherichia coli/genetics, Genetic Engineering/*methods, *Genetic Vectors, *Plasmids, Selection, GeneticGenetics
Metabolism22092764Functional characterization of the type II PamI restriction-modification system derived from plasmid pAMI7 of Paracoccus aminophilus JCM 7686.Dziewit L, Kuczkowska K, Adamczuk M, Radlinska M, Bartosik DFEMS Microbiol Lett10.1111/j.1574-6968.2011.02388.x2011Amino Acid Sequence, DNA/metabolism, DNA Restriction-Modification Enzymes/*genetics/*metabolism, Deoxyribonucleases, Type II Site-Specific/*genetics/*metabolism, Gene Transfer, Horizontal, Molecular Sequence Data, Paracoccus/*enzymology/*genetics, *Plasmids, Sequence Homology, Substrate SpecificityEnzymology
Phylogeny23653121Paracoccus zhejiangensis sp. nov., isolated from activated sludge in wastewater-treatment system.Wu ZG, Zhang DF, Liu YL, Wang F, Jiang X, Li C, Li SP, Hong Q, Li WJAntonie Van Leeuwenhoek10.1007/s10482-013-9932-22013Anti-Bacterial Agents/pharmacology, Base Composition, Base Sequence, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Lipids/analysis, Microbial Sensitivity Tests, Molecular Sequence Data, Paracoccus/classification/drug effects/genetics/growth & development/*isolation & purification/metabolism, Phenotype, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Alignment, Sequence Homology, Nucleic Acid, Sewage/*microbiology, Species Specificity, Temperature, Waste Water, *Water MicrobiologyGenetics
Genetics24517536Architecture and functions of a multipartite genome of the methylotrophic bacterium Paracoccus aminophilus JCM 7686, containing primary and secondary chromids.Dziewit L, Czarnecki J, Wibberg D, Radlinska M, Mrozek P, Szymczak M, Schluter A, Puhler A, Bartosik DBMC Genomics10.1186/1471-2164-15-1242014Base Sequence, DNA Methylation, DNA Repair, DNA Transposable Elements, Gene Regulatory Networks, *Genome, Bacterial, High-Throughput Nucleotide Sequencing, Molecular Sequence Data, Paracoccus/classification/*genetics/virology, Phylogeny, Prophages/physiology, Sequence Analysis, DNAPhylogeny
Genetics25752994Maintenance and genetic load of plasmid pKON1 of Paracoccus kondratievae, containing a highly efficient toxin-antitoxin module of the hipAB family.Czarnecki J, Dziewit L, Kowalski L, Ochnio M, Bartosik DPlasmid10.1016/j.plasmid.2015.02.0032015Amino Acid Sequence, Bacterial Toxins/*genetics, Base Composition, Base Sequence, Chromosomes, Bacterial/genetics, Genetic Loci, Molecular Sequence Data, Paracoccus/*genetics, Plasmids/*genetics, Replicon, Sequence Analysis, DNATranscriptome
26347732Genome-guided insight into the methylotrophy of Paracoccus aminophilus JCM 7686.Dziewit L, Czarnecki J, Prochwicz E, Wibberg D, Schluter A, Puhler A, Bartosik DFront Microbiol10.3389/fmicb.2015.008522015
Phylogeny26971128Paracoccus cavernae sp. nov., isolated from a show cave.Dominguez-Monino I, Jurado V, Hermosin B, Saiz-Jimenez CInt J Syst Evol Microbiol10.1099/ijsem.0.0010182016*Air Microbiology, Bacterial Typing Techniques, Base Composition, Caves/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Paracoccus/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spain, Ubiquinone/chemistryTranscriptome
Metabolism32291967Involvement of membrane vesicles in long-chain-AHL delivery in Paracoccus species.Morinaga K, Nagakubo T, Nomura N, Toyofuku MEnviron Microbiol Rep10.1111/1758-2229.128432020Acyl-Butyrolactones/*metabolism, Biological Transport, *Extracellular Vesicles, Microbial Interactions, Paracoccus/*metabolism, Paracoccus denitrificans/metabolism, *Quorum Sensing
Enzymology34112373Enzymatic synthesis of 10-oxostearic acid in high space-time yield via cascade reaction of a new oleate hydratase and an alcohol dehydrogenase.Wu YX, Pan J, Yu HL, Xu JHJ Biotechnol10.1016/j.btecx.2019.1000082019Biotechnology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3239Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8538)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8538
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
34679Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18167
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
69479João 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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
82898Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42612.1StrainInfo: A central database for resolving microbial strain identifiers
116332Curators of the CIPCollection of Institut Pasteur (CIP 106077)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106077