Strain identifier

BacDive ID: 13705

Type strain: Yes

Species: Paracoccus versutus

Strain Designation: A2

Strain history: CIP <- 2001, CCM <- B.F Taylor and D.S. Hoare

NCBI tax ID(s): 34007 (species)

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General

@ref: 299

BacDive-ID: 13705

DSM-Number: 582

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, rod-shaped

description: Paracoccus versutus A2 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 34007
  • Matching level: species

strain history

@refhistory
299<- D.P. Kelly <- D.S. Hoare, A2
67770IAM 12814 <-- Y. Katayama THI 041 <-- ATCC 25364 <-- D. S. Hoare A2.
123826CIP <- 2001, CCM <- B.F Taylor and D.S. Hoare

doi: 10.13145/bacdive13705.20250331.9.3

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 versutus
  • full scientific name: Paracoccus versutus (Harrison 1983) Katayama et al. 1996

  • synonyms

    @refsynonym
    20215Thiobacillus rapidicrescens
    20215Thiobacillus versutus

@ref: 299

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Paracoccus

species: Paracoccus versutus

full scientific name: Paracoccus versutus (Harrison 1983) Katayama et al. 1996

strain designation: A2

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
123826negativerod-shapedno
125438negative96.5
125439negative99.3

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
299STARKEYA NOVELLA MEDIUM (DSMZ Medium 69)yeshttps://mediadive.dsmz.de/medium/69Name: STARKEYA NOVELLA MEDIUM (DSMZ Medium 69) Composition: Agar 14.9667 g/l (optional) Na2HPO4 x 12 H2O 10.5765 g/l Na2S2O3 x 5 H2O 5.0 g/l KH2PO4 1.49667 g/l NH4Cl 0.299335 g/l Yeast extract 0.299335 g/l Na2-EDTA 0.25 g/l ZnSO4 x 7 H2O 0.11 g/l MgSO4 x 7 H2O 0.1 g/l CaCl2 x 2 H2O 0.0277 g/l MnCl2 x 4 H2O 0.0253 g/l FeSO4 x 7 H2O 0.025 g/l CoCl2 x 6 H2O 0.00805 g/l CuSO4 x 5 H2O 0.00785 g/l (NH4)6Mo7O24 x 4 H2O 0.0055 g/l Phenol red 0.0018 g/l Distilled water
33605MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123826CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
299CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium220.pdf

culture temp

@refgrowthtypetemperature
299positivegrowth30
33605positivegrowth25
67770positivegrowth30
123826positivegrowth25-41
123826nogrowth5
123826nogrowth10

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: obligate aerobe
  • confidence: 95.7

spore formation

@refspore formationconfidence
125438no91.123
125439no97.4

halophily

@refsaltgrowthtested relationconcentration
123826NaClpositivegrowth0-6 %
123826NaClnogrowth8 %
123826NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1238264853esculin-hydrolysis
12382617632nitrate+reduction
12382616301nitrite+reduction
12382617632nitrate+respiration

antibiotic resistance

  • @ref: 123826
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 123826
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 123826
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
123826oxidase+
123826beta-galactosidase-3.2.1.23
123826alcohol dehydrogenase-1.1.1.1
123826gelatinase-
123826amylase-
123826DNase-
123826caseinase-3.4.21.50
123826catalase+1.11.1.6
123826tween esterase+
123826lecithinase-
123826lipase-
123826lysine decarboxylase-4.1.1.18
123826ornithine decarboxylase-4.1.1.17
123826protease-
123826tryptophan deaminase-
123826urease+3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123826-+++-+-----+---+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123826++++---+-++---------+-+--++++++-++++++---+------++------++-+++++-++---++-+-+---++--+--+-++++-+--+--

Isolation, sampling and environmental information

isolation

@refsample type
299soil
67770Soil
123826Enrichment medium for Thiobacillus denitrificans

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_869.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_31;97_32;98_688;99_869&stattab=map
  • Last taxonomy: Paracoccus
  • 16S sequence: Y16932
  • Sequence Identity:
  • Total samples: 5189
  • soil counts: 932
  • aquatic counts: 2441
  • animal counts: 1611
  • plant counts: 205

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
2991Risk group (German classification)
1238261Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Paracoccus versutus gene for 16S rRNA, strain: IAM 12814D322431383nuccore34007
20218Paracoccus versutus 16S rRNA gene, strain DSM 582Y169311393nuccore34007
20218Paracoccus versutus 16S rRNA gene, strain ATCC 25364Y169321393nuccore34007
299Paracoccus versutus 16S ribosomal RNA gene, partial sequenceAY0141741457nuccore34007
67770Paracoccus versutus gene for 16S rRNA, partial sequence, strain: NBRC 14567AB6806331386nuccore34007
124043Paracoccus versutus strain NBRC 14567 16S ribosomal RNA gene, partial sequence.ON4064151386nuccore34007

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paracoccus versutus DSM 58234007.4wgspatric34007
66792Paracoccus versutus strain DSM 58234007.16wgspatric34007
66792Paracoccus versutus DSM 5822713897089draftimg34007
66792Paracoccus versutus DSM 5822615840723draftimg34007
67770Paracoccus versutus DSM 582GCA_000763885contigncbi34007
67770Paracoccus versutus DSM 582GCA_003387045scaffoldncbi34007

GC content

@refGC-contentmethod
29965.0
6777067.6genome sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno96.5no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.298no
125438spore-formingspore-formingAbility to form endo- or exosporesno91.123no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes85.08no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.435yes
125438motile2+flagellatedAbility to perform flagellated movementno52.642no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno97.4
125439BacteriaNetmotilityAbility to perform movementyes67.8
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.3
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe95.7

External links

@ref: 299

culture collection no.: DSM 582, ATCC 25364, CCM 2505, IAM 12814, JCM 20754, CIP 107117, IFO 14567, LMD 80.62, LMD 81.78, NBRC 14567, NCCB 80062, NCCB 81078, VKM B-2163

straininfo link

  • @ref: 82890
  • straininfo: 38520

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology2482223Porin from Thiobacillus versutus.Woitzik D, Benz R, Lustig A, Weckesser JFEMS Microbiol Lett10.1016/0378-1097(89)90238-31989Bacterial Outer Membrane Proteins/analysis/isolation & purification/*metabolism, Edetic Acid/pharmacology, Electrophoresis, Polyacrylamide Gel, Ion Channels/analysis/*metabolism, Macromolecular Substances, Molecular Weight, Porins, Thiobacillus/*metabolism, UltracentrifugationMetabolism
Enzymology9043125Distribution of amine oxidases and amine dehydrogenases in bacteria grown on primary amines and characterization of the amine oxidase from Klebsiella oxytoca.Hacisalihoglu A, Jongejan JA, Duine JAMicrobiology (Reading)10.1099/00221287-143-2-5051997Amines/*metabolism, Amino Acid Sequence, Copper/analysis, Dihydroxyphenylalanine/analogs & derivatives/analysis, Klebsiella/*enzymology, Magnetic Resonance Spectroscopy, Metalloproteins/classification/isolation & purification/*metabolism, Molecular Sequence Data, Oxidoreductases Acting on CH-NH Group Donors/classification/isolation & purification/*metabolism, Phenethylamines/metabolism, Sequence Analysis, Sequence Homology, Amino Acid, Spectrophotometry, Subcellular Fractions/enzymologyMetabolism
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

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
299Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 582)https://www.dsmz.de/collection/catalogue/details/culture/DSM-582
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
33605Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4518
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)
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
82890Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID38520.1StrainInfo: A central database for resolving microbial strain identifiers
123826Curators of the CIPCollection of Institut Pasteur (CIP 107117)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107117
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1