Strain identifier

BacDive ID: 13822

Type strain: Yes

Species: Phaeovulum vinaykumarii

Strain Designation: JA 123, JA123

Strain history: CIP <- 2007, CCUG <- C. Sasikala, P. Anil Kumar, Jawaharlal Nehru Technological Univ. Hyderabad, India: strain JA123

NCBI tax ID(s): 407234 (species)

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General

@ref: 7674

BacDive-ID: 13822

DSM-Number: 18714

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

description: Phaeovulum vinaykumarii JA 123 is a mesophilic, Gram-negative bacterium that was isolated from enrichment of tidal seawater.

NCBI tax id

  • NCBI tax id: 407234
  • Matching level: species

strain history

@refhistory
7674<- C. Sasikala, Bacterial Discovery Lab., Centre Environment, Inst. Sci. and Technol., J. N. T. Univ., Hyderabad, India; JA 123 <- P. A. Kumar
67770Ch. Sasikala JA123.
123844CIP <- 2007, CCUG <- C. Sasikala, P. Anil Kumar, Jawaharlal Nehru Technological Univ. Hyderabad, India: strain JA123

doi: 10.13145/bacdive13822.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Paracoccaceae
  • genus: Phaeovulum
  • species: Phaeovulum vinaykumarii
  • full scientific name: Phaeovulum vinaykumarii (Srinivas et al. 2007) Suresh et al. 2020

  • synonyms

    @refsynonym
    20215Bieblia vinaykumarii
    20215Rhodobacter vinaykumarii

@ref: 7674

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Rhodobacter

species: Rhodobacter vinaykumarii

full scientific name: Rhodobacter vinaykumarii Srinivas et al. 2007

strain designation: JA 123, JA123

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.999
123844negativerod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlink
37824MEDIUM 698 - for Rhodobacter vinaykumariiyes
123844CIP Medium 698yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=698

culture temp

@refgrowthtypetemperaturerange
37824positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no92
69480no99.967

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12384417632nitrate-reduction
12384416301nitrite-reduction

metabolite production

  • @ref: 123844
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
123844oxidase+
123844catalase+1.11.1.6
123844urease+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
123844-+++-++---+----+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
7674enrichment of tidal seawaterBay of Bengal, Visakhapatnam, Ramakrishna beachIndiaINDAsia
60136Seashore waterVisakhapatnamIndiaINDAsia2005-04-16
67770Marine tidal water
123844Environment, Water, seashoreVisakhapatnamIndiaINDAsia2005

isolation source categories

Cat1Cat2Cat3
#Engineered#Laboratory#Lab enrichment
#Environmental#Aquatic#Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_1878.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_1054;97_1232;98_1479;99_1878&stattab=map
  • Last taxonomy: Bieblia vinaykumarii subclade
  • 16S sequence: AM408117
  • Sequence Identity:
  • Total samples: 1128
  • soil counts: 98
  • aquatic counts: 843
  • animal counts: 171
  • plant counts: 16

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
76741Risk group (German classification)
1238441Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7674
  • description: Rhodobacter vinaykumarii partial 16S rRNA gene, type strain JA123T
  • accession: AM408117
  • length: 1387
  • database: ena
  • NCBI tax ID: 407234

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodobacter vinaykumarii strain DSM 18714407234.3wgspatric407234
66792Bieblia vinaykumarii DSM 187142681813513draftimg407234
67770Phaeovulum vinaykumarii DSM 18714GCA_900156695scaffoldncbi407234
67770Phaeovulum vinaykumarii JA123GCA_900217755scaffoldncbi407234

GC content

  • @ref: 7674
  • GC-content: 68.8
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno92no
gram-positiveno98.792no
anaerobicyes62.6no
halophileno59.727no
spore-formingno95.05no
glucose-utilyes65.634no
aerobicno91.063no
flagellatedno75.561no
thermophileno94.059yes
motileyes65.492no
glucose-fermentno90.66no

External links

@ref: 7674

culture collection no.: DSM 18714, CCUG 54311, JCM 14544, CIP 109721

straininfo link

  • @ref: 82999
  • straininfo: 309553

literature

  • topic: Phylogeny
  • Pubmed-ID: 36269565
  • title: Limibaculum sediminis sp. nov., isolated from mangrove sediment.
  • authors: Huang Y, Liu L, Li J, Pan J, Li M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.005580
  • year: 2022
  • mesh: RNA, Ribosomal, 16S/genetics, Phylogeny, *Sodium Chloride, Base Composition, Bacterial Typing Techniques, DNA, Bacterial/genetics, *Fatty Acids/chemistry, Sequence Analysis, DNA, Phospholipids/chemistry, Glycolipids/chemistry, Phosphatidylglycerols, Quinones, Ubiquinone/chemistry
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7674Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18714)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18714
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
37824Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7496
60136Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54311)https://www.ccug.se/strain?id=54311
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
82999Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID309553.1StrainInfo: A central database for resolving microbial strain identifiers
123844Curators of the CIPCollection of Institut Pasteur (CIP 109721)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109721