Strain identifier

BacDive ID: 13872

Type strain: Yes

Species: Rhodobium gokarnense

Strain Designation: JA173

Strain history: CIP <- 2007, JCM <- C. Sasikala, JNT Univ., Hyderabad, India: strain JA173

NCBI tax ID(s): 364296 (species)

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General

@ref: 7253

BacDive-ID: 13872

DSM-Number: 17935

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

description: Rhodobium gokarnense JA173 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from photoheterotrophic enrichments of a soil sample .

NCBI tax id

  • NCBI tax id: 364296
  • Matching level: species

strain history

@refhistory
7253<- C. Sasikala, J. N. T. Univ., Inst. Sci. Technol., Hyderabad, India; JA173 <- P. A. Kumar
67770Ch. Sasikala JA173.
119701CIP <- 2007, JCM <- C. Sasikala, JNT Univ., Hyderabad, India: strain JA173

doi: 10.13145/bacdive13872.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Rhodobiaceae
  • genus: Rhodobium
  • species: Rhodobium gokarnense
  • full scientific name: Rhodobium gokarnense Srinivas et al. 2007

@ref: 7253

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Rhodobiaceae

genus: Rhodobium

species: Rhodobium gokarnense

full scientific name: Rhodobium gokarnense Srinivas et al. 2007 emend. Urdiain et al. 2008

strain designation: JA173

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
32034negative1.5 µm0.55 µmrod-shapedno
119701negativerod-shapedyes

pigmentation

  • @ref: 32034
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlink
37806MEDIUM 698 - for Rhodobacter vinaykumariiyes
119701CIP Medium 698yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=698

culture temp

@refgrowthtypetemperaturerange
32034positiveoptimum30mesophilic
37806positivegrowth30mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
32034positivegrowth5.0-9.0alkaliphile
32034positiveoptimum7.25

Physiology and metabolism

oxygen tolerance

  • @ref: 32034
  • oxygen tolerance: facultative anaerobe

spore formation

  • @ref: 32034
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
32034NaClpositivegrowth0.5-10 %
32034NaClpositiveoptimum4 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3203430089acetate+carbon source
3203416947citrate+carbon source
3203417234glucose+carbon source
3203425115malate+carbon source
3203429864mannitol+carbon source
3203415361pyruvate+carbon source
3203430911sorbitol+carbon source
3203430031succinate+carbon source
3203417632nitrate+reduction
11970117632nitrate-reduction
11970116301nitrite-reduction

metabolite production

  • @ref: 119701
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
119701oxidase+
119701catalase+1.11.1.6
119701urease+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
119701-+++-+--+-++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
7253photoheterotrophic enrichments of a soil sample (saltern)Gokarna (14° 32' N 74° 19' E)IndiaINDAsia14.533374.3167
67770Saltern
119701Environment, Soil and waterGokarnaIndiaINDAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Laboratory#Lab enrichment
#Environmental#Terrestrial#Soil
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_60542.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_26621;97_33425;98_42966;99_60542&stattab=map
  • Last taxonomy: Rhodobium
  • 16S sequence: AM180706
  • Sequence Identity:
  • Total samples: 1047
  • soil counts: 181
  • aquatic counts: 736
  • animal counts: 81
  • plant counts: 49

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
72531Risk group (German classification)
1197011Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Rhodobium gokarnense strain ATCC BAA-1215 16S-23S ribosomal RNA intergenic spacer, partial sequenceEU786785728ena364296
7253Rhodobium gokarnense 16S rRNA gene, type strain JA173TAM1807061415ena364296

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodobium gokarnense DSM 179352929249989draftimg364296
66792Rhodobium gokarnense DSM 17935GCA_025961475contigncbi364296

GC content

@refGC-contentmethod
725372.4high performance liquid chromatography (HPLC)
3203472.4

External links

@ref: 7253

culture collection no.: DSM 17935, ATCC BAA 1215, JCM 13532, ATCC BAA 1275, CIP 109649

straininfo link

  • @ref: 83048
  • straininfo: 377532

literature

  • topic: Phylogeny
  • Pubmed-ID: 17473235
  • title: Rhodobium gokarnense sp. nov., a novel phototrophic alphaproteobacterium from a saltern.
  • authors: Srinivas TNR, Kumar PA, Sasikala C, Ramana CV, Imhoff JF
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64843-0
  • year: 2007
  • mesh: Alphaproteobacteria/chemistry/*classification/*isolation & purification/physiology, Bacteriochlorophyll A/analysis, Carbon/metabolism, Carotenoids/analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fermentation, Genes, rRNA/genetics, India, Molecular Sequence Data, Nucleic Acid Hybridization, Organelles/ultrastructure, Peptones/metabolism, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, *Water Microbiology
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
7253Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17935)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17935
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
32034Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128284
37806Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7416
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
83048Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID377532.1StrainInfo: A central database for resolving microbial strain identifiers
119701Curators of the CIPCollection of Institut Pasteur (CIP 109649)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109649