Strain identifier

BacDive ID: 135947

Type strain: Yes

Species: Rhodobacter blasticus

Strain history: CIP <- 1995, NCIMB <- C.S. Dow

NCBI tax ID(s): 1188250 (strain), 1075 (species)

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General

@ref: 35232

BacDive-ID: 135947

DSM-Number: 2131

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

description: Rhodobacter blasticus CIP 104374 is a mesophilic, Gram-negative bacterium of the family Paracoccaceae.

NCBI tax id

NCBI tax idMatching level
1188250strain
1075species

strain history

@refhistory
67772Warwick University [Basonym: Rhodopseudomonas blastica (Dow C.,1981)]
35232CIP <- 1995, NCIMB <- C.S. Dow

doi: 10.13145/bacdive135947.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Paracoccaceae
  • genus: Rhodobacter
  • species: Rhodobacter blasticus
  • full scientific name: Rhodobacter blasticus corrig. (Eckersley and Dow 1981) Kawasaki et al. 1994

  • synonyms

    @refsynonym
    20215Rhodobacter blastica
    20215Fuscovulum blasticum
    20215Rhodopseudomonas blastica
    20215Tabrizicola blastica
    20215Pseudogemmobacter blasticus

@ref: 35232

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Rhodobacter

species: Rhodobacter blasticus

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
125439negative98.8
125438negative98.3
35232negativerod-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
35232MEDIUM 120 - for Rhodobacter blasticusyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Yeast extract (2.500 g);Peptone (2.500 g)
35232CIP Medium 12yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=12

culture temp

@refgrowthtypetemperature
35232positivegrowth30
67772positiveoptimum30
35232positivegrowth30-41
35232nogrowth10

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: obligate aerobe
  • confidence: 96.8

spore formation

@refspore formationconfidence
125439no91.6
125438no91.837

halophily

@refsaltgrowthtested relationconcentration
35232NaClpositivegrowth0-2 %
35232NaClnogrowth4 %
35232NaClnogrowth6 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3523216947citrate-carbon source
352324853esculin-hydrolysis
3523217632nitrate-reduction
3523216301nitrite-reduction
3523215792malonate-assimilation
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from

antibiotic resistance

  • @ref: 35232
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 35232
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
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
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase-3.1.3.1
35232oxidase+
35232alcohol dehydrogenase-1.1.1.1
35232gelatinase-
35232amylase-
35232DNase-
35232catalase+1.11.1.6
35232tween esterase-
35232lysine decarboxylase-4.1.1.18
35232ornithine decarboxylase-4.1.1.17
35232urease-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
35232--------------------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
35232-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
35232---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refgeographic locationcountryorigin.countrycontinentsample type
35232Warwick Univ.United KingdomGBREurope
67772West Midlands, WarwickUnited KingdomGBREuropeEutrophic freshwater pond
35232WarwickUnited KingdomGBREuropeEnvironment, Small eutrophic freshwater pond

taxonmaps

  • @ref: 69479
  • File name: preview.99_22209.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_3953;97_8403;98_16751;99_22209&stattab=map
  • Last taxonomy: Rhodobacter blasticus subclade
  • 16S sequence: DQ342322
  • Sequence Identity:
  • Total samples: 598
  • soil counts: 60
  • aquatic counts: 448
  • animal counts: 43
  • plant counts: 47

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
677721
352321Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
67772Rhodobacter blasticus strain ATCC 33485 16S ribosomal RNA gene, partial sequenceDQ3423221389nuccore1188250
124043Rhodobacter blasticus 16S rRNA.D134781378nuccore1188250
124043Rhodobacter blasticus gene for 16S rRNA, strain: ATCC 33485.D164291389nuccore1188250

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Fuscovulum blasticum DSM 2131GCA_003034965contigncbi1188250
66792Rhodobacter blasticus DSM 21311188250.3wgspatric1188250
66792Rhodobacter blasticus DSM 21312898807436draftimg1188250
67772Fuscovulum blasticum 28/5GCA_003071405completencbi1075

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno98.3no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no85.391no
125438spore-formingspore-formingAbility to form endo- or exosporesno91.837no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes68.43no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.682no
125438motile2+flagellatedAbility to perform flagellated movementyes64.866no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno91.6
125439BacteriaNetmotilityAbility to perform movementyes66.2
125439BacteriaNetgram_stainReaction to gram-stainingnegative98.8
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe96.8

External links

@ref: 35232

culture collection no.: CIP 104374, ATCC 33485, DSM 2131, LMG 4305, NCIMB 11576, UCCCB1, DSM 26431, IFO 16437, NBRC 16437

straininfo link

  • @ref: 93208
  • straininfo: 4905

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16738114Rubellimicrobium thermophilum gen. nov., sp. nov., a red-pigmented, moderately thermophilic bacterium isolated from coloured slime deposits in paper machines.Denner EBM, Kolari M, Hoornstra D, Tsitko I, Kampfer P, Busse HJ, Salkinoja-Salonen MInt J Syst Evol Microbiol10.1099/ijs.0.63751-02006DNA, Bacterial/genetics/isolation & purification, Fatty Acids/analysis, Industry, Microscopy, Electron, Molecular Sequence Data, Myxococcales/*classification/genetics/growth & development/isolation & purification, Paper, Phylogeny, Rhodobacteraceae/*classification/genetics/isolation & purification/ultrastructureEnzymology
Phylogeny24158532Tabrizicola aquatica gen. nov. sp. nov., a novel alphaproteobacterium isolated from Qurugol Lake nearby Tabriz city, Iran.Tarhriz V, Thiel V, Nematzadeh G, Hejazi MA, Imhoff JF, Hejazi MSAntonie Van Leeuwenhoek10.1007/s10482-013-0042-y2013Aerobiosis, Bacterial Typing Techniques, Base Composition, Chemoautotrophic Growth, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Heterotrophic Processes, Hydrogen-Ion Concentration, Iran, Lakes/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, TemperatureGenetics
Phylogeny30798491Rhodobacter thermarum sp. nov., a novel phototrophic bacterium isolated from sediment of a hot spring.Khan IU, Habib N, Xiao M, Li MM, Xian WD, Hejazi MS, Tarhriz V, Zhi XY, Li WJAntonie Van Leeuwenhoek10.1007/s10482-018-01219-72019Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Geologic Sediments/chemistry/*microbiology, Hot Springs/chemistry/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacter/classification/genetics/*isolation & purification/metabolism, Sodium Chloride/analysis/metabolism, TibetMetabolism
Phylogeny33112224Tabrizicola oligotrophica sp. nov. and Rhodobacter tardus sp. nov., two new species of bacteria belonging to the family Rhodobacteraceae.Sheu C, Li ZH, Sheu SY, Yang CC, Chen WMInt J Syst Evol Microbiol10.1099/ijsem.0.0045262020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacter/*classification/isolation & purification, Rhodobacteraceae/*classification/isolation & purification, Sequence Analysis, DNA, Taiwan, Ubiquinone/analogs & derivatives/chemistryEnzymology
Phylogeny35380297Neotabrizicola shimadae gen. nov., sp. nov., an aerobic anoxygenic phototrophic bacterium harbouring photosynthetic genes in the family Rhodobacteraceae, isolated from a terrestrial hot spring.Muramatsu S, Hirose S, Iino T, Ohkuma M, Hanada S, Haruta SAntonie Van Leeuwenhoek10.1007/s10482-022-01728-62022Bacterial Typing Techniques, Bacteriochlorophylls/genetics, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Hot Springs/microbiology, Photosynthesis, Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhodobacteraceae, Sequence Analysis, DNATranscriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
35232Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104374Collection of Institut Pasteur (CIP 104374)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67772Curators of the UCCCBhttps://ucccb.uc.pt/
68371Automatically annotated from API 50CH acid
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
93208Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID4905.1
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG