Strain identifier

BacDive ID: 5387

Type strain: Yes

Species: Erythrobacter ramosus

Strain Designation: E5

Strain history: CIP <- 2001, IAM <- DSMZ <- V. Yurkov: strain E5

NCBI tax ID(s): 35811 (species)

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General

@ref: 3291

BacDive-ID: 5387

DSM-Number: 8510

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

description: Erythrobacter ramosus E5 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from cyanobacterial mat from a hot spring.

NCBI tax id

  • NCBI tax id: 35811
  • Matching level: species

strain history

@refhistory
3291<- V. Yurkov, E5
67770E. Yabuuchi EY4223 <-- ATCC 700003 <-- DSM 8510 <-- V. Yurkov E5.
122135CIP <- 2001, IAM <- DSMZ <- V. Yurkov: strain E5

doi: 10.13145/bacdive5387.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Erythrobacteraceae
  • genus: Erythrobacter
  • species: Erythrobacter ramosus
  • full scientific name: Erythrobacter ramosus (Yurkov et al. 1994) Xu et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Erythromicrobium ramosum

@ref: 3291

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Erythrobacteraceae

genus: Erythromicrobium

species: Erythromicrobium ramosum

full scientific name: Erythromicrobium ramosum Yurkov et al. 1994

strain designation: E5

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
23246negative1.3-2.5 µm0.6-1.0 µmrod-shapedyesmonotrichous, polar
69480negative99.875
122135negativerod-shapedyes

colony morphology

@refcolony color
23246orange
122135

pigmentation

@refproductionname
23246yesBacteriochlorophyll a
23246yescarotenoids

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3291ERYTHROMICROBIUM AND ROSEOCOCCUS MEDIUM (DSMZ Medium 767)yeshttps://mediadive.dsmz.de/medium/767Name: ERYTHROMICROBIUM AND ROSEOCOCCUS MEDIUM (DSMZ Medium 767) Composition: Yeast extract 1.0 g/l Na-acetate 1.0 g/l Bacto peptone 1.0 g/l MgSO4 x 7 H2O 0.5 g/l K2HPO4 0.3 g/l NH4Cl 0.3 g/l KCl 0.3 g/l CaCl2 x 2 H2O 0.05 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l Na2MoO4 x 2 H2O 3e-05 g/l MnCl2 x 4 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l Vitamin B12 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Distilled water
37252MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122135CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
3291positivegrowth30mesophilic
23246positiveoptimum25-30mesophilic
37252positivegrowth25mesophilic
67770positivegrowth26mesophilic
122135positivegrowth15-45
122135nogrowth5psychrophilic

culture pH

  • @ref: 23246
  • ability: positive
  • type: optimum
  • pH: 7.08-8.5
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 122135
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.98

halophily

  • @ref: 122135
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2324617790methanol-assimilation
2324622599arabinose-growth
2324616150benzoate-growth
2324615740formate-growth
2324617754glycerol-growth
2324629805glycolate-growth
2324629864mannitol-growth
2324617790methanol-growth
2324633942ribose-growth
232465291gelatin-hydrolysis
2324628017starch-hydrolysis
2324653426tween 80-hydrolysis
2324630089acetate+growth
2324617968butyrate+growth
23246casein hydrolysate+growth
2324616947citrate+growth
2324616236ethanol+growth
2324628757fructose+growth
2324629806fumarate+growth
2324617234glucose+growth
2324629987glutamate+growth
2324624996lactate+growth
2324625115malate+growth
2324617306maltose+growth
2324617272propionate+growth
2324615361pyruvate+growth
2324630031succinate+growth
2324617992sucrose+growth
23246132950tartrate+growth
23246yeast extract+growth
12213516947citrate-carbon source
1221354853esculin+hydrolysis
122135606565hippurate+hydrolysis
12213517632nitrate-builds gas from
12213517632nitrate-reduction
12213516301nitrite-builds gas from
12213516301nitrite-reduction
12213515792malonate-assimilation
12213517632nitrate-respiration

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantresistance conc.is sensitivesensitivity conc.
2324617334penicillinyesyes20 Unit (disc)
2324617076streptomycinyesyes50 µg (disc)
2324628971ampicillinyesyes
232467660nystatinyesyes
232468309polymyxin byesyes100 Unit (disc)
2324671321fusidateyesyes0.5 µg (disc)
2324617698chloramphenicolyesyes100 µg (disc)
232462637amikacinyesyes
2324628669bacitracinyesyes
2324627644chlortetracyclinyesyes
2324648923erythromycinyesyes
2324617833gentamicinyesyes
232466104kanamycinyesyes
23246100147nalidixic acidyesyes
232467507neomycinyesyes
2324628368novobiocinyesyes
232467660nystatinyesyes
2324627902tetracyclineyesyes
2324628001vancomycinyesyes
1221350129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)yesnoyes

metabolite production

  • @ref: 122135
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12213515688acetoin-
12213517234glucose+

enzymes

@refvalueactivityec
23246catalase+1.11.1.6
23246cytochrome oxidase+1.9.3.1
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
122135oxidase+
122135beta-galactosidase+3.2.1.23
122135alcohol dehydrogenase-1.1.1.1
122135gelatinase+/-
122135amylase-
122135DNase-
122135caseinase-3.4.21.50
122135catalase+1.11.1.6
122135tween esterase-
122135gamma-glutamyltransferase+2.3.2.2
122135lecithinase+
122135lipase+
122135lysine decarboxylase-4.1.1.18
122135ornithine decarboxylase-4.1.1.17
122135protease+
122135tryptophan deaminase-
122135urease-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
122135--++--+--+-+-+--+---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122135+++++-+++-+----++++++++-------++++++-----+-------+++-++----++---+--------+-----++-+---+--++--++----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
3291cyanobacterial mat from a hot springLake Baykal regionRussiaRUSAsia
23246cyanobacterial mat from an alkaline spring (pH 9.5; 25°C)
67770Cyanobacterial mat from an alkaline spring
122135Environment, Cyanobacterial mat from a hot springBaykal lakeRussian FederationRUSEurope

isolation source categories

Cat1Cat2Cat3
#Condition#Thermophilic (>45°C)
#Environmental#Aquatic#Thermal spring
#Environmental#Microbial community#Microbial mat
#Host#Microbial#Bacteria
#Condition#Alkaline

taxonmaps

  • @ref: 69479
  • File name: preview.99_22555.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_251;97_1392;98_1691;99_22555&stattab=map
  • Last taxonomy: Erythrobacter
  • 16S sequence: AF465837
  • Sequence Identity:
  • Total samples: 825
  • soil counts: 88
  • aquatic counts: 430
  • animal counts: 276
  • plant counts: 31

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
32911Risk group (German classification)
1221351Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Erythromicrobium ramosum gene for 16S rRNAAB0133551408ena35811
20218Erythromicrobium ramosum strain DSM 8510 16S ribosomal RNA gene, partial sequenceAF4658371413ena35811
20218E.ramosum gene for 16S rRNAX729091115ena35811
3291Chalcites lucidus plagosus specimen-voucher 47087 mitochondrial control region, partial sequenceAF464837425ena196527

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Erythrobacter ramosus DSM 8510GCA_014195675contigncbi35811
66792Erythromicrobium ramosum strain DSM 851035811.6wgspatric35811
66792Erythromicrobium ramosum strain JCM 1028235811.5wgspatric35811
66792Erythromicrobium ramosum DSM 85102828010827draftimg35811
67770Erythrobacter ramosus JCM 10282GCA_009828055scaffoldncbi35811

GC content

@refGC-contentmethod
6777064thermal denaturation, midpoint method (Tm)
6777064.3genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno97.966yes
anaerobicno99.415no
halophileno80.405no
spore-formingno95.391no
glucose-utilyes82.81yes
motileno84.712yes
flagellatedno93.728yes
aerobicyes93.042no
thermophileno95.044no
glucose-fermentno91.814no

External links

@ref: 3291

culture collection no.: DSM 8510, IAM 14333, NCIMB 13404, JCM 10282, ATCC 700003, CIP 106927, NBRC 102621

straininfo link

  • @ref: 74878
  • straininfo: 93008

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3291Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8510)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8510
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
23246VLADIMIR YURKOV, ERKO STACKEBRANDT, ANDREW HOLMES, JOHN A. FUERST, P. HUGENHOLTZ, JOCHEN GOLECKI, NASSER GAD'ON, VLADIMIR M. GORLENKO, ELENA I. KOMPANTSEVA, GERHART DREWS10.1099/00207713-44-3-427Phylogenetic Positions of Novel Aerobic, Bacteriochlorophyll a-Containing Bacteria and Description of Roseococcus thiosulfatophilus gen. nov., sp. nov., Erythromicrobium ramosum gen. nov., sp. nov., and Erythrobacter litoralis sp. nov.IJSEM 44: 427-434 19947520734
37252Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19112
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
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
74878Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID93008.1StrainInfo: A central database for resolving microbial strain identifiers
122135Curators of the CIPCollection of Institut Pasteur (CIP 106927)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106927