Strain identifier

BacDive ID: 5380

Type strain: Yes

Species: Erythrobacter longus

Strain history: CIP <- 1994, M. Gauthier, INSERM, Nice, France <- ATCC <- T. Shiba: strain OCh 101

NCBI tax ID(s): 1044 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 2940

BacDive-ID: 5380

DSM-Number: 6997

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

description: Erythrobacter longus DSM 6997 is a mesophilic, Gram-negative bacterium that was isolated from seaweed, Enteromorpha linza.

NCBI tax id

  • NCBI tax id: 1044
  • Matching level: species

strain history

@refhistory
2940<- T. Shiba, Otsuchi Marine Res. Center, Univ. Tokyo, OCh 101
67770T. Shiba OCh101.
120654CIP <- 1994, M. Gauthier, INSERM, Nice, France <- ATCC <- T. Shiba: strain OCh 101

doi: 10.13145/bacdive5380.20230509.8.1

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 longus
  • full scientific name: Erythrobacter longus Shiba and Simidu 1982

@ref: 2940

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Erythrobacteraceae

genus: Erythrobacter

species: Erythrobacter longus

full scientific name: Erythrobacter longus Shiba and Simidu 1982

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.981
120654negativerod-shapedyes

colony morphology

  • @ref: 120654

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2940BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
37982Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120654CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
2940positivegrowth28mesophilic
37982positivegrowth30mesophilic
67770positivegrowth26mesophilic
120654positivegrowth15-30
120654nogrowth5psychrophilic
120654nogrowth37mesophilic
120654nogrowth41thermophilic
120654nogrowth45thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.996

halophily

@refsaltgrowthtested relationconcentration
120654NaClnogrowth0 %
120654NaClnogrowth2 %
120654NaClnogrowth4 %
120654NaClnogrowth6 %
120654NaClnogrowth8 %
120654NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12065416947citrate-carbon source
1206544853esculin-hydrolysis
120654606565hippurate+hydrolysis
12065417632nitrate+reduction
12065416301nitrite-reduction
12065415792malonate-assimilation

metabolite production

  • @ref: 120654
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12065415688acetoin-
12065417234glucose-

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
120654oxidase+
120654beta-galactosidase+3.2.1.23
120654alcohol dehydrogenase-1.1.1.1
120654gelatinase+/-
120654amylase-
120654caseinase-3.4.21.50
120654catalase+1.11.1.6
120654tween esterase+
120654gamma-glutamyltransferase+2.3.2.2
120654lecithinase-
120654lipase-
120654lysine decarboxylase-4.1.1.18
120654ornithine decarboxylase-4.1.1.17
120654phenylalanine ammonia-lyase-4.3.1.24
120654protease-
120654tryptophan deaminase-
120654urease-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
120654-+++-++-++-+--------

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
2940seaweed, Enteromorpha linzaEnteromorpha linza
67770Seaweed (Enteromorpha linza)Enteromorpha linza
120654SeaweedJapanJPNAsia

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Aquatic plant

taxonmaps

  • @ref: 69479
  • File name: preview.99_3645.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_251;97_274;98_2787;99_3645&stattab=map
  • Last taxonomy: Erythrobacter longus
  • 16S sequence: L01786
  • Sequence Identity:
  • Total samples: 151
  • soil counts: 1
  • aquatic counts: 136
  • animal counts: 13
  • plant counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
29401Risk group (German classification)
1206541Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Erythrobacter longus (ATCC 33941) 16S ribosomal RNA (partial)M55493261ena1044
20218Erythrobacter longus 16S ribosomal RNAM590621488ena1044
20218Erythrobacter longus 16S rRNA, partial sequenceD126991314ena1044
20218Erythrobacter longus 16S ribosomal RNAL017861403ena1044
20218Erythrobacter longus strain OCh101 16S ribosomal RNA gene, partial sequenceM967441412ena1044
2940Erythrobacter longus strain DSM 6997 16S ribosomal RNA gene, partial sequenceAF4658351414ena1044

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Erythrobacter longus strain DSM 69971044.3wgspatric1044
66792Erythrobacter longus DSM 69972585427956draftimg1044
67770Erythrobacter longus DSM 6997GCA_000715015contigncbi1044

GC content

@refGC-contentmethod
6777060.7thermal denaturation, midpoint method (Tm)
6777057.4genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes65.593no
flagellatedno82.41no
gram-positiveno97.704no
anaerobicno99.354no
aerobicyes93.434no
halophileno77.663no
spore-formingno95.012no
thermophileno93.024yes
glucose-utilyes82.99no
glucose-fermentno93.036no

External links

@ref: 2940

culture collection no.: DSM 6997, ATCC 33941, IAM 14242, IFO 14126, JCM 6170, NBRC 14126, OCh 101, CECT 5010, CGMCC 1.8459, CIP 104268, KCTC 2829, LMG 3982, LMG 5510, NCIMB 2174

straininfo link

  • @ref: 74870
  • straininfo: 11116

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology22033765Photosynthetic characteristics of marine aerobic anoxygenic phototrophic bacteria Roseobacter and Erythrobacter strains.Sato-Takabe Y, Hamasaki K, Suzuki KArch Microbiol10.1007/s00203-011-0761-22011Bacteria, Aerobic/chemistry/growth & development/isolation & purification, Bacteriochlorophyll A/analysis, *Photosynthesis, Photosynthetic Reaction Center Complex Proteins/analysis, Roseobacter/*chemistry/growth & development/isolation & purification, Sphingomonadaceae/*chemistry/growth & developmentPhylogeny
Phylogeny22843716Erythrobacter jejuensis sp. nov., isolated from seawater.Yoon BJ, Lee DH, Oh DCInt J Syst Evol Microbiol10.1099/ijs.0.038349-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/analysis, Water MicrobiologyGenetics
Genetics25059862Draft Genome Sequences of Two Marine Phototrophic Bacteria, Erythrobacter longus Strain DSM 6997 and Erythrobacter litoralis Strain DSM 8509.Wang Y, Zhang R, Zheng Q, Jiao NGenome Announc10.1128/genomeA.00677-142014
Phylogeny34997854Erythrobacter rubeus sp. nov., a carotenoid-producing alphaproteobacterium isolated from coastal seawater.Yoon J, Lee EY, Nam SJArch Microbiol10.1007/s00203-021-02736-22022Bacterial Typing Techniques, Carotenoids, DNA, Bacterial/genetics, Fatty Acids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater, Sequence Analysis, DNA, *Sphingomonadaceae/geneticsTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2940Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6997)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6997
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
37982Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16158
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
74870Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID11116.1StrainInfo: A central database for resolving microbial strain identifiers
120654Curators of the CIPCollection of Institut Pasteur (CIP 104268)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104268