Strain identifier

BacDive ID: 5619

Type strain: Yes

Species: Muricauda ruestringensis

Strain Designation: B1

Strain history: CIP <- 2002, L. Berthe-Corti, Carl von Ossietzky Univ., Oldenburg, Germany: strain B1

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

@ref: 4983

BacDive-ID: 5619

DSM-Number: 13258

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

description: Muricauda ruestringensis B1 is a facultative anaerobe, slightly halophilic, mesophilic bacterium that forms circular colonies and was isolated from seawater sediment suspension containing hexadecane.

NCBI tax id

NCBI tax idMatching level
886377strain
111501species

strain history

@refhistory
4983<- L. Berthe-Corti <- U. Maschmann; B1
122302CIP <- 2002, L. Berthe-Corti, Carl von Ossietzky Univ., Oldenburg, Germany: strain B1

doi: 10.13145/bacdive5619.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Muricauda
  • species: Muricauda ruestringensis
  • full scientific name: Muricauda ruestringensis Bruns et al. 2001
  • synonyms

    • @ref: 20215
    • synonym: Allomuricauda ruestringensis

@ref: 4983

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Muricauda

species: Muricauda ruestringensis

full scientific name: Muricauda ruestringensis Bruns et al. 2001

strain designation: B1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43377negative1.1-2.7 µm0.3-0.6 µmrod-shapedno
69480negative99.985
122302negativerod-shapedno

colony morphology

  • @ref: 43377
  • colony size: 0.5-1 mm
  • colony color: yellow
  • colony shape: circular
  • medium used: Nutrient Agar

pigmentation

@refproductionname
43377noFlexirubin-Type
122302noFlexirubin

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_13258_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4983BACTO 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
4983MODIFIED SEA WATER AGAR (DSMZ Medium 917)yeshttps://mediadive.dsmz.de/medium/917Name: MODIFIED SEA WATER AGAR (DSMZ Medium 917) Composition: NaCl 17.7 g/l Agar 15.0 g/l MgSO4 x 7 H2O 4.46 g/l MgCl2 x 6 H2O 3.4 g/l Peptone 2.5 g/l Hexadecane 2.0 g/l Yeast extract 1.5 g/l CaCl2 x 2 H2O 0.98 g/l KCl 0.48 g/l Distilled water
34934MEDIUM 168 - for Cytophaga latercula and Flammeovirga apricayesAgar (15.000 g);Yeast extract (0.500 g);Sodium acetate (0.200 g);Tryptone (2.000 g);Beef extract (0.500 g);Synthetic sea solution - M0216 (1000.000 ml)
43377Nutrient agar (NA)yes
122302CIP Medium 168yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=168

culture temp

@refgrowthtypetemperaturerange
4983positivegrowth28mesophilic
4983positivegrowth30mesophilic
34934positivegrowth25mesophilic
43377positiveoptimum20-30
43377positivegrowth8-40
122302positivegrowth15-41
122302nogrowth5psychrophilic
122302nogrowth45thermophilic

culture pH

@refabilitytypepH
43377positivegrowth6-8
43377positiveoptimum6.5-7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 43377
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.997

halophily

@refhalophily levelsaltgrowthtested relationconcentration
43377slightly halophilicNaClpositivegrowth0.5-9.0 %(w/v)
43377NaClpositiveoptimum3 %(w/v)
122302NaClnogrowth0 %
122302NaClnogrowth2 %
122302NaClnogrowth4 %
122302NaClnogrowth6 %
122302NaClnogrowth8 %
122302NaClnogrowth10 %

observation

  • @ref: 43377
  • observation: formation of appendages as a continuum of the outer membrane

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4337730089acetate-carbon source
433772509agar-hydrolysis
4337716449alanine+carbon source
4337729016arginine+carbon source
4337717057cellobiose+carbon source
4337762968cellulose-hydrolysis
4337716236ethanol-carbon source
4337728757fructose+carbon source
433775291gelatin-hydrolysis
4337717234glucose-carbon source
4337745296hexadecane-carbon source
4337717716lactose+carbon source
4337729864mannitol-carbon source
4337737684mannose+carbon source
4337717632nitrate-reduction
43377peptone+growth
4337715361pyruvate-carbon source
4337716634raffinose+carbon source
4337717822serine-carbon source
4337728017starch-hydrolysis
4337717992sucrose+carbon source
1223024853esculin+hydrolysis
122302606565hippurate+hydrolysis
12230217632nitrate-reduction
12230216301nitrite-reduction
12230215792malonate-assimilation

antibiotic resistance

  • @ref: 122302
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
4337716136hydrogen sulfideno
4337735581indoleno
12230235581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12230215688acetoin-
12230217234glucose-

enzymes

@refvalueactivityec
43377catalase-1.11.1.6
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
122302oxidase-
122302beta-galactosidase+3.2.1.23
122302alcohol dehydrogenase-1.1.1.1
122302gelatinase-
122302amylase-
122302DNase+
122302caseinase-3.4.21.50
122302catalase-1.11.1.6
122302tween esterase+
122302gamma-glutamyltransferase+2.3.2.2
122302lecithinase-
122302lipase-
122302lysine decarboxylase-4.1.1.18
122302ornithine decarboxylase-4.1.1.17
122302phenylalanine ammonia-lyase-4.3.1.24
122302tryptophan deaminase-
122302urease-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
122302-+-+-++---++---+++--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122302------------------+--------------------------------+----------+--+---------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
4983seawater sediment suspension containing hexadecaneJadebusen BayGermanyDEUEurope
43377continuous flow culture with sedimentJadebusen bayGermanyDEUEurope
122302Environment, Suspension of intertidal sedimentGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_7995.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15779;96_885;97_4056;98_5831;99_7995&stattab=map
  • Last taxonomy: Muricauda ruestringensis
  • 16S sequence: AF218782
  • Sequence Identity:
  • Total samples: 351
  • soil counts: 24
  • aquatic counts: 313
  • animal counts: 11
  • plant counts: 3

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
49831Risk group (German classification)
1223021Risk group (French classification)

Sequence information

16S sequences

  • @ref: 4983
  • description: Muricauda ruestringensis 16S ribosomal RNA gene, partial sequence
  • accession: AF218782
  • length: 1426
  • database: ena
  • NCBI tax ID: 886377

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Allomuricauda ruestringensis DSM 13258GCA_000224085completencbi886377
66792Muricauda ruestringensis DSM 13258886377.3completepatric886377
66792Muricauda ruestringensis B1, DSM 132582505679007completeimg886377

GC content

  • @ref: 4983
  • GC-content: 41.4
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.499yes
flagellatedno96.997no
gram-positiveno98.109yes
anaerobicno99.289yes
aerobicyes79.795yes
halophileno71.424no
spore-formingno97.32no
thermophileno98.146yes
glucose-utilyes84.013yes
glucose-fermentno84.261no

External links

@ref: 4983

culture collection no.: DSM 13258, KCTC 12948, LMG 19739, CIP 107369, KCTC 62007

straininfo link

  • @ref: 75102
  • straininfo: 13469

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11760940Muricauda ruestringensis gen. nov., sp. nov., a facultatively anaerobic, appendaged bacterium from German North Sea intertidal sediment.Bruns A, Rohde M, Berthe-Corti LInt J Syst Evol Microbiol10.1099/00207713-51-6-19972001Culture Media, DNA, Ribosomal/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Gram-Negative Facultatively Anaerobic Rods/*classification/genetics/growth & development/ultrastructure, Microscopy, Electron, Molecular Sequence Data, North Sea, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNACultivation
Phylogeny15879227Muricauda flavescens sp. nov. and Muricauda aquimarina sp. nov., isolated from a salt lake near Hwajinpo Beach of the East Sea in Korea, and emended description of the genus Muricauda.Yoon JH, Lee MH, Oh TK, Park YHInt J Syst Evol Microbiol10.1099/ijs.0.03051-02005Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Flavobacteriaceae/*classification/cytology/*isolation & purification/physiology, Genes, rRNA, Gentian Violet, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenazines, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/analysis, Vitamin K 2/analogs & derivatives/analysis, *Water MicrobiologyGenetics
Phylogeny23291883Muricauda taeanensis sp. nov., isolated from a marine tidal flat.Kim JM, Jin HM, Jeon COInt J Syst Evol Microbiol10.1099/ijs.0.047647-02013Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny23543499Muricauda antarctica sp. nov., a marine member of the Flavobacteriaceae isolated from Antarctic seawater.Wu YH, Yu PS, Zhou YD, Xu L, Wang CS, Wu M, Oren A, Xu XWInt J Syst Evol Microbiol10.1099/ijs.0.048355-02013Antarctic Regions, Bacterial Typing Techniques, Base Composition, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis, Xanthophylls/analysis, ZeaxanthinsGenetics
Phylogeny31909707Muricauda alvinocaridis sp. nov., isolated from shrimp gill from the Okinawa Trough.Liu L, Yu M, Zhou S, Fu T, Sun W, Wang L, Zhang XHInt J Syst Evol Microbiol10.1099/ijsem.0.0039532020Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Decapoda/*microbiology, Fatty Acids/chemistry, Flavobacteriaceae/*classification/isolation & purification, Gills/*microbiology, Nucleic Acid Hybridization, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny33095696Muricauda maritima sp. nov., Muricauda aequoris sp. nov. and Muricauda oceanensis sp. nov., three marine bacteria isolated from seawater.Guo LL, Wu D, Sun C, Cheng H, Xu XW, Wu M, Wu YHInt J Syst Evol Microbiol10.1099/ijsem.0.0045222020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/isolation & purification, Nucleic Acid Hybridization, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny35103584Muricauda aurea sp. nov. and Muricauda profundi sp. nov., two marine bacteria isolated from deep sea sediment of Pacific Ocean.Zhao S, Liu R, Lai Q, Shao ZInt J Syst Evol Microbiol10.1099/ijsem.0.0052172022Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/isolation & purification, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, *Seawater/microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4983Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13258)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13258
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
34934Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4797
43377Alke Bruns, Manfred Rohde and Luise Berthe-Corti10.1099/00207713-51-6-1997Muricauda ruestringensis gen. nov., sp. nov., a facultatively anaerobic, appendaged bacterium from German North Sea intertidal sedimentIJSEM 51: 1997-2006 200111760940
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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
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
75102Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13469.1StrainInfo: A central database for resolving microbial strain identifiers
122302Curators of the CIPCollection of Institut Pasteur (CIP 107369)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107369