Strain identifier

BacDive ID: 12492

Type strain: Yes

Species: Byssovorax cruenta

Strain Designation: By c2

Strain history: CIP <- 2005, DSMZ <- H. Reichenbach, GBF, Braunschweig, Germany: strain By C2

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

@ref: 5294

BacDive-ID: 12492

DSM-Number: 14553

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

description: Byssovorax cruenta By c2 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from soil with rotting plant material.

NCBI tax id

NCBI tax idMatching level
1300159strain
293647species

strain history

@refhistory
5294<- H. Reichenbach; By c2
67770DSM 14553 <-- H. Reichenbach By c2.
118792CIP <- 2005, DSMZ <- H. Reichenbach, GBF, Braunschweig, Germany: strain By C2

doi: 10.13145/bacdive12492.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Deltaproteobacteria
  • order: Myxococcales
  • family: Polyangiaceae
  • genus: Byssovorax
  • species: Byssovorax cruenta
  • full scientific name: Byssovorax cruenta (ex Thaxter 1897) Reichenbach 2006
  • synonyms

    • @ref: 20215
    • synonym: Byssophaga cruenta

@ref: 5294

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Myxococcales

family: Polyangiaceae

genus: Byssovorax

species: Byssovorax cruenta

full scientific name: Byssovorax cruenta (ex Thaxter 1897) Reichenbach 2006

strain designation: By c2

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.687
118792positivecoccus-shapedno

multimedia

  • @ref: 5294
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_14553.jpg
  • caption: swarms on medium 9
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5294VY/2 AGAR (DSMZ Medium 9)yeshttps://mediadive.dsmz.de/medium/9Name: VY/2 AGAR (DSMZ Medium 9; with strain-specific modifications) Composition: Agar 15.0 g/l Baker's yeast 5.0 g/l Maltose 2.0 g/l CaCl2 x 2 H2O 1.36 g/l Vitamin B12 0.0005 g/l Distilled water
38337MEDIUM 657 - for Byssovorax cruentayesDistilled water make up to (1000.000 ml);Calcium chloride dihydrate (1.360g);Agar (15.000 g);Yeast Baker (5.000 g);Vitamin B12 solution - M01085 (100.000 ml);Maltose solution - M01084 (100.000 ml)
118792CIP Medium 657yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=657

culture temp

@refgrowthtypetemperaturerange
5294positivegrowth30mesophilic
38337positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118792
  • oxygen tolerance: facultative anaerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.995

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371lactose+builds acid from17716
68371maltose+builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
118792nitrate+reduction17632
118792nitrite-reduction16301

metabolite production

  • @ref: 118792
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
118792urease+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
118792-++-------++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118792+---+/-----++++--------+/------++-+--+/------+/---------+/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
5294soil with rotting plant materialArizona, HolbrookUSAUSANorth America
67770Soil with decaying plant materialHolbrook, AZUSAUSANorth America
118792Environment, Soil with rotting plant materialHolbrook, ArizonaUnited States of AmericaUSANorth America2001

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Decomposing plant

taxonmaps

  • @ref: 69479
  • File name: preview.99_26602.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_400;96_13255;97_16110;98_19961;99_26602&stattab=map
  • Last taxonomy: Byssovorax cruenta subclade
  • 16S sequence: AJ833647
  • Sequence Identity:
  • Total samples: 20
  • soil counts: 16
  • aquatic counts: 3
  • animal counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
52941Risk group (German classification)
1187921Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5294
  • description: Byssophaga cruenta partial 16S rRNA gene, strain DSM 14553T
  • accession: AJ833647
  • length: 1529
  • database: ena
  • NCBI tax ID: 293647

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Byssovorax cruenta JCM 12614GCA_001312805contigncbi1300159
66792Byssovorax cruenta JCM 126141300159.4wgspatric1300159
66792Byssovorax cruenta JCM 126142734481916draftimg1300159

GC content

  • @ref: 67770
  • GC-content: 69.9
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno52no
motileno84.722no
gram-positiveno86.903no
anaerobicno98.007no
halophileno90.766no
spore-formingno82.772no
thermophileno97.957yes
glucose-utilyes91.275no
flagellatedno97.585no
aerobicyes92.009no
glucose-fermentno88.22no

External links

@ref: 5294

culture collection no.: DSM 14553, JCM 12614, CIP 108850

straininfo link

  • @ref: 81711
  • straininfo: 133176

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17012562Byssovorax cruenta gen. nov., sp. nov., nom. rev., a cellulose-degrading myxobacterium: rediscovery of 'Myxococcus cruentus' Thaxter 1897.Reichenbach H, Lang E, Schumann P, Sproer CInt J Syst Evol Microbiol10.1099/ijs.0.63628-02006Base Composition, Cellulose/metabolism, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Molecular Sequence Data, Myxococcales/*classification/genetics/growth & development/ultrastructure, Myxococcus/*classification, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny25048208Vulgatibacter incomptus gen. nov., sp. nov. and Labilithrix luteola gen. nov., sp. nov., two myxobacteria isolated from soil in Yakushima Island, and the description of Vulgatibacteraceae fam. nov., Labilitrichaceae fam. nov. and Anaeromyxobacteraceae fam. nov.Yamamoto E, Muramatsu H, Nagai KInt J Syst Evol Microbiol10.1099/ijs.0.063198-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Forests, Islands, Japan, Molecular Sequence Data, Myxococcales/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny27046779Racemicystis crocea gen. nov., sp. nov., a soil myxobacterium in the family Polyangiaceae.Awal RP, Garcia R, Muller RInt J Syst Evol Microbiol10.1099/ijsem.0.0010452016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Myxococcales/*classification/genetics/isolation & purification, Philippines, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitle
5294Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14553)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14553
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
38337Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6525
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/
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.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)
81711Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID133176.1StrainInfo: A central database for resolving microbial strain identifiers
118792Curators of the CIPCollection of Institut Pasteur (CIP 108850)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108850