Strain identifier

BacDive ID: 9984

Type strain: Yes

Species: Myxococcus xanthus

Strain Designation: FB

Strain history: CIP <- 2001, CCUG <- 1972, NCIMB <- P.H.A. Sneath <- M. Dworkin: strain FB <- E.J. Ordal

NCBI tax ID(s): 34 (species)

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

@ref: 6391

BacDive-ID: 9984

DSM-Number: 16526

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

description: Myxococcus xanthus FB is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 34
  • Matching level: species

strain history

@refhistory
6391<- ATCC <- M. Dworkin; FB <- E. J. Ordal according to ATCC catalogue, culture collection Department of Bacteriology, University of California, Berkeley, USA according to reference Voelz and Dworkin 1962
123970CIP <- 2001, CCUG <- 1972, NCIMB <- P.H.A. Sneath <- M. Dworkin: strain FB <- E.J. Ordal

doi: 10.13145/bacdive9984.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Deltaproteobacteria
  • order: Myxococcales
  • family: Myxococcaceae
  • genus: Myxococcus
  • species: Myxococcus xanthus
  • full scientific name: Myxococcus xanthus Beebe 1941 (Approved Lists 1980)

@ref: 6391

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Myxococcales

family: Myxococcaceae

genus: Myxococcus

species: Myxococcus xanthus

full scientific name: Myxococcus xanthus Beebe 1941

strain designation: FB

type strain: yes

Morphology

cell morphology

  • @ref: 123970
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6391VY/2 AGAR (DSMZ Medium 9)yeshttps://mediadive.dsmz.de/medium/9Name: VY/2 AGAR (DSMZ Medium 9) Composition: Agar 15.0 g/l Baker's yeast 5.0 g/l CaCl2 x 2 H2O 1.36 g/l Vitamin B12 0.0005 g/l Distilled water
35225MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123970CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
123970CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
6391positivegrowth30mesophilic
35225positivegrowth30mesophilic
44476positivegrowth30mesophilic
123970positivegrowth25-37mesophilic
123970nogrowth5psychrophilic
123970nogrowth10psychrophilic
123970nogrowth15psychrophilic
123970nogrowth41thermophilic

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
123970NaClpositivegrowth0-2 %
123970NaClnogrowth4 %
123970NaClnogrowth6 %
123970NaClnogrowth8 %
123970NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1239704853esculin-hydrolysis
12397017632nitrate+reduction
12397016301nitrite+reduction
6837917632nitrate-reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

metabolite production

  • @ref: 123970
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68379catalase-1.11.1.6
68379gelatinase+
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase+3.5.1.B15
123970oxidase-
123970beta-galactosidase+3.2.1.23
123970alcohol dehydrogenase-1.1.1.1
123970gelatinase+
123970amylase-
123970DNase+
123970caseinase+3.4.21.50
123970catalase+1.11.1.6
123970tween esterase+
123970gamma-glutamyltransferase+2.3.2.2
123970lecithinase-
123970lipase+
123970lysine decarboxylase-4.1.1.18
123970ornithine decarboxylase-4.1.1.17
123970protease+
123970tryptophan deaminase-
123970urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELControlGLURIBXYLMANMALLACSACGLYGCAT
44476-+-+----+-+----------

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
44476-+++-++---++--------
123970-++++++-+-++--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123970---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

  • @ref: 6391
  • sample type: soil

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_1275.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_211;96_740;97_863;98_1007;99_1275&stattab=map
  • Last taxonomy: Myxococcaceae
  • 16S sequence: KC169882
  • Sequence Identity:
  • Total samples: 8929
  • soil counts: 6158
  • aquatic counts: 816
  • animal counts: 759
  • plant counts: 1196

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
63911Risk group (German classification)
1239701Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Myxococcus xanthus strain DSM16526 16S ribosomal RNA gene, partial sequenceKC1698821385ena34
20218Myxococcus xanthus gene for 16S rRNA, partial sequence, strain: NBRC 13542AB2182051463ena34
20218Myxococcus xanthus gene for 16S-23S rRNA internal transcribed spacer regions, partial sequence, strain: NBRC 13542AB218234729ena34
20218Myxococcus xanthus gene for 16S-23S rRNA internal transcribed spacer regions, partial sequence, strain: NBRC 13542AB218235634ena34
6391Myxococcus xanthus strain ATCC 25232 16S ribosomal RNA gene, partial sequenceDQ7681161493ena34

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Myxococcus xanthus strain DSM 1652634.40wgspatric34
66792Myxococcus xanthus DSM 165262693429903draftimg34
66792Myxococcus xanthus DSM 16526GCA_900106535scaffoldncbi34

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno56.391no
glucose-fermentno88.36no
flagellatedno88.674no
gram-positiveno96.169no
anaerobicno97.63no
aerobicyes79.77no
halophileno90.153no
spore-formingno81.951no
thermophileno98.171no
glucose-utilyes71.962no

External links

@ref: 6391

culture collection no.: DSM 16526, ATCC 25232, CCUG 2079, CIP 107069, IFO 13542, NBRC 13542, NCIMB 9412, ATCC 19368

straininfo link

  • @ref: 79363
  • straininfo: 8219

literature

  • topic: Metabolism
  • Pubmed-ID: 30217842
  • title: Engineering Pseudochelin Production in Myxococcus xanthus.
  • authors: Korp J, Winand L, Sester A, Nett M
  • journal: Appl Environ Microbiol
  • DOI: 10.1128/AEM.01789-18
  • year: 2018
  • mesh: Amidohydrolases/genetics/metabolism, Bacterial Proteins/genetics/metabolism, Biosynthetic Pathways, Catechols/chemistry/metabolism, Gene Expression Regulation, Bacterial, Genetic Engineering, Lysine/*analogs & derivatives/biosynthesis/chemistry, Myxococcus xanthus/genetics/*metabolism, Plasmids/genetics/metabolism, Promoter Regions, Genetic, Regulon
  • topic2: Biotechnology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6391Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16526)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16526
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
35225Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19269
44476Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 2079)https://www.ccug.se/strain?id=2079
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)
68379Automatically annotated from API Coryne
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
79363Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID8219.1StrainInfo: A central database for resolving microbial strain identifiers
123970Curators of the CIPCollection of Institut Pasteur (CIP 107069)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107069