Strain identifier

BacDive ID: 9805

Type strain: No

Species: Myxococcus virescens

Strain Designation: 38

Strain history: CIP <- 2001, JCM <- S. Yamanaka: strain 38

NCBI tax ID(s): 83456 (species)

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General

@ref: 1885

BacDive-ID: 9805

DSM-Number: 4946

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

description: Myxococcus virescens 38 is a microaerophile, Gram-negative, rod-shaped bacterium that was isolated from soil of seaside.

NCBI tax id

  • NCBI tax id: 83456
  • Matching level: species

strain history

@refhistory
1885<- JCM <- S. Yamanaka, 38
67770S. Yamanaka No. 38 (=AJ 12384).
119371CIP <- 2001, JCM <- S. Yamanaka: strain 38

doi: 10.13145/bacdive9805.20240510.9

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 virescens
  • full scientific name: Myxococcus virescens Thaxter 1892 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Myxococcus flavescens

@ref: 1885

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Myxococcales

family: Myxococcaceae

genus: Myxococcus

species: Myxococcus virescens

full scientific name: Myxococcus virescens Thaxter 1892 emend. Lang et al. 2008

strain designation: 38

type strain: no

Morphology

cell morphology

  • @ref: 119371
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1885VY/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
1885CY-AGAR (DSMZ Medium 67)yeshttps://mediadive.dsmz.de/medium/67Name: CY-AGAR (DSMZ Medium 67) Composition: Agar 15.0 g/l Casitone 3.0 g/l CaCl2 x 2 H2O 1.36 g/l Yeast extract 1.0 g/l Distilled water
33632MEDIUM 390 - for Myxococcus flavescensyesDistilled water make up to (1000.000 ml);Calcium chloride dihydrate (1.360g);Agar (15.000 g);Yeast extract (1.000 g);Casitone (3.000 g)
119371CIP Medium 390yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=390

culture temp

@refgrowthtypetemperature
1885positivegrowth30
33632positivegrowth30
67770positivegrowth30
119371positivegrowth25-37
119371nogrowth5
119371nogrowth10
119371nogrowth15
119371nogrowth41

Physiology and metabolism

oxygen tolerance

  • @ref: 119371
  • oxygen tolerance: microaerophile

halophily

@refsaltgrowthtested relationconcentration
119371NaClpositivegrowth0 %
119371NaClnogrowth2 %
119371NaClnogrowth4 %
119371NaClnogrowth6 %
119371NaClnogrowth8 %
119371NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11937116947citrate-carbon source
1193714853esculin-hydrolysis
11937117632nitrate-reduction
11937116301nitrite-reduction

antibiotic resistance

  • @ref: 119371
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 119371
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
119371oxidase-
119371beta-galactosidase+3.2.1.23
119371alcohol dehydrogenase-1.1.1.1
119371gelatinase+
119371amylase+
119371DNase+
119371catalase+1.11.1.6
119371gamma-glutamyltransferase+2.3.2.2
119371lysine decarboxylase-4.1.1.18
119371ornithine decarboxylase-4.1.1.17
119371phenylalanine ammonia-lyase-4.3.1.24
119371tryptophan deaminase-
119371urease-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
119371-+++-++---++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
1885soil of seasideKanagawaJapanJPNAsia
67770Soil of seasideKanagawa Pref.JapanJPNAsia
119371Environment, Soil, seasideKanagawaJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Terrestrial#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: AB218220
  • 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
18851Risk group (German classification)
1193711Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
1885Myxococcus virescens strain DSM 4946 16S ribosomal RNA gene, partial sequenceDQ7681301493nuccore83456
67770Myxococcus flavescens gene for 16S rRNA, partial sequence, strain: NBRC 100081AB2182201463nuccore83456
124043Myxococcus flavescens gene for 16S-23S rRNA internal transcribed spacer regions, partial sequence, strain: NBRC 100081.AB218254725nuccore83456

GC content

@refGC-contentmethod
188567.1
6777067.1thermal denaturation, midpoint method (Tm)

External links

@ref: 1885

culture collection no.: DSM 4946, ATCC 51243, IAM 13189, JCM 6245, CIP 107135, IAM 14540, KCTC 9843, NBRC 100081

straininfo link

  • @ref: 79184
  • straininfo: 42874

Reference

@idauthorscataloguedoi/urltitle
1885Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4946)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4946
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
33632Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4537
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
79184Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42874.1StrainInfo: A central database for resolving microbial strain identifiers
119371Curators of the CIPCollection of Institut Pasteur (CIP 107135)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107135
124043Dr. Isabel Schober, Dr. Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy