Strain identifier

BacDive ID: 6294

Type strain: Yes

Species: Phycicoccus duodecadis

Strain Designation: Lochhead&Burton541

Strain history: CIP <- 1970, NCIB <- R.M. Keddie <- A.G. Lochhead

NCBI tax ID(s): 173053 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 4830

BacDive-ID: 6294

DSM-Number: 12806

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic

description: Phycicoccus duodecadis Lochhead&Burton541 is an obligate aerobe, mesophilic bacterium that was isolated from field soil.

NCBI tax id

  • NCBI tax id: 173053
  • Matching level: species

strain history

@refhistory
4830<- NCIMB <- R. M. Keddie <- A. G. Lochhead
67770LMG 17308 <-- ATCC 13347 <-- A. G. Lochhead 541.
118977CIP <- 1970, NCIB <- R.M. Keddie <- A.G. Lochhead

doi: 10.13145/bacdive6294.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Intrasporangiaceae
  • genus: Phycicoccus
  • species: Phycicoccus duodecadis
  • full scientific name: Phycicoccus duodecadis (Lochhead 1958) Nouioui et al. 2018

  • synonyms

    @refsynonym
    20215Arthrobacter duodecadis
    20215Tetrasphaera duodecadis

@ref: 4830

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Intrasporangiaceae

genus: Phycicoccus

species: Phycicoccus duodecadis

full scientific name: Phycicoccus duodecadis (Lochhead 1958) Nouioui et al. 2018

strain designation: Lochhead&Burton541

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no92.713
69480100positive
118977yespositiverod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4830OXOID NUTRIENT BROTH (DSMZ Medium 948)yeshttps://mediadive.dsmz.de/medium/948Name: OXOID NUTRIENT BROTH (DSMZ Medium 948) Composition: Nutrient broth 13.0 g/l Distilled water
4830RAE MEDIUM (DSMZ Medium 848)yeshttps://mediadive.dsmz.de/medium/848Name: RAE MEDIUM (DSMZ Medium 848) Composition: Glucose 40.0 g/l Yeast extract 10.0 g/l Peptone 10.0 g/l Na2HPO4 x 2 H2O 3.38 g/l Citric acid x H2O 1.5 g/l Glacial acetic acid Absolute ethanol Distilled water
38105MEDIUM 298 - for Arthrobacter duodecadisyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g);Vitamins solution - M0539 (10.000 ml)
118977CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
4830positivegrowth28mesophilic
38105positivegrowth25mesophilic
67770positivegrowth28mesophilic
118977positivegrowth25-37mesophilic
118977nogrowth10psychrophilic
118977nogrowth15psychrophilic
118977nogrowth41thermophilic
118977nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118977
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no98
69480no99.953

halophily

@refsaltgrowthtested relationconcentration
118977NaClpositivegrowth0-4 %
118977NaClnogrowth6 %
118977NaClnogrowth8 %
118977NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11897716947citrate-carbon source
1189774853esculin+hydrolysis
118977606565hippurate-hydrolysis
11897717632nitrate-reduction
11897716301nitrite-reduction
11897717632nitrate-respiration

metabolite production

  • @ref: 118977
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11897715688acetoin-
11897717234glucose-

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
118977oxidase-
118977beta-galactosidase+3.2.1.23
118977alcohol dehydrogenase-1.1.1.1
118977gelatinase-
118977catalase+1.11.1.6
118977gamma-glutamyltransferase-2.3.2.2
118977lysine decarboxylase-4.1.1.18
118977ornithine decarboxylase-4.1.1.17
118977phenylalanine ammonia-lyase-4.3.1.24
118977tryptophan deaminase-
118977urease-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
118977-+++++++--++++-++---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118977+++-+--+-----+-+---+++----+-+-++++-++--+--------++------+--+---+--+-----++-+--+++---+-+-+++----++++

Isolation, sampling and environmental information

isolation

@refsample type
4830field soil
67770Soil
118977Environment, Field soil

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_6370.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1391;97_3482;98_4707;99_6370&stattab=map
  • Last taxonomy: Phycicoccus duodecadis
  • 16S sequence: AB072496
  • Sequence Identity:
  • Total samples: 2551
  • soil counts: 1068
  • aquatic counts: 975
  • animal counts: 480
  • plant counts: 28

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
48301Risk group (German classification)
1189771Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Tetrasphaera duodecadis gene for 16S rRNA, partial sequence
  • accession: AB072496
  • length: 1485
  • database: ena
  • NCBI tax ID: 173053

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Tetrasphaera duodecadis strain DSM 12806173053.3wgspatric173053
66792Tetrasphaera duodecadis DSM 128062630968219draftimg173053
67770Phycicoccus duodecadis DSM 12806GCA_002846495contigncbi173053

GC content

  • @ref: 67770
  • GC-content: 73
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno98no
motileno95.062no
gram-positiveyes88.758no
anaerobicno97.726no
aerobicyes91.148no
halophileno97.524no
spore-formingno86.479no
glucose-utilyes87.818no
flagellatedno98.255no
thermophileno94.523yes
glucose-fermentno88.953no

External links

@ref: 4830

culture collection no.: DSM 12806, ATCC 13347, CDA 859, IFO 12159, NBRC 12159, NCDO 1576, NCIMB 9222, JCM 11564, CIP 102696, IAM 14868, IAM 14893, IAM 14902, IFO 12959, KCTC 39573, KCTC 9649, LMG 16468, LMG 17308, NBRC 12959, VKM Ac-1108

straininfo link

  • @ref: 75769
  • straininfo: 8176

literature

  • topic: Phylogeny
  • Pubmed-ID: 16738116
  • title: Reclassification of Arthrobacter duodecadis Lochhead 1958 as Tetrasphaera duodecadis comb. nov. and emended description of the genus Tetrasphaera.
  • authors: Ishikawa T, Yokota A
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02984-0
  • year: 2006
  • mesh: Actinomycetales/*classification/cytology/genetics/isolation & purification, DNA, Neoplasm/genetics, Environment, Fatty Acids/analysis, Molecular Sequence Data, Phylogeny, Temperature
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4830Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12806)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12806
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
38105Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14410
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
75769Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID8176.1StrainInfo: A central database for resolving microbial strain identifiers
118977Curators of the CIPCollection of Institut Pasteur (CIP 102696)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102696