Strain identifier

BacDive ID: 11955

Type strain: Yes

Species: Planococcus citreus

Strain Designation: 628

Strain history: CIP <- 1981, CCM <- C.E. ZoBell: strain 628, Micrococcus aquivivus

NCBI tax ID(s): 1373 (species)

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General

@ref: 8777

BacDive-ID: 11955

DSM-Number: 20549

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, motile, oval-shaped

description: Planococcus citreus 628 is an obligate aerobe, mesophilic, motile bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 1373
  • Matching level: species

strain history

@refhistory
8777<- CCM <- C.E. ZoBell, 628 (Micrococcus aquivivus)
67770M. V. Hao HK 709 <-- AJ 3344 <-- CCM 316 <-- C. E. ZoBell 628.
118304CIP <- 1981, CCM <- C.E. ZoBell: strain 628, Micrococcus aquivivus

doi: 10.13145/bacdive11955.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Caryophanaceae
  • genus: Planococcus
  • species: Planococcus citreus
  • full scientific name: Planococcus citreus Migula 1894 (Approved Lists 1980)

@ref: 8777

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Caryophanaceae

genus: Planococcus

species: Planococcus citreus

full scientific name: Planococcus citreus Migula 1894

strain designation: 628

type strain: yes

Morphology

cell morphology

  • @ref: 118304
  • cell shape: oval-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8777NUTRIENT AGAR WITH NaCl (DSMZ Medium 101)yeshttps://mediadive.dsmz.de/medium/101Name: NUTRIENT AGAR or BROTH WITH NaCl (DSMZ Medium 101) Composition: NaCl 30.0 g/l Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
37979MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
118304CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
118304CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
8777positivegrowth26
37979positivegrowth30
67770positivegrowth30

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
118304obligate aerobe
125439aerobe91.3

murein

  • @ref: 8777
  • murein short key: A11.33
  • type: A4alpha L-Lys-D-Glu

observation

  • @ref: 67770
  • observation: quinones: MK-8 (MK-7)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11830417632nitrate-reduction
11830416301nitrite-reduction

metabolite production

  • @ref: 118304
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
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
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
118304oxidase-
118304catalase+1.11.1.6
118304urease-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
118304-+++-+-+-------+----

Isolation, sampling and environmental information

isolation

@refsample type
8777seawater
67770Seawater
118304Environment, Seawater

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_129.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_67;97_70;98_75;99_129&stattab=map
  • Last taxonomy: Planococcus
  • 16S sequence: LC379145
  • Sequence Identity:
  • Total samples: 12884
  • soil counts: 6586
  • aquatic counts: 2240
  • animal counts: 2949
  • plant counts: 1109

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
87771Risk group (German classification)
1183041Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Planococcus citreus strain DSM 20549 16S-23S rRNA intergenic spacer regionAF145717185nuccore1373
20218Planococcus citreus gene for 16S rRNA, partial sequence, strain: NBRC 15849AB6809851476nuccore1373
20218P.citreus 16S rRNAX621721432nuccore1373
67770Planococcus citreus gene for 16S rRNA, partial sequence, strain: JCM 2532LC3791451473nuccore1373
67770Planococcus citreus 5S ribosomal RNAX13005116nuccore1373
124043Planococcus citreus strain DSM 20549 16S ribosomal RNA gene, partial sequence.OQ6189631352nuccore1373
124043Planococcus citreus strain DSM 20549 16S ribosomal RNA gene, partial sequence.OQ6260071320nuccore1373

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Planococcus citreus strain DSM 205491373.6wgspatric1373
66792Planococcus citreus strain DSM 205491373.5wgspatric1373
66792Planococcus citreus DSM 205492770939644draftimg1373
67770Planococcus citreus DSM 20549GCA_004761885contigncbi1373
67770Planococcus citreus DSM 20549GCA_003664125scaffoldncbi1373

GC content

@refGC-contentmethod
877751.2
6777047.5fluorimetric
6777051.2thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes78.237no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.474yes
125438spore-formingspore-formingAbility to form endo- or exosporesyes58.223no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes80.401yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno94.339yes
125438motile2+flagellatedAbility to perform flagellated movementyes54.404no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes74.5
125439BacteriaNetmotilityAbility to perform movementyes79.3
125439BacteriaNetgram_stainReaction to gram-stainingvariable83.6
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe91.3

External links

@ref: 8777

culture collection no.: DSM 20549, ATCC 14404, CCM 316, NCMB 1493, JCM 2532, CECT 951, CGMCC 1.2714, CIP 81.74, IAM 12456, IAM 12541, IAM 13052, IFO 15849, LMG 17319, NBRC 15849, NCIMB 1493, VKM B-1307

straininfo link

  • @ref: 81168
  • straininfo: 13977

literature

  • topic: Phylogeny
  • Pubmed-ID: 14657138
  • title: Planococcus maritimus sp. nov., isolated from sea water of a tidal flat in Korea.
  • authors: Yoon JH, Weiss N, Kang KH, Oh TK, Park YH
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02557-0
  • year: 2003
  • mesh: DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Gram-Positive Bacteria/*classification/genetics/growth & development/isolation & purification, Korea, Molecular Sequence Data, *Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8777Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20549)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20549
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
37979Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11239
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/
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
81168Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13977.1StrainInfo: A central database for resolving microbial strain identifiers
118304Curators of the CIPCollection of Institut Pasteur (CIP 81.74)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2081.74
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1