Strain identifier
BacDive ID: 11955
Type strain:
Species: Planococcus citreus
Strain Designation: 628
Strain history: CIP <- 1981, CCM <- C.E. ZoBell: strain 628, Micrococcus aquivivus
NCBI tax ID(s): 1373 (species)
General
@ref: 8777
BacDive-ID: 11955
DSM-Number: 20549
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, motile
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
@ref | history |
---|---|
8777 | <- CCM <- C.E. ZoBell, 628 (Micrococcus aquivivus) |
67770 | M. V. Hao HK 709 <-- AJ 3344 <-- CCM 316 <-- C. E. ZoBell 628. |
118304 | CIP <- 1981, CCM <- C.E. ZoBell: strain 628, Micrococcus aquivivus |
doi: 10.13145/bacdive11955.20230509.8.1
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 | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | yes | 93.883 | ||
69480 | 100 | positive | ||
118304 | yes | oval-shaped |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
8777 | NUTRIENT AGAR WITH NaCl (DSMZ Medium 101) | yes | https://mediadive.dsmz.de/medium/101 | Name: 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 |
37979 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
118304 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 | |
118304 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
8777 | positive | growth | 26 | mesophilic |
37979 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 118304
- oxygen tolerance: obligate aerobe
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.219
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
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
118304 | 17632 | nitrate | - | reduction |
118304 | 16301 | nitrite | - | reduction |
metabolite production
- @ref: 118304
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
118304 | oxidase | - | |
118304 | catalase | + | 1.11.1.6 |
118304 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | + | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | - | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | - | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118304 | - | + | + | + | - | + | - | + | - | - | - | - | - | - | - | + | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
8777 | seawater |
67770 | Seawater |
118304 | Environment, 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
@ref | biosafety level | biosafety level comment |
---|---|---|
8777 | 1 | Risk group (German classification) |
118304 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Planococcus citreus strain DSM 20549 16S-23S rRNA intergenic spacer region | AF145717 | 185 | ena | 1373 |
20218 | Planococcus citreus gene for 16S rRNA, partial sequence, strain: NBRC 15849 | AB680985 | 1476 | ena | 1373 |
20218 | P.citreus 16S rRNA | X62172 | 1432 | ena | 1373 |
67770 | Planococcus citreus gene for 16S rRNA, partial sequence, strain: JCM 2532 | LC379145 | 1473 | ena | 1373 |
67770 | Planococcus citreus 5S ribosomal RNA | X13005 | 116 | ena | 1373 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Planococcus citreus strain DSM 20549 | 1373.6 | wgs | patric | 1373 |
66792 | Planococcus citreus strain DSM 20549 | 1373.5 | wgs | patric | 1373 |
66792 | Planococcus citreus DSM 20549 | 2770939644 | draft | img | 1373 |
67770 | Planococcus citreus DSM 20549 | GCA_004761885 | contig | ncbi | 1373 |
67770 | Planococcus citreus DSM 20549 | GCA_003664125 | scaffold | ncbi | 1373 |
GC content
@ref | GC-content | method |
---|---|---|
8777 | 51.2 | |
67770 | 47.5 | fluorimetric |
67770 | 51.2 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 67 | no |
motile | yes | 71.489 | no |
gram-positive | yes | 92.002 | no |
anaerobic | no | 99.092 | no |
halophile | yes | 85.244 | no |
spore-forming | yes | 59.11 | no |
thermophile | no | 99.59 | yes |
glucose-util | yes | 88.494 | no |
aerobic | yes | 96.068 | no |
flagellated | no | 59.255 | no |
glucose-ferment | no | 86.83 | no |
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
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
8777 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20549) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-20549 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
37979 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/11239 | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68382 | Automatically annotated from API zym | |||||
69479 | João 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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
81168 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID13977.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
118304 | Curators of the CIP | Collection of Institut Pasteur (CIP 81.74) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2081.74 |