Strain identifier

BacDive ID: 3922

Type strain: Yes

Species: Dermacoccus nishinomiyaensis

Strain Designation: 59, 8094

Strain history: CIP <- 1981, CCM <- Osaka University, Japan: strain 8094 <- M. Oda: strain 59

NCBI tax ID(s): 1274 (species)

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General

@ref: 8820

BacDive-ID: 3922

DSM-Number: 20448

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive, coccus-shaped

description: Dermacoccus nishinomiyaensis 59 is a facultative anaerobe, mesophilic, Gram-positive bacterium that was isolated from water.

NCBI tax id

  • NCBI tax id: 1274
  • Matching level: species

strain history

@refhistory
8820<- K.H. Schleifer <- CCM <- OUT 8094 <- M. Oda, 59
67770CCM 2140 <-- OUT 8094 <-- M. Oda 59.
121306CIP <- 1981, CCM <- Osaka University, Japan: strain 8094 <- M. Oda: strain 59

doi: 10.13145/bacdive3922.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Dermacoccaceae
  • genus: Dermacoccus
  • species: Dermacoccus nishinomiyaensis
  • full scientific name: Dermacoccus nishinomiyaensis (Oda 1935) Stackebrandt et al. 1995

  • synonyms

    • @ref: 20215
    • synonym: Micrococcus nishinomiyaensis

@ref: 8820

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Dermacoccaceae

genus: Dermacoccus

species: Dermacoccus nishinomiyaensis

full scientific name: Dermacoccus nishinomiyaensis (Oda 1935) Stackebrandt et al. 1995

strain designation: 59, 8094

type strain: yes

Morphology

cell morphology

  • @ref: 121306
  • gram stain: positive
  • cell shape: coccus-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
18747Chrome yellow10-14 days5006
18747Chrome yellow10-14 days5425
18747Chrome yellow10-14 days5428
18747Chrome yellow10-14 daysISP 2
18747Chrome yellow10-14 daysISP 6

multicellular morphology

@refforms multicellular complexmedium name
18747noISP 2
18747no5006
18747no5425
18747no5428
18747noISP 6

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8820CORYNEBACTERIUM AGAR (DSMZ Medium 53)yeshttps://mediadive.dsmz.de/medium/53Name: CORYNEBACTERIUM AGAR (DSMZ Medium 53) Composition: Agar 15.0 g/l Casein peptone 10.0 g/l NaCl 5.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Distilled water
18747ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
187475006yesMedium: 5006 Name: Composition (g/l) Sucrose 3,0 Dextrin 15,0 Meat extract 1,0 Yeast extract 2,0 Tryptone soy broth (Oxoid) 5,0 NaCl 0,5 K2HPO4 0,5 MgSO4 x 7 H2O 0,5 FeSO4 x 7 H2O 0,01 Agar 20,0 Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7,3 Usage: Maintenance Organisms: All Actinomycetes
187475425yesName: Brain Heart Infusion (BHI) Agar; 5425 Composition: Calf brain infusion 200.0 g/l Beef heart infusion 250.0 g/l Casein (meat) peptone 10.0 g/l Glucose 2.0 g/l NaCl 5.0 g/l Na2HPO4 2.5 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.4 Usage: Maintenance and revitalization Organisms: Dermatophilus congolensis, Nocardia brasieliensis, N. asteroides, Rhodococcus equi, R. fascians, R. rhodochrous, Streptomyces thermoviol aceus subsp. apingens, Coryneform species
187475428yes
18747ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
38082MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
121306CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
121306CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
18747positiveoptimum28mesophilic
8820positivegrowth30mesophilic
38082positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121306
  • oxygen tolerance: facultative anaerobe

murein

  • @ref: 8820
  • murein short key: A11.39
  • type: A4alpha L-Lys-L-Ser2-D-Glu

observation

  • @ref: 67770
  • observation: quinones: MK-8(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis
12130617632nitrate-reduction
12130616301nitrite-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

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
12130635581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-

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
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
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
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase+3.2.1.23
121306oxidase+
121306catalase+1.11.1.6
121306urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    51331C15:0 ISO10.614.621
    51331C16:0 10-methyl1516.433
    51331C16:0 iso9.315.626
    51331C16:1 ω7c13.615.819
    51331C17:0 10-methyl317.41
    51331C17:0 anteiso416.722
    51331C17:0 iso16.416.629
    51331C17:1 ω8c22.216.792
    51331C18:1 ω9c5.917.769
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18747------+--+---------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18747--+-+----+----+----
121306+++-++++-+----+-----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18747+++-+-+----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
8820water
67770Water ("miyamizu")JapanJPNAsia
121306Environment, Water

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic

taxonmaps

  • @ref: 69479
  • File name: preview.99_648.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_403;97_455;98_524;99_648&stattab=map
  • Last taxonomy: Dermacoccus
  • 16S sequence: X87757
  • Sequence Identity:
  • Total samples: 24272
  • soil counts: 2219
  • aquatic counts: 2728
  • animal counts: 18144
  • plant counts: 1181

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
187471Risk group (German classification)
88201Risk group (German classification)
1213061Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8820
  • description: M.nishinomyaensis 16S rRNA gene
  • accession: X87757
  • length: 1464
  • database: ena
  • NCBI tax ID: 1274

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dermacoccus nishinomiyaensis strain FDAARGOS_11191274.37completepatric1274
66792Dermacoccus nishinomiyaensis strain NCTC110391274.14wgspatric1274
66792Dermacoccus nishinomiyaensis NCTC 110392832479645draftimg1274
67770Dermacoccus nishinomiyaensis NCTC11039GCA_900447535contigncbi1274

GC content

@refGC-contentmethod
882067.8
6777067.8thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno96.931no
gram-positiveyes93.593no
anaerobicno98.818no
aerobicyes80.268no
halophileno94.331no
spore-formingno90.258no
thermophileno97.358no
glucose-utilyes87.435no
flagellatedno98.052no
glucose-fermentno87.853no

External links

@ref: 8820

culture collection no.: DSM 20448, ATCC 29093, CCM 2140, CCUG 33028, JCM 11613, CECT 544, CIP 81.71, IAM 13592, IFO 15356, IMSNU 21319, LMG 14222, NBRC 15356, NCDO 2358, NCIMB 702358, NCTC 11039, VKM Ac-2160, VKM B-1818

straininfo link

  • @ref: 73431
  • straininfo: 9313

literature

  • topic: Phylogeny
  • Pubmed-ID: 16738097
  • title: Dermacoccus abyssi sp. nov., a piezotolerant actinomycete isolated from the Mariana Trench.
  • authors: Pathom-Aree W, Nogi Y, Sutcliffe IC, Ward AC, Horikoshi K, Bull AT, Goodfellow M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64133-0
  • year: 2006
  • mesh: Actinomycetales/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, Geologic Sediments/microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8820Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20448)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20448
18747Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20448.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
38082Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11236
51331Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 33028)https://www.ccug.se/strain?id=33028
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/
68368Automatically annotated from API 20E
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
73431Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID9313.1StrainInfo: A central database for resolving microbial strain identifiers
121306Curators of the CIPCollection of Institut Pasteur (CIP 81.71)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2081.71