Strain identifier

BacDive ID: 11054

Type strain: Yes

Species: Smaragdicoccus niigatensis

Strain Designation: Hou_blue

Strain history: CIP <- 2007, DSMZ <- A. Katsuta, MBIC, Iwate, Japan: strain Hou_blue

NCBI tax ID(s): 1123258 (strain), 359359 (species)

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General

@ref: 12166

BacDive-ID: 11054

DSM-Number: 44881

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

description: Smaragdicoccus niigatensis Hou_blue is a mesophilic, Gram-positive, coccus-shaped bacterium that was isolated from oil springs.

NCBI tax id

NCBI tax idMatching level
1123258strain
359359species

strain history

@refhistory
12166<- A. Katsuta, MBIC (Smaragdicoccus niigataensis) <- X. Peng (mix culture)
67770IFM 10815 <-- DSM 44881 <-- A. Katsuta strain Hou-blue <-- X. Peng (mix culture).
121303CIP <- 2007, DSMZ <- A. Katsuta, MBIC, Iwate, Japan: strain Hou_blue

doi: 10.13145/bacdive11054.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Nocardiaceae
  • genus: Smaragdicoccus
  • species: Smaragdicoccus niigatensis
  • full scientific name: Smaragdicoccus niigatensis Adachi et al. 2007

@ref: 12166

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Smaragdicoccus

species: Smaragdicoccus niigatensis

full scientific name: Smaragdicoccus niigatensis Adachi et al. 2007

strain designation: Hou_blue

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapeconfidencemotility
31777positive0.86 µmcoccus-shaped
69480positive100
121303positivecoccus-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19883Olive green10-14 daysISP 2
19883Olive green10-14 daysISP 3
1988310-14 daysISP 4
1988310-14 daysISP 5
1988310-14 daysISP 6
1988310-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19883noISP 2
19883noISP 3
19883noISP 4
19883noISP 5
19883noISP 6
19883noISP 7

pigmentation

  • @ref: 31777
  • production: no

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_44881_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_44881_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_44881_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_44881_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_44881_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12166COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
12166MIDDLEBROOK MEDIUM (DSMZ Medium 645)yeshttps://mediadive.dsmz.de/medium/645Name: MIDDLEBROOK MEDIUM (DSMZ Medium 645) Composition: Bacto Middlebrook 7H10 agar 20.9945 g/l Glycerol Distilled water
19883ISP 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
19883ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19883ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19883ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19883ISP 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
19883ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
121303CIP Medium 93yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=93

culture temp

@refgrowthtypetemperaturerange
12166positivegrowth30mesophilic
19883positiveoptimum28mesophilic
31777positivegrowth04-37
31777positiveoptimum20.5psychrophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
31777no
69481no100
69480no99.897

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3177728757fructose+carbon source
3177717234glucose+carbon source
3177717992sucrose+carbon source
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
6837917632nitrate-reduction
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

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68379gelatinase-
68379urease+3.5.1.5
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
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369arginine dihydrolase-3.5.3.6
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19883--++--+-+/-+---------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19883++++++++++++--++---
12166-++-+-----+/----+/------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
12166----+/--------+----+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12166oil springsNiigataJapanJPNAsia
67770Soil from an oil springNishiyama-cho, Niigata Pref.JapanJPNAsia
121303Environment, Oil springsJapanJPNAsia

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Industrial
  • Cat3: #Oil reservoir

taxonmaps

  • @ref: 69479
  • File name: preview.99_5416.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_2626;97_3216;98_4040;99_5416&stattab=map
  • Last taxonomy: Smaragdicoccus niigatensis subclade
  • 16S sequence: AB243007
  • Sequence Identity:
  • Total samples: 2502
  • soil counts: 1610
  • aquatic counts: 431
  • animal counts: 230
  • plant counts: 231

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
121661Risk group (German classification)
198831Risk group (German classification)
1213031Risk group (French classification)

Sequence information

16S sequences

  • @ref: 31777
  • description: Smaragdicoccus niigatensis gene for 16S rRNA, partial sequence
  • accession: AB243007
  • length: 1478
  • database: nuccore
  • NCBI tax ID: 359359

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Smaragdicoccus niigatensis DSM 448811123258.3wgspatric1123258
66792Smaragdicoccus niigatensis DSM 44881 = NBRC 1035631123258.7wgspatric1123258
66792Smaragdicoccus niigatensis DSM 448812519103184draftimg1123258
66792Smaragdicoccus niigatensis NBRC 1035632731957600draftimg1123258
67770Smaragdicoccus niigatensis DSM 44881 = NBRC 103563GCA_000380645contigncbi1123258
67770Smaragdicoccus niigatensis DSM 44881 = NBRC 103563GCA_001552795contigncbi1123258

GC content

@refGC-contentmethod
3177763.7
6777063.7high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno95.856no
flagellatedno98.557no
gram-positiveyes86.394yes
anaerobicno99.142no
aerobicyes87.239no
halophileno96.603no
spore-formingno70.7no
thermophileno98.753no
glucose-utilyes86.515no
glucose-fermentno91.026no

External links

@ref: 12166

culture collection no.: DSM 44881, CIP 109538, MBIC 06267, JCM 14666, IFM 10815, NBRC 103563

straininfo link

  • @ref: 80303
  • straininfo: 297334

literature

  • topic: Phylogeny
  • Pubmed-ID: 17267967
  • title: Smaragdicoccus niigatensis gen. nov., sp. nov., a novel member of the suborder Corynebacterineae.
  • authors: Adachi K, Katsuta A, Matsuda S, Peng X, Misawa N, Shizuri Y, Kroppenstedt RM, Yokota A, Kasai H
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64254-0
  • year: 2007
  • mesh: Actinomycetales/*classification/genetics/*isolation & purification/physiology, Amino Acids, Diamino/analysis, Carbohydrates/analysis, Cell Wall/chemistry, DNA Gyrase/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Genes, rRNA, Hydrocarbons/metabolism, Japan, Molecular Sequence Data, Mycolic Acids/analysis, Peptidoglycan/chemistry, Petroleum/*microbiology, Phospholipids/analysis/chemistry, Phylogeny, Pigments, Biological/biosynthesis, Quinones/analysis/chemistry, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
12166Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44881)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44881
19883Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44881.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
31777Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2805028776041
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life28604660 35: 676-683 2017
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
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
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
80303Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297334.1StrainInfo: A central database for resolving microbial strain identifiers
121303Curators of the CIPCollection of Institut Pasteur (CIP 109538)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109538