Strain identifier

BacDive ID: 7762

Type strain: Yes

Species: Nesterenkonia halobia

Strain Designation: 28-3

Strain history: CIP <- 1981, CCM, Micrococcus halobius <- H. Onishi: strain 28-3

NCBI tax ID(s): 37922 (species)

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General

@ref: 8770

BacDive-ID: 7762

DSM-Number: 20541

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

description: Nesterenkonia halobia 28-3 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from unrefined solar salt.

NCBI tax id

  • NCBI tax id: 37922
  • Matching level: species

strain history

@refhistory
8770<- CCM <- H. Onishi, 28-3
67770CIP 81.68 <-- CCM 2591 <-- H. Onishi 28-3.
119799CIP <- 1981, CCM, Micrococcus halobius <- H. Onishi: strain 28-3

doi: 10.13145/bacdive7762.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Nesterenkonia
  • species: Nesterenkonia halobia
  • full scientific name: Nesterenkonia halobia (Onishi and Kamekura 1972) Stackebrandt et al. 1995

  • synonyms

    • @ref: 20215
    • synonym: Micrococcus halobius

@ref: 8770

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Nesterenkonia

species: Nesterenkonia halobia

full scientific name: Nesterenkonia halobia (Onishi and Kamekura 1972) Stackebrandt et al. 1995

strain designation: 28-3

type strain: yes

Morphology

cell morphology

  • @ref: 119799
  • gram stain: positive
  • cell shape: coccus-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
18756Cream10-14 days5006
18756Cream10-14 days5428
18756Cream10-14 days5428+6% NaCl
18756Cream10-14 days5530
18756Beige10-14 daysISP 2

multicellular morphology

@refforms multicellular complexmedium name
18756noISP 2
18756no5006
18756no5428+6% NaCl
18756no5428
18756no5530

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8770BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
18756ISP 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
187565006yesMedium: 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
187565428+6% NaClyes
187565428yes
187565530yes
37624Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
119799CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
18756positiveoptimum28mesophilic
8770positivegrowth28mesophilic
37624positivegrowth30mesophilic
54531positivegrowth30-37mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
54531aerobe
119799obligate aerobe

spore formation

  • @ref: 119799
  • spore formation: no

compound production

@refcompound
8770amylase, halophilic
20216Amylase (halophilic)
67770Halophilic amylase

halophily

  • @ref: 54531
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: >6 %

murein

  • @ref: 8770
  • murein short key: A11.56
  • type: A4alpha L-Lys-Gly-L-Glu

observation

  • @ref: 67770
  • observation: quinones: MK-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
11979917632nitrate-reduction
11979916301nitrite-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
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
11979935581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
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
119799oxidase+
119799catalase+1.11.1.6
119799urease-3.5.1.5
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382trypsin-3.4.21.4
68382acid phosphatase-3.1.3.2
68382alpha-galactosidase-3.2.1.22
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
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
18756-----++-+----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18756----++--------++---
119799+++++++-+-+-+-++----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18756---------+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8770unrefined solar salt
54531Unrefined solar salt
67770Unrefined solar saltNoda, Chiba Pref.JapanJPNAsia
119799Unrefined solar salt

isolation source categories

  • Cat1: #Condition
  • Cat2: #Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_6681.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1530;97_1826;98_4927;99_6681&stattab=map
  • Last taxonomy: Nesterenkonia
  • 16S sequence: X80747
  • Sequence Identity:
  • Total samples: 2426
  • soil counts: 126
  • aquatic counts: 234
  • animal counts: 1996
  • plant counts: 70

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
87701Risk group (German classification)
187561Risk group (German classification)
1197991Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: M.halobius 16S rDNA
  • accession: X80747
  • length: 1451
  • database: ena
  • NCBI tax ID: 37922

GC content

@refGC-contentmethod
877071.5
6777070fluorimetric
6777071.5thermal denaturation, midpoint method (Tm)

External links

@ref: 8770

culture collection no.: DSM 20541, ATCC 21727, CCM 2591, CCUG 38889, JCM 11483, BCRC 11656, CECT 5018, CGMCC 1.2323, CIP 81.68, IAM 13001, IFO 15353, IMET 11383, IMSNU 21325, KCTC 3518, LMG 14214, LMG 21452, MTCC 701, NBRC 15353, NCIMB 2204, VKM Ac-2256, VKM B-1317, VKM B-1421

straininfo link

  • @ref: 77205
  • straininfo: 9303

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9336934Polyphasic taxonomy of Nesterenkonia halobia.Mota RR, Marquez MC, Arahal DR, Mellado E, Ventosa AInt J Syst Bacteriol10.1099/00207713-47-4-12311997Base Composition, Cell Wall/chemistry, Culture Media/metabolism, DNA, Bacterial/*analysis, Micrococcaceae/chemistry/*classification/*genetics, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/*analysisGenetics
Phylogeny16110966[Study on isolation and systematic taxonomy of strains of genus Nesterenkonia].Chen HH, Li WJ, Zhang YQ, Wang D, Tang SKWei Sheng Wu Xue Bao2004Micrococcaceae/*classification/growth & development/*isolation & purification, PhylogenyEnzymology
Enzymology16345444Purification and Some Properties of an Extracellular Amylase from a Moderate Halophile, Micrococcus halobius.Onishi H, Sonoda KAppl Environ Microbiol10.1128/aem.38.4.616-620.19791979
Phylogeny18523178Nesterenkonia halophila sp. nov., a moderately halophilic, alkalitolerant actinobacterium isolated from a saline soil.Li WJ, Zhang YQ, Schumann P, Liu HY, Yu LY, Zhang YQ, Stackebrandt E, Xu LH, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.64226-02008Bacterial Typing Techniques, Base Sequence, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Hydrogen-Ion Concentration, Micrococcaceae/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/chemistry/genetics, Sequence Analysis, DNA, *Sodium Chloride, Soil/analysis, *Soil Microbiology, Species SpecificityGenetics
Metabolism18604501Cloning and characterization of the gene cluster for biosynthesis of ectoine from Nesterenkonia halobia DSM 20541.Zhang B, Bao X, Wang L, Yang SSJ Microbiol10.1007/s12275-008-0001-x2008Amino Acid Sequence, Amino Acids, Diamino/*biosynthesis/genetics, Bacteria/genetics, Bacterial Proteins/chemistry/*genetics/metabolism, Base Sequence, Chlorides/metabolism, *Cloning, Molecular, Escherichia coli/genetics/metabolism, Gene Expression, Micrococcaceae/chemistry/*genetics/*metabolism, Molecular Sequence Data, *Multigene Family, Osmotic Pressure, Sequence Analysis, DNA, Sequence Homology, Amino AcidEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8770Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20541)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20541
18756Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20541.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
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
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
37624Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11232
54531Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 38889)https://www.ccug.se/strain?id=38889
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
77205Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID9303.1StrainInfo: A central database for resolving microbial strain identifiers
119799Curators of the CIPCollection of Institut Pasteur (CIP 81.68)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2081.68