Strain identifier

BacDive ID: 13270

Type strain: Yes

Species: Haloechinothrix halophila

Strain history: S.-K. Tang YIM 93223.

NCBI tax ID(s): 592678 (strain), 1069073 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 15796

BacDive-ID: 13270

DSM-Number: 45216

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive

description: Haloechinothrix halophila DSM 45216 is an aerobe, spore-forming, mesophilic bacterium that was isolated from salt lake.

NCBI tax id

NCBI tax idMatching level
592678strain
1069073species

strain history

@refhistory
15796<- S.-K. Tang, YIM; YIM 93223
67770S.-K. Tang YIM 93223.

doi: 10.13145/bacdive13270.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Haloechinothrix
  • species: Haloechinothrix halophila
  • full scientific name: Haloechinothrix halophila (Tang et al. 2010) Nouioui et al. 2018

  • synonyms

    • @ref: 20215
    • synonym: Amycolatopsis halophila

@ref: 15796

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Haloechinothrix

species: Haloechinothrix halophila

full scientific name: Haloechinothrix halophila (Tang et al. 2010) Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
29403positive
69480no92.355
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
21392Sand yellow (1002)10-14 daysISP 2
21392Light ivory (1015)10-14 daysISP 3
21392Light ivory (1015)10-14 daysISP 4
21392Light ivory (1015) - Ivory (1014)10-14 daysISP 5
21392Ivory (1014) - Brown beige (1011)10-14 daysISP 7
21392Dahlia yellow (1033)10-14 daysSuter with tyrosine
21392Dahlia yellow (1033)10-14 daysSuter without tyrosine

multicellular morphology

@refforms multicellular complexmedium name
21392noISP 2
21392noISP 3
21392noISP 4
21392noISP 5
21392noISP 7
21392noSuter with tyrosine
21392noSuter without tyrosine

multimedia

  • @ref: 15796
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45216.jpg
  • caption: Medium 514 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15796BACTO 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
21392ISP 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
21392ISP 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:
21392ISP 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
21392ISP 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
21392ISP 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
21392Suter with tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
21392Suter without tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes

culture temp

@refgrowthtypetemperaturerange
15796positivegrowth37mesophilic
29403positivegrowth25-45
29403positiveoptimum37mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepH
29403positivegrowth06-08
29403positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 29403
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
29403yes
69480yes92.398

halophily

@refsaltgrowthtested relationconcentration
21392NaClpositivemaximum5 %
29403NaClpositivegrowth01-15 %
29403NaClpositiveoptimum5 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2139222599arabinose-
2139217992sucrose-
2139218222xylose-
2139217268myo-inositol-
2139237684mannose-
2139228757fructose-
2139226546rhamnose-
2139216634raffinose-
2139262968cellulose+
2940328260galactose+carbon source
2940317754glycerol+carbon source
2940316634raffinose+carbon source
2940326546rhamnose+carbon source
2940327082trehalose+carbon source
2940353258sodium citrate+carbon source
2940317151xylitol+carbon source
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

enzymes

@refvalueactivityec
29403alkaline phosphatase+3.1.3.1
29403gelatinase+
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
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
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
21392-+/-++---+-++--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
21392+++++++--++-----+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15796salt lakeXinjiang ProvinceChinaCHNAsia
67770Soil from a salt lake (Qijiaojing Lake)Xinjiang Province, north-west ChinaChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Lake (large)
#Condition#Saline

Safety information

risk assessment

  • @ref: 15796
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15796
  • description: Amycolatopsis halophila YIM 93223 16S ribosomal RNA gene, partial sequence
  • accession: FJ606836
  • length: 1530
  • database: ena
  • NCBI tax ID: 592678

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Amycolatopsis halophila YIM 93223592678.3wgspatric592678
66792Haloechinothrix halophila YIM 932232512564011draftimg592678
67770Haloechinothrix halophila YIM 93223GCA_000504245scaffoldncbi592678

GC content

@refGC-contentmethod
1579666.1high performance liquid chromatography (HPLC)
2940366.1
6777067.8genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes80no
gram-positiveyes85.856no
anaerobicno98.651no
halophileyes63.446no
spore-formingyes52.743no
glucose-utilyes87.789no
thermophileno94.917yes
flagellatedno98.244no
aerobicyes89.156yes
motileno92.61no
glucose-fermentno92.655no

External links

@ref: 15796

culture collection no.: DSM 45216, KCTC 19403, YIM 93223, JCM 18118

straininfo link

  • @ref: 82474
  • straininfo: 404701

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19666809Amycolatopsis halophila sp. nov., a halophilic actinomycete isolated from a salt lake.Tang SK, Wang Y, Guan TW, Lee JC, Kim CJ, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.012427-02009Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Fresh Water/chemistry/*microbiology, Genes, rRNA, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, Species SpecificityGenetics
Phylogeny21317279Amycolatopsis salitolerans sp. nov., a filamentous actinomycete isolated from a hypersaline habitat.Guan TW, Xia ZF, Tang SK, Wu N, Chen ZJ, Huang Y, Ruan JS, Li WJ, Zhang LLInt J Syst Evol Microbiol10.1099/ijs.0.030031-02011Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, *Environmental Microbiology, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysisGenetics
30319584Revisiting the Taxonomic Status of the Biomedically and Industrially Important Genus Amycolatopsis, Using a Phylogenomic Approach.Sangal V, Goodfellow M, Blom J, Tan GYA, Klenk HP, Sutcliffe ICFront Microbiol10.3389/fmicb.2018.022812018

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15796Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45216)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45216
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
21392Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45216.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
29403Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2581028776041
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/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
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)
82474Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID404701.1StrainInfo: A central database for resolving microbial strain identifiers