Strain identifier

BacDive ID: 7787

Type strain: Yes

Species: Yaniella halotolerans

Strain history: DSM 15476 <-- W.-J. Li YIM 70085.

NCBI tax ID(s): 1123507 (strain), 225453 (species)

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General

@ref: 5946

BacDive-ID: 7787

DSM-Number: 15476

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

description: Yaniella halotolerans DSM 15476 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from saline soil.

NCBI tax id

NCBI tax idMatching level
1123507strain
225453species

strain history

@refhistory
5946<- W.-J. Li <- CCTCC <- YIM
67770DSM 15476 <-- W.-J. Li YIM 70085.

doi: 10.13145/bacdive7787.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Yaniella
  • species: Yaniella halotolerans
  • full scientific name: Yaniella halotolerans (Li et al. 2004) Li et al. 2008

  • synonyms

    • @ref: 20215
    • synonym: Yania halotolerans

@ref: 5946

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Yaniella

species: Yaniella halotolerans

full scientific name: Yaniella halotolerans (Li et al. 2004) Li et al. 2008 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30044positive0.55 µm0.55 µmcoccus-shapedno
69480no96.92
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
18392Signal yellow (1003)10-14 daysISP 2
18392Signal yellow (1003)10-14 daysISP 6

multicellular morphology

@refforms multicellular complexmedium name
18392noISP 2
18392noISP 6

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_15476_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15476_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15476_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15476_4.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5946MODIFIED ISP5 MEDIUM (DSMZ Medium 993b)yeshttps://mediadive.dsmz.de/medium/993bName: MODIFIED ISP5 MEDIUM (DSMZ Medium 993b) Composition: KCl 100.0 g/l Agar 20.0 g/l Glycerol 10.0 g/l Yeast extract 5.0 g/l L-Asparagine 1.0 g/l K2HPO4 1.0 g/l MnCl2 x 4 H2O 0.001 g/l ZnSO4 x 7 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water
18392ISP 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
18392ISP 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

culture temp

@refgrowthtypetemperaturerange
18392positiveoptimum28mesophilic
5946positivegrowth28mesophilic
30044positivegrowth10-40
30044positiveoptimum29mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepH
30044positivegrowth7.0-8.0
30044positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 30044
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30044no
69481no100
69480no99.992

halophily

  • @ref: 30044
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-25 %

murein

  • @ref: 5946
  • murein short key: A11.56
  • type: A4alpha L-Lys-Gly-L-Glu

observation

@refobservation
30044aggregates in clumps
67770quinones: MK-8, MK-9, MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3004422599arabinose+carbon source
3004417057cellobiose+carbon source
3004428757fructose+carbon source
3004428260galactose+carbon source
3004417234glucose+carbon source
3004417716lactose+carbon source
3004417306maltose+carbon source
3004429864mannitol+carbon source
3004437684mannose+carbon source
3004417992sucrose+carbon source
3004418222xylose+carbon source
3004417632nitrate+reduction
683794853esculin-hydrolysis
6837916199urea+hydrolysis
683795291gelatin-hydrolysis
6837917992sucrose-fermentation

metabolite production

  • @ref: 30044
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

@refvalueactivityec
30044catalase+1.11.1.6
30044urease+3.5.1.5
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
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
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

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
18392--+/------+--

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18392+++-++---++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5946saline soilXijiangChinaCHNAsia
67770Saline soilXinjiang ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_5355.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_2597;97_3180;98_3993;99_5355&stattab=map
  • Last taxonomy: Yaniella halotolerans
  • 16S sequence: AY228479
  • Sequence Identity:
  • Total samples: 4154
  • soil counts: 695
  • aquatic counts: 257
  • animal counts: 3070
  • plant counts: 132

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
59461Risk group (German classification)
183921German classification

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
5946Yania halophila strain YIM 70085 16S ribosomal RNA gene, partial sequenceAY2284791503ena225453
5946Yaniella halotolerans DSM 15476, whole genome shotgun sequencing projectATVQ000000006ena1123507

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Yaniella halotolerans DSM 154761123507.4wgspatric1123507
66792Yaniella halotolerans DSM 154762524614768draftimg1123507
67770Yaniella halotolerans DSM 15476GCA_000420805contigncbi1123507

GC content

@refGC-contentmethod
594653.5
6777055.6genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.778yes
flagellatedno97.352no
gram-positiveyes87.287no
anaerobicno99.126no
aerobicyes92.352yes
halophileyes75.617no
spore-formingno94.892yes
thermophileno98.684no
glucose-utilyes75.924no
glucose-fermentno90.341no

External links

@ref: 5946

culture collection no.: DSM 15476, CCTCC AA 001023, JCM 13527, YIM 70085, NBRC 107837

straininfo link

  • @ref: 77230
  • straininfo: 131438

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15023970Yania halotolerans gen. nov., sp. nov., a novel member of the suborder Micrococcineae from saline soil in China.Li WJ, Chen HH, Xu P, Zhang YQ, Schumann P, Tang SK, Xu LH, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.02875-02004Base Composition, Base Sequence, China, DNA, Bacterial/chemistry/genetics, Micrococcaceae/*classification/genetics/growth & development/isolation & purification, Molecular Sequence Data, Phylogeny, *Soil Microbiology, TemperatureGenetics
Phylogeny16166690Proposal of Yaniaceae fam. nov. and Yania flava sp. nov. and emended description of the genus Yania.Li WJ, Schumann P, Zhang YQ, Xu P, Chen GZ, Xu LH, Stackebrandt E, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.63594-02005Actinomycetales/chemistry/*classification/genetics/physiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny20382793Yaniella fodinae sp. nov., isolated from a coal mine.Dhanjal S, Ruckmani A, Cameotra SS, Pukall R, Klenk HP, Mayilraj SInt J Syst Evol Microbiol10.1099/ijs.0.020636-02010Actinomycetales/*classification/*isolation & purification, Base Composition, Carbohydrates/analysis, Cell Wall/chemistry, Cluster Analysis, Coal, Cytoplasm/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Peptidoglycan/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysisGenetics
Phylogeny20461464Yaniella soli sp. nov., a new actinobacterium isolated from non-saline forest soil in China.Chen YG, Chen J, Chen QH, Tang SK, Zhang YQ, He JW, Li WJ, Liu YQAntonie Van Leeuwenhoek10.1007/s10482-010-9453-12010Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis/genetics, DNA, Ribosomal/analysis/genetics, Genes, rRNA, Micrococcaceae/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride, *Soil Microbiology, Trees/*microbiologyGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
5946Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15476)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15476
18392Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM15476.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
30044Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2640528776041
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/
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
77230Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID131438.1StrainInfo: A central database for resolving microbial strain identifiers