Strain identifier

BacDive ID: 3931

Type strain: Yes

Species: Yimella lutea

Strain history: <- SK Tang, Yunnan Inst. Microbiol., China

NCBI tax ID(s): 587872 (species)

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General

@ref: 8337

BacDive-ID: 3931

DSM-Number: 19828

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

description: Yimella lutea DSM 19828 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from contaminated agar plate.

NCBI tax id

  • NCBI tax id: 587872
  • Matching level: species

strain history

@refhistory
8337<- S.-K. Tang, YIM; YIM 45900
67770KCTC 19231 <-- S.-K. Tang YIM 45900.
67771<- SK Tang, Yunnan Inst. Microbiol., China

doi: 10.13145/bacdive3931.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Dermacoccaceae
  • genus: Yimella
  • species: Yimella lutea
  • full scientific name: Yimella lutea Tang et al. 2010

@ref: 8337

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Dermacoccaceae

genus: Yimella

species: Yimella lutea

full scientific name: Yimella lutea Tang et al. 2010

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29477positive1.55 µm0.8 µmcoccus-shapedno
67771positive
69480no96.005
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
19787Corn yellow (1006)10-14 daysISP 2
19787Beige (1001)10-14 daysISP 3
19787Light ivory (1015)10-14 daysISP 4
19787Golden yellow (1004)10-14 daysISP 5
19787Golden yellow (1004)10-14 daysISP 6
19787Dahlia yellow (1033)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19787noISP 2
19787noISP 3
19787noISP 4
19787noISP 5
19787noISP 6
19787noISP 7

pigmentation

  • @ref: 29477
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8337COLUMBIA 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
8337GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
19787ISP 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
19787ISP 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:
19787ISP 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
19787ISP 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
19787ISP 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
19787ISP 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

culture temp

@refgrowthtypetemperaturerange
8337positivegrowth28mesophilic
19787positiveoptimum28mesophilic
29477positivegrowth22-42
29477positiveoptimum28mesophilic
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
29477positivegrowth05-09alkaliphile
29477positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29477aerobe
67771aerobe

spore formation

@refspore formationconfidence
29477no
69481no96
69480no99.988

halophily

@refsaltgrowthtested relationconcentration
29477NaClpositivegrowth0-8 %
29477NaClpositiveoptimum0.5 %

murein

  • @ref: 8337
  • murein short key: A11.36
  • type: A4alpha L-Lys-L-Ser-D-Asp

observation

@refobservation
29477aggregates in clumps
67770quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1978762968cellulose-
1978716634raffinose-
1978726546rhamnose-
1978728757fructose+
1978729864mannitol+
1978717268myo-inositol-
1978718222xylose-
1978717992sucrose+
1978722599arabinose-
1978717234glucose+
2947730089acetate+carbon source
2947729016arginine+carbon source
2947728757fructose+carbon source
2947717234glucose+carbon source
2947717754glycerol+carbon source
2947715428glycine+carbon source
2947727570histidine+carbon source
2947717306maltose+carbon source
2947737684mannose+carbon source
2947717272propionate+carbon source
2947715361pyruvate+carbon source
2947733942ribose+carbon source
2947717992sucrose+carbon source
2947727082trehalose+carbon source
2947753423tween 40+carbon source
2947753426tween 80+carbon source
2947716704uridine+carbon source
2947718222xylose+carbon source
2947717632nitrate+reduction

enzymes

@refvalueactivityec
29477alkaline phosphatase+3.1.3.1
29477catalase+1.11.1.6
29477gelatinase+
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
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19787+++-++---++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8337contaminated agar plateYannan ProvinceChinaCHNAsia
67770Contaminated agar plate in the laboratory of Yunnan Institute of MicrobiologyChinaCHNAsia
67771From contaminated plateXinjiang ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Engineered#Laboratory#Lab enrichment

taxonmaps

  • @ref: 69479
  • File name: preview.99_33605.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_8956;97_10766;98_24869;99_33605&stattab=map
  • Last taxonomy: Yimella lutea subclade
  • 16S sequence: FJ528304
  • Sequence Identity:
  • Total samples: 2480
  • soil counts: 124
  • aquatic counts: 241
  • animal counts: 2048
  • plant counts: 67

Safety information

risk assessment

  • @ref: 8337
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8337
  • description: Yimella lutea strain YIM 45900 16S ribosomal RNA gene, partial sequence
  • accession: FJ528304
  • length: 1444
  • database: ena
  • NCBI tax ID: 587872

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Yimella lutea strain DSM 19828587872.3wgspatric587872
66792Yimella lutea DSM 198282806310639draftimg587872
67770Yimella lutea DSM 19828GCA_006715095contigncbi587872

GC content

@refGC-contentmethod
833765.8
6777065.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno96no
gram-positiveyes92.248yes
anaerobicno98.143yes
halophileno94.355yes
spore-formingno86.603yes
glucose-utilyes91.636no
thermophileno97.804no
flagellatedno98.198yes
aerobicyes88.336no
motileno96.867yes
glucose-fermentno89.981no

External links

@ref: 8337

culture collection no.: DSM 19828, CCTCC AB 207007, KCTC 19231, YIM 45900, JCM 16960

straininfo link

  • @ref: 73441
  • straininfo: 400760

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19656924Yimella lutea gen. nov., sp. nov., a novel actinobacterium of the family Dermacoccaceae.Tang SK, Wu JY, Wang Y, Schumann P, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.013920-02009Actinobacteria/*classification/genetics/*isolation & purification/metabolism, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny20562243Branchiibius hedensis gen. nov., sp. nov., an actinobacterium isolated from a Japanese codling (Physiculus japonicus).Sugimoto S, Kato T, Ito M, Sakata N, Tsuchida T, Matsumoto A, Takahashi YInt J Syst Evol Microbiol10.1099/ijs.0.023648-02010Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Animals, Base Composition, DNA, Bacterial/genetics, Fatty Acids/metabolism, Gadiformes/*microbiology, Japan, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny27469463Yimella radicis sp. nov., an endophytic actinobacterium isolated from the root of Paris polyphylla Smith var. yunnanensis.Yang LL, Jiang Z, Tang SK, Chu X, Xu LH, Zhi XYInt J Syst Evol Microbiol10.1099/ijsem.0.0013342016Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry, Melanthiaceae/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny28629492Calidifontibacter terrae sp. nov., an actinomycete isolated from soil, with potential applications in cosmetics.Dahal RH, Shim DS, Kim JY, Kim JInt J Syst Evol Microbiol10.1099/ijsem.0.0018932017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8337Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19828)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19828
19787Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM19828.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
29477Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2587928776041
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
73441Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID400760.1StrainInfo: A central database for resolving microbial strain identifiers