Strain identifier

BacDive ID: 7508

Type strain: No

Species: Amnibacterium kyonggiense

Strain Designation: KSL51201-037

Strain history: S.-S. Lee KSL51201-037.

NCBI tax ID(s): 595671 (species)

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General

@ref: 17770

BacDive-ID: 7508

DSM-Number: 24782

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

description: Amnibacterium kyonggiense KSL51201-037 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from Anyang stream.

NCBI tax id

  • NCBI tax id: 595671
  • Matching level: species

strain history

@refhistory
17770<- JCM <- S.-S. Lee; Graduate School of Kyonggi University; KSL51201-037
67770S.-S. Lee KSL51201-037.

doi: 10.13145/bacdive7508.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Amnibacterium
  • species: Amnibacterium kyonggiense
  • full scientific name: Amnibacterium kyonggiense Kim and Lee 2011

@ref: 17770

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Amnibacterium

species: Amnibacterium kyonggiense

full scientific name: Amnibacterium kyonggiense Kim and Lee 2011

strain designation: KSL51201-037

type strain: no

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29690positive0.275 µm0.175 µmrod-shapedno
69480no93.286
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
21380Lemon yellow (1012)10-14 daysISP 2
21380n.d.10-14 daysISP 3
21380none10-14 daysISP 4
21380none10-14 daysISP 5
21380none10-14 daysISP 7
21380none10-14 daysSuter with tyrosine
21380none10-14 daysSuter without tyrosine

multicellular morphology

@refforms multicellular complexmedium name
21380noISP 2
21380noISP 3
21380noISP 4
21380noISP 5
21380noISP 7
21380noSuter with tyrosine
21380noSuter without tyrosine

pigmentation

  • @ref: 29690
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17770R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
21380ISP 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
21380ISP 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:
21380ISP 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
21380ISP 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
21380ISP 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
21380Suter 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
21380Suter 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
17770positivegrowth28mesophilic
29690positivegrowth10-37
29690positiveoptimum30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepH
29690positivegrowth5.0-8.0
29690positiveoptimum6

Physiology and metabolism

oxygen tolerance

  • @ref: 29690
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
21380NaClpositivegrowth0 %
29690NaClpositivegrowth0-2 %

observation

@refobservation
29690aggregates in clumps
67770quinones: MK-11, MK-12

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2138017234glucose-
2138022599arabinose-
2138017992sucrose-
2138018222xylose-
2138017268myo-inositol-
2138037684mannose-
2138028757fructose-
2138026546rhamnose-
2138016634raffinose-
2138062968cellulose-
296904853esculin+hydrolysis
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
29690acid phosphatase+3.1.3.2
29690alpha-galactosidase+3.2.1.22
29690catalase+1.11.1.6
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
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
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
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

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
21380--------+----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
21380+/-++-++/-+/---+++--+/-++--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
17770Anyang streamRepublic of KoreaKORAsia
67770Anyang streamRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #River (Creek)

Safety information

risk assessment

  • @ref: 17770
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17770
  • description: Amnibacterium kyonggiense 16S ribosomal RNA gene, partial sequence
  • accession: FJ527819
  • length: 1459
  • database: ena
  • NCBI tax ID: 595671

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Amnibacterium kyonggiense strain DSM 24782595671.3wgspatric595671
66792Amnibacterium kyonggiense DSM 247822734482167draftimg595671
67770Amnibacterium kyonggiense DSM 24782GCA_004364555contigncbi595671

GC content

@refGC-contentmethod
1777072.7high performance liquid chromatography (HPLC)
2969072.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
gram-positiveyes90.647no
anaerobicno99.429yes
halophileno94.048no
spore-formingno93.638no
glucose-utilyes78.244yes
thermophileno99.489no
flagellatedno95.477yes
aerobicyes89.811yes
motileno63.609yes
glucose-fermentno89.039yes

External links

@ref: 17770

culture collection no.: DSM 24782, JCM 16463, KEMC 51201-037, KACC 15557, NBRC 109360

straininfo link

  • @ref: 76954
  • straininfo: 401682

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20173001Amnibacterium kyonggiense gen. nov., sp. nov., a new member of the family Microbacteriaceae.Kim SJ, Lee SSInt J Syst Evol Microbiol10.1099/ijs.0.018788-02010Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Aminobutyrates/analysis, Base Composition, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Korea, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analysisGenetics
Phylogeny23203625Naasia aerilata gen. nov., sp. nov., a member of the family Microbacteriaceae isolated from air.Weon HY, Kim SJ, Jang YH, Hamada M, Tamura T, Ahn JH, Suzuki KI, Kwon SWInt J Syst Evol Microbiol10.1099/ijs.0.046599-02012Actinomycetales/*classification/genetics/isolation & purification, *Air Microbiology, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Peptidoglycan/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analysisGenetics
Phylogeny23990652Amnibacterium soli sp. nov., an actinobacterium isolated from grass soil.Jin L, Lee HG, Kim HS, Ahn CY, Oh HMInt J Syst Evol Microbiol10.1099/ijs.0.052506-02013Actinobacteria/*classification/genetics/isolation & purification, Aminobutyrates/chemistry, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Poaceae/*microbiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistryGenetics
Phylogeny29498617Amnibacterium endophyticum sp. nov., an endophytic actinobacterium isolated from Aegiceras corniculatum.Li FN, Tuo L, Lee SM, Jin T, Liao S, Li W, Yan X, Sun CHInt J Syst Evol Microbiol10.1099/ijsem.0.0026762018Actinomycetales/*classification/genetics/isolation & purification, Aminobutyrates/chemistry, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Phospholipids/chemistry, *Phylogeny, Primulaceae/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome
Phylogeny30511915Amnibacterium flavum sp. nov., a novel endophytic actinobacterium isolated from bark of Nerium indicum Mill.Tuo L, Yan XR, Li FN, Yang C, An MB, Sun CHInt J Syst Evol Microbiol10.1099/ijsem.0.0031562018Actinomycetales/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Nerium/*microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Bark/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome
Phylogeny31332634Amnibacterium setariae sp. nov., an endophytic actinobacterium isolated from dried foxtail.Kim I, Chhetri G, Kim J, Seo TAntonie Van Leeuwenhoek10.1007/s10482-019-01302-72019Actinobacteria/*classification/genetics/*isolation & purification, Aerobiosis, Base Composition, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Endophytes/*classification/genetics/*isolation & purification, Fatty Acids/analysis, Glycolipids/analysis, Locomotion, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phospholipids/analysis, Phylogeny, Pigments, Biological/analysis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Setaria Plant/*microbiologyEnzymology
Phylogeny31738159Naasia lichenicola sp. nov., an actinobacterium isolated from lichen.Jiang LQ, Zhang K, Li GD, Wang XY, Shi SB, Li QY, An DF, Lang L, Wang LS, Jiang CL, Jiang YInt J Syst Evol Microbiol10.1099/ijsem.0.0038652020Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Germany, Lichens/*microbiology, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17770Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24782)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24782
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
21380Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM24782.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
29690Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2607528776041
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)
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
76954Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID401682.1StrainInfo: A central database for resolving microbial strain identifiers