Strain identifier

BacDive ID: 11083

Type strain: Yes

Species: Kribbella amoyensis

Strain history: <- Z. Xu, Lab. Microbial Pharmaceutical Eng., Xiamen Univ., China; XMU 198 <- Z. Lui

NCBI tax ID(s): 996641 (species)

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General

@ref: 17730

BacDive-ID: 11083

DSM-Number: 24683

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

description: Kribbella amoyensis DSM 24683 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from rhizosphere soil of the pharmaceutical plant Typhonium giganteum Engl..

NCBI tax id

  • NCBI tax id: 996641
  • Matching level: species

strain history

  • @ref: 17730
  • history: <- Z. Xu, Lab. Microbial Pharmaceutical Eng., Xiamen Univ., China; XMU 198 <- Z. Lui

doi: 10.13145/bacdive11083.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Kribbellaceae
  • genus: Kribbella
  • species: Kribbella amoyensis
  • full scientific name: Kribbella amoyensis Xu et al. 2012

@ref: 17730

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Kribbellaceae

genus: Kribbella

species: Kribbella amoyensis

full scientific name: Kribbella amoyensis Xu et al. 2012

type strain: yes

Morphology

cell morphology

  • @ref: 30314
  • gram stain: positive
  • motility: no

colony morphology

@refincubation periodcolony colormedium used
177303-7 days
69318Beige (1001)ISP 6
69318Ivory (1014)suter with tyrosine
69318Ivory (1014)suter without tyrosine
69318Ivory (1014), Light ivory (1015)ISP 2
69318Light ivory (1014)ISP 4
69318Light ivory (1014)ISP 5
69318Light ivory (1014)ISP 7
69318Light ivory (1015)ISP 3

multicellular morphology

@refforms multicellular complexcomplex namemedium namecomplex color
69318noAerial myceliumISP 2
69318yesAerial myceliumISP 3Cream (9001)
69318yesAerial myceliumISP 4Cream (9001)
69318yesAerial myceliumISP 5Signal white (9003)
69318noAerial myceliumISP 6
69318yesAerial myceliumISP 7Signal white (9003)
69318noAerial myceliumsuter with tyrosine
69318noAerial myceliumsuter without tyrosine

pigmentation

@refproductionname
30314yes
69318noMelanin
69318nosoluble pigment

multimedia

@refmultimedia contentcaptionintellectual property rights
69318DSM_24683_image3.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69318DSM_24683_image4.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17730GYM 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
17730R2A 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

culture temp

@refgrowthtypetemperaturerange
17730positivegrowth28mesophilic
30314positivegrowth10-37
30314positiveoptimum28mesophilic

culture pH

@refabilitytypepH
30314positivegrowth06-08
30314positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 30314
  • oxygen tolerance: aerobe

spore formation

  • @ref: 30314
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
30314NaClpositivegrowth<5 %
69318NaClpositivegrowth0-5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6931822599arabinose+growth
3031417234glucose+carbon source
3031429864mannitol+carbon source
3031437684mannose+carbon source
3031426546rhamnose+carbon source
3031430911sorbitol+carbon source
3031417992sucrose+carbon source
3031418222xylose+carbon source
6931862968cellulose-growth
6931828757fructose+growth
6931817234glucose+growth
6931817268inositol+growth
6931837684mannose+growth
6931816634raffinose+growth
6931826546rhamnose+growth
6931817992sucrose+growth
6931818222xylose+growth
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
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
68382alkaline phosphatase+3.1.3.1
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-mannosidase+3.2.1.24
68382alpha-fucosidase+3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69318++++-+----+--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69318++/-+/--++/-+/---+/-+/-+/-+-+/-+/-+/-++

Isolation, sampling and environmental information

isolation

  • @ref: 17730
  • sample type: rhizosphere soil of the pharmaceutical plant Typhonium giganteum Engl.
  • host species: Typhonium giganteum
  • geographic location: Fujian, Xiamen City
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

taxonmaps

  • @ref: 69479
  • File name: preview.99_118417.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_440;97_503;98_578;99_118417&stattab=map
  • Last taxonomy: Kribbella amoyensis
  • 16S sequence: HM368615
  • Sequence Identity:
  • Total samples: 111
  • soil counts: 100
  • aquatic counts: 2
  • plant counts: 9

Safety information

risk assessment

  • @ref: 17730
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17730
  • description: Kribbella amoyensis strain XMU 198 16S ribosomal RNA gene, partial sequence
  • accession: HM368615
  • length: 1420
  • database: ena
  • NCBI tax ID: 996641

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kribbella amoyensis DSM 24683GCA_007828865contigncbi996641
66792Kribbella amoyensis strain DSM 24683996641.3wgspatric996641
66792Kribbella amoyensis DSM 246832816332119draftimg996641

GC content

@refGC-contentmethod
1773069.3high performance liquid chromatography (HPLC)
3031469.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno92.254no
flagellatedno97.951yes
gram-positiveyes86.431no
anaerobicno99.204yes
halophileno94.101no
spore-formingyes90.763yes
thermophileno98.296yes
glucose-utilyes87.913no
aerobicyes90.699yes
glucose-fermentno90.361yes

External links

@ref: 17730

culture collection no.: DSM 24683, NBRC 107914, XMU 198

straininfo link

  • @ref: 80332
  • straininfo: 397999

literature

  • topic: Phylogeny
  • Pubmed-ID: 21705443
  • title: Kribbella amoyensis sp. nov., isolated from rhizosphere soil of a pharmaceutical plant, Typhonium giganteum Engl.
  • authors: Xu Z, Xu Q, Zheng Z, Huang Y
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.033290-0
  • year: 2011
  • mesh: Actinomycetales/*classification/genetics/*isolation & purification, Araceae/*microbiology, Bacterial Typing Techniques, Carbohydrates/analysis, China, Cluster Analysis, Cytosol/chemistry, DNA Gyrase/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, Plants, Medicinal/microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17730Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24683)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24683
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
30314Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2665528776041
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)
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69318Wink, J.https://cdn.dsmz.de/wink/DSM%2024683.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
80332Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID397999.1StrainInfo: A central database for resolving microbial strain identifiers