Strain identifier

BacDive ID: 13563

Type strain: Yes

Species: Kaistia adipata

Strain Designation: CHj 404

Strain history: CIP <- 2005, IAM <- S.T. Lee

NCBI tax ID(s): 1122131 (strain), 166954 (species)

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General

@ref: 7199

BacDive-ID: 13563

DSM-Number: 17808

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative

description: Kaistia adipata CHj 404 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil .

NCBI tax id

NCBI tax idMatching level
166954species
1122131strain

strain history

@refhistory
7199<- S.-T. Lee, KAIST; CHj 404 <- H.-S. Bae
67771<- ST Lee, KAIST
116045CIP <- 2005, IAM <- S.T. Lee

doi: 10.13145/bacdive13563.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Kaistiaceae
  • genus: Kaistia
  • species: Kaistia adipata
  • full scientific name: Kaistia adipata Im et al. 2005

@ref: 7199

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Kaistiaceae

genus: Kaistia

species: Kaistia adipata

full scientific name: Kaistia adipata Im et al. 2005

strain designation: CHj 404

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
67771negative
69480negative99.976
116045negativecoccus-shapedno

colony morphology

  • @ref: 116045
  • hemolysis ability: 1

pigmentation

  • @ref: 116045
  • production: no
  • name: Flexirubin

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_17808_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_17808_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_17808_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_17808_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_17808_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7199NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
33991MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116045CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7199positivegrowth28mesophilic
33991positivegrowth37mesophilic
67771positivegrowth30-37mesophilic
116045positivegrowth15-37
116045nogrowth5psychrophilic
116045nogrowth41thermophilic
116045nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
67771aerobe
116045obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.997

halophily

  • @ref: 116045
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

observation

  • @ref: 67771
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11604516947citrate-carbon source
1160454853esculin+hydrolysis
116045606565hippurate+hydrolysis
11604517632nitrate-builds gas from
11604517632nitrate+reduction
11604516301nitrite-builds gas from
11604516301nitrite-reduction
11604515792malonate-assimilation
11604517234glucose+degradation

metabolite production

  • @ref: 116045
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11604515688acetoin-
11604517234glucose+

enzymes

@refvalueactivityec
116045oxidase-
116045beta-galactosidase-3.2.1.23
116045alcohol dehydrogenase-1.1.1.1
116045gelatinase+/-
116045amylase-
116045DNase+
116045caseinase-3.4.21.50
116045catalase+1.11.1.6
116045tween esterase-
116045gamma-glutamyltransferase-2.3.2.2
116045lecithinase-
116045lipase+
116045lysine decarboxylase-4.1.1.18
116045ornithine decarboxylase-4.1.1.17
116045phenylalanine ammonia-lyase-4.3.1.24
116045tryptophan deaminase-
116045urease+3.5.1.5
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 zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116045-++--++---++---++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7199soil (sediment)near the Chung-Ju industrial complexRepublic of KoreaKORAsia
67771From soilRepublic of KoreaKORAsia
116045Environment, Soil sample collected in an industrial streamNear the Chung-Ju industrial complexRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Sediment
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_51541.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_3060;97_4363;98_5583;99_51541&stattab=map
  • Last taxonomy: Kaistia
  • 16S sequence: AY039817
  • Sequence Identity:
  • Total samples: 322
  • soil counts: 137
  • aquatic counts: 67
  • animal counts: 74
  • plant counts: 44

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
71991Risk group (German classification)
1160451Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7199
  • description: Kaistia adipata 16S ribosomal RNA gene, complete sequence
  • accession: AY039817
  • length: 1413
  • database: ena
  • NCBI tax ID: 166954

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kaistia adipata DSM 17808GCA_000423225scaffoldncbi1122131
66792Kaistia adipata DSM 178081122131.7wgspatric1122131
66792Kaistia adipata DSM 178082524614770draftimg1122131

GC content

  • @ref: 7199
  • GC-content: 67.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno90.902no
flagellatedno97.434no
gram-positiveno97.196yes
anaerobicno98.864yes
aerobicyes90.383yes
halophileno91.674no
spore-formingno96.777no
glucose-utilyes91.639no
thermophileno97.668yes
glucose-fermentno90.741no

External links

@ref: 7199

culture collection no.: DSM 17808, IAM 15023, JCM 21486, KCTC 12095, CIP 108816

straininfo link

  • @ref: 82751
  • straininfo: 107095

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15747229Kaistia adipata gen. nov., sp. nov., a novel alpha-proteobacterium.Im WT, Yokota A, Kim MK, Lee STJ Gen Appl Microbiol10.2323/jgam.50.2492004Alphaproteobacteria/*classification, Base Sequence, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny21131499Kaistia geumhonensis sp. nov. and Kaistia dalseonensis sp. nov., two members of the class Alphaproteobacteria.Jin L, Kim KK, Baek SH, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.028894-02010Base Composition, DNA, Bacterial/genetics, Fatty Acids/metabolism, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobiaceae/*classification/genetics/*isolation & purification/metabolism, Rivers/*microbiologyMetabolism
Phylogeny22247212Kaistia defluvii sp. nov., isolated from river sediment.Jin L, Kim KK, Lee HG, Ahn CY, Oh HMInt J Syst Evol Microbiol10.1099/ijs.0.038687-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhizobiaceae/*classification/genetics/isolation & purification, Rivers/*microbiology, Sequence Analysis, DNA, Sewage/microbiology, Ubiquinone/analogs & derivatives/analysisGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7199Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17808)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17808
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
33991Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6487
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 life 35: 676-683 201728604660
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
82751Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID107095.1StrainInfo: A central database for resolving microbial strain identifiers
116045Curators of the CIPCollection of Institut Pasteur (CIP 108816)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108816