Strain identifier

BacDive ID: 58

Type strain: Yes

Species: Kozakia baliensis

Strain Designation: YO-3

Strain history: NRIC 0488 <-- P. Lisdiyanti Yo-3.

NCBI tax ID(s): 1307929 (strain), 153496 (species)

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General

@ref: 5337

BacDive-ID: 58

DSM-Number: 14400

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

description: Kozakia baliensis YO-3 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from palm brown sugar.

NCBI tax id

NCBI tax idMatching level
153496species
1307929strain

strain history

@refhistory
5337<- S. Okada; YO-3 <- P. Lisdiyanti <- Y. Yamada
67770NRIC 0488 <-- P. Lisdiyanti Yo-3.

doi: 10.13145/bacdive58.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodospirillales
  • family: Acetobacteraceae
  • genus: Kozakia
  • species: Kozakia baliensis
  • full scientific name: Kozakia baliensis Lisdiyanti et al. 2002

@ref: 5337

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Acetobacteraceae

genus: Kozakia

species: Kozakia baliensis

full scientific name: Kozakia baliensis Lisdiyanti et al. 2002

strain designation: YO-3

type strain: yes

Morphology

cell morphology

  • @ref: 23245
  • gram stain: negative
  • cell length: 2.0-3.0 µm
  • cell width: 0.6-0.8 µm
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5337GLUCONOBACTER OXYDANS MEDIUM (DSMZ Medium 105)yeshttps://mediadive.dsmz.de/medium/105Name: GLUCONOBACTER OXYDANS MEDIUM (DSMZ Medium 105) Composition: Glucose 100.0 g/l CaCO3 20.0 g/l Agar 15.0 g/l Yeast extract 10.0 g/l Distilled water
5337AG MEDIUM (DSMZ Medium 955)yeshttps://mediadive.dsmz.de/medium/955Name: AG MEDIUM (DSMZ Medium 955) Composition: Agar 15.0 g/l CaCO3 7.0 g/l Yeast extract 5.0 g/l Peptone 5.0 g/l Malt extract 2.0 g/l Glycerol 1.5 g/l Glucose 1.0 g/l Distilled water
23245AG mediumyes0.1% D-Glucose, 1.5% Glycerol, 0.5% Peptone, 0.5% Yeast Extract, 0.2% Malt Extract, 0.7% CaCO3 and 1.5% agar (w/v)

culture temp

@refgrowthtypetemperaturerange
5337positivegrowth28mesophilic
5337positivegrowth30mesophilic
23245positivegrowth30mesophilic
58344positivegrowth30mesophilic
67770positivegrowth30mesophilic

culture pH

  • @ref: 23245
  • ability: positive
  • type: growth
  • pH: 3
  • PH range: acidophile

Physiology and metabolism

tolerance

  • @ref: 23245
  • compound: Acetic acid
  • percentage: 0.35

oxygen tolerance

  • @ref: 23245
  • oxygen tolerance: obligate aerobe

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2324515824D-fructose-builds acid from
2324516899D-mannitol-builds acid from
2324517924D-sorbitol-builds acid from
2324516813galactitol-builds acid from
2324562345L-rhamnose-builds acid from
2324517266L-sorbose-builds acid from
2324517790methanol-growth
2324517632nitrate-reduction
2324512936D-galactose+builds acid from
2324517634D-glucose+builds acid from
2324516024D-mannose+builds acid from
2324565327D-xylose+builds acid from
2324516236ethanol+builds acid from
2324517754glycerol+builds acid from
2324530849L-arabinose+builds acid from
2324528053melibiose+builds acid from
2324516634raffinose+builds acid from
2324529864mannitol+growth
2324516236ethanol+oxidation
2324517108D-arabinose+/-builds acid from
2324517992sucrose+/-builds acid from
2324530089acetate+/-oxidation
2324524996lactate+/-oxidation

metabolite production

@refChebi-IDmetaboliteproduction
2324535581indoleno
2324516136hydrogen sulfideno
2324528938ammoniumno
23245114492,5-didehydro-D-gluconateno
2324516016dihydroxyacetoneyes
2324518391D-gluconateyes
2324530089acetateyes
23245174265-dehydro-D-gluconateyes
23245168082-dehydro-D-gluconateyes

enzymes

@refvalueactivityec
23245catalase+1.11.1.6
23245cytochrome oxidase-1.9.3.1
23245gelatinase-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment culture composition
5337palm brown sugarBaliIndonesiaIDNAsia
232451,0% D-Glucose, 0,5% Ethanol, 0,3% Acetic acid, 1,5% Peptone, 0,8% Yeast Extract and 100 p.p.m. Cycloheximide (w/v), and adjusted to pH 3,5 with HCl
58344Palm brown sugarBaliIndonesiaIDNAsia
67770Palm brown sugarBaliIndonesiaIDNAsia

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Tree

taxonmaps

  • @ref: 69479
  • File name: preview.99_1130.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_29;96_661;97_765;98_884;99_1130&stattab=map
  • Last taxonomy: Kozakia baliensis
  • 16S sequence: AB681100
  • Sequence Identity:
  • Total samples: 3525
  • soil counts: 1028
  • aquatic counts: 502
  • animal counts: 885
  • plant counts: 1110

Safety information

risk assessment

  • @ref: 5337
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Kozakia baliensis gene for 16S rRNA, partial sequence, strain: NBRC 16664AB6811001418ena153496
5337Kozakia baliensis gene for 16S rRNA, strain:Yo-3AB0563211415ena153496

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kozakia baliensis DSM 14400GCA_001787335completencbi153496
66792Kozakia baliensis strain DSM 14400153496.19plasmidpatric153496
66792Kozakia baliensis strain DSM 14400153496.12completepatric153496
66792Kozakia baliensis strain DSM 14400153496.18plasmidpatric153496
66792Kozakia baliensis strain DSM 14400153496.16plasmidpatric153496
66792Kozakia baliensis strain DSM 14400153496.20plasmidpatric153496
66792Kozakia baliensis strain DSM 14400153496.17plasmidpatric153496
66792Kozakia baliensis strain DSM 14400153496.15plasmidpatric153496
66792Kozakia baliensis strain NBRC 16664153496.32wgspatric153496
66792Kozakia baliensis DSM 144002718217748completeimg153496
67770Kozakia baliensis NBRC 16664GCA_007989365contigncbi153496

GC content

@refGC-contentmethod
533757.2
2324557.20
6777057.2high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno88.422yes
gram-positiveno96.592no
anaerobicno99.188yes
aerobicyes88.881yes
halophileno91.472no
spore-formingno93.958no
glucose-utilyes90.846no
thermophileno96.847yes
motileyes70.571yes
glucose-fermentno87.858no

External links

@ref: 5337

culture collection no.: DSM 14400, IFO 16664, JCM 11301, NBRC 16664, NRIC 0488, CCUG 48823, CCM 7137, NCIMB 14242

straininfo link

  • @ref: 69742
  • straininfo: 100709

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12054243Kozakia baliensis gen. nov., sp. nov., a novel acetic acid bacterium in the alpha-proteobacteria.Lisdiyanti P, Kawasaki H, Widyastuti Y, Saono S, Seki T, Yamada Y, Uchimura T, Komagata KInt J Syst Evol Microbiol10.1099/00207713-52-3-8132002Acetic Acid/*metabolism, Acetobacteraceae/*classification/*genetics/physiology, Alphaproteobacteria/classification/genetics/physiology, Bacterial Typing Techniques, Base Composition, DNA, Ribosomal/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Metabolism23399151Structural analysis of fructans produced by acetic acid bacteria reveals a relation to hydrocolloid function.Jakob F, Pfaff A, Novoa-Carballal R, Rubsam H, Becker T, Vogel RFCarbohydr Polym10.1016/j.carbpol.2012.10.0542012Acetic Acid/*metabolism, Acetobacteraceae/*metabolism, Colloids, Food Handling, Fructans/*biosynthesis/*chemistry/isolation & purification, Molecular Conformation, Molecular Weight, Structure-Activity RelationshipEnzymology
Metabolism27716345Dissection of exopolysaccharide biosynthesis in Kozakia baliensis.Brandt JU, Jakob F, Behr J, Geissler AJ, Vogel RFMicrob Cell Fact10.1186/s12934-016-0572-x2016Acetic Acid/*metabolism, Acetobacteraceae/*genetics/growth & development/*metabolism, Bacterial Proteins/genetics, Base Sequence, Cellulose/biosynthesis/genetics, Computer Simulation, DNA Transposable Elements, Fructans/biosynthesis, *Genome, Bacterial, Gluconacetobacter xylinus/genetics, Glycerol/metabolism, Mannitol/metabolism, Operon, Polysaccharides, Bacterial/*biosynthesis/chemistry/genetics, Sequence Analysis, DNA, Sucrose/metabolismGenetics
Metabolism28797225Environmentally triggered genomic plasticity and capsular polysaccharide formation are involved in increased ethanol and acetic acid tolerance in Kozakia baliensis NBRC 16680.Brandt JU, Born FL, Jakob F, Vogel RFBMC Microbiol10.1186/s12866-017-1070-y2017Acetic Acid/*metabolism, Acetobacteraceae/genetics/*metabolism, Bacterial Capsules/genetics/*metabolism, Ecosystem, Environment, Ethanol/*metabolism, Genomics, Phenotype, Polysaccharides/*biosynthesisGenetics
Biotechnology35631879Candidate Acetic Acid Bacteria Strains for Levan Production.Anguluri K, La China S, Brugnoli M, De Vero L, Pulvirenti A, Cassanelli S, Gullo MPolymers (Basel)10.3390/polym141020002022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5337Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14400)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14400
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
23245Puspita Lisdiyanti, Hiroko Kawasaki, Yantyati Widyastuti, Susono Saono, Tatsuji Seki, Yuzo Yamada, Tai Uchimura, Kazuo Komagata10.1099/00207713-52-3-813Kozakia baliensis gen. nov., sp. nov., a novel acetic acid bacterium in the alpha-proteobacteria.IJSEM 52: 813-818 200212054243
58344Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 48823)https://www.ccug.se/strain?id=48823
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
69742Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100709.1StrainInfo: A central database for resolving microbial strain identifiers