Strain identifier

BacDive ID: 88

Type strain: Yes

Species: Komagataeibacter xylinus

Strain history: CIP <- 2019, DSMZ <- 1988, NCIB <- 1949, NCTC <- 1933, G. Bertrand, sorbose bacterium, Acetobacter xylinus

NCBI tax ID(s): 1220579 (strain), 28448 (species)

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General

@ref: 2710

BacDive-ID: 88

DSM-Number: 6513

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

description: Komagataeibacter xylinus DSM 6513 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from mountains ash berries.

NCBI tax id

NCBI tax idMatching level
1220579strain
28448species

strain history

@refhistory
2710<- NCIMB <- NCTC <- G. Bertrand
67770NCIB 11664 <-- NCTC 4112 <-- G. Bertrand.
124001CIP <- 2019, DSMZ <- 1988, NCIB <- 1949, NCTC <- 1933, G. Bertrand, sorbose bacterium, Acetobacter xylinus

doi: 10.13145/bacdive88.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodospirillales
  • family: Acetobacteraceae
  • genus: Komagataeibacter
  • species: Komagataeibacter xylinus
  • full scientific name: Komagataeibacter xylinus (Brown 1886) Yamada et al. 2013

  • synonyms

    @refsynonym
    20215Komagatabacter xylinus
    20215Bacterium xylinum
    20215Acetobacter xylinus
    20215Gluconoacetobacter xylinus
    20215Acetobacter aceti subsp. xylinus
    20215Acetobacter xylinum
    20215Acetobacter aceti subsp. xylinum
    20215Gluconacetobacter xylinus

@ref: 2710

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Acetobacteraceae

genus: Komagataeibacter

species: Komagataeibacter xylinus

full scientific name: Komagataeibacter xylinus (Brown 1886) Yamada et al. 2013

type strain: yes

Morphology

cell morphology

  • @ref: 124001
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2710YPM MEDIUM (DSMZ Medium 360)yeshttps://mediadive.dsmz.de/medium/360Name: YPM MEDIUM (DSMZ Medium 360) Composition: Mannitol 25.0 g/l Agar 12.0 g/l Yeast extract 5.0 g/l Peptone 3.0 g/l Distilled water
2710GLUCONOBACTER 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
36961MEDIUM 1 - for Acetobacter, Azotobacter, Gluconobacter, Gluconacetobacter, Mesorhizodium ciceri and Pseudomonas doudoroffiiyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Yeast extract (5.000 g);Peptone (3.000 g);Mannitol (25.000 g)
38117MEDIUM 1 - for Acetobacter, Azotobacter, Gluconobacter, Gluconacetobacter, Mesorhizodium ciceri and Pseudomonas doudoroffiiyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Yeast extract (5.000 g);Peptone (3.000 g);Mannitol (25.000 g)
124001CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
124001CIP Medium 1yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=1

culture temp

@refgrowthtypetemperaturerange
2710positivegrowth28mesophilic
36961positivegrowth30mesophilic
38117positivegrowth30mesophilic
67770positivegrowth30mesophilic
124001positivegrowth22-30
124001nogrowth10psychrophilic
124001nogrowth37mesophilic
124001nogrowth41thermophilic
124001nogrowth45thermophilic

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
124001NaClpositivegrowth0 %
124001NaClnogrowth2 %
124001NaClnogrowth4 %
124001NaClnogrowth6 %
124001NaClnogrowth8 %
124001NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
124001606565hippurate-hydrolysis
12400117632nitrate-reduction
12400116301nitrite-reduction

antibiotic resistance

  • @ref: 124001
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 124001
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
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
124001oxidase-
124001beta-galactosidase-3.2.1.23
124001gelatinase-
124001catalase+1.11.1.6
124001gamma-glutamyltransferase-2.3.2.2
124001urease+3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
124001--+--------+--------

Isolation, sampling and environmental information

isolation

@refsample typeisolation date
2710mountains ash berries
67770Mountain ash berries
124001Plant, Mountain ash berries1896

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Shrub (Scrub)
#Host#Plants#Tree
#Host Body-Site#Plant#Fruit (Seed)

taxonmaps

  • @ref: 69479
  • File name: preview.99_79.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_29;96_64;97_67;98_72;99_79&stattab=map
  • Last taxonomy: Komagataeibacter
  • 16S sequence: X75619
  • Sequence Identity:
  • Total samples: 4067
  • soil counts: 662
  • aquatic counts: 523
  • animal counts: 2327
  • plant counts: 555

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
27101Risk group (German classification)
1240011Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Gluconacetobacter xylinus gene for 16S rRNA, partial sequence, strain: JCM 7644AB2052181445ena1234668
20218Gluconacetobacter xylinus gene for 16S rRNA, partial sequence, strain: JCM 7644AB6457371411ena1234668
20218Gluconacetobacter xylinus gene for 16S rRNA, partial sequence, strain: NBRC 15237AB6808151414ena28448
20218Gluconacetobacter xylinus strain LMG 1515 16S ribosomal RNA gene, partial sequenceJF7940131352ena28448
20218Gluconacetobacter xylinus strain LMG 1515T 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequenceKC478458790ena28448
20218Gluconacetobacter xylinus strain DSM 6513T 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequenceKC478459807ena28448
20218A.xylinum DNA for 16S-23S spacer region (NCIB 11664, LMG 1515 strain)X85405882ena28448
2710Gluconacetobacter xylinus gene for 16S rRNA, partial sequence, strain: NBRC 15237AB2052161393ena28448
2710A.xylinum gene for 16S ribosomal RNAX756191481ena28448

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Komagataeibacter xylinus NBRC 152371220579.3wgspatric1220579
66792Komagataeibacter xylinus strain LMG 151528448.11wgspatric28448
66792Komagataeibacter xylinus NBRC 152372731957626draftimg1220579
66792Komagataeibacter xylinus LMG 15152846462022draftimg28448
67770Komagataeibacter xylinus NBRC 15237GCA_001571345contigncbi1220579
67770Komagataeibacter xylinus LMG 1515GCA_003207915contigncbi28448

GC content

  • @ref: 67770
  • GC-content: 61.8
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno85.795no
gram-positiveno96.49no
anaerobicno97.995no
aerobicyes73.588no
halophileno92.509no
spore-formingno95.386no
glucose-utilyes91.288no
flagellatedno96.136no
thermophileno96.267yes
glucose-fermentno85.282no

External links

@ref: 2710

culture collection no.: DSM 6513, ATCC 23767, BCC 7226, JCM 7644, LMG 1515, NBRC 15237, NCIMB 11664, BCRC 12952, CCM 3611, CCUG 37299, CECT 7351, CIP 103107, IFO 15237, NCTC 4112, VTT E-97831

straininfo link

  • @ref: 69771
  • straininfo: 92679

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism30553964Bacterial cellulose production by Acetobacter xylinum ATCC 23767 using tobacco waste extract as culture medium.Ye J, Zheng S, Zhang Z, Yang F, Ma K, Feng Y, Zheng J, Mao D, Yang XBioresour Technol10.1016/j.biortech.2018.12.0282018Carbohydrate Metabolism, Carbon/metabolism, Cellulose/*metabolism, China, Culture Media, Fermentation, Gluconacetobacter xylinus/*metabolism, Spectroscopy, Fourier Transform Infrared, Tobacco/*metabolismCultivation
Metabolism31983038Genome sequencing and phylogenetic analysis of K1G4: a new Komagataeibacter strain producing bacterial cellulose from different carbon sources.La China S, Bezzecchi A, Moya F, Petroni G, Di Gregorio S, Gullo MBiotechnol Lett10.1007/s10529-020-02811-62020Acetobacteraceae/*classification/genetics/metabolism, Carbon/*metabolism, Cellulose/genetics/*metabolism, Genome Size, Glucose/metabolism, Glucosyltransferases/genetics, Glycerol/metabolism, Mannitol/metabolism, Operon, Phylogeny, Whole Genome Sequencing/*methodsPhylogeny
Phylogeny32756518Description of Komagataeibacter melaceti sp. nov. and Komagataeibacter melomenusus sp. nov. Isolated from Apple Cider Vinegar.Maric L, Cleenwerck I, Accetto T, Vandamme P, Trcek JMicroorganisms10.3390/microorganisms80811782020

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2710Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6513)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6513
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
36961Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/9598
38117Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14869
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/
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
69771Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92679.1StrainInfo: A central database for resolving microbial strain identifiers
124001Curators of the CIPCollection of Institut Pasteur (CIP 103107)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103107