Strain identifier

BacDive ID: 3806

Type strain: Yes

Species: Hymenobacter gelipurpurascens

Strain Designation: Tx g1 (MyxV2), Txg1

Strain history: CIP <- 2007, H.J. Busse, Veterin. Univ., Vienna, Austria: strain Txg1

NCBI tax ID(s): 1121956 (strain), 89968 (species)

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General

@ref: 4210

BacDive-ID: 3806

DSM-Number: 11116

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

description: Hymenobacter gelipurpurascens Tx g1 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
89968species
1121956strain

strain history

@refhistory
4210<- H. Reichenbach, Tx g1 (MyxV2)
378142007, H.J. Busse, Veterin. Univ., Vienna, Austria: strain Txg1
378152007, H.J. Busse, Veterin. Univ., Vienna, Austria: strain Myx 2105
119568CIP <- 2007, H.J. Busse, Veterin. Univ., Vienna, Austria: strain Txg1

doi: 10.13145/bacdive3806.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Hymenobacteraceae
  • genus: Hymenobacter
  • species: Hymenobacter gelipurpurascens
  • full scientific name: Hymenobacter gelipurpurascens Buczolits et al. 2006

@ref: 4210

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Hymenobacteraceae

genus: Hymenobacter

species: Hymenobacter gelipurpurascens

full scientific name: Hymenobacter gelipurpurascens Buczolits et al. 2006

strain designation: Tx g1 (MyxV2), Txg1

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.975
119568negativerod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4210R2A 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
37814MEDIUM 296 - for RhizobiumyesDistilled water make up to (800.000 ml);Agar (15.000 g);Yeast extract (1.000 g);Mannitol (10.000 g);Earth extract - M0541 (200.000 ml)
37815MEDIUM 296 - for RhizobiumyesDistilled water make up to (800.000 ml);Agar (15.000 g);Yeast extract (1.000 g);Mannitol (10.000 g);Earth extract - M0541 (200.000 ml)
119568CIP Medium 296yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=296

culture temp

@refgrowthtypetemperaturerange
4210positivegrowth30mesophilic
37814positivegrowth30mesophilic
37815positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119568
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.993

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11956817632nitrate+reduction
11956816301nitrite+reduction

metabolite production

  • @ref: 119568
  • 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
119568oxidase-
119568catalase+1.11.1.6
119568urease-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
119568-+++-+++-+++---+-+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
4210soilAlbertaCanadaCANNorth America
119568Environment, SoilAlbertaCanadaCANNorth America

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
42101Risk group (German classification)
1195681Risk group (French classification)

Sequence information

16S sequences

  • @ref: 4210
  • description: Hymenobacter gelipurpurascens 16S rRNA gene, type strain Txg1T
  • accession: Y18836
  • length: 1506
  • database: ena
  • NCBI tax ID: 89968

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Hymenobacter gelipurpurascens DSM 11116GCA_900187375scaffoldncbi89968
66792Hymenobacter gelipurpurascens strain DSM 1111689968.4wgspatric89968
66792Hymenobacter gelipurpurascens DSM 111162728369218draftimg89968

GC content

  • @ref: 4210
  • GC-content: 58.1
  • method: Buoyant density centrifugation (BD)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.867no
flagellatedno97.287no
gram-positiveno97.218no
anaerobicno99.568no
aerobicyes90.516no
halophileno93.735no
spore-formingno94.881no
thermophileno98.108yes
glucose-utilyes82.858no
glucose-fermentno89.348no

External links

@ref: 4210

culture collection no.: DSM 11116, LMG 21873, CIP 109676

straininfo link

  • @ref: 73318
  • straininfo: 49038

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16957101Proposal of Hymenobacter norwichensis sp. nov., classification of 'Taxeobacter ocellatus', 'Taxeobacter gelupurpurascens' and 'Taxeobacter chitinovorans' as Hymenobacter ocellatus sp. nov., Hymenobacter gelipurpurascens sp. nov. and Hymenobacter chitinivorans sp. nov., respectively, and emended description of the genus Hymenobacter Hirsch et al. 1999.Buczolits S, Denner EBM, Kampfer P, Busse HJInt J Syst Evol Microbiol10.1099/ijs.0.64371-02006Bacterial Typing Techniques, Cytophagaceae/chemistry/*classification/genetics, DNA, Bacterial/analysis, Fatty Acids/*analysis, Molecular Sequence Data, Polyamines/*analysis, RNA, Ribosomal, 16S/analysis/geneticsGenetics
Phylogeny32749954Hymenobacter fodinae sp. nov. and Hymenobacter metallicola sp. nov., isolated from abandoned lead-zinc mine.Feng GD, Zhang J, Chen W, Wang SN, Zhu HInt J Syst Evol Microbiol10.1099/ijsem.0.0043132020Bacterial Typing Techniques, Base Composition, China, Cytophagaceae/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lead, *Mining, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, ZincTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4210Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11116)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11116
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
37814Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7445
37815Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7448
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
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
73318Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49038.1StrainInfo: A central database for resolving microbial strain identifiers
119568Curators of the CIPCollection of Institut Pasteur (CIP 109676)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109676