Strain identifier

BacDive ID: 3805

Type strain: Yes

Species: Hymenobacter chitinivorans

Strain Designation: Tx c1 (MyxT299,M6), Tx c1 (MyxT299;M6), Txc1

Strain history: CIP <- 2007, H.J. Busse, Veterin. Univ., Vienna, Austria: strain Txc1

NCBI tax ID(s): 1121954 (strain), 89969 (species)

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General

@ref: 4209

BacDive-ID: 3805

DSM-Number: 11115

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

description: Hymenobacter chitinivorans Tx c1 (MyxT299 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
89969species
1121954strain

strain history

@refhistory
4209<- H. Reichenbach, Tx c1 (MyxT299;M6)
364282007, H.J. Busse, Veterin. Univ., Vienna, Austria: strain Txc1
118236CIP <- 2007, H.J. Busse, Veterin. Univ., Vienna, Austria: strain Txc1

doi: 10.13145/bacdive3805.20230509.8.1

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 chitinivorans
  • full scientific name: Hymenobacter chitinivorans Buczolits et al. 2006

@ref: 4209

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Hymenobacteraceae

genus: Hymenobacter

species: Hymenobacter chitinivorans

full scientific name: Hymenobacter chitinivorans Buczolits et al. 2006

strain designation: Tx c1 (MyxT299,M6), Tx c1 (MyxT299;M6), Txc1

type strain: yes

Morphology

cell morphology

  • @ref: 118236
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4209R2A 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
36428MEDIUM 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)
118236CIP Medium 296yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=296

culture temp

@refgrowthtypetemperaturerange
4209positivegrowth30mesophilic
36428positivegrowth30mesophilic

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11823617632nitrate-reduction
11823616301nitrite-reduction

metabolite production

  • @ref: 118236
  • 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
118236oxidase-
118236catalase+1.11.1.6
118236urease+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
118236-+++-+++--++----++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
4209soilCreteGreeceGRCEurope
118236Environment, SoilCreteGreeceGRCEurope

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
42091Risk group (German classification)
1182361Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Hymenobacter chitinivorans 16S rRNA gene, type strain Txc1T
  • accession: Y18837
  • length: 1507
  • database: ena
  • NCBI tax ID: 89969

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Hymenobacter chitinivorans DSM 11115GCA_002797555contigncbi1121954
66792Hymenobacter chitinivorans DSM 111151121954.3wgspatric1121954
66792Hymenobacter chitinivorans DSM 111152731639182draftimg89969

GC content

  • @ref: 4209
  • GC-content: 61.5
  • method: Buoyant density centrifugation (BD)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno92.597no
flagellatedno95.631no
gram-positiveno96.707no
anaerobicno99.517no
halophileno94.05no
spore-formingno92.947no
thermophileno99.143yes
glucose-utilyes78.251no
aerobicyes90.924no
glucose-fermentno90.675no

External links

@ref: 4209

culture collection no.: DSM 11115, LMG 21951, CIP 109677

straininfo link

  • @ref: 73317
  • straininfo: 49037

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
4209Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11115)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11115
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
36428Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7446
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
73317Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49037.1StrainInfo: A central database for resolving microbial strain identifiers
118236Curators of the CIPCollection of Institut Pasteur (CIP 109677)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109677