Strain identifier

BacDive ID: 3807

Type strain: Yes

Species: Hymenobacter ocellatus

Strain Designation: Txo1

Strain history: CIP <- 2007, H.J. Busse, Veterin. Univ., Vienna, Austria: strain Myx 2105

NCBI tax ID(s): 36878 (species)

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General

@ref: 4211

BacDive-ID: 3807

DSM-Number: 11117

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

description: Hymenobacter ocellatus Txo1 is a mesophilic, Gram-negative, oval-shaped bacterium that was isolated from dung of antelope.

NCBI tax id

  • NCBI tax id: 36878
  • Matching level: species

strain history

@refhistory
4211<- H. Reichenbach, Tx o1 (Myx 2105)
121383CIP <- 2007, H.J. Busse, Veterin. Univ., Vienna, Austria: strain Myx 2105

doi: 10.13145/bacdive3807.20230509.8.1

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

  • synonyms

    • @ref: 20215
    • synonym: Parahymenobacter ocellatus

@ref: 4211

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Hymenobacteraceae

genus: Hymenobacter

species: Hymenobacter ocellatus

full scientific name: Hymenobacter ocellatus Buczolits et al. 2006

strain designation: Txo1

type strain: yes

Morphology

cell morphology

  • @ref: 121383
  • gram stain: negative
  • cell shape: oval-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4211R2A 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
4211CY-AGAR (DSMZ Medium 67)yeshttps://mediadive.dsmz.de/medium/67Name: CY-AGAR (DSMZ Medium 67) Composition: Agar 15.0 g/l Casitone 3.0 g/l CaCl2 x 2 H2O 1.36 g/l Yeast extract 1.0 g/l Distilled water
4211VY/2 AGAR (DSMZ Medium 9)yeshttps://mediadive.dsmz.de/medium/9Name: VY/2 AGAR (DSMZ Medium 9) Composition: Agar 15.0 g/l Baker's yeast 5.0 g/l CaCl2 x 2 H2O 1.36 g/l Vitamin B12 0.0005 g/l Distilled water
4211MYX AGAR (DSMZ Medium 729)yeshttps://mediadive.dsmz.de/medium/729Name: MYX AGAR (DSMZ Medium 729) Composition: Agar 15.0 g/l Na2-glutamate 5.0 g/l Glucose 2.0 g/l MgSO4 x 7 H2O 1.0 g/l Yeast extract 1.0 g/l Distilled water
121383CIP Medium 296yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=296

culture temp

  • @ref: 4211
  • growth: positive
  • type: growth
  • temperature: 30
  • range: mesophilic

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12138317632nitrate-reduction
12138316301nitrite-reduction

metabolite production

  • @ref: 121383
  • 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
121383oxidase-
121383catalase+1.11.1.6
121383urease-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
121383-+++-+++--++---+-+--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
4211dung of antelopeSouth AfricaZAFAfrica
121383Antelope dungSouth AfricaZAFAfrica

isolation source categories

Cat1Cat2Cat3
#Host Body Product#Gastrointestinal tract#Feces (Stool)
#Host#Mammals#Bovinae (Cow, Cattle)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
42111Risk group (German classification)
1213831Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Hymenobacter ocellatus 16S rRNA gene, type strain Myx 2105T
  • accession: Y18835
  • length: 1505
  • database: ena
  • NCBI tax ID: 36878

GC content

  • @ref: 4211
  • GC-content: 64.6
  • method: Buoyant density centrifugation (BD)

External links

@ref: 4211

culture collection no.: DSM 11117, LMG 21874, Myx 2105, CIP 109678, LMG 21873

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
Phylogeny26801373Hymenobacter paludis sp. nov., isolated from a marsh.Chen WM, Chen ZH, Young CC, Sheu SYInt J Syst Evol Microbiol10.1099/ijsem.0.0009152016
Phylogeny28984220Hymenobacter gummosus sp. nov., isolated from a spring.Chen WM, Chen WT, Young CC, Sheu SYInt J Syst Evol Microbiol10.1099/ijsem.0.0023722017Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Natural Springs/*microbiology, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/chemistry, Taiwan, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny29956123Hymenobacter jeollabukensis sp. nov., isolated from soil.Ten LN, Han YE, Park KI, Kang IK, Han JS, Jung HYJ Microbiol10.1007/s12275-018-8085-42018Bacterial Typing Techniques, Base Composition, Cytophagaceae/chemistry/*classification/genetics/*isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Phosphatidylethanolamines/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome
Phylogeny31165292Hymenobacter oligotrophus sp. nov., isolated from a contaminated agar plate.Geng Y, Zhang Y, Tian J, Liu J, Qin K, Huang Y, Wei Z, Peng FAntonie Van Leeuwenhoek10.1007/s10482-019-01279-32019Agar, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/*isolation & purification/physiology, Base Composition, Cluster Analysis, Culture Media, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, *Environmental Microbiology, Fatty Acids/analysis, Locomotion, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, TemperatureCultivation
Phylogeny31287394Hymenobacter edaphi sp. nov., isolated from abandoned arsenic-contaminated farmland soil.Nie L, Fan X, Xiang D, Liao S, Wang GInt J Syst Evol Microbiol10.1099/ijsem.0.0035782019*Arsenic, Bacterial Typing Techniques, Base Composition, China, Cytophagaceae/*classification/isolation & purification, DNA, Bacterial/genetics, *Farms, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4211Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11117)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11117
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
68382Automatically annotated from API zym
121383Curators of the CIPCollection of Institut Pasteur (CIP 109678)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109678