Strain identifier
BacDive ID: 17917
Type strain: 
Species: Orbus hercynius
Strain history: <- G. Wilharm, Robert-Koch-Institut, Wernigerode, Germany; CN3 <- M. Volkmann
NCBI tax ID(s): 593135 (species)
version 8.1 (current version)
General
@ref: 16215
BacDive-ID: 17917
DSM-Number: 22228
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, ovoid-shaped
description: Orbus hercynius DSM 22228 is a facultative anaerobe, mesophilic, ovoid-shaped bacterium that was isolated from faeces of wild boar.
NCBI tax id
- NCBI tax id: 593135
- Matching level: species
strain history
- @ref: 16215
- history: <- G. Wilharm, Robert-Koch-Institut, Wernigerode, Germany; CN3 <- M. Volkmann
doi: 10.13145/bacdive17917.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Orbales
- family: Orbaceae
- genus: Orbus
- species: Orbus hercynius
- full scientific name: Orbus hercynius Volkmann et al. 2010
@ref: 16215
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Orbales
family: Orbaceae
genus: Orbus
species: Orbus hercynius
full scientific name: Orbus hercynius Volkmann et al. 2010
type strain: yes
Morphology
cell morphology
| @ref | cell length | cell width | cell shape | motility | gram stain | confidence |
|---|---|---|---|---|---|---|
| 29700 | 1-1.5 µm | 0.8 µm | ovoid-shaped | no | ||
| 69480 | negative | 99.981 |
pigmentation
- @ref: 29700
- production: no
Culture and growth conditions
culture medium
- @ref: 16215
- name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
- growth: yes
- link: https://mediadive.dsmz.de/medium/535
- composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 16215 | positive | growth | 28 | mesophilic |
| 29700 | positive | growth | 04-37 | |
| 29700 | positive | optimum | 20-30 | |
| 61393 | positive | growth | 30 | mesophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 29700 | positive | growth | 06-08 |
| 29700 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 29700 | facultative anaerobe |
| 61393 | aerobe |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.998 |
observation
- @ref: 29700
- observation: aggregates in chains
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29700 | 17234 | glucose | + | carbon source |
| 29700 | 4853 | esculin | + | hydrolysis |
| 29700 | 17632 | nitrate | + | reduction |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 29700 | catalase | + | 1.11.1.6 |
| 29700 | cytochrome oxidase | + | 1.9.3.1 |
| 29700 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | sampling date |
|---|---|---|---|---|---|---|
| 16215 | faeces of wild boar | Halberstadt | Germany | DEU | Europe | |
| 61393 | Wild boar,feces | Halberstadt | Germany | DEU | Europe | 2008-08-11 |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Mammals | #Suidae (Pig,Swine) |
| #Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
taxonmaps
- @ref: 69479
- File name: preview.99_52514.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_84;96_13469;97_16396;98_37629;99_52514&stattab=map
- Last taxonomy: Orbus hercynius subclade
- 16S sequence: FJ612598
- Sequence Identity:
- Total samples: 449
- soil counts: 2
- aquatic counts: 27
- animal counts: 417
- plant counts: 3
Safety information
risk assessment
- @ref: 16215
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16215
- description: Orbus hercynius strain CN3 16S ribosomal RNA gene, partial sequence
- accession: FJ612598
- length: 1522
- database: ena
- NCBI tax ID: 593135
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Orbus hercynius DSM 22228 | GCA_003634275 | scaffold | ncbi | 593135 |
| 66792 | Orbus hercynius strain DSM 22228 | 593135.5 | wgs | patric | 593135 |
| 66792 | Orbus hercynius DSM 22228 | 2770939645 | draft | img | 593135 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 16215 | 36.4 | high performance liquid chromatography (HPLC) |
| 29700 | 36.4 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 91.676 | yes |
| flagellated | no | 95.754 | no |
| gram-positive | no | 97.028 | no |
| anaerobic | no | 84.448 | no |
| aerobic | no | 82.493 | no |
| halophile | no | 54.008 | no |
| spore-forming | no | 97.586 | no |
| glucose-util | yes | 87.606 | yes |
| thermophile | no | 99.782 | yes |
| glucose-ferment | yes | 72.243 | no |
External links
@ref: 16215
culture collection no.: DSM 22228, CCUG 57622, CN 3
straininfo link
- @ref: 86906
- straininfo: 402530
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 20023064 | Orbus hercynius gen. nov., sp. nov., isolated from faeces of wild boar, is most closely related to members of the orders 'Enterobacteriales' and Pasteurellales. | Volkmann M, Skiebe E, Kerrinnes T, Faber F, Lepka D, Pfeifer Y, Holland G, Bannert N, Wilharm G | Int J Syst Evol Microbiol | 10.1099/ijs.0.019026-0 | 2009 | Animals, Base Composition, DNA, Bacterial/genetics, Fatty Acids/metabolism, Feces/*microbiology, Gammaproteobacteria/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sus scrofa/*microbiology | Metabolism |
| Phylogeny | 22941300 | Orbus sasakiae sp. nov., a bacterium isolated from the gut of the butterfly Sasakia charonda, and emended description of the genus Orbus. | Kim JY, Lee J, Shin NR, Yun JH, Whon TW, Kim MS, Jung MJ, Roh SW, Hyun DW, Bae JW | Int J Syst Evol Microbiol | 10.1099/ijs.0.041871-0 | 2012 | Animals, Bacterial Typing Techniques, Base Composition, Butterflies/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Gammaproteobacteria/*classification/genetics/isolation & purification, Gastrointestinal Tract/*microbiology, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/analysis | Genetics |
| Phylogeny | 23041637 | Cultivation and characterization of the gut symbionts of honey bees and bumble bees: description of Snodgrassella alvi gen. nov., sp. nov., a member of the family Neisseriaceae of the Betaproteobacteria, and Gilliamella apicola gen. nov., sp. nov., a member of Orbaceae fam. nov., Orbales ord. nov., a sister taxon to the order 'Enterobacteriales' of the Gammaproteobacteria. | Kwong WK, Moran NA | Int J Syst Evol Microbiol | 10.1099/ijs.0.044875-0 | 2012 | Animals, Bacterial Typing Techniques, Base Composition, Bees/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Gammaproteobacteria/*classification/genetics/isolation & purification, Gastrointestinal Tract/*microbiology, Molecular Sequence Data, Neisseriaceae/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Symbiosis, Ubiquinone/analysis | Enzymology |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 16215 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22228) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22228 | ||||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | ||||
| 29700 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 26083 | 28776041 | ||
| 61393 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 57622) | https://www.ccug.se/strain?id=57622 | ||||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
| 69479 | João 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 | ||||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | ||||
| 86906 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID402530.1 | StrainInfo: A central database for resolving microbial strain identifiers |