Strain identifier
BacDive ID: 22934
Type strain:
Species: Domibacillus robiginosus
Strain Designation: WS 4628, isolate G 6512, WS 4628, isolate G 6512
Strain history: <- H. Seiler, TU Munich, (ZIEL), Freising-Weihenstephan, Germany; WS 4628 <- M. Wenning <- G. Rieser
NCBI tax ID(s): 1071054 (species)
General
@ref: 19342
BacDive-ID: 22934
DSM-Number: 25058
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, motile, rod-shaped
description: Domibacillus robiginosus WS 4628 is an aerobe, spore-forming, mesophilic bacterium that was isolated from air from the clean room a pharmaceutical manufacturing site.
NCBI tax id
- NCBI tax id: 1071054
- Matching level: species
strain history
- @ref: 19342
- history: <- H. Seiler, TU Munich, (ZIEL), Freising-Weihenstephan, Germany; WS 4628 <- M. Wenning <- G. Rieser
doi: 10.13145/bacdive22934.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Bacillaceae
- genus: Domibacillus
- species: Domibacillus robiginosus
- full scientific name: Domibacillus robiginosus Seiler et al. 2013
@ref: 19342
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Bacillaceae
genus: Domibacillus
species: Domibacillus robiginosus
full scientific name: Domibacillus robiginosus Seiler et al. 2013
strain designation: WS 4628, isolate G 6512, WS 4628, isolate G 6512
type strain: yes
Morphology
cell morphology
- @ref: 30789
- gram stain: positive
- cell length: 3.5 µm
- cell width: 0.9 µm
- cell shape: rod-shaped
- motility: yes
pigmentation
- @ref: 30789
- production: yes
Culture and growth conditions
culture medium
- @ref: 19342
- name: CASO AGAR (MERCK 105458) (DSMZ Medium 220)
- growth: yes
- link: https://mediadive.dsmz.de/medium/220
- composition: Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
19342 | positive | growth | 30 | mesophilic |
30789 | positive | growth | 13-45 | |
30789 | positive | optimum | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
30789 | positive | growth | 6.5-8.5 | alkaliphile |
30789 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 30789
- oxygen tolerance: aerobe
spore formation
- @ref: 30789
- spore formation: yes
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
30789 | NaCl | positive | growth | 0-8.5 % |
30789 | NaCl | positive | optimum | 0.5 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30789 | 58143 | 5-dehydro-D-gluconate | + | carbon source |
30789 | 22599 | arabinose | + | carbon source |
30789 | 17057 | cellobiose | + | carbon source |
30789 | 28757 | fructose | + | carbon source |
30789 | 28260 | galactose | + | carbon source |
30789 | 24265 | gluconate | + | carbon source |
30789 | 17306 | maltose | + | carbon source |
30789 | 28053 | melibiose | + | carbon source |
30789 | 506227 | N-acetylglucosamine | + | carbon source |
30789 | 16634 | raffinose | + | carbon source |
30789 | 26546 | rhamnose | + | carbon source |
30789 | 17814 | salicin | + | carbon source |
30789 | 18222 | xylose | + | carbon source |
30789 | 4853 | esculin | + | hydrolysis |
enzymes
@ref | value | activity | ec |
---|---|---|---|
30789 | alkaline phosphatase | + | 3.1.3.1 |
30789 | catalase | + | 1.11.1.6 |
30789 | pyrazinamidase | + | 3.5.1.B15 |
Isolation, sampling and environmental information
isolation
- @ref: 19342
- sample type: air from the clean room a pharmaceutical manufacturing site
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Built environment | #Clean room |
#Engineered | #Industrial | |
#Environmental | #Air | #Indoor Air |
taxonmaps
- @ref: 69479
- File name: preview.99_73939.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_1025;97_1195;98_3327;99_73939&stattab=map
- Last taxonomy: Domibacillus
- 16S sequence: HE577175
- Sequence Identity:
- Total samples: 1137
- soil counts: 879
- aquatic counts: 95
- animal counts: 139
- plant counts: 24
Safety information
risk assessment
- @ref: 19342
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 19342
- description: Domibacillus robiginosus partial 16S rRNA gene, type strain WS 4628T, isolate G 6512
- accession: HE577175
- length: 1483
- database: ena
- NCBI tax ID: 1071054
Genome sequences
- @ref: 66792
- description: Domibacillus robiginosus WS 4628
- accession: GCA_000966195
- assembly level: contig
- database: ncbi
- NCBI tax ID: 1071054
GC content
@ref | GC-content | method |
---|---|---|
19342 | 44.1 | high performance liquid chromatography (HPLC) |
30789 | 44.1 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 89.875 | yes |
flagellated | yes | 91.333 | no |
gram-positive | yes | 93.769 | yes |
anaerobic | no | 97.737 | yes |
aerobic | yes | 90.481 | yes |
halophile | no | 86.189 | yes |
spore-forming | yes | 90.842 | no |
thermophile | no | 97.75 | no |
glucose-util | yes | 90.554 | no |
glucose-ferment | no | 85.921 | no |
External links
@ref: 19342
culture collection no.: DSM 25058, LMG 26645
straininfo link
- @ref: 87182
- straininfo: 400107
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 23064349 | Domibacillus robiginosus gen. nov., sp. nov., isolated from a pharmaceutical clean room. | Seiler H, Wenning M, Scherer S | Int J Syst Evol Microbiol | 10.1099/ijs.0.044396-0 | 2012 | Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Environment, Controlled, Fatty Acids/analysis, Molecular Sequence Data, Peptidoglycan/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
Phylogeny | 24907266 | Description of Domibacillus indicus sp. nov., isolated from ocean sediments and emended description of the genus Domibacillus. | Sharma A, Dhar SK, Prakash O, Vemuluri VR, Thite V, Shouche YS | Int J Syst Evol Microbiol | 10.1099/ijs.0.064295-0 | 2014 | Bacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, India, Molecular Sequence Data, Oceans and Seas, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
Phylogeny | 25242536 | Domibacillus enclensis sp. nov., isolated from marine sediment, and emended description of the genus Domibacillus. | Sonalkar VV, Mawlankar R, Krishnamurthi S, Tang SK, Dastager SG | Int J Syst Evol Microbiol | 10.1099/ijs.0.068924-0 | 2014 | Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, India, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, Pigments, Biological/chemistry, RNA, Ribosomal, 16S/genetics, Seawater, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
Phylogeny | 26637819 | Description of Domibacillus iocasae sp. nov., isolated from deep-sea sediment, and emended description of the genus Domibacillus. | Sun QL, Sun L | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000823 | 2015 | ||
Phylogeny | 27073919 | Domibacillus antri sp. nov., isolated from the soil of a cave. | Xu D, Wang L, Wang G, Zheng S | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001080 | 2016 | Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Caves/*microbiology, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
19342 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25058) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25058 | |||
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 | |||
30789 | 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 | 27120 | 28776041 | |
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) | |||
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 | |||
87182 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID400107.1 | StrainInfo: A central database for resolving microbial strain identifiers |