Strain identifier

BacDive ID: 22934

Type strain: Yes

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)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refgrowthtypetemperaturerange
19342positivegrowth30mesophilic
30789positivegrowth13-45
30789positiveoptimum30mesophilic

culture pH

@refabilitytypepHPH range
30789positivegrowth6.5-8.5alkaliphile
30789positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 30789
  • oxygen tolerance: aerobe

spore formation

  • @ref: 30789
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
30789NaClpositivegrowth0-8.5 %
30789NaClpositiveoptimum0.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
30789581435-dehydro-D-gluconate+carbon source
3078922599arabinose+carbon source
3078917057cellobiose+carbon source
3078928757fructose+carbon source
3078928260galactose+carbon source
3078924265gluconate+carbon source
3078917306maltose+carbon source
3078928053melibiose+carbon source
30789506227N-acetylglucosamine+carbon source
3078916634raffinose+carbon source
3078926546rhamnose+carbon source
3078917814salicin+carbon source
3078918222xylose+carbon source
307894853esculin+hydrolysis

enzymes

@refvalueactivityec
30789alkaline phosphatase+3.1.3.1
30789catalase+1.11.1.6
30789pyrazinamidase+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

Cat1Cat2Cat3
#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

@refGC-contentmethod
1934244.1high performance liquid chromatography (HPLC)
3078944.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes89.875yes
flagellatedyes91.333no
gram-positiveyes93.769yes
anaerobicno97.737yes
aerobicyes90.481yes
halophileno86.189yes
spore-formingyes90.842no
thermophileno97.75no
glucose-utilyes90.554no
glucose-fermentno85.921no

External links

@ref: 19342

culture collection no.: DSM 25058, LMG 26645

straininfo link

  • @ref: 87182
  • straininfo: 400107

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23064349Domibacillus robiginosus gen. nov., sp. nov., isolated from a pharmaceutical clean room.Seiler H, Wenning M, Scherer SInt J Syst Evol Microbiol10.1099/ijs.0.044396-02012Bacillaceae/*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, DNAGenetics
Phylogeny24907266Description 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 YSInt J Syst Evol Microbiol10.1099/ijs.0.064295-02014Bacteria/*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/chemistryGenetics
Phylogeny25242536Domibacillus enclensis sp. nov., isolated from marine sediment, and emended description of the genus Domibacillus.Sonalkar VV, Mawlankar R, Krishnamurthi S, Tang SK, Dastager SGInt J Syst Evol Microbiol10.1099/ijs.0.068924-02014Bacillaceae/*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/chemistryGenetics
Phylogeny26637819Description of Domibacillus iocasae sp. nov., isolated from deep-sea sediment, and emended description of the genus Domibacillus.Sun QL, Sun LInt J Syst Evol Microbiol10.1099/ijsem.0.0008232015
Phylogeny27073919Domibacillus antri sp. nov., isolated from the soil of a cave.Xu D, Wang L, Wang G, Zheng SInt J Syst Evol Microbiol10.1099/ijsem.0.0010802016Bacillaceae/*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/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
19342Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25058)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25058
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
30789Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2712028776041
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)
69479João 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
87182Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID400107.1StrainInfo: A central database for resolving microbial strain identifiers