Strain identifier

BacDive ID: 1383

Type strain: Yes

Species: Ornithinibacillus contaminans

Strain history: <- P. Kämpfer, Univ. Giessen, Germany; CCUG 53201

NCBI tax ID(s): 694055 (species)

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General

@ref: 16631

BacDive-ID: 1383

DSM-Number: 22953

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, mesophilic, Gram-positive, rod-shaped, colony-forming

description: Ornithinibacillus contaminans DSM 22953 is an obligate aerobe, spore-forming, mesophilic bacterium that forms circular colonies and was isolated from contaminant from a blood sample of a 75-year-old woman.

NCBI tax id

  • NCBI tax id: 694055
  • Matching level: species

strain history

  • @ref: 16631
  • history: <- P. Kämpfer, Univ. Giessen, Germany; CCUG 53201

doi: 10.13145/bacdive1383.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Ornithinibacillus
  • species: Ornithinibacillus contaminans
  • full scientific name: Ornithinibacillus contaminans Kämpfer et al. 2010

@ref: 16631

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Ornithinibacillus

species: Ornithinibacillus contaminans

full scientific name: Ornithinibacillus contaminans Kämpfer et al. 2010

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
23015positive2.0-3.0 µm0.8-1.0 µmrod-shapedno
69480yes97.502
69480positive100

colony morphology

  • @ref: 23015
  • colony color: beige
  • colony shape: circular

Culture and growth conditions

culture medium

  • @ref: 16631
  • 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; with strain-specific modifications) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l MnSO4 0.01 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16631positivegrowth28mesophilic
23015positivegrowth20.0-45.0
23015nogrowth10.0psychrophilic
23015nogrowth50.0thermophilic
23015nogrowth5.0psychrophilic
23015positivegrowth40.0thermophilic
23015positivegrowth37.0mesophilic
23015positiveoptimum30.0mesophilic
59829positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
23015positivegrowth6.5-9.5alkaliphile
23015positiveoptimum7.0-9.0
23015nogrowth5.7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23015obligate aerobe
59829microaerophile

spore formation

@refspore descriptiontype of sporespore formationconfidence
23015centralendosporeyes
69481yes100
69480yes100

halophily

  • @ref: 23015
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <6.0 %(w/v)

murein

@refmurein short keytype
16631A21.04A4ß L-Orn-D-Asp
23015A21.04A4ß L-Orn-D-Asp

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2301517634D-glucose+builds acid from
2301516899D-mannitol+builds acid from
2301565327D-xylose+builds acid from

enzymes

@refvalueactivityec
23015catalase+1.11.1.6
23015cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture temperaturesampling date
16631contaminant from a blood sample of a 75-year-old womanGöteborgSwedenSWEEurope
23015tryptone soy agar (TSA; Oxoid)30.0
59829Human blood,75-yr-old womanBoråsSwedenSWEEurope2006-07-02

isolation source categories

Cat1Cat2Cat3
#Engineered#Laboratory#Contaminant
#Infection#Patient
#Host Body Product#Fluids#Blood
#Host#Human#Female

taxonmaps

  • @ref: 69479
  • File name: preview.99_4882.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_2404;97_2926;98_3655;99_4882&stattab=map
  • Last taxonomy: Ornithinibacillus contaminans subclade
  • 16S sequence: FN597064
  • Sequence Identity:
  • Total samples: 43
  • soil counts: 15
  • aquatic counts: 4
  • animal counts: 24

Safety information

risk assessment

  • @ref: 16631
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Ornithinibacillus contaminans strain CCUG 53201 16S ribosomal RNA gene, partial sequenceKF4255161524ena694055
16631Ornithinibacillus contaminans partial 16S rRNA gene, type strain CCUG 53201TFN5970641254ena694055

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ornithinibacillus contaminans DSM 22953GCA_001038425contigncbi694055
66792Ornithinibacillus contaminans strain DSM 22953694055.4wgspatric694055
66792Ornithinibacillus contaminans DSM 229532645727623draftimg694055

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes91.455yes
anaerobicno99.416yes
halophileyes90.371yes
spore-formingyes94.556yes
glucose-utilyes86.64no
thermophileno91.409no
flagellatedyes84.558no
motileyes84.978yes
aerobicyes88.389no
glucose-fermentno87.724no

External links

@ref: 16631

culture collection no.: DSM 22953, CCUG 53201

straininfo link

  • @ref: 71034
  • straininfo: 370878

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20118298Ornithinibacillus contaminans sp. nov., an endospore-forming species.Kampfer P, Falsen E, Lodders N, Langer S, Busse HJ, Schumann PInt J Syst Evol Microbiol10.1099/ijs.0.021337-02010Aged, Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Female, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sweden, Vitamin K 2/analogs & derivatives/chemistryPathogenicity
Phylogeny26706221Comparative genomic study of three species within the genus Ornithinibacillus, reflecting the adaption to different habitats.Jiang XW, Cheng H, Zheng BW, Li A, Lv LX, Ling ZX, Yan R, Jiang HY, Cheng YW, Gu SL, Li LJGene10.1016/j.gene.2015.12.0252015*Adaptation, Physiological, Bacillaceae/*classification/*genetics/isolation & purification, Base Composition, Drug Resistance, Bacterial, Genome Size, *Genome, Bacterial, Geologic Sediments/microbiology, Phylogeny, Sequence Analysis, DNA/methods, Stress, PhysiologicalGenetics
Phylogeny29125459Pseudogracilibacillus endophyticus sp. nov., a moderately thermophilic and halophilic species isolated from plant root.Park J, Kim MK, Yun BR, Han JH, Kim SBInt J Syst Evol Microbiol10.1099/ijsem.0.0024752017Bacillaceae/classification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Oenothera biennis/*microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny31364965Two novel species of the family Bacillaceae: Oceanobacillus piezotolerans sp. nov. and Bacillus piezotolerans sp. nov., from deep-sea sediment samples of Yap Trench.Yu L, Tang X, Wei S, Qiu Y, Xu X, Xu G, Wang Q, Yang QInt J Syst Evol Microbiol10.1099/ijsem.0.0035592019Bacillaceae/*classification/isolation & purification, Bacillus/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Pacific Ocean, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16631Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22953)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22953
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
23015P. Kämpfer,E. Falsen,N. Lodders,S. Langer,H.-J. Busse,P. Schumann10.1099/ijs.0.021337-0Ornithinibacillus contaminans sp. nov., an endospore-forming speciesIJSEM 60: 2930-2934 201020118298
59829Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53201)https://www.ccug.se/strain?id=53201
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
71034Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID370878.1StrainInfo: A central database for resolving microbial strain identifiers