Strain identifier

BacDive ID: 1382

Type strain: Yes

Species: Ornithinibacillus californiensis

Strain Designation: MB-9

Strain history: CIP <- 2006, CCM <- H.J. Busse, Vienna Univ., Vienna, Austria <- R. Mayr, Munich Univ., Munich, Germany <- B.M. Tebo: strain MB-9

NCBI tax ID(s): 161536 (species)

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General

@ref: 6532

BacDive-ID: 1382

DSM-Number: 16628

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

description: Ornithinibacillus californiensis MB-9 is an obligate aerobe, spore-forming, mesophilic bacterium that forms circular colonies and was isolated from marine sediment.

NCBI tax id

  • NCBI tax id: 161536
  • Matching level: species

strain history

@refhistory
6532<- H.J. Busse <- R. Mayr <- Fracis, Tebo, strain MB-9
117104CIP <- 2006, CCM <- H.J. Busse, Vienna Univ., Vienna, Austria <- R. Mayr, Munich Univ., Munich, Germany <- B.M. Tebo: strain MB-9

doi: 10.13145/bacdive1382.20230509.8.1

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 californiensis
  • full scientific name: Ornithinibacillus californiensis Mayr et al. 2006

@ref: 6532

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Ornithinibacillus

species: Ornithinibacillus californiensis

full scientific name: Ornithinibacillus californiensis Mayr et al. 2006

strain designation: MB-9

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
23014positive2.0-6.0 µm0.4 µmrod-shapedyes
69480yes98.471
69480positive100
117104positiverod-shapedyes

colony morphology

  • @ref: 23014
  • type of hemolysis: alpha/beta
  • hemolysis ability: 1
  • colony size: 5.0 mm
  • colony color: slightly brownish/orange
  • colony shape: circular
  • incubation period: 11 days
  • medium used: trypticase soy agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6532BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
23014trypticase soy agaryes
37501MEDIUM 682 - for Ornithinibacillus californiensisyes
117104CIP Medium 682yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=682

culture temp

@refgrowthtypetemperaturerange
6532positivegrowth30mesophilic
23014positivegrowth10.0psychrophilic
23014positivegrowth37.0mesophilic
23014nogrowth7.0psychrophilic
23014nogrowth42.0thermophilic
23014positiveoptimum30.0mesophilic
37501positivegrowth30mesophilic

culture pH

  • @ref: 23014
  • ability: positive
  • type: growth
  • pH: 5.0-9.0
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23014obligate aerobe
117104obligate aerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
23014oval,terminal,in swollen sporangia ((width approx. 0.8 mm) appears racket-shaped)endosporeyes
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentrationhalophily level
23014NaClpositivegrowth0.5-12.0 %(w/v)
23014NaCloptimum0.5-8.0 %
23014moderately halophilic

murein

@refmurein short keytype
6532A21.04A4ß L-Orn-D-Asp
23014A21.04A4ß L-Orn-D-Asp

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
23014168082-dehydro-D-gluconate-builds acid from
2301415963ribitol-builds acid from
2301427613amygdalin-builds acid from
2301418305arbutin-builds acid from
2301417057cellobiose-builds acid from
2301417108D-arabinose-builds acid from
2301418333D-arabitol-builds acid from
2301428847D-fucose-builds acid from
2301462318D-lyxose-builds acid from
2301416024D-mannose-builds acid from
2301416634raffinose-builds acid from
2301432528turanose-builds acid from
2301465327D-xylose-builds acid from
2301416813galactitol-builds acid from
2301417113erythritol-builds acid from
2301428260galactose-builds acid from
2301428066gentiobiose-builds acid from
2301424265gluconate-builds acid from
2301428087glycogen-builds acid from
2301417268myo-inositol-builds acid from
2301430849L-arabinose-builds acid from
2301418403L-arabitol-builds acid from
2301418287L-fucose-builds acid from
2301417266L-sorbose-builds acid from
2301465328L-xylose-builds acid from
2301417716lactose-builds acid from
2301429864mannitol-builds acid from
230146731melezitose-builds acid from
2301428053melibiose-builds acid from
23014320061methyl alpha-D-glucopyranoside-builds acid from
2301443943methyl alpha-D-mannoside-builds acid from
2301474863methyl beta-D-xylopyranoside-builds acid from
2301426546rhamnose-builds acid from
2301430911sorbitol-builds acid from
2301417151xylitol-builds acid from
2301428017starch-degradation
2301417632nitrate-reduction
2301415588D-malate-respiration
2301416651(S)-lactate-respiration
23014172562-deoxyadenosine-respiration
23014645522-hydroxybutyrate-respiration
23014620642,3-butanediol-respiration
23014739183-O-methyl-D-glucose-respiration
23014167244-hydroxybutyrate-respiration
23014181014-hydroxyphenylacetic acid-respiration
2301416335adenosine-respiration
2301440585alpha-cyclodextrin-respiration
2301417925alpha-D-glucose-respiration
2301436219alpha-lactose-respiration
2301416027amp-respiration
2301427613amygdalin-respiration
2301415570D-alanine-respiration
2301418333D-arabitol-respiration
2301417057cellobiose-respiration
2301415824D-fructose-respiration
2301478697D-fructose 6-phosphate-respiration
2301412936D-galactose-respiration
2301418024D-galacturonic acid-respiration
230148391D-gluconate-respiration
2301414314D-glucose 6-phosphate-respiration
2301416899D-mannitol-respiration
2301416024D-mannose-respiration
230146731melezitose-respiration
2301428053melibiose-respiration
2301427605D-psicose-respiration
2301416634raffinose-respiration
2301416988D-ribose-respiration
2301417924D-sorbitol-respiration
2301416443D-tagatose-respiration
2301465327D-xylose-respiration
2301428066gentiobiose-respiration
2301429042glucose 1-phosphate-respiration
2301417596inosine-respiration
2301421217L-alaninamide-respiration
2301473786L-alanylglycine-respiration
2301430849L-arabinose-respiration
2301417196L-asparagine-respiration
2301418287L-fucose-respiration
2301429985L-glutamate-respiration
2301462345L-rhamnose-respiration
2301475144lactamide-respiration
230146359lactulose-respiration
2301417306maltose-respiration
2301461993maltotriose-respiration
2301428808mannan-respiration
2301474611methyl (R)-lactate-respiration
2301455507methyl alpha-D-galactoside-respiration
23014320061methyl alpha-D-glucopyranoside-respiration
2301443943methyl alpha-D-mannoside-respiration
2301417540methyl beta-D-galactoside-respiration
23014320055methyl beta-D-glucopyranoside-respiration
2301475146monomethyl succinate-respiration
2301417268myo-inositol-respiration
2301444337N-acetyl-L-glutamate-respiration
2301463154N-acetyl-beta-D-mannosamine-respiration
23014506227N-acetylglucosamine-respiration
2301473784glycyl-l-glutamate-respiration
2301418394palatinose-respiration
2301417148putrescine-respiration
2301432488sedoheptulosan-respiration
2301417164stachyose-respiration
23014143136succinamate-respiration
2301430031succinate-respiration
2301417992sucrose-respiration
2301417748thymidine-respiration
2301463528thymidine 5'-monophosphate-respiration
2301432528turanose-respiration
2301416695uridine 5'-monophosphate-respiration
2301417151xylitol-respiration
23014174265-dehydro-D-gluconate+builds acid from
2301417634D-glucose+builds acid from
2301416443D-tagatose+builds acid from
2301417754glycerol+builds acid from
2301417306maltose+builds acid from
2301433942ribose+builds acid from
2301417814salicin+builds acid from
2301428017starch+builds acid from
2301417992sucrose+builds acid from
2301427082trehalose+builds acid from
23014286442-oxopentanoate+respiration
23014370543-hydroxybutyrate+respiration
2301430089acetate+respiration
2301415361pyruvate+respiration
2301415589L-malate+/-respiration
2301451850methyl pyruvate+/-respiration
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose-builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
11710417632nitrate-reduction
11710416301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
2301435581indoleno
2301416136hydrogen sulfideno
2301415688acetoinno
11710435581indoleno

enzymes

@refvalueactivityec
23014arginine dihydrolase-3.5.3.6
23014beta-galactosidase-3.2.1.23
23014catalase+1.11.1.6
23014cytochrome oxidase+1.9.3.1
23014gelatinase+
23014lecithinase-
23014lysine decarboxylase-4.1.1.18
23014ornithine decarboxylase-4.1.1.17
23014tryptophan deaminase-4.1.99.1
23014urease-3.5.1.5
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
117104oxidase+
117104catalase+1.11.1.6
117104urease-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
117104-++--+---+-+---+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
117104+/----+/------+------------+++-+--++---+/--------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment culture
6532marine sedimentMission Bay, San DiegoUSAUSANorth America
23014surface sediment samples collected at the waterline from the shoreMn(II)-containing K agar
117104Environment, Marine sedimentsMission bay, San Diego, CaliforniaUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
65321Risk group (German classification)
1171041Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6532
  • description: Ornithinibacillus californiensis strain MB-9 16S ribosomal RNA gene, partial sequence
  • accession: AF326365
  • length: 1528
  • database: ena
  • NCBI tax ID: 161536

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ornithinibacillus californiensis DSM 16628GCA_001038485contigncbi161536
66792Ornithinibacillus californiensis strain DSM 16628161536.5wgspatric161536
66792Ornithinibacillus californiensis DSM 166282627854193draftimg161536

GC content

@refGC-contentmethod
653240.8
2301440.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes89.775no
gram-positiveyes88.23yes
anaerobicno98.843yes
aerobicyes92.795no
halophileyes82.595no
spore-formingyes91.772yes
thermophileno98.958no
glucose-utilyes78.592yes
flagellatedyes83.022no
glucose-fermentno89.248no

External links

@ref: 6532

culture collection no.: DSM 16628, CCM 7237, CIP 109288

straininfo link

  • @ref: 71033
  • straininfo: 139328

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16738118Ornithinibacillus gen. nov., with the species Ornithinibacillus bavariensis sp. nov. and Ornithinibacillus californiensis sp. nov.Mayr R, Busse HJ, Worliczek HL, Ehling-Schulz M, Scherer SInt J Syst Evol Microbiol10.1099/ijs.0.64038-02006Catalase/metabolism, Fatty Acids/analysis, Gram-Positive Bacteria/*classification/*genetics/isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, Species SpecificityMetabolism
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
Phylogeny24002474Salinibacillus xinjiangensis sp. nov., a halophilic bacterium from a hypersaline lake.Yang N, Ren B, Liu ZH, Dai HQ, Wang J, Zhou YG, Song FH, Zhang LXInt J Syst Evol Microbiol10.1099/ijs.0.053306-02013Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Lakes/*microbiology, Molecular Sequence Data, Phosphatidylglycerols/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, Sodium Chloride/chemistry, Vitamin K 2/analogs & derivatives/chemistryGenetics
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

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6532Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16628)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16628
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
23014R. Mayr,H.-J. Busse,H. L. Worliczek,M. Ehling-Schulz,S. Scherer10.1099/ijs.0.64038-0Ornithinibacillus gen. nov., with the species Ornithinibacillus bavariensis sp. nov. and Ornithinibacillus californiensis sp. nov.IJSEM 56: 1383-1389 200616738118
37501Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7012
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)
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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
71033Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID139328.1StrainInfo: A central database for resolving microbial strain identifiers
117104Curators of the CIPCollection of Institut Pasteur (CIP 109288)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109288