Strain identifier

BacDive ID: 1221

Type strain: Yes

Species: Siminovitchia fordii

Strain Designation: R-7190

Strain history: CIP <- 2005, DSMZ <- P. Scheldeman, Flemish Com. Ministry, Belgium: strain R-7190

NCBI tax ID(s): 254759 (species)

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General

@ref: 6152

BacDive-ID: 1221

DSM-Number: 16014

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

description: Siminovitchia fordii R-7190 is an obligate aerobe, spore-forming, mesophilic bacterium that forms irregular colonies and was isolated from raw milk.

NCBI tax id

  • NCBI tax id: 254759
  • Matching level: species

strain history

@refhistory
6152<- P. Scheldeman
119425CIP <- 2005, DSMZ <- P. Scheldeman, Flemish Com. Ministry, Belgium: strain R-7190

doi: 10.13145/bacdive1221.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Siminovitchia
  • species: Siminovitchia fordii
  • full scientific name: Siminovitchia fordii (Scheldeman et al. 2004) Gupta et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Bacillus fordii

@ref: 6152

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Siminovitchia

species: Siminovitchia fordii

full scientific name: Siminovitchia fordii (Scheldeman et al. 2004) Gupta et al. 2020

strain designation: R-7190

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
23313negative1.6-3.5 µm0.6-0.8 µmrod-shapedyes
69480yes94.93
69480positive100
119425positiverod-shapedyes

colony morphology

@refcolony sizecolony colorcolony shapeincubation periodmedium used
233132 mmcreamirregular3 daysNutrient agar
23313faint pinkcasein agar
119425

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6152CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: 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
23313casein agaryes
38323MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119425CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6152positivegrowth30mesophilic
23313positivegrowth30-45
23313inconsistentgrowth20psychrophilic
38323positivegrowth30mesophilic
119425positivegrowth22-45
119425nogrowth10psychrophilic
119425nogrowth55thermophilic

culture pH

@refabilitytypepHPH range
23313positivegrowth9.0alkaliphile
23313inconsistentgrowth5.0
119425positivegrowth6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23313obligate aerobe
119425obligate aerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
23312ellispoidal, paracentral or subterminal, occasionally slightly swollen sporangiaendosporeyes
69481yes100
69480yes100
119425yes

halophily

@refsaltgrowthtested relationconcentration
23313NaClpositivegrowth7 %
119425NaClpositivegrowth0-10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
23313168082-dehydro-D-gluconate-builds acid from
23313174265-dehydro-D-gluconate-builds acid from
2331327613amygdalin-builds acid from
2331318305arbutin-builds acid from
2331315963ribitol-builds acid from
2331317108D-arabinose-builds acid from
2331318333D-arabitol-builds acid from
2331317057cellobiose-builds acid from
2331315824D-fructose-builds acid from
2331328847D-fucose-builds acid from
2331312936D-galactose-builds acid from
2331317634D-glucose-builds acid from
2331317716lactose-builds acid from
2331362318D-lyxose-builds acid from
2331317306maltose-builds acid from
2331316899D-mannitol-builds acid from
2331316024D-mannose-builds acid from
233136731melezitose-builds acid from
2331328053melibiose-builds acid from
2331316634raffinose-builds acid from
2331316988D-ribose-builds acid from
2331317992sucrose-builds acid from
2331317924D-sorbitol-builds acid from
2331316443D-tagatose-builds acid from
2331316551D-trehalose-builds acid from
2331332528turanose-builds acid from
2331365327D-xylose-builds acid from
2331316813galactitol-builds acid from
2331317113erythritol-builds acid from
2331328066gentiobiose-builds acid from
2331324265gluconate-builds acid from
2331317754glycerol-builds acid from
2331328087glycogen-builds acid from
2331317268myo-inositol-builds acid from
2331315443inulin-builds acid from
2331330849L-arabinose-builds acid from
2331318403L-arabitol-builds acid from
2331318287L-fucose-builds acid from
2331362345L-rhamnose-builds acid from
2331317266L-sorbose-builds acid from
2331365328L-xylose-builds acid from
23313320061methyl alpha-D-glucopyranoside-builds acid from
2331343943methyl alpha-D-mannoside-builds acid from
2331374863methyl beta-D-xylopyranoside-builds acid from
23313506227N-acetylglucosamine-builds acid from
2331317814salicin-builds acid from
2331328017starch-builds acid from
2331317151xylitol-builds acid from
23313510573-phenylpropionate-carbon source
2331316865gamma-aminobutyric acid-carbon source
2331315963ribitol-carbon source
2331336219alpha-lactose-carbon source
2331317750betaine-carbon source
2331327689decanoate-carbon source
2331325646octanoate-carbon source
2331316383cis-aconitate-carbon source
2331316947citrate-carbon source
2331323399coumarate-carbon source
2331315570D-alanine-carbon source
2331317057cellobiose-carbon source
2331315824D-fructose-carbon source
2331312936D-galactose-carbon source
2331330612D-glucarate-carbon source
233138391D-gluconate-carbon source
2331317634D-glucose-carbon source
2331315588D-malate-carbon source
2331316899D-mannitol-carbon source
2331316024D-mannose-carbon source
233136731melezitose-carbon source
2331328053melibiose-carbon source
2331316988D-ribose-carbon source
2331317924D-sorbitol-carbon source
2331316443D-tagatose-carbon source
2331330927D-tartrate-carbon source
2331316551D-trehalose-carbon source
2331332528turanose-carbon source
2331316813galactitol-carbon source
2331317113erythritol-carbon source
2331316537galactarate-carbon source
2331328066gentiobiose-carbon source
2331317754glycerol-carbon source
2331317240itaconate-carbon source
2331316977L-alanine-carbon source
2331329991L-aspartate-carbon source
2331318287L-fucose-carbon source
2331329985L-glutamate-carbon source
2331315589L-malate-carbon source
2331317203L-proline-carbon source
2331362345L-rhamnose-carbon source
2331317115L-serine-carbon source
2331317266L-sorbose-carbon source
2331330924L-tartrate-carbon source
233136359lactulose-carbon source
2331315792malonate-carbon source
2331368428maltitol-carbon source
2331317306maltose-carbon source
2331361993maltotriose-carbon source
2331355507methyl alpha-D-galactoside-carbon source
23313320061methyl alpha-D-glucopyranoside-carbon source
2331317540methyl beta-D-galactoside-carbon source
23313320055methyl beta-D-glucopyranoside-carbon source
2331317268myo-inositol-carbon source
2331318394palatinose-carbon source
2331317272propionate-carbon source
2331317992sucrose-carbon source
2331315708trans-aconitate-carbon source
2331318123trigonelline-carbon source
2331316765tryptamine-carbon source
2331317151xylitol-carbon source
23313casein-hydrolysis
233134853esculin-hydrolysis
2331328017starch-hydrolysis
2331317521(-)-quinic acid+carbon source
23313168082-dehydro-D-gluconate+carbon source
23313309162-oxoglutarate+carbon source
23313178794-hydroxybenzoate+carbon source
23313158875-aminovaleric acid+carbon source
23313174265-dehydro-D-gluconate+carbon source
2331316150benzoate+carbon source
2331318024D-galacturonic acid+carbon source
2331317315D-glucosamine+carbon source
2331315748D-glucuronate+carbon source
2331362318D-lyxose+carbon source
2331316634raffinose+carbon source
2331365327D-xylose+carbon source
23313370543-hydroxybutyrate+carbon source
2331333871glycerate+carbon source
2331324996lactate+carbon source
233134853esculin+carbon source
2331316000ethanolamine+carbon source
2331358044gentisate+carbon source
2331317859glutaric acid+carbon source
2331318295histamine+carbon source
2331330849L-arabinose+carbon source
2331316828L-tryptophan+carbon source
2331317895L-tyrosine+carbon source
2331325115malate+carbon source
2331330928meso-tartrate+carbon source
23313506227N-acetylglucosamine+carbon source
2331318401phenylacetate+carbon source
2331336241protocatechuate+carbon source
2331317148putrescine+carbon source
2331362517tricarballylate+carbon source
2331329806fumarate+/-carbon source
2331315971L-histidine+/-carbon source
2331330031succinate+/-carbon source
11942516947citrate-carbon source
1194254853esculin-hydrolysis
119425606565hippurate+hydrolysis
11942517632nitrate-reduction
11942516301nitrite-reduction
11942517632nitrate-respiration

metabolite production

  • @ref: 119425
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11942515688acetoin-
11942517234glucose-

enzymes

@refvalueactivityec
23313catalase+1.11.1.6
23313cytochrome oxidase+1.9.3.1
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
119425oxidase+
119425beta-galactosidase-3.2.1.23
119425alcohol dehydrogenase-1.1.1.1
119425gelatinase-
119425amylase-
119425DNase+
119425caseinase-3.4.21.50
119425catalase+1.11.1.6
119425tween esterase-
119425gamma-glutamyltransferase+2.3.2.2
119425lecithinase-
119425lipase-
119425lysine decarboxylase-4.1.1.18
119425ornithine decarboxylase-4.1.1.17
119425phenylalanine ammonia-lyase+4.3.1.24
119425protease-
119425tryptophan deaminase-
119425urease-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
119425--++-++--+++--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119425-------------------+------------------++--------+++--+----++++-------++-++++--++++-+-++--+++-+-+-++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6152raw milkWuustwezelBelgiumBELEurope
119425Food, Raw milkBelgiumBELEurope

isolation source categories

Cat1Cat2Cat3
#Host Body Product#Fluids#Milk
#Host#Mammals

taxonmaps

  • @ref: 69479
  • File name: preview.99_67862.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_18045;97_22259;98_29335;99_67862&stattab=map
  • Last taxonomy: Bacillus
  • 16S sequence: AY443039
  • Sequence Identity:
  • Total samples: 107
  • soil counts: 45
  • aquatic counts: 13
  • animal counts: 38
  • plant counts: 11

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
61521Risk group (German classification)
1194251Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6152
  • description: Bacillus fordii strain R-7190 16S ribosomal RNA gene, partial sequence
  • accession: AY443039
  • length: 1462
  • database: ena
  • NCBI tax ID: 254759

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Siminovitchia fordii DSM 16014 = CIP 108821GCA_000374565scaffoldncbi1121090
66792Bacillus fordii DSM 160141121090.3wgspatric1121090
66792Bacillus fordii DSM 160142517572148draftimg1121090

GC content

@refGC-contentmethod
615241.9
2331341.9high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes90.369no
flagellatedyes81.456no
gram-positiveyes79.534yes
anaerobicno98.93no
aerobicyes93.444yes
halophileyes87.387yes
spore-formingyes94.171yes
glucose-utilyes76.652yes
thermophileno97.034yes
glucose-fermentno94.788no

External links

@ref: 6152

culture collection no.: DSM 16014, CIP 108821, LMG 22080

straininfo link

  • @ref: 70877
  • straininfo: 21205

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15280314Bacillus farraginis sp. nov., Bacillus fortis sp. nov. and Bacillus fordii sp. nov., isolated at dairy farms.Scheldeman P, Rodriguez-Diaz M, Goris J, Pil A, De Clerck E, Herman L, De Vos P, Logan NA, Heyndrickx MInt J Syst Evol Microbiol10.1099/ijs.0.63095-02004Aerobiosis, Animal Feed/*microbiology, Animals, Bacillus/*classification/cytology/*isolation & purification/physiology, Bacterial Proteins/analysis/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA Fingerprinting, DNA, Bacterial/analysis/chemistry/isolation & purification, DNA, Ribosomal/chemistry, *Dairying, *Equipment Contamination, Fatty Acids/analysis, Genes, rRNA, Hot Temperature, Milk/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Proteome, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Repetitive Sequences, Nucleic Acid, Sequence Analysis, DNA, Sequence Homology, Spores, Bacterial/cytologyEnzymology
Phylogeny23396719Bacillus composti sp. nov. and Bacillus thermophilus sp. nov., two thermophilic, Fe(III)-reducing bacteria isolated from compost.Yang G, Chen M, Yu Z, Lu Q, Zhou SInt J Syst Evol Microbiol10.1099/ijs.0.049106-02013Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Ferric Compounds/*metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny27983469Bacillus terrae sp. nov. isolated from Cistus ladanifer rhizosphere soil.Diez-Mendez A, Rivas R, Mateos PF, Martinez-Molina E, Santin PJ, Sanchez-Rodriguez JA, Velazquez EInt J Syst Evol Microbiol10.1099/ijsem.0.0017422017Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cistus/*microbiology, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Spain, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny30747616Bacillus acidinfaciens sp. nov., isolated from farmland soil.Sun L, Chen Y, Tian W, Yao L, Chen Z, Ouyang WInt J Syst Evol Microbiol10.1099/ijsem.0.0032712019Bacillus/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, *Farms, 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/urltitlejournalpubmed
6152Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16014)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16014
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
23312Jeroen Heyrman, Bram Vanparys, Niall A. Logan, An Balcaen, Marina Rodríguez-Díaz, Andreas Felske, Paul De Vos10.1099/ijs.0.02723-0Bacillus novalis sp. nov., Bacillus vireti sp. nov., Bacillus soli sp. nov., Bacillus bataviensis sp. nov. and Bacillus drentensis sp. nov., from the Drentse A grasslandsIJSEM 54: 47-57 200414742458
23313Patsy Scheldeman, Marina Rodríguez-Díaz, Johan Goris, Annelies Pil, Elke De Clerck, Lieve Herman, Paul De Vos, Niall A. Logan, Marc Heyndrickx10.1099/ijs.0.63095-0Bacillus farraginis sp. nov., Bacillus fortis sp. nov. and Bacillus fordii sp. nov., isolated at dairy farmsIJSEM 54: 1355-1364 200415280314
38323Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6492
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)
68382Automatically annotated from API zym
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
70877Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID21205.1StrainInfo: A central database for resolving microbial strain identifiers
119425Curators of the CIPCollection of Institut Pasteur (CIP 108821)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108821