Strain identifier

BacDive ID: 1220

Type strain: Yes

Species: Siminovitchia farraginis

Strain Designation: R-6540

Strain history: CIP <- 2005, DSMZ <- P. Scheldeman, Flemish Com. Ministry, Belgium: strain R-6540

NCBI tax ID(s): 254757 (species)

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General

@ref: 6151

BacDive-ID: 1220

DSM-Number: 16013

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

description: Siminovitchia farraginis R-6540 is an obligate aerobe, spore-forming, mesophilic bacterium that forms irregular colonies and was isolated from milking apparatus, cluster.

NCBI tax id

  • NCBI tax id: 254757
  • Matching level: species

strain history

@refhistory
6151<- P. Scheldeman; R-6540
119286CIP <- 2005, DSMZ <- P. Scheldeman, Flemish Com. Ministry, Belgium: strain R-6540

doi: 10.13145/bacdive1220.20230509.8.1

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

  • synonyms

    • @ref: 20215
    • synonym: Bacillus farraginis

@ref: 6151

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Siminovitchia

species: Siminovitchia farraginis

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

strain designation: R-6540

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
23313negative1.2-4.0 µm0.5-0.8 µmrod-shapedyes
69480yes98.073
69480positive100
119286positiverod-shapedyes

colony morphology

@refcolony sizecolony colorcolony shapeincubation periodmedium used
233131 mmcream or translucentirregular3 daysNutrient agar
119286

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6151CASO 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
38322MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119286CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6151positivegrowth30mesophilic
23313positivegrowth30-45
23313inconsistentgrowth20psychrophilic
38322positivegrowth30mesophilic
119286positivegrowth22-55
119286nogrowth10psychrophilic

culture pH

@refabilitytypepH
23313inconsistentgrowth9.0
23313nogrowth5.0
119286positivegrowth6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23313obligate aerobe
119286obligate aerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
23312ellispoidal, paracentral or subterminal, occasionally slightly swollen sporangiaendosporeyes
69481yes100
69480yes100
119286yes

halophily

@refsaltgrowthtested relationconcentration
23313NaClpositivegrowth7 %
119286NaClpositivegrowth0-4 %
119286NaClnogrowth6 %
119286NaClnogrowth8 %
119286NaClnogrowth10 %

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
2331317521(-)-quinic acid-carbon source
23313168082-dehydro-D-gluconate-carbon source
23313510573-phenylpropionate-carbon source
23313178794-hydroxybenzoate-carbon source
23313174265-dehydro-D-gluconate-carbon source
2331315963ribitol-carbon source
2331336219alpha-lactose-carbon source
2331316150benzoate-carbon source
2331317750betaine-carbon source
2331327689decanoate-carbon source
2331325646octanoate-carbon source
2331316383cis-aconitate-carbon source
2331316947citrate-carbon source
2331323399coumarate-carbon source
2331318333D-arabitol-carbon source
2331317057cellobiose-carbon source
2331315824D-fructose-carbon source
2331312936D-galactose-carbon source
2331318024D-galacturonic acid-carbon source
2331330612D-glucarate-carbon source
233138391D-gluconate-carbon source
2331317634D-glucose-carbon source
2331315748D-glucuronate-carbon source
2331362318D-lyxose-carbon source
2331316899D-mannitol-carbon source
2331316024D-mannose-carbon source
233136731melezitose-carbon source
2331328053melibiose-carbon source
2331316634raffinose-carbon source
2331316443D-tagatose-carbon source
2331330927D-tartrate-carbon source
2331316551D-trehalose-carbon source
2331332528turanose-carbon source
2331365327D-xylose-carbon source
2331333871glycerate-carbon source
2331317113erythritol-carbon source
233134853esculin-carbon source
2331316000ethanolamine-carbon source
2331316537galactarate-carbon source
2331328066gentiobiose-carbon source
2331358044gentisate-carbon source
2331317754glycerol-carbon source
2331317240itaconate-carbon source
2331330849L-arabinose-carbon source
2331318403L-arabitol-carbon source
2331318287L-fucose-carbon source
2331362345L-rhamnose-carbon source
2331317115L-serine-carbon source
2331317266L-sorbose-carbon source
2331330924L-tartrate-carbon source
233136359lactulose-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
23313506227N-acetylglucosamine-carbon source
2331318394palatinose-carbon source
2331318401phenylacetate-carbon source
2331317272propionate-carbon source
2331336241protocatechuate-carbon source
2331317992sucrose-carbon source
2331315708trans-aconitate-carbon source
2331362517tricarballylate-carbon source
2331318123trigonelline-carbon source
2331316765tryptamine-carbon source
2331317151xylitol-carbon source
23313casein-hydrolysis
233134853esculin-hydrolysis
2331328017starch-hydrolysis
23313309162-oxoglutarate+carbon source
2331316865gamma-aminobutyric acid+carbon source
23313158875-aminovaleric acid+carbon source
2331315570D-alanine+carbon source
2331317315D-glucosamine+carbon source
2331315588D-malate+carbon source
2331316988D-ribose+carbon source
2331317924D-sorbitol+carbon source
23313370543-hydroxybutyrate+carbon source
2331324996lactate+carbon source
2331316813galactitol+carbon source
2331329806fumarate+carbon source
2331317859glutaric acid+carbon source
2331318295histamine+carbon source
2331316977L-alanine+carbon source
2331329991L-aspartate+carbon source
2331329985L-glutamate+carbon source
2331315971L-histidine+carbon source
2331315589L-malate+carbon source
2331317203L-proline+carbon source
2331316828L-tryptophan+carbon source
2331317895L-tyrosine+carbon source
2331325115malate+carbon source
2331315792malonate+carbon source
2331330928meso-tartrate+carbon source
2331317148putrescine+carbon source
2331330031succinate+carbon source
11928616947citrate-carbon source
1192864853esculin-hydrolysis
119286606565hippurate-hydrolysis
11928617632nitrate-reduction
11928616301nitrite-reduction
11928617632nitrate-respiration

metabolite production

  • @ref: 119286
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11928615688acetoin-
11928617234glucose-

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
119286oxidase+
119286beta-galactosidase-3.2.1.23
119286alcohol dehydrogenase-1.1.1.1
119286gelatinase+/-
119286amylase-
119286DNase-
119286caseinase-3.4.21.50
119286catalase+1.11.1.6
119286tween esterase-
119286gamma-glutamyltransferase+2.3.2.2
119286lecithinase-
119286lipase-
119286lysine decarboxylase-4.1.1.18
119286ornithine decarboxylase-4.1.1.17
119286urease-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
119286--++-++--+-+--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119286---------++--------++----+---+---++-------------++--------+-+---------+-++-+--++++-+--+-++++-+-+-++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6151milking apparatus, clusterLovendegemBelgiumBELEurope
119286Milking apparratus, clusterBelgiumBELEurope

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Industrial
  • Cat3: #Engineered product

taxonmaps

  • @ref: 69479
  • File name: preview.99_114484.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_3737;97_58336;98_77488;99_114484&stattab=map
  • Last taxonomy: Bacillus farraginis subclade
  • 16S sequence: AY443036
  • Sequence Identity:
  • Total samples: 268
  • soil counts: 73
  • aquatic counts: 11
  • animal counts: 170
  • plant counts: 14

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
61511Risk group (German classification)
1192861Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6151
  • description: Bacillus farraginis strain R-6540 16S ribosomal RNA gene, partial sequence
  • accession: AY443036
  • length: 1416
  • database: ena
  • NCBI tax ID: 254757

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Siminovitchia farraginis DSM 16013GCA_001439965scaffoldncbi254757
66792Bacillus farraginis strain DSM 16013254757.3wgspatric254757

GC content

@refGC-contentmethod
615143.7
2331343.7high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedyes71.412no
gram-positiveyes67.303yes
anaerobicno98.811yes
aerobicyes89.668yes
halophileyes54.63yes
spore-formingyes97.281yes
glucose-utilyes83.418yes
motileyes90.572yes
thermophileno98.367yes
glucose-fermentno87.337no

External links

@ref: 6151

culture collection no.: DSM 16013, CIP 108820, LMG 22081

straininfo link

  • @ref: 70876
  • straininfo: 20613

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
Genetics27313303Draft Genome Sequence of Bacillus farraginis R-6540T (DSM 16013), a Spore-Forming Bacterium Isolated at Dairy Farms.Wang JP, Liu B, Liu GH, Ge CB, Xiao RF, Zheng XF, Shi HGenome Announc10.1128/genomeA.00562-162016Phylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6151Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16013)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16013
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
38322Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6491
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
70876Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID20613.1StrainInfo: A central database for resolving microbial strain identifiers
119286Curators of the CIPCollection of Institut Pasteur (CIP 108820)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108820