Strain identifier

BacDive ID: 1519

Type strain: Yes

Species: Terribacillus saccharophilus

Strain Designation: 002-048

Strain history: CIP <- 2007, IAM

NCBI tax ID(s): 361277 (species)

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General

@ref: 15770

BacDive-ID: 1519

DSM-Number: 21619

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

description: Terribacillus saccharophilus 002-048 is an aerobe, spore-forming, mesophilic bacterium that was isolated from field soil.

NCBI tax id

  • NCBI tax id: 361277
  • Matching level: species

strain history

@refhistory
15770<- JCM <- IAM <- A. Yokota; 002-048
381502007, IAM
67770IAM 15309 <-- A. Yokota 002-048.
67771<- A Yokota, IAM
122340CIP <- 2007, IAM

doi: 10.13145/bacdive1519.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Terribacillus
  • species: Terribacillus saccharophilus
  • full scientific name: Terribacillus saccharophilus An et al. 2007

@ref: 15770

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Terribacillus

species: Terribacillus saccharophilus

full scientific name: Terribacillus saccharophilus An et al. 2007

strain designation: 002-048

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31809positive3.55 µm0.85 µmrod-shapedno
67771rod-shapedno
67771positive
69480positive100
122340positiverod-shapedyes

pigmentation

  • @ref: 31809
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15770BACTO 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
38150MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122340CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
15770positivegrowth30mesophilic
31809positivegrowth05-45
31809positiveoptimum25mesophilic
38150positivegrowth30mesophilic
67770positivegrowth30mesophilic
67771positivegrowth25-30mesophilic

culture pH

@refabilitytypepHPH range
31809positivegrowth06-10alkaliphile
31809positiveoptimum8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31809aerobe
67771aerobe
122340obligate aerobe

spore formation

@refspore formationtype of sporeconfidence
31809yes
67771yesendospore
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
31809NaClpositivegrowth0-16 %
31809NaClpositiveoptimum01-05 %

observation

@refobservation
67770quinones: MK-7
67771quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3180917057cellobiose+carbon source
3180928757fructose+carbon source
3180928260galactose+carbon source
3180917234glucose+carbon source
3180917754glycerol+carbon source
3180917716lactose+carbon source
3180929864mannitol+carbon source
3180937684mannose+carbon source
3180928053melibiose+carbon source
31809506227N-acetylglucosamine+carbon source
3180916634raffinose+carbon source
3180926546rhamnose+carbon source
3180917814salicin+carbon source
3180917992sucrose+carbon source
3180927082trehalose+carbon source
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-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
6837128017starch-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
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from
12234017632nitrate-reduction
12234016301nitrite-reduction

metabolite production

  • @ref: 122340
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31809catalase+1.11.1.6
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
122340oxidase-
122340catalase+1.11.1.6
122340urease-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
122340-+++-+---++-++--+---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122340+--------++++-+--+---++++++-++++--+---+--+----+/---

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
15770field soilJapanJPNAsia
67770Field soil from Tama CityJapanJPNAsiaTokyo
67771From field soil in JapanJapanJPNAsia
122340Environment, SoilJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_10385.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_2557;97_3126;98_3926;99_10385&stattab=map
  • Last taxonomy: Terribacillus
  • 16S sequence: AB243845
  • Sequence Identity:
  • Total samples: 10598
  • soil counts: 5792
  • aquatic counts: 1104
  • animal counts: 1158
  • plant counts: 2544

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
157701Risk group (German classification)
1223401Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15770
  • description: Terribacillus saccharophilus rrs gene for 16S rRNA, partial sequence, strain: 002-048
  • accession: AB243845
  • length: 1515
  • database: ena
  • NCBI tax ID: 361277

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Terribacillus saccharophilus strain DSM 21619361277.15wgspatric361277
66792Terribacillus saccharophilus strain DSM 21619361277.14wgspatric361277
66792Terribacillus saccharophilus DSM 216192636416060draftimg361277
67770Terribacillus saccharophilus DSM 21619GCA_900110015scaffoldncbi361277
67770Terribacillus saccharophilus DSM 21619GCA_002335735scaffoldncbi361277

GC content

@refGC-contentmethod
1577044
6777044high performance liquid chromatography (HPLC)
6777144.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes92.871yes
anaerobicno98.382no
halophileyes68.106no
spore-formingyes94.102no
glucose-utilyes90.011yes
motileyes83.227yes
flagellatedno50yes
thermophileno99.499yes
aerobicyes89.158yes
glucose-fermentno78.07no

External links

@ref: 15770

culture collection no.: DSM 21619, IAM 15309, JCM 21759, KCTC 13936, CGMCC 1.7685, CIP 109483

straininfo link

  • @ref: 71165
  • straininfo: 297339

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17220440Terribacillus saccharophilus gen. nov., sp. nov. and Terribacillus halophilus sp. nov., spore-forming bacteria isolated from field soil in Japan.An SY, Asahara M, Goto K, Kasai H, Yokota AInt J Syst Evol Microbiol10.1099/ijs.0.64340-02007Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Gram-Positive Endospore-Forming Rods/*classification/genetics/isolation & purification/physiology, Japan, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spores, Bacterial/physiologyGenetics
Phylogeny18842842Proposal for transfer of Pelagibacillus goriensis Kim et al. 2007 to the genus Terribacillus as Terribacillus goriensis comb. nov.Krishnamurthi S, Chakrabarti TInt J Syst Evol Microbiol10.1099/ijs.0.65579-02008Bacillaceae/chemistry/*classification/*genetics, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Genes, rRNA, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil MicrobiologyPhenotype
Phylogeny20118295Terribacillus aidingensis sp. nov., a moderately halophilic bacterium.Liu W, Jiang L, Guo C, Yang SSInt J Syst Evol Microbiol10.1099/ijs.0.017228-02010Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Lakes/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15770Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21619)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21619
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
31809Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2807828776041
38150Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7231
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68371Automatically annotated from API 50CH acid
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
71165Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297339.1StrainInfo: A central database for resolving microbial strain identifiers
122340Curators of the CIPCollection of Institut Pasteur (CIP 109483)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109483