Strain identifier

BacDive ID: 11976

Type strain: Yes

Species: Sporosarcina globispora

Strain Designation: W 25, W25

Strain history: CIP <- 1988, DSM <- ATCC <- J.L. Stokes: strain W25

NCBI tax ID(s): 1459 (species)

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General

@ref: 2012

BacDive-ID: 11976

DSM-Number: 4

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, psychrophilic, motile

description: Sporosarcina globispora W 25 is an aerobe, spore-forming, psychrophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 1459
  • Matching level: species

strain history

@refhistory
2012<- ATCC <- J.L. Stokes, W 25
67770CCM 2119 <-- J. L. Stokes W25.
119647CIP <- 1988, DSM <- ATCC <- J.L. Stokes: strain W25

doi: 10.13145/bacdive11976.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Caryophanaceae
  • genus: Sporosarcina
  • species: Sporosarcina globispora
  • full scientific name: Sporosarcina globispora (Larkin and Stokes 1967) Yoon et al. 2001

  • synonyms

    • @ref: 20215
    • synonym: Bacillus globisporus

@ref: 2012

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Caryophanaceae

genus: Sporosarcina

species: Sporosarcina globispora

full scientific name: Sporosarcina globispora (Larkin and Stokes 1967) Yoon et al. 2001

strain designation: W 25, W25

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes94.608
69480100positive
119647yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
40585MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
2012BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yesName: 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 waterhttps://mediadive.dsmz.de/medium/514
119647CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
119647CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
2012positivegrowth20psychrophilic
40585positivegrowth15psychrophilic
44988positivegrowth30mesophilic
67770positivegrowth20psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
44988aerobe
119647obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

  • @ref: 2012
  • compound: labilomycin

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
68368L-arabinose-fermentation30849
68368amygdalin-fermentation27613
68368melibiose-fermentation28053
68368sucrose-fermentation17992
68368L-rhamnose-fermentation62345
68368sorbitol-fermentation30911
68368myo-inositol-fermentation17268
68368D-mannitol-fermentation16899
68368D-glucose-fermentation17634
68368gelatin-hydrolysis5291
68368tryptophan-energy source27897
68368urea+hydrolysis16199
68368citrate-assimilation16947
68368ornithine-degradation18257
68368lysine-degradation25094
68368arginine-hydrolysis29016
119647nitrate-reduction17632
119647nitrite-reduction16301
68379nitrate-reduction17632
68379esculin-hydrolysis4853
68379urea+hydrolysis16199
68379gelatin-hydrolysis5291
68379D-ribose-fermentation16988
68379D-xylose-fermentation65327
68379D-mannitol-fermentation16899
68379maltose-fermentation17306
68379lactose-fermentation17716
68379sucrose-fermentation17992
68379glycogen-fermentation28087

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
11964735581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68379catalase+1.11.1.6
68379gelatinase-
68379urease+3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase-3.5.1.B15
68368cytochrome oxidase+1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23
119647oxidase-
119647catalase+1.11.1.6
119647urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELControlRIBXYLMANMALLACSACGLYGCAT
44988--++-+---+---------+

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119647-+++-+---+++++------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
44988+-----+--+----------+

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
44988--------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample type
2012soil
44988Soil
119647Environment, Soil

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_4843.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_1276;97_1516;98_3626;99_4843&stattab=map
  • Last taxonomy: Sporosarcina
  • 16S sequence: AM237400
  • Sequence Identity:
  • Total samples: 18424
  • soil counts: 10719
  • aquatic counts: 2194
  • animal counts: 3706
  • plant counts: 1805

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
20121Risk group (German classification)
1196471Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Sporosarcina globispora syn. Bacillus globisporus partial 16S rRNA gene, isolate OS-253AM2374001463ena1459
20218Staphylococcus epidermidis strain DSM-4 16S ribosomal RNA gene, partial sequenceJQ638379619ena1282
20218Vibrio sp. DSM4 16S ribosomal RNA gene, partial sequenceKC439200800ena1343243
20218B.globisporus gene for 16S rRNAX684151554ena1459
20218Sporosarcina globispora gene for 16S rRNA, partial sequenceAB006926275ena1459
20218Sporosarcina globispora gene for 16S rRNA, partial sequence, strain: NBRC 16082AB6810451477ena1459
20218B.globisporus 16S ribosomal RNAX606441430ena1459
20218B. globisporus rDNA for 16S rRNA (strain W25)X549671553ena1459

Genome sequences

  • @ref: 67770
  • description: Sporosarcina globispora DSM 4
  • accession: GCA_001274725
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 1459

GC content

@refGC-contentmethod
201239.8thermal denaturation, midpoint method (Tm)
201239.7Buoyant density centrifugation (BD)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes86.012no
flagellatedyes76.744no
gram-positiveyes85.704no
anaerobicno97.888yes
halophileno76.391no
spore-formingyes95.274no
thermophileno97.757yes
glucose-utilyes87.629no
aerobicyes89.824yes
glucose-fermentno92.971yes

External links

@ref: 2012

culture collection no.: DSM 4, ATCC 23301, CCM 2119, NCIMB 11434, CCUG 7419, CIP 103266, LMG 6928, JCM 10046, IFO 16082, CGMCC 1.3607, IAM 14760, JCM 2509, KCTC 3736, NBRC 16082, NRRL B-3396, NRRL NRS-1533, VKM B-1435

straininfo link

@refstraininfo
811881121
81189312111

literature

topicPubmed-IDtitleauthorsjournalDOIyeartopic2mesh
Genetics26494677Draft Genome Sequence of Sporosarcina globispora W 25T (DSM 4), a Psychrophilic Bacterium Isolated from Soil and River Water.Wang JP, Liu B, Liu GH, Xiao RF, Zheng XF, Shi H, Ge CBGenome Announc10.1128/genomeA.01230-152015Phylogeny
Phylogeny34877615Sporosarcina beigongshangi sp. nov., isolated from pit mud of Baijiu.Sun Z, Guo L, Yan Y, Zhang X, Wang J, Liu B, Xu J, Ren QArch Microbiol10.1007/s00203-021-02601-22021TranscriptomeBacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sporosarcina/genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2012Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4
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
40585Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15044
44988Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 7419)https://www.ccug.se/strain?id=7419
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
68379Automatically annotated from API Coryne
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
81188Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID1121.1StrainInfo: A central database for resolving microbial strain identifiers
81189Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID312111.1StrainInfo: A central database for resolving microbial strain identifiers
119647Curators of the CIPCollection of Institut Pasteur (CIP 103266)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103266