Strain identifier

BacDive ID: 1532

Type strain: Yes

Species: Lysinibacillus sphaericus

Strain Designation: Gibson 1013, 1013

Strain history: CIP <- 1965, ATCC <- R.E. Gordon, New Jersey Agri. Exper. Stat., New Brunswick, USA <- T. Gibson: strain 1013 <- Kràl Collection, Vienna, Austria <- M. Wund <- E. Neide

NCBI tax ID(s): 1354027 (strain), 1421 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 2029

BacDive-ID: 1532

DSM-Number: 28

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

description: Lysinibacillus sphaericus Gibson 1013 is an aerobe, spore-forming, mesophilic human pathogen that was isolated from Unknown source.

NCBI tax id

NCBI tax idMatching level
1354027strain
1421species

strain history

@refhistory
2029<- ATCC <- R.E. Gordon <- T. Gibson, 1013 <- Král Collection <- M. Wund <- E. Neide
67770CCM 2120 <-- R. E. Gordon <-- T. Gibson 1013 <-- Král Collection <-- Wund <-- E. Neide.
123252CIP <- 1965, ATCC <- R.E. Gordon, New Jersey Agri. Exper. Stat., New Brunswick, USA <- T. Gibson: strain 1013 <- Kràl Collection, Vienna, Austria <- M. Wund <- E. Neide

doi: 10.13145/bacdive1532.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Caryophanaceae
  • genus: Lysinibacillus
  • species: Lysinibacillus sphaericus
  • full scientific name: Lysinibacillus sphaericus (Meyer and Neide 1904) Ahmed et al. 2007
  • synonyms

    @refsynonym
    20215Lysinibacillus varians
    20215Bacillus sphaericus
    20215Lysinibacillus mangiferahumi
    20215Lysinibacillus mangiferihumi
    20215Lysinibacillus tabacifolii

@ref: 2029

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Caryophanaceae

genus: Lysinibacillus

species: Lysinibacillus sphaericus

full scientific name: Lysinibacillus sphaericus (Meyer and Neide 1904) Ahmed et al. 2007

strain designation: Gibson 1013, 1013

type strain: yes

Morphology

cell morphology

  • @ref: 123252
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 123252
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2029NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
35013MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
123252CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
2029positivegrowth30mesophilic
35013positivegrowth30mesophilic
44997positivegrowth30-37mesophilic
67770positivegrowth30mesophilic
123252positivegrowth22-45
123252nogrowth10psychrophilic
123252nogrowth55thermophilic

culture pH

  • @ref: 123252
  • ability: positive
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
44997aerobe
123252obligate aerobe

spore formation

  • @ref: 123252
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
123252NaClpositivegrowth0-4 %
123252NaClnogrowth6 %
123252NaClnogrowth8 %
123252NaClnogrowth10 %

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
123252citrate-carbon source16947
123252esculin-hydrolysis4853
123252hippurate-hydrolysis606565
123252nitrate-reduction17632
123252nitrite-reduction16301
123252nitrate-respiration17632

metabolite production

  • @ref: 123252
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12325215688acetoin-
12325217234glucose-

enzymes

@refvalueactivityec
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
123252oxidase+
123252beta-galactosidase-3.2.1.23
123252alcohol dehydrogenase-1.1.1.1
123252gelatinase+/-
123252amylase-
123252DNase+
123252caseinase-3.4.21.50
123252catalase+1.11.1.6
123252tween esterase+
123252gamma-glutamyltransferase-2.3.2.2
123252lecithinase-
123252lipase-
123252lysine decarboxylase-4.1.1.18
123252ornithine decarboxylase-4.1.1.17
123252protease-
123252urease-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
123252-+++-+-+-++---------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123252-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123252------------------+--------------------------------------------------------+------------++------+--

Isolation, sampling and environmental information

isolation

  • @ref: 123252
  • sample type: Unknown source

taxonmaps

  • @ref: 69479
  • File name: preview.99_4772.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_503;97_577;98_664;99_4772&stattab=map
  • Last taxonomy: Lysinibacillus
  • 16S sequence: AJ310084
  • Sequence Identity:
  • Total samples: 337
  • soil counts: 72
  • aquatic counts: 49
  • animal counts: 210
  • plant counts: 6

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
2029yes, in single casesyes1Risk group (German classification)
1232521Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacillus sphaericus clone BSPH-1R 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF478090540ena1421
20218Bacillus sphaericus 16S rRNA gene, strain DSM 28AJ3100841515ena1421
20218Bacillus sphaericus strain ATCC 14577 16S ribosomal RNA gene, partial sequenceDQ2862991419ena1421
20218Bacillus sphaericus complete 16S ribosomal RNA geneL140101493ena1421
2029Bacillus sphaericus 16S ribosomal RNA gene, partial sequenceAF1694951410ena1421
67770Bacillus sphaericus gene for 16S rRNA, partial sequenceAB2717421477ena1421
67770Lysinibacillus sphaericus gene for 16S rRNA, strain: IAM 13420D162801484ena1421
67770B.sphaericus 16S ribosomal RNAX606391430ena1421

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lysinibacillus sphaericus KCTC 33461354027.3wgspatric1354027
66792Lysinibacillus sphaericus strain NBRC 150951421.85wgspatric1421
66792Lysinibacillus sphaericus strain NCTC103381421.65wgspatric1421
66792Lysinibacillus sphaericus NCTC 103382855314903draftimg1421
66792Lysinibacillus sphaericus KCTC 33462554235285draftimg1354027
67770Lysinibacillus sphaericus KCTC 3346 KCTC 3346(T)GCA_000427235contigncbi1354027
67770Lysinibacillus sphaericus NBRC 15095GCA_006539805contigncbi1421
67770Lysinibacillus sphaericus DSM 28GCA_002982115completencbi1421
67770Lysinibacillus sphaericus NRRL B-23268GCA_005217555contigncbi1421
67770Lysinibacillus sphaericus NCTC10338GCA_900445465contigncbi1421

GC content

@refGC-contentmethod
202937.3thermal denaturation, midpoint method (Tm)
202937.1Buoyant density centrifugation (BD)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes85.24no
gram-positiveyes90.08no
anaerobicno95.957no
halophileno91.681no
spore-formingyes96.58no
thermophileno99.922no
glucose-utilyes84.578no
flagellatedyes80.105no
aerobicyes87.917yes
glucose-fermentno89.599no

External links

@ref: 2029

culture collection no.: DSM 28, ATCC 14577, CCM 2120, JCM 2502, NCIB 9370, NCTC 10338, CCUG 7428, LMG 7134, BCRC 12825, CECT 33, CIP 65.30, IAM 13420, IFO 15095, KCTC 3346, NBRC 15095, NCCB 75018, NCIMB 9370, NRRL B-23268, VKM B-509, NCDO 1767

straininfo link

  • @ref: 71178
  • straininfo: 7137

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology4015092Substrate-induced changes in sulfhydryl reactivity of bacterial D-amino acid transaminase.Soper TS, Ueno H, Manning JMArch Biochem Biophys10.1016/0003-9861(85)90001-31985Bacillus/enzymology, Bacteria/*enzymology, Binding Sites, D-Alanine Transaminase, *Disulfides, Dithionitrobenzoic Acid/pharmacology, Ethylamines/pharmacology, Hydrogen-Ion Concentration, Kinetics, Propionates/pharmacology, Protein Conformation, Pyridines/pharmacology, Sulfhydryl Compounds/*metabolism, Sulfhydryl Reagents/pharmacology, Transaminases/antagonists & inhibitors/*metabolismMetabolism
Pathogenicity89226352-D protein crystals as an immobilization matrix for producing reaction zones in dipstick-style immunoassays.Breitwieser A, Kupcu S, Howorka S, Weigert S, Langer C, Hoffmann-Sommergruber K, Scheiner O, Sleytr UB, Sara MBiotechniques10.2144/96215rr051996Antibodies, Monoclonal/analysis, Bacillus, Bacterial Proteins, Crystallization, Humans, Immunoassay/*methods, Immunoglobulin G/analysis, Staphylococcal Protein A, Streptavidin
Pathogenicity9055417Comparison of the cellular fatty acid composition of a bacterium isolated from a human and alleged to be Bacillus sphaericus with that of Bacillus sphaericus isolated from a mosquito larvicide.Siegel JP, Smith AR, Novak RJAppl Environ Microbiol10.1128/aem.63.3.1006-1010.19971997Animals, Bacillus/*chemistry/*classification, Culicidae, Fatty Acids/*analysis, Humans, Larva, Lung/microbiology, Pest Control, Biological, Reproducibility of ResultsPhylogeny
Phylogeny12901420Genetic polymorphism by RAPD-PCR and phenotypic characteristics of isolated thermotolerant Bacillus strains from hot spring sources.Hazem A, Manar ANew Microbiol2003Bacillus/*classification/*genetics/metabolism, Cluster Analysis, DNA Fingerprinting, DNA, Bacterial/chemistry/genetics, Hot Temperature, Hydrogen-Ion Concentration, Jordan, Microbial Sensitivity Tests, Phenotype, Phylogeny, Polymorphism, Genetic, Random Amplified Polymorphic DNA Technique, *Water MicrobiologyStress
Phylogeny17473244Bacillus decisifrondis sp. nov., isolated from soil underlying decaying leaf foliage.Zhang L, Xu Z, Patel BKCInt J Syst Evol Microbiol10.1099/ijs.0.64440-02007Amino Acids/metabolism, Australia, Bacillus/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, Cell Wall/ultrastructure, Culture Media, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Flagella/ultrastructure, Genes, rRNA/genetics, Hydrogen-Ion Concentration, Microscopy, Electron, Transmission, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Spores, Bacterial/cytology, Temperature, Thymidine/metabolism, Trees, Uridine/metabolismMetabolism
Phylogeny17473269Proposal of Lysinibacillus boronitolerans gen. nov. sp. nov., and transfer of Bacillus fusiformis to Lysinibacillus fusiformis comb. nov. and Bacillus sphaericus to Lysinibacillus sphaericus comb. nov.Ahmed I, Yokota A, Yamazoe A, Fujiwara TInt J Syst Evol Microbiol10.1099/ijs.0.63867-02007Bacillaceae/chemistry/*classification/genetics/metabolism, Bacterial Typing Techniques, Base Composition, Boron/metabolism, Cell Wall/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, *Soil Microbiology, TemperatureMetabolism
Phylogeny19502328Lysinibacillus parviboronicapiens sp. nov., a low-boron-containing bacterium isolated from soil.Miwa H, Ahmed I, Yokota A, Fujiwara TInt J Syst Evol Microbiol10.1099/ijs.0.65455-02009Bacterial Typing Techniques, Base Composition, Boron/*metabolism, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genotype, Gram-Positive Asporogenous Rods/*classification/genetics/isolation & purification/physiology, Molecular Sequence Data, Peptidoglycan/analysis, Phenotype, Phylogeny, Polymerase Chain Reaction/methods, Polymorphism, Restriction Fragment Length, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, TurkeyGenetics
Enzymology22266829Cloning of the surface layer gene sllB from Bacillus sphaericus ATCC 14577 and its heterologous expression and purification.Cui YB, Zhou Y, Liu WN, Chen QW, Ma GF, Shi WH, Wang YG, Yang LInt J Mol Med10.3892/ijmm.2012.8902012Amino Acid Sequence, Bacillus/*genetics/metabolism, Bacterial Proteins/*genetics/metabolism, Blotting, Western, *Cloning, Molecular, DNA Primers, DNA, Bacterial/genetics, Escherichia coli/genetics/isolation & purification, Gene Expression Regulation, Bacterial, Membrane Glycoproteins/*genetics/metabolism, Microscopy, Electron, Transmission, Molecular Sequence Data, Plasmids, Recombinant Proteins/genetics/metabolism, Sequence Analysis, DNAMetabolism
Phylogeny23435244Lysinibacillus contaminans sp. nov., isolated from surface water.Kampfer P, Martin K, Glaeser SPInt J Syst Evol Microbiol10.1099/ijs.0.049593-02013Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis, *Water MicrobiologyGenetics
Genetics23950128Genome Sequence of Lysinibacillus sphaericus Strain KCTC 3346T.Jeong H, Jeong DE, Sim YM, Park SH, Choi SKGenome Announc10.1128/genomeA.00625-132013
Phylogeny25070216Lysinibacillus varians sp. nov., an endospore-forming bacterium with a filament-to-rod cell cycle.Zhu C, Sun G, Chen X, Guo J, Xu MInt J Syst Evol Microbiol10.1099/ijs.0.068320-02014Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Cycle, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny27595771Comparative genomics reveals Lysinibacillus sphaericus group comprises a novel species.Gomez-Garzon C, Hernandez-Santana A, Dussan JBMC Genomics10.1186/s12864-016-3056-92016Bacillus/*classification/genetics, Evolution, Molecular, Gene Transfer, Horizontal, Genome, Bacterial, Genomics/*methods, Phylogeny, Sequence Analysis, DNA/*methods, Species SpecificityGenetics
Metabolism35834592A taxonomically representative strain collection to explore xenobiotic and secondary metabolism in bacteria.Kontomina E, Garefalaki V, Fylaktakidou KC, Evmorfidou D, Eleftheraki A, Avramidou M, Udoh K, Panopoulou M, Felfoldi T, Marialigeti K, Fakis G, Boukouvala SPLoS One10.1371/journal.pone.02711252022*Bacteria, Firmicutes, Proteobacteria, Secondary Metabolism, *Xenobiotics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2029Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28)https://www.dsmz.de/collection/catalogue/details/culture/DSM-28
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
35013Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/10215
44997Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 7428)https://www.ccug.se/strain?id=7428
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/
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
71178Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID7137.1StrainInfo: A central database for resolving microbial strain identifiers
123252Curators of the CIPCollection of Institut Pasteur (CIP 65.30)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2065.30