Strain identifier

BacDive ID: 683

Type strain: Yes

Species: Lederbergia lenta

Strain Designation: 670, Gibson 165, 883, 165

Strain history: CIP <- 1952, R.E. Gordon, New Jersey Agri. Exper. Stat., New Brunswick, USA: strain 883 <- 1940, J.R. Porter <- T. Gibson: strain 165

NCBI tax ID(s): 1348624 (strain), 1467 (species)

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General

@ref: 2016

BacDive-ID: 683

DSM-Number: 9

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

description: Lederbergia lenta 670 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
1467species
1348624strain

strain history

@refhistory
2016<- ATCC <- N.R. Smith, 670 <- T. Gibson, 165
67770CCM 2214 <-- NCIB 8773 <-- NCTC 4824 <-- T. Gibson 165.
120583CIP <- 1952, R.E. Gordon, New Jersey Agri. Exper. Stat., New Brunswick, USA: strain 883 <- 1940, J.R. Porter <- T. Gibson: strain 165

doi: 10.13145/bacdive683.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Lederbergia
  • species: Lederbergia lenta
  • full scientific name: Lederbergia lenta corrig. (Gibson 1935) Gupta et al. 2020

  • synonyms

    @refsynonym
    20215Bacillus lentus
    20215Lederbergia lentus

@ref: 2016

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Lederbergia

species: Lederbergia lenta

full scientific name: Lederbergia lenta (Gibson 1935) Gupta et al. 2020

strain designation: 670, Gibson 165, 883, 165

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.548
69480100positive
120583yespositiverod-shaped

colony morphology

  • @ref: 120583

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
37728MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
2016CASO AGAR (MERCK 105458) (DSMZ Medium 220)yesName: CASO AGAR (Merck 105458) (DSMZ Medium 220; with strain-specific modifications) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Urea 1.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/220
120583CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
120583CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
2016positivegrowth26mesophilic
37728positivegrowth30mesophilic
44431positivegrowth30-37mesophilic
67770positivegrowth30mesophilic
120583positivegrowth10-37
120583nogrowth45thermophilic
120583nogrowth55thermophilic

culture pH

  • @ref: 120583
  • ability: positive
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
44431aerobe
120583obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes99.998
120583yes

halophily

@refsaltgrowthtested relationconcentration
120583NaClpositivegrowth4-6 %
120583NaClnogrowth0 %
120583NaClnogrowth2 %
120583NaClnogrowth8 %
120583NaClnogrowth10 %

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
68368D-glucose-fermentation17634
68368gelatin-hydrolysis5291
68368tryptophan-energy source27897
68368urea+hydrolysis16199
68368citrate-assimilation16947
68368ornithine-degradation18257
68368lysine-degradation25094
68368arginine-hydrolysis29016
120583citrate-carbon source16947
120583esculin+hydrolysis4853
120583hippurate+hydrolysis606565
120583nitrate-reduction17632
120583nitrite-reduction16301
120583nitrate-respiration17632
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
12058335581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12058315688acetoin-
12058317234glucose-

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
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
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
120583oxidase+
120583beta-galactosidase+3.2.1.23
120583alcohol dehydrogenase-1.1.1.1
120583gelatinase-
120583amylase+
120583DNase-
120583caseinase-3.4.21.50
120583catalase+1.11.1.6
120583tween esterase-
120583gamma-glutamyltransferase-2.3.2.2
120583lysine decarboxylase-4.1.1.18
120583ornithine decarboxylase-4.1.1.17
120583urease+3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELControlRIBXYLMANMALLACSACGLYGCAT
44431---++++-++----------

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120583-+++---------+-+----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLU
44431+-----+--+--

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
44431-------------------------+--------------+---------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120583------------------++---------------------------------------+--------------------------+------------

Isolation, sampling and environmental information

isolation

@refsample type
2016soil
44431Soil
67770Soil
120583Environment, Soil

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_5103.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_2484;97_3034;98_3809;99_5103&stattab=map
  • Last taxonomy: Lederbergia lentus subclade
  • 16S sequence: D16272
  • Sequence Identity:
  • Total samples: 494
  • soil counts: 300
  • aquatic counts: 15
  • animal counts: 167
  • plant counts: 12

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
20161Risk group (German classification)
1205831Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacillus lentus clone EK-36_f 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF478107510ena1467
20218Bacillus lentus clone EK-33_f 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF478108541ena1467
20218Bacillus lentus clone EK-2N_f 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF478109459ena1467
20218Bacillus lentus clone EK-3N_F 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF478110669ena1467
20218Bacillus lentus gene for 16S rRNA, partial sequenceAB006928276ena1467
20218Bacillus lentus gene for 16S rRNA, partial sequence, strain: IAM 12466D162721486ena1467
20218Bacillus lentus strain JCM2511 DNA for 16S ribosomal RNA, partial sequenceD783151433ena1467
20218Bacillus lentus gene for 16S rRNA, partial sequenceAB2717461477ena1467
20218B.lentus 16S ribosomal RNAX606011429ena1467
20218Bacillus lentus gene for 16S ribosomal RNAAB0211891535ena1467

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lederbergia lenta NCTC4824GCA_900478165completencbi1467
66792Bacillus lentus NBRC 164441348624.3wgspatric1348624
66792Bacillus lentus strain NCTC48241467.3completepatric1467
66792Bacillus lentus NCTC 48242808606624completeimg1467
66792Bacillus lentus NBRC 164442731957655draftimg1348624
67770Lederbergia lenta NBRC 16444GCA_001591545contigncbi1348624

GC content

@refGC-contentmethod
201636.4Buoyant density centrifugation (BD)
201636.3thermal denaturation, midpoint method (Tm)
6777036.5
6777037

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedyes84.253no
gram-positiveyes88.781no
anaerobicno98.904yes
aerobicyes92.413yes
halophileyes64.067no
spore-formingyes94.804no
thermophileno99.692yes
glucose-utilyes84.412no
motileyes87.958no
glucose-fermentno88.736yes

External links

@ref: 2016

culture collection no.: DSM 9, ATCC 10840, CCM 2214, NCIB 8773, NCTC 4824, CCUG 1816, NRS 670, JCM 2511, BCRC 11735, CECT 18, CIP 52.74, HAMBI 1918, IAM 12466, IAM 14178, IFO 15655, IFO 16413, IFO 16444, LMG 12355, LMG 16798, LMG 9579, NBRC 15655, NBRC 16413, NBRC 16444, NCCB 48017, NCFB 1127, NCIMB 8713, NCIMB 8773, NRRL B-396, NRRL NRS-883, VKM B-500, NCDO 1127, CIP 52.73

straininfo link

  • @ref: 70358
  • straininfo: 92140

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20656804Bacillus graminis sp. nov., an endophyte isolated from a coastal dune plant.Bibi F, Chung EJ, Jeon CO, Chung YRInt J Syst Evol Microbiol10.1099/ijs.0.023820-02010Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Elymus/*microbiology, Endophytes/classification/genetics/isolation & purification, Fatty Acids/chemistry, Molecular Sequence Data, Peptidoglycan/chemistry, *Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, Salt-Tolerant Plants/microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryEnzymology
Phylogeny24277860Bacillus panacisoli sp. nov., isolated from ginseng soil.Choi JH, Cha CJInt J Syst Evol Microbiol10.1099/ijs.0.054320-02013Bacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Panax/*microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2016Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 9)https://www.dsmz.de/collection/catalogue/details/culture/DSM-9
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
37728Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/13367
44431Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 1816)https://www.ccug.se/strain?id=1816
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)
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
70358Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92140.1StrainInfo: A central database for resolving microbial strain identifiers
120583Curators of the CIPCollection of Institut Pasteur (CIP 52.74)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2052.74