Strain identifier

BacDive ID: 7340

Type strain: Yes

Species: Leifsonia shinshuensis

Strain Designation: DB102, DBI02

Strain history: CIP <- 2000, JCM <- T. Yorifuji: strain DBI02

NCBI tax ID(s): 150026 (species)

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General

@ref: 5734

BacDive-ID: 7340

DSM-Number: 15165

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

description: Leifsonia shinshuensis DB102 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from forest soil.

NCBI tax id

  • NCBI tax id: 150026
  • Matching level: species

strain history

@refhistory
5734<- JCM <- T. Yorifuji; DB102
67770T. Yorifuji DB102.
122590CIP <- 2000, JCM <- T. Yorifuji: strain DBI02

doi: 10.13145/bacdive7340.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Leifsonia
  • species: Leifsonia shinshuensis
  • full scientific name: Leifsonia shinshuensis Suzuki et al. 2000

@ref: 5734

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Leifsonia

species: Leifsonia shinshuensis

full scientific name: Leifsonia shinshuensis Suzuki et al. 2000

strain designation: DB102, DBI02

type strain: yes

Morphology

cell morphology

  • @ref: 122590
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 122590

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5734TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
39586MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122590CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5734positivegrowth28mesophilic
39586positivegrowth30mesophilic
59368positivegrowth30mesophilic
67770positivegrowth30mesophilic
122590positivegrowth25-37mesophilic
122590nogrowth10psychrophilic
122590nogrowth15psychrophilic
122590nogrowth41thermophilic
122590nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
59368aerobe
122590obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
122590NaClpositivegrowth0-4 %
122590NaClnogrowth6 %
122590NaClnogrowth8 %
122590NaClnogrowth10 %

murein

  • @ref: 5734
  • murein short key: B07
  • type: B2gamma {Gly} [L-Dab] D-Glu-D-Dab

observation

  • @ref: 67770
  • observation: quinones: MK-11, MK-10

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
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
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
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
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
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
122590esculin+hydrolysis4853
122590hippurate-hydrolysis606565
122590nitrate-reduction17632
122590nitrite-reduction16301
122590nitrate-respiration17632

antibiotic resistance

  • @ref: 122590
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 122590
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12259015688acetoin-
12259017234glucose-

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
122590oxidase-
122590beta-galactosidase+3.2.1.23
122590alcohol dehydrogenase-1.1.1.1
122590gelatinase-
122590amylase-
122590DNase-
122590caseinase-3.4.21.50
122590catalase+1.11.1.6
122590tween esterase+
122590gamma-glutamyltransferase-2.3.2.2
122590lecithinase-
122590lipase-
122590lysine decarboxylase-4.1.1.18
122590ornithine decarboxylase-4.1.1.17
122590phenylalanine ammonia-lyase-4.3.1.24
122590tryptophan deaminase-
122590urease-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
122590--++-+----++-+-++-+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122590+/--------+/---+/-----+/-+/-------+/-+/-+/-+/-----+/-----------+/---+/---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122590-+----------+-----+--------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5734forest soilNagano pref.JapanJPNAsia
59368SoilNagano Pref.JapanJPNAsia
67770SoilNagano Pref.JapanJPNAsia
122590Environment, SoilNaganoJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_1148.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_671;97_777;98_901;99_1148&stattab=map
  • Last taxonomy: Leifsonia
  • 16S sequence: AB028940
  • Sequence Identity:
  • Total samples: 3840
  • soil counts: 2218
  • aquatic counts: 554
  • animal counts: 672
  • plant counts: 396

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
57341Risk group (German classification)
1225901Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Leifsonia shinshuensis strain DB102 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceDQ2326142145ena150026
5734Microbacteriaceae str. DB102 gene for 16S rRNA, partial sequenceAB0289401395ena97974

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Leifsonia shinshuensis strain DSM 15165150026.7wgspatric150026
66792Leifsonia shinshuensis DSM 151652856442703draftimg150026
67770Leifsonia shinshuensis DSM 15165GCA_013410375contigncbi150026

GC content

  • @ref: 5734
  • GC-content: 70.7
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes51.667no
gram-positiveyes86.324no
anaerobicno99.367no
aerobicyes94.526no
halophileno95.154no
spore-formingno90.717no
glucose-utilyes88.505no
flagellatedno93.972no
thermophileno99.427yes
glucose-fermentno83.98no

External links

@ref: 5734

culture collection no.: CCUG 51930, CIP 106805, DSM 15165, JCM 10591, BCRC 17580, IAM 15088, KCTC 19444, NBRC 103132

straininfo link

  • @ref: 76790
  • straininfo: 69140

literature

Pubmed-IDtitleauthorsjournalDOIyeartopicmeshtopic2
12501368Leifsonia gen. nov., a genus for 2,4-diaminobutyric acid-containing actinomycetes to accommodate "Corynebacterium aquaticum" Leifson 1962 and Clavibacter xyli subsp. cynodontis Davis et al. 1984.Suzuki KI, Suzuki M, Sasaki J, Park YH, Komagata KKJ Gen Appl Microbiol10.2323/jgam.45.2531999
19126716Leifsonia kribbensis sp. nov., isolated from soil.Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJInt J Syst Evol Microbiol10.1099/ijs.0.001925-02009PhylogenyActinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, Korea, Phenotype, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5734Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15165)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15165
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
39586Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18975
59368Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 51930)https://www.ccug.se/strain?id=51930
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
76790Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID69140.1StrainInfo: A central database for resolving microbial strain identifiers
122590Curators of the CIPCollection of Institut Pasteur (CIP 106805)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106805