Strain identifier

BacDive ID: 7341

Type strain: Yes

Species: Leifsonia naganoensis

Strain Designation: DB103, DBI03

Strain history: CIP <- 2000, JCM <- T. Yorifuji: strain DBI03

NCBI tax ID(s): 150025 (species)

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General

@ref: 5735

BacDive-ID: 7341

DSM-Number: 15166

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

description: Leifsonia naganoensis DB103 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from forest soil.

NCBI tax id

  • NCBI tax id: 150025
  • Matching level: species

strain history

@refhistory
5735<- JCM <- T. Yorifuji; DB103
67770T. Yorifuji DB103.
121222CIP <- 2000, JCM <- T. Yorifuji: strain DBI03

doi: 10.13145/bacdive7341.20250331.9.3

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 naganoensis
  • full scientific name: Leifsonia naganoensis Suzuki et al. 2000

@ref: 5735

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Leifsonia

species: Leifsonia naganoensis

full scientific name: Leifsonia naganoensis Suzuki et al. 2000

strain designation: DB103, DBI03

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
121222positiverod-shapedyes
125439positive99.1

colony morphology

  • @ref: 121222

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5735TRYPTICASE 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
39585MEDIUM 112 - for JanibacteryesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (1.000 g);Agar (20.000 g);Yeast extract (5.000 g);Peptone (10.000 g);Tween 80 (50.000 mg);Glycerol (2.000 g);Malt extract (5.000 g);Beef extract (2.000 g);Casamino acids (5.000 g);Ca
121222CIP Medium 112yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=112

culture temp

@refgrowthtypetemperature
5735positivegrowth28
39585positivegrowth30
59369positivegrowth30
67770positivegrowth30
121222positivegrowth10-37
121222nogrowth41
121222nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
59369aerobe
121222obligate aerobe
125439obligate aerobe97.3

halophily

@refsaltgrowthtested relationconcentration
121222NaClpositivegrowth0-6 %
121222NaClnogrowth8 %
121222NaClnogrowth10 %

murein

  • @ref: 5735
  • murein short key: B07
  • type: B2gamma {Gly} [L-Dab] D-Glu-D-Dab

observation

  • @ref: 67770
  • observation: quinones: MK-11, MK-12

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1212224853esculin+hydrolysis
121222606565hippurate+hydrolysis
12122217632nitrate-reduction
12122216301nitrite-reduction
12122217632nitrate-respiration
68371Potassium 5-ketogluconate-builds acid from
68371320061methyl alpha-D-glucopyranoside-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
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
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
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

antibiotic resistance

  • @ref: 121222
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 121222
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12122215688acetoin-
12122217234glucose+

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
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
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
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
121222oxidase+
121222beta-galactosidase+3.2.1.23
121222alcohol dehydrogenase-1.1.1.1
121222gelatinase-
121222amylase+
121222DNase+
121222caseinase-3.4.21.50
121222catalase+1.11.1.6
121222tween esterase-
121222gamma-glutamyltransferase-2.3.2.2
121222lecithinase-
121222lipase-
121222lysine decarboxylase-4.1.1.18
121222ornithine decarboxylase-4.1.1.17
121222phenylalanine ammonia-lyase-4.3.1.24
121222tryptophan deaminase-
121222urease-3.5.1.5
68382alpha-mannosidase-3.2.1.24
68382alpha-galactosidase+3.2.1.22

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121222-++++++++-++++-+++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121222+--+++--+++++-+/---++---+++++++--------+++/-------+/---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121222+++++--+-+++++-+++++++++-+--+--+-+++--------------------+-----------------------------+------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5735forest soilNagano pref.JapanJPNAsia
59369SoilNaganoJapanJPNAsia
67770SoilNagano Pref.JapanJPNAsia
121222Environment, SoilNaganoJapanJPNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_5106.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_671;97_777;98_901;99_5106&stattab=map
  • Last taxonomy: Leifsonia
  • 16S sequence: AB028941
  • Sequence Identity:
  • Total samples: 1088
  • soil counts: 509
  • aquatic counts: 123
  • animal counts: 333
  • plant counts: 123

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
57351Risk group (German classification)
1212221Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Leifsonia naganoensis strain DB103 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceDQ2326122111nuccore150025
5735Microbacteriaceae str. DB103 gene for 16S rRNA, partial sequenceAB0289411410nuccore97973

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Leifsonia naganoensis strain DSM 15166150025.3wgspatric150025
66792Leifsonia naganoensis DSM 151662856447022draftimg150025
67770Leifsonia naganoensis DSM 15166GCA_013410615contigncbi150025

GC content

  • @ref: 5735
  • GC-content: 70.5
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes88.027no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.478yes
125438spore-formingspore-formingAbility to form endo- or exosporesno74.83no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes87.595no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95.929yes
125438motile2+flagellatedAbility to perform flagellated movementno76.5no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes53.5
125439BacteriaNetmotilityAbility to perform movementno79.7
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.1
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe97.3

External links

@ref: 5735

culture collection no.: DSM 15166, JCM 10592, CCUG 51931, CIP 106799, IAM 15089, KCTC 19441, NBRC 103131

straininfo link

  • @ref: 76791
  • straininfo: 69139

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
24535740Diaminobutyricibacter tongyongensis gen. nov., sp. nov. and Homoserinibacter gongjuensis gen. nov., sp. nov. belong to the family Microbacteriaceae.Kim SJ, Ahn JH, Weon HY, Hamada M, Suzuki K, Kwon SWJ Microbiol10.1007/s12275-014-3278-y2014PhylogenyActinomycetales/classification/*genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5735Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15166)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15166
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
39585Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18969
59369Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 51931)https://www.ccug.se/strain?id=51931
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
76791Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID69139.1StrainInfo: A central database for resolving microbial strain identifiers
121222Curators of the CIPCollection of Institut Pasteur (CIP 106799)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106799
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1