Strain identifier

BacDive ID: 12621

Type strain: Yes

Species: Luteococcus japonicus

Strain history: CIP <- 1994, IFO <- M. Oda, Japan: strain OUT 8086

NCBI tax ID(s): 33984 (species)

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General

@ref: 3920

BacDive-ID: 12621

DSM-Number: 10546

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

description: Luteococcus japonicus DSM 10546 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 33984
  • Matching level: species

strain history

@refhistory
3920<- IFO <- M. Oda, OUT 8086
67770IFO 12422 <-- M. Oda OUT 8086.
120321CIP <- 1994, IFO <- M. Oda, Japan: strain OUT 8086

doi: 10.13145/bacdive12621.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Propionibacteriaceae
  • genus: Luteococcus
  • species: Luteococcus japonicus
  • full scientific name: Luteococcus japonicus Tamura et al. 1994

@ref: 3920

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Propionibacteriaceae

genus: Luteococcus

species: Luteococcus japonicus

full scientific name: Luteococcus japonicus Tamura et al. 1994

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
120321positivecoccus-shapedno
125439positive99.7
125439no92.2
125438no93.1

colony morphology

@refcolony colorincubation periodmedium used
18430Pastel orange (2003)10-14 days5006
18430Beige (1001)10-14 days5425
18430Pastel orange (2003)10-14 days5428
18430Pastel orange (2003)10-14 days5530
18430Transparent10-14 daysISP 2
120321

multicellular morphology

@refforms multicellular complexmedium name
18430noISP 2
18430no5006
18430no5425
18430no5530

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3920TRYPTICASE 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
18430ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
184305006yesMedium: 5006 Name: Composition (g/l) Sucrose 3,0 Dextrin 15,0 Meat extract 1,0 Yeast extract 2,0 Tryptone soy broth (Oxoid) 5,0 NaCl 0,5 K2HPO4 0,5 MgSO4 x 7 H2O 0,5 FeSO4 x 7 H2O 0,01 Agar 20,0 Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7,3 Usage: Maintenance Organisms: All Actinomycetes
184305425yesName: Brain Heart Infusion (BHI) Agar; 5425 Composition: Calf brain infusion 200.0 g/l Beef heart infusion 250.0 g/l Casein (meat) peptone 10.0 g/l Glucose 2.0 g/l NaCl 5.0 g/l Na2HPO4 2.5 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.4 Usage: Maintenance and revitalization Organisms: Dermatophilus congolensis, Nocardia brasieliensis, N. asteroides, Rhodococcus equi, R. fascians, R. rhodochrous, Streptomyces thermoviol aceus subsp. apingens, Coryneform species
184305428yes
184305530yes
36877MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
120321CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
3920positivegrowth28
18430positiveoptimum28
36877positivegrowth30
54422positivegrowth30-37
67770positivegrowth30
120321positivegrowth15-30
120321nogrowth10
120321nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
54422aerobe
120321facultative anaerobe
125439obligate aerobe95.9

murein

  • @ref: 3920
  • murein short key: A41.01
  • type: A3gamma LL-Dpm-Gly

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6837928087glycogen-fermentation
6837917992sucrose-fermentation
6837917306maltose+fermentation
6837916899D-mannitol+fermentation
6837965327D-xylose-fermentation
6837916988D-ribose-fermentation
683795291gelatin-hydrolysis
6837917634D-glucose+fermentation
6837917632nitrate+reduction
683794853esculin+hydrolysis
12032117632nitrate-reduction
12032116301nitrite-reduction
12032135020tributyrin-hydrolysis
12032117632nitrate+respiration
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837917716lactose-fermentation
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate+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
6837132528turanose+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
6837162345L-rhamnose-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
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
12032135581indoleno
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
12032115688acetoin-
6836815688acetoin-
6836835581indole-

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-
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 (C 4)-
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
120321oxidase+
120321beta-galactosidase+3.2.1.23
120321alcohol dehydrogenase-1.1.1.1
120321gelatinase-
120321DNase-
120321caseinase-3.4.21.50
120321catalase+1.11.1.6
120321coagulase-
120321lecithinase-
120321lysine decarboxylase-4.1.1.18
120321ornithine decarboxylase-4.1.1.17
120321urease-3.5.1.5
68379gelatinase-
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase+3.2.1.20
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase+3.5.3.6
68379beta-glucosidase+3.2.1.21
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
68368beta-galactosidase+3.2.1.23

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    54422C14:00.814
    54422C15:08.415
    54422C16:05.316
    54422C17:03.817
    54422C18:00.918
    54422C15:1 ω6c14.714.856
    54422C15:1 ω8c4.914.792
    54422C16:1 ω5c0.915.908
    54422C16:1 ω7c1215.819
    54422C16:1 ω9c0.815.774
    54422C17:1 ω6c22.816.862
    54422C17:1 ω8c20.316.792
    54422C18:1 ω9c217.769
    54422C18:2 ω6,9c/C18:0 ANTE2.317.724
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18430+-++-+++++/--+--++---

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18430+-+-+--+++-++-+++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18430+++++-+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120321++-++--+-++++---+++--+-++--+--+++++++-++----+++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
3920soilJapan, Tokara islandsJapanJPNAsia
54422SoilTokara islandsJapanJPNAsia
67770SoilTokara IslandsJapanJPNAsia
120321Environment, SoilTokara IslandsJapanJPNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_38497.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15360;96_18195;97_22442;98_28237;99_38497&stattab=map
  • Last taxonomy: Luteococcus japonicus subclade
  • 16S sequence: Z78208
  • Sequence Identity:
  • Total samples: 3270
  • soil counts: 283
  • aquatic counts: 1712
  • animal counts: 1192
  • plant counts: 83

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
184301German classification
39201Risk group (German classification)
1203211Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Luteococcus japonicus gene for 16S ribosomal RNA, partial sequenceD854871471nuccore33984
20218L.japonicus 16S rRNA geneZ782081466nuccore33984
124043Luteococcus japonicus gene for 16S rRNA, partial sequence.D212451207nuccore33984

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Luteococcus japonicus strain DSM 1054633984.3wgspatric33984
66792Luteococcus japonicus DSM 105462781126037draftimg33984
67770Luteococcus japonicus DSM 10546GCA_003752415contigncbi33984

GC content

  • @ref: 3920
  • GC-content: 67
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes86.09no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no86.649yes
125438spore-formingspore-formingAbility to form endo- or exosporesno76.436no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes59.049no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno93.018yes
125438motile2+flagellatedAbility to perform flagellated movementno93.1no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes73
125439BacteriaNetmotilityAbility to perform movementno92.2
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.7
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe95.9

External links

@ref: 3920

culture collection no.: DSM 10546, ATCC 51526, CIP 104067, IFO 12422, JCM 9415, NBRC 12422, OUT 8086, CCUG 38731, IMSNU 21283, KCTC 9794, NCIMB 13388, NRIC 1092, VKM Ac-1951

straininfo link

  • @ref: 81835
  • straininfo: 43033

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny8186101Luteococcus japonicus gen. nov., sp. nov., a new gram-positive coccus with LL-diaminopimelic acid in the cell wall.Tamura T, Takeuchi M, Yokota AInt J Syst Bacteriol10.1099/00207713-44-2-3481994Base Composition, Base Sequence, Cell Wall/*chemistry, DNA, Ribosomal/genetics, Diaminopimelic Acid/*analysis, Fatty Acids/analysis, Gram-Positive Cocci/*chemistry/*classification/ultrastructure, Molecular Sequence Data, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Stereoisomerism, Vitamin K/analysisGenetics
Phylogeny24812361Luteococcus sediminum sp. nov., isolated from deep subseafloor sediment of the South Pacific Gyre.Fan X, Zhang Z, Li Z, Zhang XHInt J Syst Evol Microbiol10.1099/ijs.0.058529-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Pacific Ocean, Peptidoglycan/chemistry, Phosphatidylglycerols/chemistry, *Phylogeny, Propionibacteriaceae/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny25842902[Reactivating factor of Luteococcus japonicus subsp. casei: isolation and characterization].Vorob'eva LI, Rogozhin EA, Khodzhaev EIu, Nikolaev IV, Turova TPPrikl Biokhim Mikrobiol10.7868/s05551099140601662015Bacterial Proteins/genetics/*isolation & purification/*metabolism, Culture Media, Metabolomics, *Phylogeny, Propionibacteriaceae/*genetics, RNA, Ribosomal, 16S/genetics, Spectrometry, Mass, Matrix-Assisted Laser Desorption-IonizationCultivation

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3920Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10546)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10546
18430Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM10546.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
36877Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15934
54422Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 38731)https://www.ccug.se/strain?id=38731
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/
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
81835Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID43033.1StrainInfo: A central database for resolving microbial strain identifiers
120321Curators of the CIPCollection of Institut Pasteur (CIP 104067)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104067
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
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