Strain identifier

BacDive ID: 6260

Type strain: Yes

Species: Janibacter terrae

Strain Designation: CS12

Strain history: CIP <- 2001, JCM <- J.H. Yoon: strain CS12

NCBI tax ID(s): 1216972 (strain), 103817 (species)

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General

@ref: 5187

BacDive-ID: 6260

DSM-Number: 13876

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic

description: Janibacter terrae CS12 is an aerobe, mesophilic bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
103817species
1216972strain

strain history

@refhistory
5187<- JCM <- J.-H. Yoon; CS12
67770J.-H. Yoon CS12.
123458CIP <- 2001, JCM <- J.H. Yoon: strain CS12

doi: 10.13145/bacdive6260.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Intrasporangiaceae
  • genus: Janibacter
  • species: Janibacter terrae
  • full scientific name: Janibacter terrae Yoon et al. 2000

  • synonyms

    • @ref: 20215
    • synonym: Janibacter brevis

@ref: 5187

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Intrasporangiaceae

genus: Janibacter

species: Janibacter terrae

full scientific name: Janibacter terrae Yoon et al. 2000 emend. Lang et al. 2003

strain designation: CS12

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no94.446
69480100positive
123458nopositivecoccus-shaped

colony morphology

@refcolony colorincubation periodmedium used
18377Light ivory (1015)10-14 daysISP 2
18377Light ivory (1015)10-14 daysISP 3
18377Light ivory (1015)10-14 daysISP 4
18377Light ivory (1015)10-14 daysISP 5
18377Light ivory (1015)10-14 daysISP 6
18377Light ivory (1015)10-14 daysISP 7
123458

multicellular morphology

@refforms multicellular complexmedium name
18377noISP 2
18377noISP 3
18377noISP 4
18377noISP 5
18377noISP 6
18377noISP 7

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
18377ISP 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
18377ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
18377ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
18377ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
18377ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
18377ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
39633MEDIUM 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
5187COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yesName: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar basehttps://mediadive.dsmz.de/medium/693
5187TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yesName: 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 waterhttps://mediadive.dsmz.de/medium/92
123458CIP Medium 112yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=112

culture temp

@refgrowthtypetemperaturerange
18377positiveoptimum28mesophilic
39633positivegrowth30mesophilic
56747positivegrowth28-37mesophilic
67770positivegrowth28mesophilic
5187positivegrowth28mesophilic
123458positivegrowth25-37mesophilic
123458nogrowth10psychrophilic
123458nogrowth15psychrophilic
123458nogrowth41thermophilic
123458nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
56747aerobe
123458obligate aerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.988

halophily

  • @ref: 123458
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

murein

  • @ref: 5187
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12345816947citrate-carbon source
1234584853esculin-hydrolysis
123458606565hippurate+hydrolysis
12345817632nitrate+reduction
12345816301nitrite-reduction
12345817632nitrate-respiration
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea+hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation

antibiotic resistance

  • @ref: 123458
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 123458
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12345815688acetoin-
12345817234glucose-

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
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase+3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382alkaline phosphatase-3.1.3.1
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
123458oxidase-
123458beta-galactosidase-3.2.1.23
123458alcohol dehydrogenase-1.1.1.1
123458gelatinase+
123458amylase+
123458DNase-
123458caseinase+3.4.21.50
123458catalase+1.11.1.6
123458tween esterase+
123458gamma-glutamyltransferase+2.3.2.2
123458lecithinase-
123458lipase-
123458lysine decarboxylase-4.1.1.18
123458ornithine decarboxylase-4.1.1.17
123458phenylalanine ammonia-lyase-4.3.1.24
123458tryptophan deaminase-
123458urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    56747C14:00.714
    56747C15:01.815
    56747C16:02.516
    56747C17:01.217
    56747C18:01.218
    56747C12:0 ISO0.511.608
    56747C14:0 ISO1.513.618
    56747C15:0 ANTEISO1.414.711
    56747C15:0 ISO8.614.621
    56747C15:1 ω6c0.714.856
    56747C16:0 iso22.515.626
    56747C16:1 ISO H0.815.461
    56747C16:1 ω7c7.815.819
    56747C17:0 10-methyl1.717.41
    56747C17:0 anteiso716.722
    56747C17:0 iso5.816.629
    56747C17:1 ω8c9.916.792
    56747C17:1 ω9c ANTEISO0.716.525
    56747C17:1 ω9c ISO4.816.416
    56747C18:1 ω7c /12t/9t1.517.824
    56747C18:1 ω9c12.117.769
    56747C18:2 ω6,9c/C18:0 ANTE4.317.724
    56747C19:1 ω11c/19:1 ω9c0.918.762
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18377-+----+--+-------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18377---++-++------+----
123458-++-+-+---+---+-----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123458-+-+---+----------+----------------------------------------++-+--+---------+-----------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
5187soilRepublic of KoreaKORAsia
67770Soil around a wastewater treatment plantRepublic of KoreaKORAsia
123458Environment, Soil around a wastewater treatment plantRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_6884.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_927;97_1079;98_1288;99_6884&stattab=map
  • Last taxonomy: Janibacter terrae
  • 16S sequence: AF176948
  • Sequence Identity:
  • Total samples: 57
  • soil counts: 20
  • aquatic counts: 15
  • animal counts: 20
  • plant counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
183771German classification
51871Risk group (German classification)
1234581Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Janibacter terrae DNA, 16S-23S rRNA spacer region sequenceAB292736375ena103817
5187Janibacter terrae 16S ribosomal RNA gene, partial sequenceAF1769481480ena103817

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Janibacter terrae NBRC 1078531216972.3wgspatric1216972
66792Janibacter terrae NBRC 1078532690315844draftimg1216972
67770Janibacter terrae NBRC 107853GCA_001591405contigncbi1216972

GC content

  • @ref: 5187
  • GC-content: 69
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno95.173no
gram-positiveyes89.699no
anaerobicno98.127yes
aerobicyes93.322yes
halophileno86.698no
spore-formingno94.511no
thermophileno98.284yes
glucose-utilyes87.055no
flagellatedno98.091no
glucose-fermentno88.761yes

External links

@ref: 5187

culture collection no.: DSM 13876, JCM 10705, KCCM 80001, CCUG 45369, ATCC BAA 130, CIP 107018, KCTC 19953, NBRC 107853, NCIMB 14349, NBRC 107842

straininfo link

  • @ref: 75738
  • straininfo: 49535

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11034493Janibacter terrae sp. nov., a bacterium isolated from soil around a wastewater treatment plant.Yoon JH, Lee KC, Kang SS, Kho YH, Kang KH, Park YHInt J Syst Evol Microbiol10.1099/00207713-50-5-18212000Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis/genetics, DNA, Ribosomal/analysis/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Waste Disposal, FluidGenetics
Genetics29387173Genome sequence and comparative genomic analysis of a clinically important strain CD11-4 of Janibacter melonis isolated from celiac disease patient.Chander AM, Kochhar R, Dhawan DK, Bhadada SK, Mayilraj SGut Pathog10.1186/s13099-018-0229-x2018

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5187Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13876)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13876
18377Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM13876.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
39633Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19213
56747Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 45369)https://www.ccug.se/strain?id=45369
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/
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
75738Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49535.1StrainInfo: A central database for resolving microbial strain identifiers
123458Curators of the CIPCollection of Institut Pasteur (CIP 107018)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107018