Strain identifier

BacDive ID: 6261

Type strain: No

Species: Janibacter terrae

Strain Designation: 10N

Strain history: CIP <- 2001, IAM <- Y. Imamura: strain 10N

NCBI tax ID(s): 1053688 (strain), 103817 (species)

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General

@ref: 5193

BacDive-ID: 6261

DSM-Number: 13953

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

description: Janibacter terrae 10N is an obligate aerobe, mesophilic bacterium that was isolated from polluted groundwater.

NCBI tax id

NCBI tax idMatching level
1053688strain
103817species

strain history

@refhistory
5193<- IAM <- Y. Imamura; 10N
67770IAM 14781 <-- Y. Imamura 10N.
123457CIP <- 2001, IAM <- Y. Imamura: strain 10N

doi: 10.13145/bacdive6261.20230509.8.1

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: 5193

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: 10N

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no93.398
69480100positive
123457nopositiverod-shaped

colony morphology

@refcolony colorincubation periodmedium used
18314Light ivory (1015)10-14 daysISP 2
18314Light ivory (1015)10-14 daysISP 3
18314Light ivory (1015)10-14 daysISP 4
18314Light ivory (1015)10-14 daysISP 5
18314Light ivory (1015)10-14 daysISP 6
18314Light ivory (1015)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18314noISP 2
18314noISP 3
18314noISP 4
18314noISP 5
18314noISP 6
18314noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5193TRYPTICASE 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
18314ISP 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
18314ISP 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:
18314ISP 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
18314ISP 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
18314ISP 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
18314ISP 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
35219MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123457CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
18314positiveoptimum28mesophilic
5193positivegrowth28mesophilic
35219positivegrowth30mesophilic
67770positivegrowth28mesophilic
123457positivegrowth15-37
123457nogrowth10psychrophilic
123457nogrowth41thermophilic
123457nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123457
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.98

halophily

  • @ref: 123457
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

murein

  • @ref: 5193
  • 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
12345716947citrate-carbon source
1234574853esculin-hydrolysis
123457606565hippurate+hydrolysis
12345717632nitrate+reduction
12345716301nitrite-reduction
12345717632nitrate-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: 123457
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 123457
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12345715688acetoin-
12345717234glucose-

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
68382trypsin+3.4.21.4
68382cystine arylamidase+3.4.11.3
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
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
123457oxidase-
123457beta-galactosidase-3.2.1.23
123457alcohol dehydrogenase-1.1.1.1
123457gelatinase+
123457amylase-
123457DNase-
123457caseinase+3.4.21.50
123457catalase+1.11.1.6
123457tween esterase-
123457gamma-glutamyltransferase-2.3.2.2
123457lysine decarboxylase-4.1.1.18
123457ornithine decarboxylase-4.1.1.17
123457phenylalanine ammonia-lyase-4.3.1.24
123457tryptophan deaminase-
123457urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18314-+/--+--+--+-------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18314+-++++++-+----+----
123457+++-+-++-++---+-----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123457------------+--------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
5193polluted groundwaterJapanJPNAsia
67770Contaminated groundwaterJapanJPNAsia
123457Environment, Polluted groundwaterJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Environmental#Aquatic#Groundwater

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: AJ310085
  • 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
183141German classification
51931Risk group (German classification)
1234571Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Janibacter brevis 16S rRNA gene, strain DSM 13953TAJ3100851496ena1053688
5193Janibacter brevis gene for 16S rRNA, partial sequence, strain:10NAB0164381487ena103817

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Janibacter terrae NBRC 107854 = JCM 12887GCA_001313905contigncbi1053688
66792Janibacter terrae NBRC 107854 = JCM 128871053688.3wgspatric1053688
66792Janibacter terrae NBRC 107854 = JCM 128871053688.4wgspatric1053688
66792Janibacter terrae JCM 128872734481964draftimg1053688
66792Janibacter terrae NBRC 1078542731957720draftimg1053688
67770Janibacter terrae NBRC 107854 = JCM 12887GCA_001598955contigncbi1053688

GC content

  • @ref: 5193
  • GC-content: 72
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.95no
flagellatedno98.018no
gram-positiveyes85.538no
anaerobicno98.751no
aerobicyes96.892no
halophileno88.26no
spore-formingno96.448no
thermophileno98.159yes
glucose-utilyes83.822no
glucose-fermentno94.465yes

External links

@ref: 5193

culture collection no.: DSM 13953, IAM 14781, JCM 12887, CIP 106967, KCTC 19032, KCTC 9986, NBRC 107854

straininfo link

  • @ref: 75739
  • straininfo: 49537

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5193Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13953)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13953
18314Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM13953.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
35219Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19156
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
75739Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49537.1StrainInfo: A central database for resolving microbial strain identifiers
123457Curators of the CIPCollection of Institut Pasteur (CIP 106967)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106967