Strain identifier

BacDive ID: 6248

Type strain: Yes

Species: Janibacter limosus

Strain Designation: 2003-10

Strain history: IFO 16128 <-- DSM 11140 <-- K. Martin HKI 83.

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 4220

BacDive-ID: 6248

DSM-Number: 11140

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

description: Janibacter limosus 2003-10 is an aerobe, mesophilic bacterium that was isolated from sludge of waste water treatment.

NCBI tax id

NCBI tax idMatching level
1216970strain
53458species

strain history

doi: 10.13145/bacdive6248.20220920.7

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 limosus
  • full scientific name: Janibacter limosus Martin et al. 1997

@ref: 4220

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Intrasporangiaceae

genus: Janibacter

species: Janibacter limosus

full scientific name: Janibacter limosus Martin et al. 1997

strain designation: 2003-10

type strain: yes

Morphology

colony morphology

@refcolony colorincubation periodmedium used
18433Beige (1001)10-14 daysISP 2
18433Beige (1001)10-14 daysISP 3
18433Beige (1001)10-14 daysISP 4
18433Beige (1001)10-14 daysISP 5
18433Beige (1001)10-14 daysISP 6
18433Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18433noISP 2
18433noISP 3
18433noISP 4
18433noISP 5
18433noISP 6
18433noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4220RICH MEDIUM (DSMZ Medium 736)yeshttps://bacmedia.dsmz.de/medium/736Name: RICH MEDIUM (DSMZ Medium 736) Composition: Agar 20.0 g/l Bacto peptone 10.0 g/l Yeast extract 5.0 g/l Casamino acids 5.0 g/l Malt extract 5.0 g/l Meat extract 2.0 g/l Glycerol 2.0 g/l MgSO4 x 7 H2O 1.0 g/l Tween 80 0.05 g/l Distilled water
4220TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://bacmedia.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
18433ISP 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
18433ISP 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:
18433ISP 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
18433ISP 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
18433ISP 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
18433ISP 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
39249MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)

culture temp

@refgrowthtypetemperaturerange
18433positiveoptimum28mesophilic
4220positivegrowth28mesophilic
39249positivegrowth30mesophilic
53995positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 53995
  • oxygen tolerance: aerobe

murein

  • @ref: 4220
  • 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
6837928087glycogen-fermentation
6837917992sucrose+fermentation
6837917716lactose-fermentation
6837917306maltose-fermentation
6837916899D-mannitol-fermentation
6837965327D-xylose-fermentation
6837916988D-ribose-fermentation
6837917634D-glucose-fermentation
683795291gelatin-hydrolysis
6837916199urea+hydrolysis
683794853esculin-hydrolysis
6837917632nitrate-reduction
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

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

enzymes

@refvalueactivityec
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
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase-3.2.1.23
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    53995C15:00.415
    53995C16:02.716
    53995C17:06.217
    53995C18:03.818
    53995C19:00.419
    53995C15:0 ISO0.314.621
    53995C16:0 10-methyl0.516.433
    53995C16:0 iso16.415.626
    53995C16:1 ω7c2.415.819
    53995C17:0 10-methyl5.817.41
    53995C17:0 anteiso0.516.722
    53995C17:0 iso1.316.629
    53995C17:1 ω8c20.116.792
    53995C18:0 ISO3.317.632
    53995C18:1 ω7c /12t/9t1.917.824
    53995C18:1 ω9c23.117.769
    53995C18:2 ω6,9c/C18:0 ANTE1.317.724
    53995C19:1 ω11c/19:1 ω9c6.118.762
    53995TBSA 10Me18:02.418.392
    53995Unidentified1.218.79
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18433-+----+--+-------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18433--+-+----++---+++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18433-++++-+--+-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
4220sludge of waste water treatmentGermanyDEUEurope
53995Sludge of waste water treatment
677701-Year-old sludge from a wastewater treatment plantGermanyDEUEuropenear Jena

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste#Wastewater
#Environmental#Terrestrial#Mud (Sludge)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
184331Risk group (German classification)
42201Risk group (German classification)

Sequence information

16S sequences

  • @ref: 4220
  • description: J.limosus 16S rRNA gene
  • accession: Y08539
  • length: 1473
  • database: ena
  • NCBI tax ID: 53458

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Janibacter limosus NBRC 16128 NBRC 16128GCA_001570985contigncbi1216970
66792Janibacter limosus NBRC 161281216970.3wgspatric1216970
66792Janibacter limosus NBRC 161282731957613draftimg1216970
67770Janibacter limosus NBRC 16128, whole genome shotgun sequencing projectBCSS00000000ncbi1216970

GC content

  • @ref: 4220
  • GC-content: 70
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 4220

culture collection no.: DSM 11140, IAM 14889, IFO 16128, NBRC 16128, CCUG 37980, HKI 83, ATCC 700321, CIP 105276, JCM 10980, KCTC 9994

straininfo link

@refpassport
20218http://www.straininfo.net/strains/125442
20218http://www.straininfo.net/strains/151695
20218http://www.straininfo.net/strains/151696
20218http://www.straininfo.net/strains/336834

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9103644Janibacter limosus gen. nov., sp. nov., a new actinomycete with meso-diaminopimelic acid in the cell wall.Martin K, Schumann P, Rainey FA, Schuetze B, Groth IInt J Syst Bacteriol10.1099/00207713-47-2-5291997Actinomycetales/*classification/genetics/*metabolism, Base Composition, Cell Wall/*metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Diaminopimelic Acid/*metabolism, Fatty Acids/analysis, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species Specificity, Waste Disposal, Fluid, Water MicrobiologyMetabolism
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

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4220Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11140)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11140
18433Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM11140.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
39249Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17277
53995Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 37980)https://www.ccug.se/strain?id=37980
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym