Strain identifier

BacDive ID: 7356

Type strain: Yes

Species: Leucobacter chromiireducens subsp. solipictus

Strain Designation: ID 06-074

Strain history: DSM 18340 <-- R. E. Muir TAN 31504.

NCBI tax ID(s): 398235 (subspecies)

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General

@ref: 7514

BacDive-ID: 7356

DSM-Number: 18340

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

description: Leucobacter chromiireducens subsp. solipictus ID 06-074 is a mesophilic bacterium that was isolated from C. elegans, appeared as a contaminant.

NCBI tax id

  • NCBI tax id: 398235
  • Matching level: subspecies

strain history

@refhistory
7514<- R.E. Muir, TAN 31504
67770DSM 18340 <-- R. E. Muir TAN 31504.

doi: 10.13145/bacdive7356.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Leucobacter
  • species: Leucobacter chromiireducens subsp. solipictus
  • full scientific name: Leucobacter chromiireducens subsp. solipictus Muir and Tan 2007

@ref: 7514

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Leucobacter

species: Leucobacter chromiireducens subsp. solipictus

full scientific name: Leucobacter chromiireducens subsp. solipictus Muir and Tan 2007

strain designation: ID 06-074

type strain: yes

Morphology

colony morphology

@refcolony colorincubation periodmedium used
18412Beige (1001)10-14 daysISP 2
18412Beige (1001)10-14 daysISP 3
18412Beige (1001)10-14 daysISP 4
18412Beige (1001)10-14 daysISP 5
18412Beige (1001)10-14 daysISP 6
18412Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18412noISP 2
18412noISP 3
18412noISP 4
18412noISP 5
18412noISP 6
18412noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7514TRYPTICASE 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
18412ISP 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
18412ISP 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:
18412ISP 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
18412ISP 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
18412ISP 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
18412ISP 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

culture temp

@refgrowthtypetemperaturerange
7514positivegrowth25-28mesophilic
18412positiveoptimum28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

observation

  • @ref: 67770
  • observation: quinones: MK-11, MK-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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

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+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
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
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

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18412---------+---------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18412-++++++--++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinenthost species
7514C. elegans, appeared as a contaminantStanford, CaliforniaUSAUSANorth America
67770Nematode Caenorhabditis elegansStanford, CAUSAUSANorth AmericaCaenorhabditis elegans

isolation source categories

Cat1Cat2Cat3
#Engineered#Laboratory#Contaminant
#Host#Invertebrates (Other)#Nematoda

taxonmaps

  • @ref: 69479
  • File name: preview.99_5958.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1203;97_3124;98_4426;99_5958&stattab=map
  • Last taxonomy: Leucobacter chromiireducens subclade
  • 16S sequence: DQ845457
  • Sequence Identity:
  • Total samples: 275
  • soil counts: 61
  • aquatic counts: 72
  • animal counts: 113
  • plant counts: 29

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
75141Risk group (German classification)
184121German classification

Sequence information

16S sequences

  • @ref: 7514
  • description: Leucobacter chromiireducens subsp. solipictus strain TAN 31504 16S ribosomal RNA gene, partial sequence
  • accession: DQ845457
  • length: 1508
  • database: ena
  • NCBI tax ID: 398235

Genome sequences

  • @ref: 66792
  • description: Leucobacter chromiireducens subsp. solipictus strain TAN 31504
  • accession: 398235.3
  • assembly level: wgs
  • database: patric
  • NCBI tax ID: 398235

GC content

@refGC-contentmethod
751469.5
6777069.5high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveyes90.264no
anaerobicno99.405no
halophileno65.88no
spore-formingno94.72no
glucose-utilyes73.481no
aerobicyes94.798no
motileno89.759no
flagellatedno97.367no
thermophileno99.819yes
glucose-fermentno93.057yes

External links

@ref: 7514

culture collection no.: DSM 18340, ATCC BAA 1336, JCM 15573, KCTC 19684, NCIMB 14548

straininfo link

  • @ref: 76806
  • straininfo: 293708

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18048723Leucobacter chromiireducens subsp. solipictus subsp. nov., a pigmented bacterium isolated from the nematode Caenorhabditis elegans, and emended description of L. chromiireducens.Muir RE, Tan MWInt J Syst Evol Microbiol10.1099/ijs.0.64822-02007Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Aerobiosis/physiology, Aminobutyrates/analysis, Animals, Bacterial Typing Techniques, Base Composition, Caenorhabditis elegans/*microbiology, Cell Wall/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Locomotion/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Vitamin K 2/analysisGenetics
Phylogeny29569109A novel pigmented and heavy metal biosorptive bacterium, Leucobacter epilobiisoli sp. nov., isolated from rhizosphere soil of Epilobium hirsutum L.Hou SY, Wang F, Zhang MY, Cheng J, Zhang YXAntonie Van Leeuwenhoek10.1007/s10482-018-1071-32018Actinobacteria/*classification/genetics/isolation & purification/*metabolism, Adaptation, Biological, Biotransformation, Epilobium/*microbiology, Metabolomics/methods, Metals, Heavy/*metabolism, Molecular Typing, Phenotype, Phylogeny, Pigments, Biological/*metabolism, RNA, Ribosomal, 16S/genetics, *Rhizosphere, *Soil MicrobiologyMetabolism

Reference

@idauthorscataloguedoi/urltitle
7514Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18340)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18340
18412Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM18340.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
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
76806Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID293708.1StrainInfo: A central database for resolving microbial strain identifiers