Strain identifier

BacDive ID: 7357

Type strain: Yes

Species: Leucobacter chromiireducens

Strain Designation: L-1, L1

Strain history: CIP <- 2004, P. Morais, Coimbra, Portugal: strain L1

NCBI tax ID(s): 283877 (species)

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General

@ref: 6938

BacDive-ID: 7357

DSM-Number: 17381

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

description: Leucobacter chromiireducens L-1 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from Activated sludge.

NCBI tax id

  • NCBI tax id: 283877
  • Matching level: species

strain history

@refhistory
6938<- CIP <- P. Morais, Portugal, strain L1
344872004, P. Morais, Coimbra, Portugal: strain L1
67770LMG 22506 <-- P. V. Morais L-1 <-- R. Francisco.
67772Francisco, R. University of Coimbra [Synonym: Leucobacter chromiireducens subsp. chromiireducens (Morais et al. 2005) Muir and Tan 2007]
118259CIP <- 2004, P. Morais, Coimbra, Portugal: strain L1

doi: 10.13145/bacdive7357.20230509.8.1

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
  • full scientific name: Leucobacter chromiireducens Morais et al. 2005

@ref: 6938

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Leucobacter

species: Leucobacter chromiireducens subsp. chromiireducens

full scientific name: Leucobacter chromiireducens subsp. chromiireducens (Morais et al. 2005) Muir and Tan 2007

strain designation: L-1, L1

type strain: yes

Morphology

cell morphology

  • @ref: 118259
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 118259

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6938TRYPTICASE 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
34487MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118259CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6938positivegrowth28mesophilic
34487positivegrowth30mesophilic
67770positivegrowth28mesophilic
67772positiveminimum20psychrophilic
67772positiveoptimum28mesophilic
67772positivemaximum37mesophilic
118259positivegrowth10-37
118259nogrowth41thermophilic
118259nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118259
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
118259NaClpositivegrowth0-8 %
118259NaClnogrowth10 %

murein

  • @ref: 6938
  • murein short key: B11
  • type: B2delta {Gly} [L-Ala] D-Glu-D-Dab-L-Thr

observation

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

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
118259citrate-carbon source16947
118259esculin-hydrolysis4853
118259hippurate+hydrolysis606565
118259nitrate-reduction17632
118259nitrite-reduction16301
118259nitrate-respiration17632

metabolite production

  • @ref: 118259
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11825915688acetoin-
11825917234glucose-

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
118259oxidase-
118259beta-galactosidase-3.2.1.23
118259alcohol dehydrogenase-1.1.1.1
118259gelatinase-
118259amylase-
118259DNase-
118259caseinase-3.4.21.50
118259catalase+1.11.1.6
118259tween esterase-
118259gamma-glutamyltransferase-2.3.2.2
118259lecithinase-
118259lipase-
118259lysine decarboxylase-4.1.1.18
118259ornithine decarboxylase-4.1.1.17
118259phenylalanine ammonia-lyase-4.3.1.24
118259tryptophan deaminase-
118259urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118259--+--+----++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118259+/--------------+/-----------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118259------------------------------------------------------------------------+--------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling datelatitudelongitudeisolation date
6938Activated sludgeCoimbraPortugalPRTEurope
67770Activated sludge of a treatment plant receiving chromium-contaminated wastewater from the tannery industry
67772Activated sludge of a treatment plant that receives wastewater from the tannery industry contaminated with chromiumRibatejo, AlcanenaPortugalPRTEurope199739.4667-8.66667
118259Environment, Activated sludgePortugalPRTEurope2000

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Activated sludge

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: AJ781046
  • 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
69381Risk group (German classification)
677721
1182591Risk group (French classification)

Sequence information

16S sequences

  • @ref: 67772
  • description: Leucobacter chromiireducens subsp. chromiireducens partial 16S rRNA gene, type strain L-1T
  • accession: AJ781046
  • length: 1516
  • database: ena
  • NCBI tax ID: 660067

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Leucobacter chromiireducens subsp. chromiireducens L-1GCA_016758255contigncbi660067
66792Leucobacter chromiireducens subsp. chromiireducens strain L-1660067.3wgspatric660067
67772Leucobacter chromiireducens LYC-2GCA_003917135scaffoldncbi283877

GC content

@refGC-contentmethod
693866.7
6777066.7high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveyes89.559no
anaerobicno99.335no
halophileno78.623no
spore-formingno93.806no
glucose-utilyes68.354no
thermophileno99.871yes
flagellatedno97.062no
motileno88.767no
aerobicyes93.795no
glucose-fermentno91.754no

External links

@ref: 6938

culture collection no.: DSM 17381, CIP 108389, LMG 22506, JCM 13322, IAM 15254, KCTC 19683, UCCCB10

straininfo link

  • @ref: 76807
  • straininfo: 131629

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17392186Leucobacter iarius sp. nov., in the family Microbacteriaceae.Somvanshi VS, Lang E, Schumann P, Pukall R, Kroppenstedt RM, Ganguly S, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.64683-02007Actinomycetales/*classification/genetics, Animals, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Nematoda/*microbiology, Phylogeny, RNA, Ribosomal, 16S/geneticsGenetics
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

Reference

@idauthorscataloguedoi/urltitle
6938Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17381)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17381
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
34487Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6005
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/
67772Curators of the UCCCBhttps://ucccb.uc.pt/
68371Automatically annotated from API 50CH acid
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
76807Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID131629.1StrainInfo: A central database for resolving microbial strain identifiers
118259Curators of the CIPCollection of Institut Pasteur (CIP 108389)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108389