Strain identifier

BacDive ID: 138800

Type strain: Yes

Species: Leifsonia rubra

Strain history: CIP <- 2008, DSMZ <- CCMB, Hyderabad, India: strain CMS 76r

NCBI tax ID(s): 191389 (species)

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General

@ref: 40699

BacDive-ID: 138800

DSM-Number: 21193

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, psychrophilic, Gram-positive, rod-shaped

description: Leifsonia rubra CIP 107783 is a facultative anaerobe, psychrophilic, Gram-positive bacterium of the family Microbacteriaceae.

NCBI tax id

  • NCBI tax id: 191389
  • Matching level: species

strain history

@refhistory
67770S. Shivaji CMS 76r.
40699CIP <- 2008, DSMZ <- CCMB, Hyderabad, India: strain CMS 76r

doi: 10.13145/bacdive138800.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Leifsonia
  • species: Leifsonia rubra
  • full scientific name: Leifsonia rubra Reddy et al. 2003

@ref: 40699

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Micrococcales

family: Microbacteriaceae

genus: Leifsonia

species: Leifsonia rubra

type strain: yes

Morphology

cell morphology

  • @ref: 40699
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 40699

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
40699MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
40699CIP Medium 358yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=358
40699CIP Medium 338yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=338
40699CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
40699positivegrowth18psychrophilic
67770positivegrowth18psychrophilic
40699positivegrowth10-15psychrophilic
40699nogrowth25mesophilic
40699nogrowth30mesophilic
40699nogrowth37mesophilic
40699nogrowth41thermophilic
40699nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 40699
  • oxygen tolerance: facultative anaerobe

halophily

@refsaltgrowthtested relationconcentration
40699NaClpositivegrowth0-2 %
40699NaClnogrowth4 %
40699NaClnogrowth6 %
40699NaClnogrowth8 %
40699NaClnogrowth10 %

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-rhamnose-builds acid from62345
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
68371glycerol-builds acid from17754
40699hippurate+hydrolysis606565
40699nitrate+reduction17632
40699nitrite-reduction16301

metabolite production

  • @ref: 40699
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
4069915688acetoin-
4069917234glucose-

enzymes

@refvalueactivityec
40699oxidase-
40699beta-galactosidase-3.2.1.23
40699alcohol dehydrogenase-1.1.1.1
40699gelatinase+/-
40699amylase-
40699DNase-
40699caseinase+3.4.21.50
40699catalase+1.11.1.6
40699tween esterase-
40699gamma-glutamyltransferase-2.3.2.2
40699lecithinase-
40699lipase-
40699lysine decarboxylase-4.1.1.18
40699ornithine decarboxylase-4.1.1.17
40699phenylalanine ammonia-lyase-4.3.1.24
40699protease-
40699tryptophan deaminase-
40699urease-3.5.1.5
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

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
40699--++-+-----+---+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
40699-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
40699+--+---+--+---++---------------+------+---------------------++------------++------++------++-++-++-

Isolation, sampling and environmental information

isolation

@refgeographic locationcountryorigin.countrycontinentsample typeisolation date
40699Mc MurdoAntarcticaATAAntarctica
67770Wright Valley, McMurdoAntarcticaATAAntarcticaCyanobacterial mat from a pond
40699McMurdoAntarcticaATAAntarcticaCyanobacterial material samples1995

taxonmaps

  • @ref: 69479
  • File name: preview.99_6465.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_895;97_3383;98_4770;99_6465&stattab=map
  • Last taxonomy: Microbacteriaceae
  • 16S sequence: AJ438585
  • Sequence Identity:
  • Total samples: 104
  • soil counts: 30
  • aquatic counts: 62
  • animal counts: 7
  • plant counts: 5

Safety information

risk assessment

  • @ref: 40699
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 67770
  • description: Leifsonia rubeus 16S rRNA gene, type strain CMS 76r
  • accession: AJ438585
  • length: 1526
  • database: ena
  • NCBI tax ID: 191389

Genome sequences

  • @ref: 67770
  • description: Leifsonia rubra CMS 76R
  • accession: GCA_000477555
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 1348338

GC content

@refGC-contentmethod
6777066thermal denaturation, midpoint method (Tm)
6777059.2genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno88.805no
flagellatedno97.968no
gram-positiveyes92.556no
anaerobicno99.234no
aerobicyes94.166no
halophileno71.622no
spore-formingno93.622no
thermophileno99.657yes
glucose-utilyes86.923no
glucose-fermentno89.935no

External links

@ref: 40699

culture collection no.: CIP 107783, MTCC 4210, DSM 21193, LMG 24410, JCM 15064, CMS 76r

straininfo link

  • @ref: 95448
  • straininfo: 113590

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12892114Leifsonia rubra sp. nov. and Leifsonia aurea sp. nov., psychrophiles from a pond in Antarctica.Reddy GSN, Prakash JSS, Srinivas R, Matsumoto GI, Shivaji SInt J Syst Evol Microbiol10.1099/ijs.0.02396-02003Actinomycetales/classification/genetics/*isolation & purification/*metabolism, Antarctic Regions, Base Composition, DNA, Bacterial/chemistry/genetics, Fatty Acids/metabolism, Fresh Water/microbiology, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Terminology as TopicMetabolism
Phylogeny25288665The properties given at the time of publication for the designated type strain of Leifsonia rubra Reddy et al. 2003, CMS 76r, do not correspond with those of MTCC 4210, DSM 15304, CIP 107783 and JCM 12471 that are deposited as representing the type strain: Opinion 96. Judicial Commission of the International Committee on Systematics of Prokaryotes.Tindall BJInt J Syst Evol Microbiol10.1099/ijs.0.069229-02014Actinomycetales/*classification, Phylogeny, *Terminology as Topic

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
40699Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107783Collection of Institut Pasteur (CIP 107783)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
95448Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID113590.1