Strain identifier

BacDive ID: 132648

Type strain: Yes

Species: Lysobacter firmicutimachus

Strain Designation: PB-6250, PB6250

Strain history: <- H. Groß, Pharmaceutical Biology, University of Tuebingen, Germany <- NITE-IPOD <- T. Yoshida <- Shionogi Research Laboratories, Shionogi Co, Ltd., Osaka, Japan; PB-6250

NCBI tax ID(s): 1792846 (species)

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General

@ref: 24437

BacDive-ID: 132648

DSM-Number: 102073

keywords: 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped, colony-forming

description: Lysobacter firmicutimachus PB-6250 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from soil.

NCBI tax id

  • NCBI tax id: 1792846
  • Matching level: species

strain history

  • @ref: 24437
  • history: <- H. Groß, Pharmaceutical Biology, University of Tuebingen, Germany <- NITE-IPOD <- T. Yoshida <- Shionogi Research Laboratories, Shionogi Co, Ltd., Osaka, Japan; PB-6250

doi: 10.13145/bacdive132648.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Lysobacterales
  • family: Lysobacteraceae
  • genus: Lysobacter
  • species: Lysobacter firmicutimachus
  • full scientific name: Lysobacter firmicutimachus Miess et al. 2016

@ref: 24437

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Lysobacteraceae

genus: Lysobacter

species: Lysobacter firmicutimachus

full scientific name: Lysobacter firmicutimachus Miess et al. 2016

strain designation: PB-6250, PB6250

type strain: yes

Morphology

cell morphology

  • @ref: 24955
  • gram stain: negative
  • cell length: 2.0-4.0 µm
  • cell width: 0.9 µm
  • cell shape: rod-shaped

colony morphology

  • @ref: 24955
  • colony color: cream-yellow
  • colony shape: circular

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
24437NUTRIENT AGAR (DSMZ Medium 1)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1.pdf
24955NA (Nutrient Agar)yes
24955Reasoner's 2A agar (R2A)yes
24955LB medium (lysogeny broth)yes
24955TSA (Trypticase soy agar)yes
24955Marine agar (MA)yes
24955MacConkey agaryes
24437TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
24955positivegrowth15.0-37.0
24955positiveoptimum25.0-28.0mesophilic
24955nogrowth42thermophilic
24437positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
24955positivegrowth5.5-9.0alkaliphile
24955positiveoptimum5.5

Physiology and metabolism

oxygen tolerance

  • @ref: 24955
  • oxygen tolerance: aerobe

spore formation

  • @ref: 24955
  • spore formation: no

compound production

  • @ref: 24437
  • compound: plusbacins

halophily

  • @ref: 24955
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <0.5 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2495517234glucose-fermentation
2495517632nitrate-reduction
249554853esculin+hydrolysis
249555291gelatin+hydrolysis
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose-assimilation
683695291gelatin+hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

@refChebi-IDmetaboliteproduction
2495515688acetoinno
6836935581indoleno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-testindole test
2495517234glucose-
2495515688acetoin-
6836935581indole-

enzymes

@refvalueactivityec
24955acid phosphatase+3.1.3.2
24955alkaline phosphatase+3.1.3.1
24955alpha-fucosidase-3.2.1.51
24955alpha-galactosidase-3.2.1.22
24955alpha-glucosidase-3.2.1.20
24955alpha-mannosidase-3.2.1.24
24955beta-galactosidase-3.2.1.23
24955beta-glucosidase-3.2.1.21
24955beta-glucuronidase-3.2.1.31
24955catalase+1.11.1.6
24955cystine arylamidase-3.4.11.3
24955cytochrome oxidase+1.9.3.1
24955esterase (C 4)+
24955esterase lipase (C 8)+
24955leucine arylamidase+3.4.11.1
24955lipase (C 14)-
24955N-acetyl-beta-glucosaminidase+3.2.1.52
24955naphthol-AS-BI-phosphohydrolase+
24955trypsin+3.4.21.4
24955valine arylamidase-
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
24437-----++---+-++---+--+
24437-----++-+-+-++---+--+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture temperature
24437soilOkinawa Prefecture, Okinawa-hontoJapanJPNAsia
24955tryptic soy agar (TSA, BBL 11768)28

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_5004.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_647;97_2985;98_3740;99_5004&stattab=map
  • Last taxonomy: Lysobacter firmicutimachus
  • 16S sequence: KU593484
  • Sequence Identity:
  • Total samples: 447
  • soil counts: 251
  • aquatic counts: 112
  • animal counts: 45
  • plant counts: 39

Safety information

risk assessment

  • @ref: 24437
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24437
  • description: Lysobacter firmicutimachus strain PB-6250 16S ribosomal RNA gene, partial sequence
  • accession: KU593484
  • length: 1551
  • database: ena
  • NCBI tax ID: 1792846

GC content

  • @ref: 24437
  • GC-content: 68.7
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 24437

culture collection no.: DSM 102073, FERM BP-2938, LMG 28994

straininfo link

  • @ref: 90961
  • straininfo: 398165

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27468934Reclassification of Pseudomonas sp. PB-6250T as Lysobacter firmicutimachus sp. nov.Miess H, van Trappen S, Cleenwerck I, De Vos P, Gross HInt J Syst Evol Microbiol10.1099/ijsem.0.0013292016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Japan, Lysobacter/*classification, Nucleic Acid Hybridization, *Phylogeny, Pseudomonas/*classification, Quinones/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome
Phylogeny30540245Lysobacter tabacisoli sp. nov., isolated from rhizosphere soil of Nicotiana tabacum L.Xiao M, Zhou XK, Chen X, Duan YQ, Alkhalifah DHM, Im WT, Hozzein WN, Chen W, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0031642018Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lysobacter/*classification/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Tobacco/*microbiology, Ubiquinone/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
24437Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-102073Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 102073)
24955H. v. T. Miess, Stefanie,Cleenwerck, Ilse,De Vos, Paul,Gross, HaraldReclassification of Pseudomonas sp. PB-6250T as Lysobacter firmicutimachus sp. nov10.1099/ijsem.0.001329IJSEM 66: 4162-4166 201627468934
68369Automatically annotated from API 20NE
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/
90961Reimer, 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-ID398165.1