Strain identifier

BacDive ID: 164545

Type strain: Yes

Species: Pseudomonas juntendi

Strain Designation: BML3

Strain history: <- M. Tohya, Univ. Juntendo School of Medicine; BML3

NCBI tax ID(s): 2666183 (species)

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General

@ref: 67770

BacDive-ID: 164545

DSM-Number: 109244

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

description: Pseudomonas juntendi BML3 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from Sputum of a patient in Japan in 2018.

NCBI tax id

  • NCBI tax id: 2666183
  • Matching level: species

strain history

@refhistory
67770M. Tohya and T. Kirikae; Juntendo Univ. Sch. of Med., Japan; BML3.
68606<- M. Tohya, Univ. Juntendo School of Medicine; BML3

doi: 10.13145/bacdive164545.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pseudomonadales
  • family: Pseudomonadaceae
  • genus: Pseudomonas
  • species: Pseudomonas juntendi
  • full scientific name: Pseudomonas juntendi Tohya et al. 2019

@ref: 67770

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas juntendi

full scientific name: Pseudomonas juntendi Tohya et al. 2019

strain designation: BML3

type strain: yes

Morphology

cell morphology

  • @ref: 68201
  • gram stain: negative
  • cell length: 1-2 µm
  • cell width: 0.5-0.8 µm
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 68201
  • colony size: 1-2 mm
  • colony color: creamy colour
  • colony shape: circular
  • incubation period: 2 days

pigmentation

  • @ref: 68201
  • production: yes
  • name: fluorescent pigments

Culture and growth conditions

culture medium

@refnamegrowthlink
68606NUTRIENT AGAR (DSMZ Medium 1)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1.pdf
68606TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf

culture temp

@refgrowthtypetemperaturerange
68606positivegrowth28mesophilic
67770positivegrowth30mesophilic
68201positivegrowth4-40

Physiology and metabolism

oxygen tolerance

  • @ref: 68201
  • oxygen tolerance: aerobe

spore formation

  • @ref: 68201
  • spore formation: no

halophily

  • @ref: 68201
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 1-7 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6820117925alpha-D-glucose+assimilation
6820112936D-galactose+assimilation
6820128847D-fucose+assimilation
6820117596inosine+assimilation
6820117754glycerol+assimilation
6820178697D-fructose 6-phosphate+assimilation
6820116523D-serine+assimilation
6820116977L-alanine+assimilation
6820190350L-arginine-2-naphthylamide+assimilation
6820129991L-aspartate+assimilation
6820129985L-glutamate+assimilation
6820115971L-histidine+assimilation
6820118183L-pyroglutamic acid+assimilation
6820117115L-serine+assimilation
6820118024D-galacturonic acid+assimilation
682018391D-gluconate+assimilation
6820115748D-glucuronate+assimilation
6820132323glucuronamide+assimilation
6820135390galactarate+assimilation
6820117521(-)-quinic acid+assimilation
6820133801D-saccharate+assimilation
68201L-lactate+assimilation
6820116947citrate+assimilation
68201645522-hydroxybutyrate+assimilation
6820116865gamma-aminobutyric acid+assimilation
68201370543-hydroxybutyrate+assimilation
6820117272propionate+assimilation
6820116411acetic acid+assimilation
6820115740formate+assimilation
682011 % sodium lactate+growth
6820171321fusidate+growth
6820116523D-serine+growth
6820145735troleandomycin+growth
6820129673rifamycin sv+growth
6820150694minocycline+growth
682016472lincomycin+growth
6820132735guanidinium chloride+growth
6820175273niaproof+growth
6820128001vancomycin+growth
6820175193tetrazolium violet+growth
6820175198tetrazolium blue+growth
68201100147nalidixic acid+growth
6820148607lithium chloride+growth
6820175248potassium tellurite+growth
68201161680aztreonam+growth
6820164103sodium butyrate+growth
6820175229sodium bromate+growth
6820116467L-arginine+assimilation
6820117234glucose+assimilation
6820130849L-arabinose+assimilation
6820116024D-mannose+assimilation
6820132032potassium gluconate+assimilation
6820117120hexanoate+assimilation
6820115588D-malate+assimilation
6820115589L-malate+assimilation
6820153258sodium citrate+assimilation
6820117128adipate-growth

enzymes

@refvalueactivityec
68201catalase+1.11.1.6
68201cytochrome oxidase+1.9.3.1
68201esterase (C 4)+
68201esterase Lipase (C 8)+
68201leucine arylamidase+3.4.11.1
68201valine arylamidase+
68201acid phosphatase+3.1.3.2
68201naphthol-AS-BI-phosphohydrolase+
68201alkaline phosphatase-3.1.3.1

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    68201C10:0 3OH3.3
    68201C12:01.5
    68201C12:0 2OH2.6
    68201C12:0 3OH4.4
    68201C16:029
    68201C17:0 cyclo2.6
    68201C16:1 w7c/C16:1 w6c28.5
    68201C18:1 w7c/C18:1 w6c23.1
  • type of FA analysis: whole cell analysis
  • incubation medium: tryptic soy broth agar
  • incubation temperature: 30
  • incubation time: 1
  • software version: Sherlock 6.0
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
67770Sputum of a patient in Japan in 2018
68201sputum sample of a patientJapanJPNAsia2018-01-01

taxonmaps

  • @ref: 69479
  • File name: preview.99_239.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_89;98_203;99_239&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: MK680061
  • Sequence Identity:
  • Total samples: 2133
  • soil counts: 368
  • aquatic counts: 543
  • animal counts: 799
  • plant counts: 423

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
68201Pseudomonas sp. strain BML3 16S ribosomal RNA gene, partial sequenceMK6800611540ena2666183
68606Pseudomonas juntendi strain BML3 16S ribosomal RNA gene, partial sequenceMK5834631432ena2666183

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas juntendi strain BML32666183.3wgspatric2666183
68201Pseudomonas juntendi BML3GCA_009932375contigncbi2666183

GC content

  • @ref: 68201
  • GC-content: 62.66
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes90.8yes
gram-positiveno98.598yes
anaerobicno97.89yes
aerobicyes95.551no
halophileno84.773no
spore-formingno96.282yes
glucose-utilyes91.059yes
thermophileno99.909yes
flagellatedyes81.731no
glucose-fermentno90.189no

External links

@ref: 67770

culture collection no.: JCM 33395, DMS 109244, DSM 109244

straininfo link

  • @ref: 114176
  • straininfo: 403019

literature

  • topic: Phylogeny
  • Pubmed-ID: 31368883
  • title: Pseudomonas juntendi sp. nov., isolated from patients in Japan and Myanmar.
  • authors: Tohya M, Watanabe S, Teramoto K, Shimojima M, Tada T, Kuwahara-Arai K, War MW, Mya S, Tin HH, Kirikae T
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003623
  • year: 2019
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Humans, Japan, Myanmar, Nucleic Acid Hybridization, *Phylogeny, Pseudomonas/*classification/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sputum/*microbiology, Urine/*microbiology
  • topic2: Pathogenicity

Reference

@idauthorstitledoi/urljournalcatalogue
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
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68201Mari Tohya, Shin Watanabe, Kanae Teramoto, Masahiro Shimojima, Tatsuya Tada, Kyoko Kuwahara-Arai, May Wint War, San Mya, Htay Htay Tin and Teruo KirikaePseudomonas juntendi sp. nov., isolated from patients in Japan and Myanmar10.1099/ijsem.0.003623IJSEM 69: 3377-3384 2019
68606Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-109244Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 109244)
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/
114176Reimer, 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-ID403019.1