Strain identifier

BacDive ID: 5603

Type strain: Yes

Species: Leeuwenhoekiella palythoae

Strain history: <- O. I. Nedashkovskaya, Pacific Inst. Bioorg. Chem., RAS, Vladivostok <- V. V. Mikhailov, Inst. Marine Biol. FEB RAS, Vladivostok

NCBI tax ID(s): 573501 (species)

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General

@ref: 8357

BacDive-ID: 5603

DSM-Number: 19859

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

description: Leeuwenhoekiella palythoae DSM 19859 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from coral Palythoa sp..

NCBI tax id

  • NCBI tax id: 573501
  • Matching level: species

strain history

  • @ref: 8357
  • history: <- O. I. Nedashkovskaya, Pacific Inst. Bioorg. Chem., RAS, Vladivostok <- V. V. Mikhailov, Inst. Marine Biol. FEB RAS, Vladivostok

doi: 10.13145/bacdive5603.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Leeuwenhoekiella
  • species: Leeuwenhoekiella palythoae
  • full scientific name: Leeuwenhoekiella palythoae Nedashkovskaya et al. 2009

@ref: 8357

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Leeuwenhoekiella

species: Leeuwenhoekiella palythoae

full scientific name: Leeuwenhoekiella palythoae Nedashkovskaya et al. 2009

type strain: yes

Morphology

cell morphology

  • @ref: 29293
  • gram stain: negative
  • cell length: 2.3 µm
  • cell width: 0.45 µm
  • cell shape: rod-shaped
  • motility: yes
  • flagellum arrangement: gliding

pigmentation

  • @ref: 29293
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 8357
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
8357positivegrowth28mesophilic
29293positivegrowth04-38
29293positiveoptimum23-25

Physiology and metabolism

oxygen tolerance

  • @ref: 29293
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
29293NaClpositivegrowth0-12 %
29293NaClpositiveoptimum03-04 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2929322599arabinose+carbon source
2929317057cellobiose+carbon source
2929328260galactose+carbon source
2929317234glucose+carbon source
2929317716lactose+carbon source
2929325017leucine+carbon source
2929317306maltose+carbon source
2929326546rhamnose+carbon source
2929317992sucrose+carbon source
2929327082trehalose+carbon source
292934853esculin+hydrolysis

enzymes

@refvalueactivityec
29293acid phosphatase+3.1.3.2
29293alpha-galactosidase+3.2.1.22

Isolation, sampling and environmental information

isolation

  • @ref: 8357
  • sample type: coral Palythoa sp.
  • host species: Palythoa
  • geographic location: South China Sea, Vanfong Bay
  • country: Vietnam
  • origin.country: VNM
  • continent: Asia

isolation source categories

  • Cat1: #Host
  • Cat2: #Invertebrates (Other)
  • Cat3: #Cnidaria (Corals)

taxonmaps

  • @ref: 69479
  • File name: preview.99_5239.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_74;96_712;97_832;98_968;99_5239&stattab=map
  • Last taxonomy: Leeuwenhoekiella palythoae
  • 16S sequence: FJ405187
  • Sequence Identity:
  • Total samples: 1880
  • soil counts: 55
  • aquatic counts: 1763
  • animal counts: 59
  • plant counts: 3

Safety information

risk assessment

  • @ref: 8357
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8357
  • description: Leeuwenhoekiella palythoae strain KMM 6264 16S ribosomal RNA gene, partial sequence
  • accession: FJ405187
  • length: 1480
  • database: ena
  • NCBI tax ID: 573501

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Leeuwenhoekiella palythoae DSM 19859GCA_900130045scaffoldncbi573501
66792Leeuwenhoekiella palythoae LMG 24856GCA_004104045contigncbi573501
66792Leeuwenhoekiella palythoae strain DSM 19859573501.8wgspatric573501
66792Leeuwenhoekiella palythoae strain LMG 24856573501.11wgspatric573501
66792Leeuwenhoekiella palythoae DSM 198592622736499draftimg573501
66792Leeuwenhoekiella palythoae LMG 248562772190912draftimg573501

GC content

@refGC-contentmethod
835741.2thermal denaturation, midpoint method (Tm)
2929341.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno86.216no
flagellatedno94.87yes
gram-positiveno97.367no
anaerobicno99.613no
aerobicyes91.739yes
halophileno56.676no
spore-formingno95.473no
thermophileno99.521yes
glucose-utilyes88.435yes
glucose-fermentno87.183no

External links

@ref: 8357

culture collection no.: DSM 19859, KCTC 22020, KMM 6264, LMG 24856

straininfo link

  • @ref: 75085
  • straininfo: 264790

literature

  • topic: Phylogeny
  • Pubmed-ID: 19643875
  • title: Leeuwenhoekiella palythoae sp. nov., a new member of the family Flavobacteriaceae.
  • authors: Nedashkovskaya OI, Vancanneyt M, Kim SB, Zhukova NV, Han JH, Mikhailov VV
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.010371-0
  • year: 2009
  • mesh: Animals, Anthozoa/*microbiology, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Flavobacteriaceae/*classification/genetics/*isolation & purification, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8357Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19859)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19859
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
29293Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2570928776041
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)
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
75085Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID264790.1StrainInfo: A central database for resolving microbial strain identifiers