Strain identifier

BacDive ID: 17212

Type strain: Yes

Species: Persicirhabdus sediminis

Strain Designation: YM20-087

Strain history: <- JW Yoon, Tokyo Univ. <- Y Matsuo, MBI

NCBI tax ID(s): 1122952 (strain), 454144 (species)

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General

@ref: 16352

BacDive-ID: 17212

DSM-Number: 22463

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

description: Persicirhabdus sediminis YM20-087 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from marine sediment.

NCBI tax id

NCBI tax idMatching level
454144species
1122952strain

strain history

@refhistory
16352<- A. Katsuta, Kitasato Univ., Kamaishi, Iwate, Japan <- Y. Matsuo, Marine Biotechnol. Inst., Kamaishi, Japan; YM20-087
67771<- JW Yoon, Tokyo Univ. <- Y Matsuo, MBI

doi: 10.13145/bacdive17212.20240510.9

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/verrucomicrobiota
  • domain: Bacteria
  • phylum: Verrucomicrobiota
  • class: Verrucomicrobiia
  • order: Verrucomicrobiales
  • family: Verrucomicrobiaceae
  • genus: Persicirhabdus
  • species: Persicirhabdus sediminis
  • full scientific name: Persicirhabdus sediminis Yoon et al. 2008

@ref: 16352

domain: Bacteria

phylum: Verrucomicrobia

class: Verrucomicrobiae

order: Verrucomicrobiales

family: Verrucomicrobiaceae

genus: Persicirhabdus

species: Persicirhabdus sediminis

full scientific name: Persicirhabdus sediminis Yoon et al. 2008

strain designation: YM20-087

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
32455negative1.25 µm0.65 µmrod-shapedno
67771rod-shapedno
67771negative

pigmentation

  • @ref: 32455
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 16352
  • name: HALF STRENGTH R2A MEDIUM IN 75% SEAWATER (DSMZ Medium 1320)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1320
  • composition: Name: HALF STRENGTH R2A MEDIUM IN 75% SEAWATER (DSMZ Medium 1320) Composition: Agar 15.0 g/l Yeast extract 0.5 g/l Proteose peptone 0.5 g/l Casamino acids 0.5 g/l Glucose 0.5 g/l Starch 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperature
16352positivegrowth21
32455positivegrowth20-30
32455positiveoptimum25
67771positivegrowth25-30

culture pH

  • @ref: 32455
  • ability: positive
  • type: growth
  • pH: 6.5-8.5
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32455aerobe
67771aerobe

spore formation

  • @ref: 32455
  • spore formation: no

halophily

  • @ref: 32455
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <2.5 %

observation

  • @ref: 67771
  • observation: quinones: MK-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3245522599arabinose+carbon source
3245523652dextrin+carbon source
3245527082trehalose+carbon source
3245553426tween 80+carbon source
3245517632nitrate+reduction

enzymes

@refvalueactivityec
32455acid phosphatase+3.1.3.2
32455alkaline phosphatase+3.1.3.1
32455cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
16352marine sedimentChiba, Shore of Sodegaura-Kaihinkouen (35°27'17.0'' N 139°57'03.8'' E)JapanJPNAsia35.4547139.951
67771From marine sedimentshore of Sodegaura-Kaihinkouen(35°27'17.0'' N 139°57'03.8'' E), ChibaJapanJPNAsia35.4547139.951

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_92131.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1051;96_38004;97_48353;98_63437;99_92131&stattab=map
  • Last taxonomy: Persicirhabdus sediminis subclade
  • 16S sequence: AB331886
  • Sequence Identity:
  • Total samples: 1551
  • soil counts: 42
  • aquatic counts: 1261
  • animal counts: 241
  • plant counts: 7

Safety information

risk assessment

  • @ref: 16352
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16352
  • description: Persicirhabdus sediminis gene for 16S rRNA, partial sequence, strain: YM20-087
  • accession: AB331886
  • length: 1480
  • database: nuccore
  • NCBI tax ID: 1122952

GC content

  • @ref: 16352
  • GC-content: 50.4

External links

@ref: 16352

culture collection no.: DSM 22463, KCTC 22039, MBIC 08313

straininfo link

  • @ref: 86211
  • straininfo: 401548

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18398209Description of Persicirhabdus sediminis gen. nov., sp. nov., Roseibacillus ishigakijimensis gen. nov., sp. nov., Roseibacillus ponti sp. nov., Roseibacillus persicicus sp. nov., Luteolibacter pohnpeiensis gen. nov., sp. nov. and Luteolibacter algae sp. nov., six marine members of the phylum 'Verrucomicrobia', and emended descriptions of the class Verrucomicrobiae, the order Verrucomicrobiales and the family Verrucomicrobiaceae.Yoon J, Matsuo Y, Adachi K, Nozawa M, Matsuda S, Kasai H, Yokota AInt J Syst Evol Microbiol10.1099/ijs.0.65520-02008Base Composition, Carotenoids/biosynthesis, DNA, Bacterial/chemistry/genetics, Fatty Acids/metabolism, Genes, Bacterial, Gram-Negative Bacteria/*classification/genetics/*isolation & purification/metabolism, Marine Biology, Microscopy, Electron, Transmission, Molecular Sequence Data, Peptidoglycan/metabolism, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Terminology as TopicMetabolism
Phylogeny34468960Oceaniferula marina gen.nov., sp.nov., an anti-fluoroquinolone bacterium isolated from marine sediment.Jin CB, Feng X, Zou QH, Ye MQ, Du ZJAntonie Van Leeuwenhoek10.1007/s10482-021-01645-02021Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids, *Fluoroquinolones, *Geologic Sediments, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, VerrucomicrobiaTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16352Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22463)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22463
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
32455Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2867728776041
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
86211Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID401548.1StrainInfo: A central database for resolving microbial strain identifiers