Strain identifier

BacDive ID: 23125

Type strain: Yes

Species: Phytohabitans rumicis

Strain Designation: K11-0047

Strain history: A. Matsumoto K11-0047.

NCBI tax ID(s): 1076125 (species)

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General

@ref: 19190

BacDive-ID: 23125

DSM-Number: 45865

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive

description: Phytohabitans rumicis K11-0047 is an aerobe, spore-forming, mesophilic bacterium that was isolated from roots of Rumex acetosa.

NCBI tax id

  • NCBI tax id: 1076125
  • Matching level: species

strain history

@refhistory
19190<- JCM; JCM 17829 <- A. Matsumoto; K11-0047
67770A. Matsumoto K11-0047.

doi: 10.13145/bacdive23125.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micromonosporales
  • family: Micromonosporaceae
  • genus: Phytohabitans
  • species: Phytohabitans rumicis
  • full scientific name: Phytohabitans rumicis Inahashi et al. 2012

@ref: 19190

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Phytohabitans

species: Phytohabitans rumicis

full scientific name: Phytohabitans rumicis Inahashi et al. 2012

strain designation: K11-0047

type strain: yes

Morphology

cell morphology

@refgram stainconfidence
30512positive
69480positive100

pigmentation

  • @ref: 30512
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
19190GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium65.pdf
19190N-Z-AMINE-MEDIUM (DSMZ Medium 554)yeshttps://mediadive.dsmz.de/medium/554Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
19190positivegrowth28mesophilic
30512positivegrowth20-34
30512positiveoptimum27mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
30512positivegrowth07-11alkaliphile
30512positiveoptimum8

Physiology and metabolism

oxygen tolerance

  • @ref: 30512
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30512yes
69481yes100
69480yes99.999

observation

  • @ref: 67770
  • observation: quinones: MK-10(H8), MK-10(H6)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3051222599arabinose+carbon source
3051228757fructose+carbon source
3051217234glucose+carbon source
3051217306maltose+carbon source
3051229864mannitol+carbon source
3051230911sorbitol+carbon source
3051217992sucrose+carbon source
3051217632nitrate+reduction

enzymes

@refvalueactivityec
30512acid phosphatase+3.1.3.2
30512alkaline phosphatase+3.1.3.1
30512gelatinase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinenthost species
19190roots of Rumex acetosaKanagawa Pref.JapanJPNAsia
67770Roots of Rumex acetosaKanagawa Pref.JapanJPNAsiaRumex acetosa

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)

Safety information

risk assessment

  • @ref: 19190
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 19190
  • description: Phytohabitans rumicis gene for 16S rRNA, partial sequence
  • accession: AB663559
  • length: 1470
  • database: ena
  • NCBI tax ID: 1076125

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Phytohabitans rumicis NBRC 108638GCA_011764445contigncbi1076125
66792Phytohabitans rumicis strain NBRC 1086381076125.3wgspatric1076125

GC content

@refGC-contentmethod
1919072
6777072high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno93.623no
flagellatedno97.675no
gram-positiveyes87.546yes
anaerobicno98.962yes
aerobicyes92.25yes
halophileno96.204no
spore-formingyes92.669no
thermophileno97.988yes
glucose-utilyes86.552yes
glucose-fermentno90.501no

External links

@ref: 19190

culture collection no.: DSM 45865, BCC 48146, JCM 17829, NBRC 108638

straininfo link

  • @ref: 87361
  • straininfo: 404075

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22228668Phytohabitans flavus sp. nov., Phytohabitans rumicis sp. nov. and Phytohabitans houttuyneae sp. nov., isolated from plant roots, and emended description of the genus Phytohabitans.Inahashi Y, Matsumoto A, Omura S, Takahashi YInt J Syst Evol Microbiol10.1099/ijs.0.037747-02012Bacterial Typing Techniques, DNA, Bacterial/genetics, Houttuynia/microbiology, Japan, Micromonosporaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Rumex/microbiology, Sequence Analysis, DNAGenetics
33120960Polyketide Synthase and Nonribosomal Peptide Synthetase Gene Clusters in Type Strains of the Genus Phytohabitans.Komaki H, Tamura TLife (Basel)10.3390/life101102572020

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
19190Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45865)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45865
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
30512Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2684428776041
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
87361Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID404075.1StrainInfo: A central database for resolving microbial strain identifiers