Strain identifier

BacDive ID: 23124

Type strain: Yes

Species: Phytohabitans houttuyneae

Strain Designation: K11-0057

Strain history: A. Matsumoto K11-0057.

NCBI tax ID(s): 1076126 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 19189

BacDive-ID: 23124

DSM-Number: 45864

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

description: Phytohabitans houttuyneae K11-0057 is an aerobe, spore-forming, mesophilic bacterium that was isolated from roots of Houttuynia cordata.

NCBI tax id

  • NCBI tax id: 1076126
  • Matching level: species

strain history

@refhistory
19189<- JCM; JCM 17830 <- A. Matsumoto; K11-0057
67770A. Matsumoto K11-0057.

doi: 10.13145/bacdive23124.20230509.8.1

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 houttuyneae
  • full scientific name: Phytohabitans houttuyneae Inahashi et al. 2012

@ref: 19189

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Phytohabitans

species: Phytohabitans houttuyneae

full scientific name: Phytohabitans houttuyneae Inahashi et al. 2012

strain designation: K11-0057

type strain: yes

Morphology

cell morphology

@refgram stainconfidence
30512positive
69480positive100

pigmentation

  • @ref: 30512
  • production: yes

multimedia

  • @ref: 19189
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45864.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
19189GPHF-MEDIUM (DSMZ Medium 553)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium553.pdf
19189N-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
19189GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
19189positivegrowth28mesophilic
30512positivegrowth20-42
30512positiveoptimum30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
30512positivegrowth06-11alkaliphile
30512positiveoptimum8

Physiology and metabolism

oxygen tolerance

  • @ref: 30512
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30512yes
69481yes98
69480yes100

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
3051226546rhamnose+carbon source
3051217992sucrose+carbon source
3051218222xylose+carbon source

enzymes

@refvalueactivityec
30512acid phosphatase+3.1.3.2
30512alkaline phosphatase+3.1.3.1
30512alpha-galactosidase+3.2.1.22
30512gelatinase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinenthost species
19189roots of Houttuynia cordataKanagawa Pref.JapanJPNAsia
67770Roots of Houttuynia cordataKanagawa Pref.JapanJPNAsiaHouttuynia cordata

isolation source categories

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

Safety information

risk assessment

  • @ref: 19189
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 19189
  • description: Phytohabitans houttuyneae gene for 16S rRNA, partial sequence
  • accession: AB663560
  • length: 1468
  • database: ena
  • NCBI tax ID: 1076126

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Phytohabitans houttuyneae NBRC 108639GCA_011764425contigncbi1076126
66792Phytohabitans houttuyneae strain NBRC 1086391076126.3wgspatric1076126

GC content

@refGC-contentmethod
1918973
6777073high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes98no
motileno90.231no
flagellatedno97.555no
gram-positiveyes84.674no
anaerobicno98.946yes
aerobicyes91.875yes
halophileno94.115no
spore-formingyes90.54no
thermophileno97.614yes
glucose-utilyes88.28yes
glucose-fermentno90.31no

External links

@ref: 19189

culture collection no.: DSM 45864, BCC 48147, JCM 17830, NBRC 108639

straininfo link

  • @ref: 87360
  • straininfo: 404222

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
Phylogeny27126122Phytohabitans kaempferiae sp. nov., an endophytic actinomycete isolated from the leaf of Kaempferia larsenii.Niemhom N, Chutrakul C, Suriyachadkun C, Thawai CInt J Syst Evol Microbiol10.1099/ijsem.0.0011212016Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Micromonosporaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Leaves/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Thailand, Vitamin K 2/chemistry, Zingiberaceae/*microbiologyTranscriptome
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
19189Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45864)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45864
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
87360Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID404222.1StrainInfo: A central database for resolving microbial strain identifiers