Strain identifier

BacDive ID: 8050

Type strain: Yes

Species: Phytohabitans suffuscus

Strain Designation: K07-0523

Strain history: DSM 45306 <-- Y. Takahashi; Kitasato Univ., Japan; K07-0523.

NCBI tax ID(s): 624315 (species)

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General

@ref: 16165

BacDive-ID: 8050

DSM-Number: 45306

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

description: Phytohabitans suffuscus K07-0523 is an aerobe, spore-forming, mesophilic bacterium that was isolated from roots of an orchid.

NCBI tax id

  • NCBI tax id: 624315
  • Matching level: species

strain history

@refhistory
16165<- Y. Takahashi, Kitasato Univ., Tokyo, Japan; K07-0523 <- Y. Inahashi
67770DSM 45306 <-- Y. Takahashi; Kitasato Univ., Japan; K07-0523.

doi: 10.13145/bacdive8050.20230509.8.1

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 suffuscus
  • full scientific name: Phytohabitans suffuscus Inahashi et al. 2010

@ref: 16165

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Phytohabitans

species: Phytohabitans suffuscus

full scientific name: Phytohabitans suffuscus Inahashi et al. 2010

strain designation: K07-0523

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
29587positiverod-shapedno
69480positive100

pigmentation

  • @ref: 29587
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16165TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
16165GYM 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
16165GPHF-MEDIUM (DSMZ Medium 553)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium553.pdf

culture temp

@refgrowthtypetemperaturerange
16165positivegrowth28mesophilic
29587positivegrowth26-35mesophilic
29587positiveoptimum27mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
29587positivegrowth07-10alkaliphile
29587positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 29587
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
29587yes
69481yes100
69480yes100

observation

  • @ref: 67770
  • observation: quinones: MK-10(H6), MK-10(H4), MK-9(H6), MK-10(H8), MK-9(H8)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2958722599arabinose+carbon source
2958728757fructose+carbon source
2958728260galactose+carbon source
2958717234glucose+carbon source
2958729864mannitol+carbon source
2958737684mannose+carbon source
2958716634raffinose+carbon source
2958726546rhamnose+carbon source
2958717992sucrose+carbon source
2958718222xylose+carbon source

enzymes

  • @ref: 29587
  • value: gelatinase
  • activity: +

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16165roots of an orchidOkinawa PrefectureJapanJPNAsia
67770Roots of an orchidOkinawa Pref.JapanJPNAsia

isolation source categories

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

Safety information

risk assessment

  • @ref: 16165
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16165
  • description: Phytohabitans suffuscus gene for 16S ribosomal RNA, partial sequence
  • accession: AB490769
  • length: 1469
  • database: ena
  • NCBI tax ID: 624315

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Phytohabitans suffuscus NBRC 105367GCA_011764565completencbi624315
66792Phytohabitans suffuscus strain NBRC 105367624315.3completepatric624315

GC content

@refGC-contentmethod
1616573high performance liquid chromatography (HPLC)
2958773

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno90.39no
flagellatedno97.466no
gram-positiveyes85.851yes
anaerobicno98.898yes
aerobicyes92.279yes
halophileno95.811no
spore-formingyes92.371yes
glucose-utilyes87.289yes
thermophileno97.41no
glucose-fermentno90.049no

External links

@ref: 16165

culture collection no.: DSM 45306, BCC 55028, JCM 31213, NBRC 105367, TBRC 2211

straininfo link

  • @ref: 77478
  • straininfo: 371119

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20042750Phytohabitans suffuscus gen. nov., sp. nov., an actinomycete of the family Micromonosporaceae isolated from plant roots.Inahashi Y, Matsumoto A, Danbara H, Omura S, Takahashi YInt J Syst Evol Microbiol10.1099/ijs.0.016477-02009Base Composition, DNA, Bacterial/genetics, Fatty Acids/metabolism, Micromonosporaceae/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Orchidaceae/*microbiology, Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/geneticsMetabolism
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
16165Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45306)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45306
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
29587Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2597928776041
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
77478Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID371119.1StrainInfo: A central database for resolving microbial strain identifiers