Strain identifier

BacDive ID: 141048

Type strain: Yes

Species: Ramlibacter rhizophilus

Strain Designation: THG-YS3.2.7

Strain history: <- Tae-Hoo Yi, Kyung Hee Univ.

NCBI tax ID(s): 1781167 (species)

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General

@ref: 43928

BacDive-ID: 141048

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

description: Ramlibacter rhizophilus THG-YS3.2.7 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from rhizosphere soil of a Mugunghwa flower collected from Kyung Hee University, Yongin, South Korea.

NCBI tax id

  • NCBI tax id: 1781167
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Tae-Hoo Yi, Kyung Hee Univ.

doi: 10.13145/bacdive141048.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Ramlibacter
  • species: Ramlibacter rhizophilus
  • full scientific name: Ramlibacter rhizophilus Yan et al. 2017

@ref: 43928

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Ramlibacter

species: Ramlibacter rhizophilus

strain designation: THG-YS3.2.7

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43928negative10-12 µm0.5-1.0 µmrod-shapedno
439280.5-0.6 µm0.5-0.6 µmcoccus-shaped
69480negative99.999

colony morphology

  • @ref: 43928
  • colony color: yellow
  • colony shape: circular
  • incubation period: 7 days
  • medium used: Nutrient agar

Culture and growth conditions

culture medium

@refnamegrowth
43928LB (Luria-Bertani) MEDIUMyes
43928MacConkey agarno
43928Marine agar (MA)yes
43928Nutrient agar (NA)yes
43928Reasoner's 2A agar (R2A)yes
43928Tryptone soya agaryes

culture temp

@refgrowthtypetemperaturerange
43928positivegrowth10-40
43928positiveoptimum28-37mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepH
43928positivegrowth6.0-8.0
43928positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43928aerobe
67771aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.987

halophily

@refsaltgrowthtested relationconcentration
43928NaClpositivegrowth0-5 %(w/v)
43928NaClpositiveoptimum1 %(w/v)

observation

  • @ref: 43928
  • observation: quinone Q-8

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
43928casein-hydrolysis
43928chitin-hydrolysis17029
43928L-tyrosine-hydrolysis17895
43928tween 20-hydrolysis53424
43928tween 80-hydrolysis53426
43928nitrate-reduction17632
439283-hydroxybenzoate+carbon source16193
439283-hydroxybutyrate+carbon source37054
43928glycogen+carbon source28087
43928L-proline+carbon source17203
43928sodium malonate+carbon source62983
43928suberic acid+carbon source9300
43928adipate+hydrolysis17128
43928cellulose+hydrolysis62968
43928dna+hydrolysis16991
43928gluconate+hydrolysis24265
43928starch+hydrolysis28017

metabolite production

  • @ref: 43928
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43928catalase+1.11.1.6
43928cytochrome oxidase+1.9.3.1
43928arginine dihydrolase+3.5.3.6
43928urease+3.5.1.5
43928alkaline phosphatase+3.1.3.1
43928esterase (C 4)+
43928esterase Lipase (C 8)+
43928lipase (C 14)+
43928leucine arylamidase+3.4.11.1
43928valine arylamidase+
43928cystine arylamidase+3.4.11.3
43928trypsin+3.4.21.4
43928alpha-chymotrypsin+3.4.21.1
43928acid phosphatase+3.1.3.2
43928naphthol-AS-BI-phosphohydrolase+

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43928C10:03.3
    43928C10:0 3OH3.8
    43928C16:031.1
    43928C16:1ω7c / C16:1ω6c11.6
    43928C17:0 cyclo19.6
    43928C17:0 cyclo1.9
    43928C18:09.9
    43928C18:1ω7c / C18:1ω6c12.1
    43928C18:3ω6c3.5
    43928C9:00.7
  • type of FA analysis: whole cell analysis
  • incubation medium: Nutrient agar
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 7
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • method/protocol: Sasser, 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperature
43928rhizosphere soil of a Mugunghwa flower (Hibiscus syriacus L.) collected from Kyung Hee University, Yongin, South KoreaKyung Hee University, YonginRepublic of KoreaKORAsia37.2758127.178Nutrient agar1 week30
67771From soilYonginRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

Sequence information

16S sequences

  • @ref: 43928
  • description: 16S rRNA gene sequence
  • accession: KT962170
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ramlibacter rhizophilus CCTCC AB2015357GCA_004681965contigncbi1781167
66792Ramlibacter rhizophilus strain CCTCC AB20153571781167.3wgspatric1781167
66792Ramlibacter rhizophilus CCTCC AB20153572881101125draftimg1781167

GC content

  • @ref: 43928
  • GC-content: 69.4
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno83.466yes
gram-positiveno98.02yes
anaerobicno98.655yes
aerobicyes94.484yes
halophileno90.712yes
spore-formingno93.373no
thermophileno96.604yes
glucose-utilno56.014no
flagellatedno92.999yes
glucose-fermentno88.565no

External links

@ref: 43928

culture collection no.: KCTC 52083, CCTCC AB 2015357

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28879839Ramlibacter rhizophilus sp. nov., isolated from rhizosphere soil of national flower Mugunghwa from South Korea.Yan ZF, Trinh H, Moya G, Lin P, Li CT, Kook M, Yi THInt J Syst Evol Microbiol10.1099/ijsem.0.0021912017Bacterial Typing Techniques, Base Composition, Comamonadaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hibiscus/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryTranscriptome
Phylogeny31433291Ramlibacter humi sp. nov., isolated from tropical forest soil.Zhang XJ, Feng GD, Yao Q, Wang YH, Yang SZ, Zhu HHInt J Syst Evol Microbiol10.1099/ijsem.0.0036412019Bacterial Typing Techniques, Base Composition, China, Comamonadaceae/classification, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Tropical Climate, Ubiquinone/chemistryTranscriptome

Reference

@idauthorstitledoi/urljournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
43928Zheng-Fei Yan, Huan Trinh, Gabriela Moya, Pei Lin, Chang-Tian Li, MooChang Kook, Tae-Hoo YiRamlibacter rhizophilus sp. nov., isolated from rhizosphere soil of national flower Mugunghwa from South Korea10.1099/ijsem.0.002191IJSEM 67: 3773-3777 201728879839
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1