Strain identifier

BacDive ID: 158615

Type strain: Yes

Species: Hymenobacter rubripertinctus

Strain Designation: NY03-3-30

Strain history: <- Fan Jiang, Wuhan Univ.

NCBI tax ID(s): 2029981 (species)

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General

@ref: 65337

BacDive-ID: 158615

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

description: Hymenobacter rubripertinctus NY03-3-30 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from From soil.

NCBI tax id

  • NCBI tax id: 2029981
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Fan Jiang, Wuhan Univ.

doi: 10.13145/bacdive158615.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Hymenobacteraceae
  • genus: Hymenobacter
  • species: Hymenobacter rubripertinctus
  • full scientific name: Hymenobacter rubripertinctus Jiang et al. 2018

@ref: 65337

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Hymenobacteraceae

genus: Hymenobacter

species: Hymenobacter rubripertinctus

strain designation: NY03-3-30

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
65337negative2.1-5.6 µm0.8-1 µmrod-shapedno
67771rod-shapedno
67771negative
69480negative99.998

colony morphology

  • @ref: 65337
  • colony color: red
  • colony shape: circular
  • medium used: R2A

pigmentation

@refproductionname
65337noflexirubin-type pigments
65337yescarotinoid pigments

Culture and growth conditions

culture medium

@refnamegrowth
65337Reasoner's 2A agar (R2A)yes
653370.3 x R2Ayes
65337tryptic soy agaryes
65337Marine agar (MA)yes
65337nutriet agaryes
65337LB (Luria-Bertani) MEDIUMyes
65337MacConkey agarno

culture temp

@refgrowthtypetemperaturerange
65337positivegrowth4-28
65337positiveoptimum20psychrophilic
67771positivegrowth20psychrophilic

culture pH

@refabilitytypepHPH range
65337positivegrowth6-9alkaliphile
65337positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
65337aerobe
67771aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.99

halophily

@refsaltgrowthtested relationconcentration
65337NaClpositivegrowth0-1 %(w/v)
65337NaClpositiveoptimum0 %(w/v)

observation

  • @ref: 67771
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
65337161933-hydroxybenzoate-assimilation
65337370543-hydroxybutyrate-assimilation
65337178794-hydroxybenzoate-assimilation
6533717128adipate-assimilation
6533727689decanoate-assimilation
6533717634D-glucose-fermentation
6533716899D-mannitol-assimilation
6533716024D-mannose-assimilation
6533716988D-ribose-assimilation
6533717924D-sorbitol-assimilation
653374853esculin-hydrolysis
653375291gelatin-hydrolysis
6533728087glycogen+assimilation
6533717268myo-inositol-assimilation
6533717240itaconate-assimilation
6533716977L-alanine-assimilation
6533730849L-arabinose-assimilation
6533718287L-fucose-assimilation
6533715971L-histidine-assimilation
6533717203L-proline-assimilation
6533762345L-rhamnose-assimilation
6533717115L-serine-assimilation
6533724996lactate-assimilation
6533725115malate-assimilation
6533717306maltose+assimilation
6533728053melibiose-assimilation
6533717632nitrate+reduction
6533718401phenylacetate-assimilation
65337potassium 2-dehydro-D-gluconate-assimilation
65337potassium 5-dehydro-D-gluconate-assimilation
6533732032potassium gluconate-assimilation
6533717272propionate-assimilation
6533717814salicin-assimilation
6533732954sodium acetate-assimilation
6533753258sodium citrate-assimilation
6533762983sodium malonate-assimilation
653379300suberic acid-assimilation
6533717992sucrose-assimilation
6533731011valerate-assimilation

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
65337100241ciprofloxacinyesyes5 µg (disc)
6533728971ampicillinyesyes10 µg (disc)
6533748923erythromycinyesyes15 µg (disc)
65337161680aztreonamyesyes30 µg (disc)
6533729007ceftriaxoneyesyes30 µg (disc)
6533717698chloramphenicolyesyes30 µg (disc)
653376104kanamycinyesyes30 µg (disc)
653378309polymyxin byesyes30 µg (disc)
6533727902tetracyclineyesyes30 µg (disc)
6533728001vancomycinyesyes30 µg (disc)
6533728864tobramycinyesyes10 µg (disc)

metabolite production

  • @ref: 65337
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
65337catalase+1.11.1.6
65337cytochrome oxidase+1.9.3.1
65337alkaline phosphatase+3.1.3.1
65337leucine arylamidase+3.4.11.1
65337valine arylamidase+
65337cystine arylamidase+3.4.11.3
65337naphthol-AS-BI-phosphohydrolase+
65337acid phosphatase+3.1.3.2
65337alpha-glucosidase+3.2.1.20
65337beta-glucosidase+3.2.1.21
65337N-acetyl-beta-glucosaminidase+3.2.1.52
65337esterase (C 4)+
65337esterase Lipase (C 8)+
65337lipase (C 14)-
65337trypsin-3.4.21.4
65337alpha-chymotrypsin-3.4.21.1
65337alpha-galactosidase-3.2.1.22
65337beta-galactosidase-3.2.1.23
65337beta-glucuronidase-3.2.1.31
65337alpha-mannosidase-3.2.1.24
65337alpha-fucosidase-3.2.1.51
65337urease-3.5.1.5
65337arginine dihydrolase-3.5.3.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling datelatitudelongitudeenrichment cultureisolation procedure
67771From soilInexpressible Island, Northern Victoria Land of the Antarctic Ross Orogen, AntarcticaAntarcticaATAAustralia and Oceania
65337soil sampleInexpressible Island, Northern Victoria Land of the Antarctic Ross OrogenAntarcticaATAAustralia and Oceania2015-02-74.9169163.716R2A agardilution plating technique

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Sequence information

16S sequences

  • @ref: 65337
  • description: 16S rRNA gene sequence
  • accession: MF770258
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Hymenobacter rubripertinctus CCM 8852GCA_003583925contigncbi2029981
66792Hymenobacter rubripertinctus strain CCM 88522029981.3wgspatric2029981
66792Hymenobacter rubripertinctus CCM 88522881489277draftimg2029981

GC content

@refGC-contentmethod
6533759.4high performance liquid chromatography (HPLC)
6777159.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno82no
motileno93.939no
gram-positiveno97.782yes
anaerobicno98.99yes
aerobicyes90.432yes
halophileno93.093no
spore-formingno93.879no
glucose-utilyes75.151no
flagellatedno97.521yes
thermophileno96.533yes
glucose-fermentno91.58yes

External links

@ref: 65337

culture collection no.: CCTCC AB 2017095, KCTC 62163, CCM 8852

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29388548Hymenobacter rubripertinctus sp. nov., isolated from Antarctic tundra soil.Jiang F, Danzeng W, Zhang Y, Zhang Y, Jiang L, Liu J, Lu L, Fan W, Peng FInt J Syst Evol Microbiol10.1099/ijsem.0.0025632018Antarctic Regions, Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Tundra, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny30587382Hymenobacter amundsenii sp. nov. resistant to ultraviolet radiation, isolated from regoliths in Antarctica.Sedlacek I, Pantucek R, Kralova S, Maslanova I, Holochova P, Stankova E, Vrbovska V, Svec P, Busse HJSyst Appl Microbiol10.1016/j.syapm.2018.12.0042018Antarctic Regions, Bacteroidetes/chemistry/*classification/genetics/*physiology, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Genome, Bacterial/genetics, Lipids/analysis, Phylogeny, Pigmentation, Quinones/analysis, RNA, Ribosomal, 16S/genetics, *Radiation Tolerance, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics

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
65337Fan Jiang, Wangmu Danzeng, Yuming Zhang, Yan Zhang, Li Jiang, Jia Liu, Lu Lu, Wei Fan, Fang PengHymenobacter rubripertinctus sp. nov., isolated from Antarctic tundra soil10.1099/ijsem.0.002563IJSEM 68: 663-668 201829388548
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
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