Strain identifier

BacDive ID: 3804

Type strain: Yes

Species: Hymenobacter psychrotolerans

Strain Designation: Tibet-IIU11

Strain history: <- G. Zhang, School of Life Sci., Lanzhou Univ., China; Tibet-IIU11

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

@ref: 7529

BacDive-ID: 3804

DSM-Number: 18569

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

description: Hymenobacter psychrotolerans Tibet-IIU11 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from permafrost sediment sample.

NCBI tax id

NCBI tax idMatching level
1121959strain
344998species

strain history

  • @ref: 7529
  • history: <- G. Zhang, School of Life Sci., Lanzhou Univ., China; Tibet-IIU11

doi: 10.13145/bacdive3804.20230509.8.1

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 psychrotolerans
  • full scientific name: Hymenobacter psychrotolerans Zhang et al. 2008

@ref: 7529

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Hymenobacteraceae

genus: Hymenobacter

species: Hymenobacter psychrotolerans

full scientific name: Hymenobacter psychrotolerans Zhang et al. 2008

strain designation: Tibet-IIU11

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32500negative1.25 µm0.5 µmrod-shapedno
69480negative99.998

pigmentation

  • @ref: 32500
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 7529
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
7529positivegrowth20-25
32500positivegrowth04-28
32500positiveoptimum18psychrophilic

culture pH

@refabilitytypepHPH range
32500positivegrowth05-10alkaliphile
32500positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 32500
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
32500no
69481no100
69480no99.998

halophily

  • @ref: 32500
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-1.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3250017234glucose+carbon source
3250037684mannose+carbon source
3250017272propionate+carbon source
3250017992sucrose+carbon source
3250017632nitrate+reduction

enzymes

@refvalueactivityec
32500acid phosphatase+3.1.3.2
32500alkaline phosphatase+3.1.3.1
32500catalase+1.11.1.6
32500cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 7529
  • sample type: permafrost sediment sample
  • geographic location: Qinghai–Tibet Plateau, Beilu river basin (34° 50' N 92° 56' E, 4676 m above sea level)
  • country: China
  • origin.country: CHN
  • continent: Asia
  • latitude: 34.8333
  • longitude: 92.9333

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Permafrost

Safety information

risk assessment

  • @ref: 7529
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7529
  • description: Hymenobacter psychrotolerans strain Tibet-IIU11 16S ribosomal RNA gene, partial sequence
  • accession: DQ177475
  • length: 1484
  • database: ena
  • NCBI tax ID: 1121959

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Hymenobacter psychrotolerans DSM 18569GCA_900142395contigncbi1121959
66792Hymenobacter psychrotolerans DSM 185691121959.3wgspatric1121959
66792Hymenobacter psychrotolerans DSM 185692585428192draftimg1121959

GC content

@refGC-content
752960.0
3250060

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.078yes
flagellatedno97.372yes
gram-positiveno97.441no
anaerobicno99.173no
halophileno92.795yes
spore-formingno94.186yes
thermophileno93.267no
glucose-utilyes82.962yes
aerobicyes90.819yes
glucose-fermentno90.758no

External links

@ref: 7529

culture collection no.: DSM 18569, CGMCC 1.6365

straininfo link

  • @ref: 73316
  • straininfo: 312287

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18450716Hymenobacter psychrotolerans sp. nov., isolated from the Qinghai--Tibet Plateau permafrost region.Zhang G, Niu F, Busse HJ, Ma X, Liu W, Dong M, Feng H, An L, Cheng GInt J Syst Evol Microbiol10.1099/ijs.0.65588-02008Bacterial Typing Techniques, Base Composition, China, *Cold Temperature, Cytophagaceae/*classification/genetics/isolation & purification/physiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Geologic Sediments/*microbiology, Ice Cover/*microbiology, Molecular Sequence Data, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny24682704Hymenobacter kanuolensis sp. nov., a novel radiation-resistant bacterium.Su S, Chen M, Teng C, Jiang S, Zhang C, Lin M, Zhang WInt J Syst Evol Microbiol10.1099/ijs.0.051680-02014Bacterial Typing Techniques, Base Composition, China, Cytophagaceae/*classification/genetics/isolation & purification/*radiation effects, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gamma Rays, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Radiation Tolerance, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny27374800Hymenobacter glacieicola sp. nov., isolated from glacier ice.Liu K, Liu Y, Wang N, Gu Z, Shen L, Xu B, Zhou Y, Liu H, Jiao NInt J Syst Evol Microbiol10.1099/ijsem.0.0012662016Bacterial Typing Techniques, Base Composition, China, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Ice Cover/*microbiology, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny29148363Hymenobacter defluvii sp. nov., isolated from wastewater of an acidic water neutralization facility.Kang JW, Choi S, Choe HN, Seong CNInt J Syst Evol Microbiol10.1099/ijsem.0.0024972017Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Spermidine/analogs & derivatives/chemistry, Tibet, Vitamin K 2/analogs & derivatives/chemistry, Waste Water/*microbiologyTranscriptome
Phylogeny29458543Hymenobacter profundi sp. nov., isolated from deep-sea water.Sun J, Xing M, Wang W, Dai F, Liu J, Hao JInt J Syst Evol Microbiol10.1099/ijsem.0.0026212018
Phylogeny34259886Hymenobacter guriensis sp. nov., and Hymenobacter duratus sp. nov., Radiation-Resistant Species Isolated from Soil in South Korea.Damdintogtokh T, Cha IT, Kim MKCurr Microbiol10.1007/s00284-021-02517-62021Bacterial Typing Techniques, Bacteroidetes, Base Composition, *Cytophagaceae/genetics, DNA, Bacterial/genetics, Fatty Acids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil, Soil Microbiology, TibetTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7529Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18569)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18569
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
32500Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2872028776041
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)
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
73316Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID312287.1StrainInfo: A central database for resolving microbial strain identifiers