Strain identifier
BacDive ID: 3804
Type strain:
Species: Hymenobacter psychrotolerans
Strain Designation: Tibet-IIU11
Strain history: <- G. Zhang, School of Life Sci., Lanzhou Univ., China; Tibet-IIU11
NCBI tax ID(s): 1121959 (strain), 344998 (species)
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 id | Matching level |
---|---|
1121959 | strain |
344998 | species |
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
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
32500 | negative | 1.25 µm | 0.5 µm | rod-shaped | no | |
69480 | negative | 99.998 |
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
@ref | growth | type | temperature | range |
---|---|---|---|---|
7529 | positive | growth | 20-25 | |
32500 | positive | growth | 04-28 | |
32500 | positive | optimum | 18 | psychrophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
32500 | positive | growth | 05-10 | alkaliphile |
32500 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 32500
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
32500 | no | |
69481 | no | 100 |
69480 | no | 99.998 |
halophily
- @ref: 32500
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-1.5 %
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32500 | 17234 | glucose | + | carbon source |
32500 | 37684 | mannose | + | carbon source |
32500 | 17272 | propionate | + | carbon source |
32500 | 17992 | sucrose | + | carbon source |
32500 | 17632 | nitrate | + | reduction |
enzymes
@ref | value | activity | ec |
---|---|---|---|
32500 | acid phosphatase | + | 3.1.3.2 |
32500 | alkaline phosphatase | + | 3.1.3.1 |
32500 | catalase | + | 1.11.1.6 |
32500 | cytochrome 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
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Hymenobacter psychrotolerans DSM 18569 | GCA_900142395 | contig | ncbi | 1121959 |
66792 | Hymenobacter psychrotolerans DSM 18569 | 1121959.3 | wgs | patric | 1121959 |
66792 | Hymenobacter psychrotolerans DSM 18569 | 2585428192 | draft | img | 1121959 |
GC content
@ref | GC-content |
---|---|
7529 | 60.0 |
32500 | 60 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 92.078 | yes |
flagellated | no | 97.372 | yes |
gram-positive | no | 97.441 | no |
anaerobic | no | 99.173 | no |
halophile | no | 92.795 | yes |
spore-forming | no | 94.186 | yes |
thermophile | no | 93.267 | no |
glucose-util | yes | 82.962 | yes |
aerobic | yes | 90.819 | yes |
glucose-ferment | no | 90.758 | no |
External links
@ref: 7529
culture collection no.: DSM 18569, CGMCC 1.6365
straininfo link
- @ref: 73316
- straininfo: 312287
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 18450716 | Hymenobacter 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 G | Int J Syst Evol Microbiol | 10.1099/ijs.0.65588-0 | 2008 | Bacterial 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 Specificity | Genetics |
Phylogeny | 24682704 | Hymenobacter kanuolensis sp. nov., a novel radiation-resistant bacterium. | Su S, Chen M, Teng C, Jiang S, Zhang C, Lin M, Zhang W | Int J Syst Evol Microbiol | 10.1099/ijs.0.051680-0 | 2014 | Bacterial 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/chemistry | Genetics |
Phylogeny | 27374800 | Hymenobacter glacieicola sp. nov., isolated from glacier ice. | Liu K, Liu Y, Wang N, Gu Z, Shen L, Xu B, Zhou Y, Liu H, Jiao N | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001266 | 2016 | Bacterial 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/chemistry | Transcriptome |
Phylogeny | 29148363 | Hymenobacter defluvii sp. nov., isolated from wastewater of an acidic water neutralization facility. | Kang JW, Choi S, Choe HN, Seong CN | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002497 | 2017 | Bacterial 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/*microbiology | Transcriptome |
Phylogeny | 29458543 | Hymenobacter profundi sp. nov., isolated from deep-sea water. | Sun J, Xing M, Wang W, Dai F, Liu J, Hao J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002621 | 2018 | ||
Phylogeny | 34259886 | Hymenobacter guriensis sp. nov., and Hymenobacter duratus sp. nov., Radiation-Resistant Species Isolated from Soil in South Korea. | Damdintogtokh T, Cha IT, Kim MK | Curr Microbiol | 10.1007/s00284-021-02517-6 | 2021 | Bacterial 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, Tibet | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
7529 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18569) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18569 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
32500 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28720 | 28776041 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
73316 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID312287.1 | StrainInfo: A central database for resolving microbial strain identifiers |