Strain identifier
BacDive ID: 162605
Type strain: 
Species: Hymenobacter qilianensis
Strain history: J. Lv DK6-37.
NCBI tax ID(s): 1385715 (species)
version 9.3 (current version)
General
@ref: 67770
BacDive-ID: 162605
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Hymenobacter qilianensis JCM 19763 is a mesophilic, Gram-negative bacterium that was isolated from Subsurface sandstone sediment in the permafrost region of Qilian Mountains.
NCBI tax id
- NCBI tax id: 1385715
- Matching level: species
strain history
- @ref: 67770
- history: J. Lv DK6-37.
doi: 10.13145/bacdive162605.20250331.9.3
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 qilianensis
- full scientific name: Hymenobacter qilianensis Han et al. 2014
@ref: 67770
domain: Bacteria
phylum: Bacteroidetes
class: Cytophagia
order: Cytophagales
family: Hymenobacteraceae
genus: Hymenobacter
species: Hymenobacter qilianensis
full scientific name: Hymenobacter qilianensis Han et al. 2014
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 125439 | negative | 99.4 |
| 125438 | negative | 95.482 |
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 28
Physiology and metabolism
spore formation
- @ref: 125439
- spore formation: no
- confidence: 98.7
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Subsurface sandstone sediment (356 m in depth) in the permafrost region of Qilian Mountains
- country: China
- origin.country: CHN
- continent: Asia
Sequence information
16S sequences
- @ref: 67770
- description: Hymenobacter qilianensis strain DK6-37 16S ribosomal RNA gene, partial sequence
- accession: KF723715
- length: 1393
- database: nuccore
- NCBI tax ID: 1385715
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Hymenobacter qilianensis CGMCC 1.12720 | GCA_014638675 | contig | ncbi | 1385715 |
| 66792 | Hymenobacter qilianensis JCM 19763 | GCA_014489555 | complete | ncbi | 1385715 |
| 66792 | Hymenobacter qilianensis strain CGMCC 1.12720 | 1385715.4 | wgs | patric | 1385715 |
| 66792 | Hymenobacter qilianensis strain JCM 19763 | 1385715.3 | complete | patric | 1385715 |
| 66792 | Hymenobacter qilianensis JCM 19763 | 2897422876 | complete | img | 1385715 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 95.482 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 96.546 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 88.52 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 86.761 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 96.381 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 83.526 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 98.7 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 51.5 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 99.4 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | aerobe | 87.1 |
External links
@ref: 67770
culture collection no.: JCM 19763, CGMCC 1.12720
literature
- topic: Phylogeny
- Pubmed-ID: 24677143
- title: Hymenobacter qilianensis sp. nov., isolated from a subsurface sandstone sediment in the permafrost region of Qilian Mountains, China and emended description of the genus Hymenobacter.
- authors: Han L, Wu SJ, Qin CY, Zhu YH, Lu ZQ, Xie B, Lv J
- journal: Antonie Van Leeuwenhoek
- DOI: 10.1007/s10482-014-0155-y
- year: 2014
- mesh: Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, Cytophagaceae/*classification/genetics/*isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology
- topic2: Genetics
Reference
| @id | authors | title | doi/url |
|---|---|---|---|
| 20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |