Strain identifier
BacDive ID: 131335
Type strain: 
Species: Hymenobacter luteus
Strain history: W.-J. Li; Yunnan Inst. of Microbiol., Yunnan Univ., China; YIM 77921.
NCBI tax ID(s): 1411122 (species)
version 9.3 (current version)
General
@ref: 22562
BacDive-ID: 131335
DSM-Number: 26718
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative
description: Hymenobacter luteus DSM 26718 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from freshwater sediment.
NCBI tax id
- NCBI tax id: 1411122
- Matching level: species
strain history
| @ref | history |
|---|---|
| 22562 | <- S.-K. Tang, YIM; YIM 77921 <- E.-M. Zhou |
| 67770 | W.-J. Li; Yunnan Inst. of Microbiol., Yunnan Univ., China; YIM 77921. |
doi: 10.13145/bacdive131335.20250331.9.3
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 luteus
- full scientific name: Hymenobacter luteus Liu et al. 2015
@ref: 22562
domain: Bacteria
phylum: Bacteroidetes
class: Cytophagia
order: Cytophagales
family: Hymenobacteraceae
genus: Hymenobacter
species: Hymenobacter luteus
full scientific name: Hymenobacter luteus Liu et al. 2015
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 125439 | negative | 95.1 |
| 125438 | negative | 95.937 |
Culture and growth conditions
culture medium
- @ref: 22562
- name: ISP2 MEDIUM (DSMZ Medium 987)
- growth: yes
- link: https://mediadive.dsmz.de/medium/987
- composition: Name: ISP 2 MEDIUM (DSMZ Medium 987) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 22562 | positive | growth | 28 |
| 67770 | positive | growth | 28 |
Physiology and metabolism
oxygen tolerance
- @ref: 125438
- oxygen tolerance: aerobe
- confidence: 90.823
spore formation
- @ref: 125439
- spore formation: no
- confidence: 90.8
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 22562 | freshwater sediment | Yunnan province, Yiliang county, Jiuxiang tourist cave (E 103° 22.791', N 25° 04.270') | China | CHN | Asia | 25.0712 | 103.38 |
| 67770 | Freshwater sediment of Jiuxiang tourist cave in Yiliang country | Yunnan Province | China | CHN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Sediment |
| #Environmental | #Aquatic | #Freshwater |
taxonmaps
- @ref: 69479
- File name: preview.99_84110.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_263;96_21517;97_26865;98_34197;99_84110&stattab=map
- Last taxonomy: Hymenobacter
- 16S sequence: AB859261
- Sequence Identity:
- Total samples: 1217
- soil counts: 123
- aquatic counts: 150
- animal counts: 891
- plant counts: 53
Safety information
risk assessment
- @ref: 22562
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22562
- description: Hymenobacter luteus gene for 16S ribosomal RNA, partial sequence
- accession: AB859261
- length: 1545
- database: nuccore
- NCBI tax ID: 1411122
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Hymenobacter luteus DSM 26718 | GCA_014202325 | scaffold | ncbi | 1411122 |
| 66792 | Hymenobacter luteus strain DSM 26718 | 1411122.3 | wgs | patric | 1411122 |
| 66792 | Hymenobacter luteus DSM 26718 | 2861397439 | draft | img | 1411122 |
GC content
- @ref: 22562
- GC-content: 59.6
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 95.937 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 96.038 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 90.823 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 87.55 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 94.631 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 85.526 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 90.8 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 68.4 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 95.1 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | aerobe | 87.3 |
External links
@ref: 22562
culture collection no.: DSM 26718, CCTCC AB 2012947, JCM 30328, YIM 77921
straininfo link
- @ref: 89776
- straininfo: 407889
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 25348876 | Hymenobacter latericoloratus sp. nov. and Hymenobacter luteus sp. nov., isolated from freshwater sediment. | Liu L, Zhou EM, Jiao JY, Manikprabhu D, Ming H, Liu WH, Hozzein WN, Shu WS, Li WJ | Antonie Van Leeuwenhoek | 10.1007/s10482-014-0314-1 | 2014 | Aerobiosis, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, Cytophagaceae/*classification/genetics/*isolation & purification, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fresh Water/*microbiology, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
| Phylogeny | 31961285 | Hymenobacter sediminis sp. nov., isolated from lake sediment. | Wang C, Liu BT, Zhang R, Liu CL, Du ZJ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003990 | 2020 | Bacterial Typing Techniques, Base Composition, China, Cytophagaceae/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Lakes/*microbiology, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 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 | |
| 22562 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-26718 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26718) | |
| 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/ | ||
| 69479 | João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |
| 89776 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID407889.1 | |
| 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 |