Strain identifier
BacDive ID: 131501
Type strain: 
Species: Hymenobacter mucosus
Strain history: <- Wen-Jun Li, Yunnan Inst. Microbiol.
NCBI tax ID(s): 1411120 (species)
version 8.1 (current version)
General
@ref: 22728
BacDive-ID: 131501
DSM-Number: 28041
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, rod-shaped
description: Hymenobacter mucosus DSM 28041 is an aerobe, mesophilic, rod-shaped bacterium that was isolated from soil.
NCBI tax id
- NCBI tax id: 1411120
- Matching level: species
strain history
| @ref | history |
|---|---|
| 22728 | <- W.-J. Li, YIM; YIM 77969 |
| 67770 | W.-J. Li YIM 77969. |
| 67771 | <- Wen-Jun Li, Yunnan Inst. Microbiol. |
doi: 10.13145/bacdive131501.20230509.8.1
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 mucosus
- full scientific name: Hymenobacter mucosus Liu et al. 2015
@ref: 22728
domain: Bacteria
phylum: Bacteroidetes
class: Cytophagia
order: Cytophagales
family: Hymenobacteraceae
genus: Hymenobacter
species: Hymenobacter mucosus
full scientific name: Hymenobacter mucosus Liu et al. 2015
type strain: yes
Morphology
cell morphology
| @ref | cell shape | motility | gram stain | confidence |
|---|---|---|---|---|
| 67771 | rod-shaped | no | ||
| 67771 | negative | |||
| 69480 | negative | 99.922 | ||
| 69480 | no | 90.082 |
Culture and growth conditions
culture medium
- @ref: 22728
- 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 |
|---|---|---|---|---|
| 22728 | positive | growth | 28 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
| 67771 | positive | growth | 28 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.974 |
observation
- @ref: 67771
- observation: quinones: MK-7
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 22728 | soil | Yunnan province, Yiliang county, Jiuxiang cave | China | CHN | Asia |
| 67770 | Soil of Jiuxiang cave in Yiliang County | Yunnan Province | China | CHN | Asia |
| 67771 | From soil, Jiuxiang cave, a tourism cave | Yiliang county, Yunnan province | China | CHN | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_7730.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_263;96_3593;97_4412;98_5652;99_7730&stattab=map
- Last taxonomy: Hymenobacter mucosus subclade
- 16S sequence: AB859259
- Sequence Identity:
- Total samples: 2200
- soil counts: 378
- aquatic counts: 387
- animal counts: 1199
- plant counts: 236
Safety information
risk assessment
- @ref: 22728
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22728
- description: Hymenobacter mucosus gene for 16S ribosomal RNA, partial sequence
- accession: AB859259
- length: 1540
- database: ena
- NCBI tax ID: 1411120
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Hymenobacter mucosus strain DSM 28041 | 1411120.3 | wgs | patric | 1411120 |
| 66792 | Hymenobacter mucosus DSM 28041 | 2724679735 | draft | img | 1411120 |
| 67770 | Hymenobacter mucosus DSM 28041 | GCA_900188255 | contig | ncbi | 1411120 |
GC content
- @ref: 67771
- GC-content: 55.2
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 91.606 | no |
| gram-positive | no | 96.624 | yes |
| anaerobic | no | 99.237 | no |
| halophile | no | 93.899 | no |
| spore-forming | no | 93.602 | no |
| glucose-util | yes | 83.887 | no |
| thermophile | no | 98.054 | yes |
| aerobic | yes | 90.768 | yes |
| flagellated | no | 95.646 | no |
| glucose-ferment | no | 88.169 | no |
External links
@ref: 22728
culture collection no.: DSM 28041, KCTC 32567, YIM 77969, JCM 19647
straininfo link
- @ref: 89917
- straininfo: 408027
literature
- topic: Phylogeny
- Pubmed-ID: 26303395
- title: Hymenobacter mucosus sp. nov., isolated from a karst cave soil sample.
- authors: Liu L, Zhou EM, Jiao JY, Manikprabhu D, Ming H, Huang MJ, Yin YR, Li WJ
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.000550
- year: 2015
- mesh: Bacterial Typing Techniques, Base Composition, Caves/*microbiology, China, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry
- topic2: 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 | |
| 22728 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-28041 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28041) | |
| 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/ | ||
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||
| 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/ | |
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions 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 | |
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |
| 89917 | 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-ID408027.1 |