Strain identifier
BacDive ID: 23264
Type strain: 
Species: Novosphingobium sediminicola
Strain Designation: HU1-AH51
Strain history: <- ST Lee, KAIST
NCBI tax ID(s): 563162 (species)
version 8.1 (current version)
General
@ref: 19124
BacDive-ID: 23264
DSM-Number: 27057
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative
description: Novosphingobium sediminicola HU1-AH51 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from freshwater sediment from littoral zone.
NCBI tax id
- NCBI tax id: 563162
- Matching level: species
strain history
| @ref | history |
|---|---|
| 19124 | <- LMG <- S. T. Lee, KAIST <- J. Lim, KAIST, Korea Advanced Institute of Science and Technology, Daejeon, Rep. Korea |
| 67771 | <- ST Lee, KAIST |
doi: 10.13145/bacdive23264.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Sphingomonadales
- family: Erythrobacteraceae
- genus: Novosphingobium
- species: Novosphingobium sediminicola
- full scientific name: Novosphingobium sediminicola Baek et al. 2011
@ref: 19124
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Sphingomonadales
family: Erythrobacteraceae
genus: Novosphingobium
species: Novosphingobium sediminicola
full scientific name: Novosphingobium sediminicola Baek et al. 2011
strain designation: HU1-AH51
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 67771 | negative | |
| 69480 | negative | 99.969 |
multimedia
- @ref: 19124
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_27057.jpg
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
- @ref: 19124
- 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 |
|---|---|---|---|---|
| 19124 | positive | growth | 28 | mesophilic |
| 67771 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 98 |
| 69480 | no | 99.942 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 19124 | freshwater sediment from littoral zone | Lake Hakha | Republic of Korea | KOR | Asia |
| 67771 | From freshwater sediment | Daejeon | Republic of Korea | KOR | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Freshwater |
| #Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_58538.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_3914;97_4812;98_6168;99_58538&stattab=map
- Last taxonomy: Novosphingobium sediminicola
- 16S sequence: FJ177534
- Sequence Identity:
- Total samples: 41
- soil counts: 2
- aquatic counts: 24
- animal counts: 4
- plant counts: 11
Safety information
risk assessment
- @ref: 19124
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 19124
- description: Novosphingobium sediminicola strain HU1-AH51 16S ribosomal RNA gene, partial sequence
- accession: FJ177534
- length: 1387
- database: ena
- NCBI tax ID: 563162
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Novosphingobium sediminicola DSM 27057 | GCA_014196525 | scaffold | ncbi | 563162 |
| 66792 | Novosphingobium sediminicola strain DSM 27057 | 563162.3 | wgs | patric | 563162 |
| 66792 | Novosphingobium sediminicola DSM 27057 | 2829917985 | draft | img | 563162 |
GC content
- @ref: 19124
- GC-content: 62.6
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 98 | no |
| flagellated | no | 87.862 | no |
| gram-positive | no | 97.115 | yes |
| anaerobic | no | 98.167 | yes |
| aerobic | yes | 83.383 | yes |
| halophile | no | 96.079 | no |
| spore-forming | no | 91.817 | no |
| glucose-util | yes | 92.628 | no |
| thermophile | no | 98.323 | yes |
| motile | yes | 58.7 | no |
| glucose-ferment | no | 88.525 | no |
External links
@ref: 19124
culture collection no.: DSM 27057, KCTC 22311, LMG 24320
straininfo link
- @ref: 87487
- straininfo: 319132
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 21097643 | Novosphingobium sediminicola sp. nov. isolated from freshwater sediment. | Baek SH, Lim JH, Jin L, Lee HG, Lee ST | Int J Syst Evol Microbiol | 10.1099/ijs.0.024307-0 | 2010 | Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fresh Water/*microbiology, Geologic Sediments/*microbiology, Glycosphingolipids/analysis, Molecular Sequence Data, Phylogeny, Pigments, Biological/metabolism, Polyamines/analysis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sphingomonadaceae/*classification/genetics/*isolation & purification/physiology | Genetics |
| Phylogeny | 26514117 | Novosphingobium oryzae sp. nov., a potential plant-promoting endophytic bacterium isolated from rice roots. | Zhang L, Gao JS, Kim SG, Zhang CW, Jiang JQ, Ma XT, Zhang J, Zhang XX | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000718 | 2015 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza/*microbiology, Phospholipids/chemistry, *Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistry | Genetics |
| Phylogeny | 27515386 | Novosphingobium lotistagni sp. nov., isolated from a lotus pond. | Ngo HTT, Trinh H, Kim JH, Yang JE, Won KH, Kim JH, Kook M, Yi TH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001418 | 2016 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lotus, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Ponds/*microbiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistry | Transcriptome |
| Phylogeny | 28829033 | Novosphingobium humi sp. nov., isolated from soil of a military shooting range. | Hyeon JW, Kim K, Son AR, Choi E, Lee SK, Jeon CO | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002089 | 2017 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Firearms, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 19124 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27057) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-27057 | |
| 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 | |
| 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) | |
| 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |
| 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 | |
| 87487 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID319132.1 | StrainInfo: A central database for resolving microbial strain identifiers |