Strain identifier
BacDive ID: 132339
Type strain: 
Species: Novosphingobium endophyticum
Strain history: W.-J. Li; Yunnan Inst. of Microbiol., Yunnan Univ., China; EGI 60015.
NCBI tax ID(s): 1955250 (species)
version 9.3 (current version)
General
@ref: 24128
BacDive-ID: 132339
DSM-Number: 29948
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Novosphingobium endophyticum DSM 29948 is a mesophilic, Gram-negative bacterium that was isolated from surface sterilized healthy roots of Chinese liquorice Glycyrrhiza uralensis.
NCBI tax id
- NCBI tax id: 1955250
- Matching level: species
strain history
| @ref | history |
|---|---|
| 24128 | <- W.-J. Li, YIM Yunnan Institute of Microbiology <- Y. Li, YIM <- L. Li, YIM |
| 67770 | W.-J. Li; Yunnan Inst. of Microbiol., Yunnan Univ., China; EGI 60015. |
doi: 10.13145/bacdive132339.20250331.9.3
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 endophyticum
- full scientific name: Novosphingobium endophyticum Li et al. 2016
@ref: 24128
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Pseudomonadales
family: Erythrobacteraceae
genus: Novosphingobium
species: Novosphingobium endophyticum
full scientific name: Novosphingobium endophyticum Li et al. 2016
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 125438 | negative | 95.762 |
| 125439 | negative | 99.6 |
Culture and growth conditions
culture medium
- @ref: 24128
- 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 |
|---|---|---|---|
| 24128 | positive | growth | 28 |
| 67770 | positive | growth | 30 |
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: obligate aerobe
- confidence: 96
spore formation
- @ref: 125439
- spore formation: no
- confidence: 98.3
observation
- @ref: 67770
- observation: quinones: Q-10
Isolation, sampling and environmental information
isolation
| @ref | sample type | host species | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|---|
| 24128 | surface sterilized healthy roots of Chinese liquorice Glycyrrhiza uralensis | Glycyrrhiza uralensis | Xinjiang province, Yili County | China | CHN | Asia |
| 67770 | Healthy roots of Glycyrrhiza uralensis F. collected from Yili County | Glycyrrhiza uralensis | Xinjiang Province, northwest China | China | CHN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Host Body-Site | #Plant | #Root (Rhizome) |
| #Host Body-Site | #Plant | #Sterilized plant part |
taxonmaps
- @ref: 69479
- File name: preview.99_184426.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_795;97_15120;98_46773;99_184426&stattab=map
- Last taxonomy: Novosphingobium endophyticum
- 16S sequence: KP721487
- Sequence Identity:
- Total samples: 979
- soil counts: 317
- aquatic counts: 522
- animal counts: 80
- plant counts: 60
Safety information
risk assessment
- @ref: 24128
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24128
- description: Novosphingobium endophyticum strain EGI 60015 16S ribosomal RNA gene, partial sequence
- accession: KP721487
- length: 1492
- database: nuccore
- NCBI tax ID: 1955250
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Novosphingobium endophyticum CGMCC 1.15095 | GCA_014640675 | contig | ncbi | 1955250 |
| 66792 | Novosphingobium endophyticum strain CGMCC 1.15095 | 1955250.3 | wgs | patric | 1955250 |
GC content
- @ref: 24128
- GC-content: 66.6
- 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 | 95.762 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 88.543 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 87.08 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 85.84 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 96.058 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 68.346 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 98.3 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 68.6 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 99.6 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 96 |
External links
@ref: 24128
culture collection no.: DSM 29948, CGMCC 1.15095, KCTC 42486, EGI 600015, JCM 30707
straininfo link
- @ref: 90685
- straininfo: 405299
literature
- topic: Phylogeny
- Pubmed-ID: 26047607
- title: Novosphingobium endophyticum sp. nov. isolated from roots of Glycyrrhiza uralensis.
- authors: Li YQ, Li L, Chen W, Duan YQ, Nimaichand S, Guo JW, Gao R, Li WJ
- journal: Arch Microbiol
- DOI: 10.1007/s00203-015-1124-1
- year: 2015
- mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Glycyrrhiza uralensis/*microbiology, Phylogeny, Plant Roots/*microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Species Specificity, Sphingomonadaceae/*classification/genetics/isolation & purification
- topic2: Enzymology
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 | |
| 24128 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-29948 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29948) | |
| 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/ | |
| 90685 | 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-ID405299.1 | |
| 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 |