Strain identifier
BacDive ID: 131427
Type strain: 
Species: Sphingomonas morindae
Strain Designation: NBD5
Strain history: <- Yang Liu, CICC, China.
NCBI tax ID(s): 1541170 (species)
version 8.1 (current version)
General
@ref: 22654
BacDive-ID: 131427
DSM-Number: 29151
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic
description: Sphingomonas morindae NBD5 is an aerobe, mesophilic bacterium that was isolated from Noni L.; inner tissue of healthy branches, as endophyte.
NCBI tax id
- NCBI tax id: 1541170
- Matching level: species
strain history
| @ref | history |
|---|---|
| 22654 | <- Y. Ge, China Natl. Res. Inst. of Food and Fermentation Ind., Beijing, China; NBD5 <- Y. Liu <- Y. Cao |
| 67771 | <- Yang Liu, CICC, China. |
doi: 10.13145/bacdive131427.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Sphingomonadales
- family: Sphingomonadaceae
- genus: Sphingomonas
- species: Sphingomonas morindae
- full scientific name: Sphingomonas morindae Liu et al. 2015
@ref: 22654
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Pseudomonadales
family: Sphingomonadaceae
genus: Sphingomonas
species: Sphingomonas morindae
full scientific name: Sphingomonas morindae Liu et al. 2015
strain designation: NBD5
type strain: yes
Morphology
multimedia
- @ref: 22654
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_29151.jpg
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
- @ref: 22654
- name: NUTRIENT AGAR (DSMZ Medium 1)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1
- composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 22654 | positive | growth | 28 | mesophilic |
| 67771 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
Isolation, sampling and environmental information
isolation
| @ref | sample type | host species | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|---|
| 22654 | Noni (Morinda citrifolia) L.; inner tissue of healthy branches, as endophyte | Morinda citrifolia | Hainan, Sanya, Hainan Noni Biological Engineering Development (18° 18' 01'' N 109° 31' 36'' E) | China | CHN | Asia | 18.3003 | 109.527 |
| 67771 | From Noni(Morinda Citrifolia L.) | China | CHN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Tree |
| #Host Body-Site | #Plant | #Stem (Branch) |
taxonmaps
- @ref: 69479
- File name: preview.99_130454.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_3122;97_43184;98_87336;99_130454&stattab=map
- Last taxonomy: Sphingomonas morindae subclade
- 16S sequence: KJ934256
- Sequence Identity:
- Total samples: 94
- soil counts: 37
- aquatic counts: 12
- animal counts: 26
- plant counts: 19
Safety information
risk assessment
- @ref: 22654
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22654
- description: Sphingomonas morindae strain NBD5 16S ribosomal RNA gene, partial sequence
- accession: KJ934256
- length: 1446
- database: ena
- NCBI tax ID: 1541170
Genome sequences
- @ref: 66792
- description: Sphingomonas morindae NBD5
- accession: GCA_023822065
- assembly level: complete
- database: ncbi
- NCBI tax ID: 1541170
GC content
- @ref: 22654
- GC-content: 67.6
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| flagellated | no | 87.368 | no |
| gram-positive | no | 96.342 | no |
| anaerobic | no | 98.805 | yes |
| aerobic | yes | 91.164 | no |
| halophile | no | 94.505 | no |
| spore-forming | no | 94.004 | no |
| motile | yes | 80.137 | no |
| glucose-ferment | no | 89.333 | no |
| thermophile | no | 96.965 | no |
| glucose-util | yes | 90.823 | no |
External links
@ref: 22654
culture collection no.: DSM 29151, CICC 10879, KCTC 42183
straininfo link
- @ref: 89855
- straininfo: 406158
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 25985831 | Sphingomonas morindae sp. nov., isolated from Noni (Morinda citrifolia L.) branch. | Liu Y, Yao S, Lee YJ, Cao Y, Zhai L, Zhang X, Su J, Ge Y, Kim SG, Cheng C | Int J Syst Evol Microbiol | 10.1099/ijs.0.000340 | 2015 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Endophytes/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Molecular Sequence Data, Morinda/*microbiology, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistry | Enzymology |
| Phylogeny | 29091024 | Sphingomonas difficilis sp. nov., a difficultly cultivable bacterium that grows on solid but not in liquid medium, isolated from an abandoned lead-zinc mine. | Feng GD, Xiong X, Zhu HH, Li HP | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002461 | 2017 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, *Mining, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistry, *Zinc | 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 | |
| 22654 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-29151 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29151) | |
| 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 | |
| 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/ | |
| 89855 | 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-ID406158.1 |