Strain identifier
BacDive ID: 130591
Type strain: 
Species: Saccharothrix carnea
Strain Designation: NEAU-yn17
Strain history: CGMCC 4.7097 <-- C. Liu; Northeast Agric. Univ., China; NEAU-yn17.
NCBI tax ID(s): 1280637 (species)
version 8.1 (current version)
General
@ref: 21774
BacDive-ID: 130591
DSM-Number: 45878
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic
description: Saccharothrix carnea NEAU-yn17 is a spore-forming, mesophilic bacterium that was isolated from soil from a wastewater discharge site of a pesticide factory.
NCBI tax id
- NCBI tax id: 1280637
- Matching level: species
strain history
| @ref | history |
|---|---|
| 21774 | <- C. Liu, Northeast Agricultural Univ., Harbin, China; NEAU-yn17 <- S. Wang, Harbin,China |
| 67770 | CGMCC 4.7097 <-- C. Liu; Northeast Agric. Univ., China; NEAU-yn17. |
doi: 10.13145/bacdive130591.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Pseudonocardiales
- family: Pseudonocardiaceae
- genus: Saccharothrix
- species: Saccharothrix carnea
- full scientific name: Saccharothrix carnea Liu et al. 2014
@ref: 21774
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Pseudonocardiaceae
genus: Saccharothrix
species: Saccharothrix carnea
full scientific name: Saccharothrix carnea Liu et al. 2014
strain designation: NEAU-yn17
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | no | 90.758 | |
| 69480 | 100 | positive |
Culture and growth conditions
culture medium
- @ref: 21774
- name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
- growth: yes
- link: https://mediadive.dsmz.de/medium/65
- composition: Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 21774 | positive | growth | 28 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 100 |
| 69480 | yes | 100 |
observation
- @ref: 67770
- observation: quinones: MK-9(H4)
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 21774 | soil from a wastewater discharge site of a pesticide factory | Heilongjiang Province, Harbin (45° 45' N 126° 41' E) | China | CHN | Asia | 45.75 | 126.683 |
| 67770 | Soil at the wastewater discharge site of a pesticide factory in Harbin | China | CHN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Industrial | #Plant (Factory) |
| #Engineered | #Waste | #Wastewater |
| #Environmental | #Terrestrial | #Soil |
Safety information
risk assessment
- @ref: 21774
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 21774
- description: Saccharothrix carnea strain NEAU-yn17 16S ribosomal RNA gene, partial sequence
- accession: KC195859
- length: 1511
- database: ena
- NCBI tax ID: 1280637
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Saccharothrix carnea strain CGMCC 4.7097 | 1280637.3 | wgs | patric | 1280637 |
| 66792 | Saccharothrix carnea CGMCC 4.7097 | 2718217663 | draft | img | 1280637 |
| 67770 | Saccharothrix carnea CGMCC 4.7097 | GCA_003014735 | contig | ncbi | 1280637 |
GC content
- @ref: 21774
- GC-content: 74.5
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| motile | no | 91.366 | no |
| gram-positive | yes | 90.81 | no |
| anaerobic | no | 99.241 | no |
| aerobic | yes | 92.59 | no |
| halophile | no | 90.003 | no |
| spore-forming | yes | 96.141 | no |
| thermophile | no | 98.66 | no |
| glucose-util | yes | 87.521 | no |
| flagellated | no | 97.516 | no |
| glucose-ferment | no | 89.666 | no |
External links
@ref: 21774
culture collection no.: DSM 45878, CGMCC 4.7097, JCM 32496
straininfo link
- @ref: 89106
- straininfo: 404911
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 25256705 | Saccharothrix carnea sp. nov., an actinobacterium isolated from soil. | Liu C, Guan X, Wang S, Zhao J, Wang H, He H, Xiang W, Wang X | Int J Syst Evol Microbiol | 10.1099/ijs.0.065557-0 | 2014 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Industrial Waste, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Pesticides, Phospholipids/chemistry, *Phylogeny, Pigments, Biological/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistry, Waste Water | Genetics |
| Phylogeny | 36268867 | Saccharothrix luteola sp. nov., a novel cellulose-degrading actinobacterium isolated from soil and emended description of the genus Saccharothrix. | He C, Sun X, Huang Z, Wang Z, Luo X, Song J, Wang X, Zhao J, Xiang W | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005572 | 2022 | RNA, Ribosomal, 16S/genetics, *Soil, *Phosphatidylethanolamines, Soil Microbiology, Vitamin K 2, Cellulose, Cardiolipins, Congo Red, Galactose, Mannose, Ribose, Base Composition, Phylogeny, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Sequence Analysis, DNA, Phosphatidylinositols, Phospholipids | 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 | |
| 21774 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45878 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45878) | |
| 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/ | ||
| 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 | |
| 89106 | 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-ID404911.1 |