Strain identifier
BacDive ID: 24446
Type strain:
Species: Pseudonocardia sediminis
Strain history: S.-K. Tang YIM M13141.
NCBI tax ID(s): 1397368 (species)
General
@ref: 20748
BacDive-ID: 24446
DSM-Number: 45779
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic
description: Pseudonocardia sediminis DSM 45779 is a spore-forming, mesophilic bacterium that was isolated from marine sediment.
NCBI tax id
- NCBI tax id: 1397368
- Matching level: species
strain history
@ref | history |
---|---|
20748 | <- S.-K. Tang, Yunnan Univ., Yunnan Inst. Microbiol. (YIM), Kunming, China; YIM M13141 <- D.-F. Zhang, YIM |
67770 | S.-K. Tang YIM M13141. |
doi: 10.13145/bacdive24446.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Pseudonocardiales
- family: Pseudonocardiaceae
- genus: Pseudonocardia
- species: Pseudonocardia sediminis
- full scientific name: Pseudonocardia sediminis Zhang et al. 2014
@ref: 20748
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Pseudonocardiaceae
genus: Pseudonocardia
species: Pseudonocardia sediminis
full scientific name: Pseudonocardia sediminis Zhang et al. 2014
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | no | 94.667 | |
69480 | 100 | positive |
Culture and growth conditions
culture medium
- @ref: 20748
- name: GPHF-MEDIUM (DSMZ Medium 553)
- growth: yes
- link: https://mediadive.dsmz.de/medium/553
- composition: Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
20748 | positive | growth | 28 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
- @ref: 69481
- spore formation: yes
- confidence: 99
observation
- @ref: 67770
- observation: quinones: MK-8(H4)
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
---|---|---|---|---|---|---|---|
20748 | marine sediment | South China Sea (21° 23.2029 N 117° 37.2089 E) at a depth of 652 m | China | CHN | Asia | 21.3867 | 117.62 |
67770 | Marine sediment from the South China Sea |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_122167.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_1626;97_61724;98_82188;99_122167&stattab=map
- Last taxonomy: Pseudonocardia sediminis subclade
- 16S sequence: KF564279
- Sequence Identity:
- Total samples: 942
- soil counts: 90
- aquatic counts: 32
- animal counts: 278
- plant counts: 542
Safety information
risk assessment
- @ref: 20748
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20748
- description: Pseudonocardia sediminis strain YIM M13141 16S ribosomal RNA gene, complete sequence
- accession: KF564279
- length: 1541
- database: ena
- NCBI tax ID: 1397368
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pseudonocardia sediminis strain DSM 45779 | 1397368.3 | wgs | patric | 1397368 |
66792 | Pseudonocardia sediminis DSM 45779 | 2806310546 | draft | img | 1397368 |
67770 | Pseudonocardia sediminis DSM 45779 | GCA_004217185 | contig | ncbi | 1397368 |
GC content
- @ref: 20748
- GC-content: 73.1
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 99 | no |
motile | no | 92.069 | no |
gram-positive | yes | 91.441 | no |
anaerobic | no | 99.177 | no |
halophile | no | 84.46 | no |
spore-forming | yes | 69.5 | no |
thermophile | no | 99.565 | yes |
glucose-util | yes | 88.798 | no |
aerobic | yes | 93.846 | no |
flagellated | no | 97.534 | no |
glucose-ferment | no | 90.8 | no |
External links
@ref: 20748
culture collection no.: DSM 45779, JCM 18540, YIM M13141
straininfo link
- @ref: 88323
- straininfo: 404135
literature
- topic: Phylogeny
- Pubmed-ID: 24198055
- title: Pseudonocardia sediminis sp. nov., isolated from marine sediment.
- authors: Zhang DF, Jiang Z, Li L, Liu BB, Zhang XM, Tian XP, Zhang S, Li WJ
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.057844-0
- year: 2013
- mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Oceans and Seas, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
- topic2: Genetics
Reference
@id | authors | title | doi/url | catalogue | journal | pubmed |
---|---|---|---|---|---|---|
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 | |||
20748 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45779 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45779) | |||
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 | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
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/ | |||
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 | |||
88323 | 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-ID404135.1 |