Strain identifier
BacDive ID: 24253
Type strain: 
Species: Nocardioides pacificus
Strain Designation: XH274
Strain history: X.-H. Zhang and X. Fan XH274.
NCBI tax ID(s): 1343103 (species)
version 8.1 (current version)
General
@ref: 20686
BacDive-ID: 24253
DSM-Number: 27278
keywords: 16S sequence, Bacteria, mesophilic
description: Nocardioides pacificus XH274 is a mesophilic bacterium that was isolated from deep sub-seafloor sediment.
NCBI tax id
- NCBI tax id: 1343103
- Matching level: species
strain history
| @ref | history |
|---|---|
| 20686 | <- X.-H. Zhang, Ocean Univ. China, Qingdao, P. R. China; XH274 |
| 67770 | X.-H. Zhang and X. Fan XH274. |
doi: 10.13145/bacdive24253.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Propionibacteriales
- family: Nocardioidaceae
- genus: Nocardioides
- species: Nocardioides pacificus
- full scientific name: Nocardioides pacificus Fan et al. 2014
@ref: 20686
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Nocardioidaceae
genus: Nocardioides
species: Nocardioides pacificus
full scientific name: Nocardioides pacificus Fan et al. 2014
strain designation: XH274
type strain: yes
Culture and growth conditions
culture medium
- @ref: 20686
- name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514
- composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 20686 | positive | growth | 28 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
observation
- @ref: 67770
- observation: quinones: MK-8(H4)
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | latitude | longitude |
|---|---|---|---|---|
| 20686 | deep sub-seafloor sediment | South Pacific Gyre at station U1371 (41° 58' S 163° 11' W) at a depth of 107.3–107.4 m below the sea floor | -45.9667 | -163.183 |
| 67770 | Deep sub-seafloor sediment from the South Pacific Gyre |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_21564.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_2111;97_13208;98_16261;99_21564&stattab=map
- Last taxonomy: Nocardioides pacificus subclade
- 16S sequence: KC986355
- Sequence Identity:
- Total samples: 1395
- soil counts: 710
- aquatic counts: 88
- animal counts: 170
- plant counts: 427
Safety information
risk assessment
- @ref: 20686
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20686
- description: Nocardioides pacificus strain XH274 16S ribosomal RNA gene, partial sequence
- accession: KC986355
- length: 1442
- database: ena
- NCBI tax ID: 1343103
GC content
- @ref: 20686
- GC-content: 74.6
- method: high performance liquid chromatography (HPLC)
External links
@ref: 20686
culture collection no.: DSM 27278, JCM 19260
straininfo link
- @ref: 88195
- straininfo: 397444
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 24699067 | Nocardioides pacificus sp. nov., isolated from deep sub-seafloor sediment. | Fan X, Qiao Y, Gao X, Zhang XH | Int J Syst Evol Microbiol | 10.1099/ijs.0.059873-0 | 2014 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
| Phylogeny | 25805631 | Nocardioides echinoideorum sp. nov., isolated from sea urchins (Tripneustes gratilla). | Lin SY, Wen CZ, Hameed A, Liu YC, Hsu YH, Shen FT, Lai WA, Young CC | Int J Syst Evol Microbiol | 10.1099/ijs.0.000206 | 2015 | Actinomycetales/*classification/genetics/isolation & purification, Animals, Bacteria, Aerobic/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sea Urchins/*microbiology, Seafood/*microbiology, Sequence Analysis, DNA, Taiwan, Vitamin K 2/analogs & derivatives/chemistry | Enzymology |
| Phylogeny | 25893957 | Nocardioides solisilvae sp. nov., isolated from a forest soil. | Sultanpuram VR, Mothe T, Mohammed F | Antonie Van Leeuwenhoek | 10.1007/s10482-015-0455-x | 2015 | Actinobacteria/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Forests, India, Molecular Sequence Data, Peptidoglycan/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysis | Genetics |
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 | |
| 20686 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-27278 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27278) | |
| 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/ | |
| 88195 | 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-ID397444.1 |