Strain identifier
BacDive ID: 24051
Type strain:
Species: Sinomicrobium oceani
Strain history: <- X.-P. Tian, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; SCSIO 03483
NCBI tax ID(s): 1150368 (species)
General
@ref: 21245
BacDive-ID: 24051
DSM-Number: 25598
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Sinomicrobium oceani DSM 25598 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from deep-sea sediment.
NCBI tax id
- NCBI tax id: 1150368
- Matching level: species
strain history
- @ref: 21245
- history: <- X.-P. Tian, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; SCSIO 03483
doi: 10.13145/bacdive24051.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Flavobacteriia
- order: Flavobacteriales
- family: Flavobacteriaceae
- genus: Sinomicrobium
- species: Sinomicrobium oceani
- full scientific name: Sinomicrobium oceani Xu et al. 2013
@ref: 21245
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Sinomicrobium
species: Sinomicrobium oceani
full scientific name: Sinomicrobium oceani Xu et al. 2013
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
30680 | negative | 4.3 µm | 0.6 µm | rod-shaped | yes | |
69480 | negative | 99.979 |
pigmentation
- @ref: 30680
- production: yes
Culture and growth conditions
culture medium
- @ref: 21245
- 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 |
---|---|---|---|---|
21245 | positive | growth | 28 | mesophilic |
30680 | positive | growth | 10-45 | |
30680 | positive | optimum | 32.5 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
30680 | positive | growth | 06-08 |
30680 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 30680
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
30680 | no | |
69481 | no | 100 |
69480 | no | 99.99 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
30680 | NaCl | positive | growth | 0-10 % |
30680 | NaCl | positive | optimum | 2 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30680 | 28757 | fructose | + | carbon source |
30680 | 17234 | glucose | + | carbon source |
30680 | 17754 | glycerol | + | carbon source |
30680 | 17716 | lactose | + | carbon source |
30680 | 37684 | mannose | + | carbon source |
30680 | 26546 | rhamnose | + | carbon source |
30680 | 18222 | xylose | + | carbon source |
30680 | 17632 | nitrate | + | reduction |
enzymes
@ref | value | activity | ec |
---|---|---|---|
30680 | catalase | + | 1.11.1.6 |
30680 | gelatinase | + |
Isolation, sampling and environmental information
isolation
- @ref: 21245
- sample type: deep-sea sediment
- geographic location: South China Sea, Nansha Islands sea area (6° 0.733' N 113° 28.842' E) at a depth of 2548 m
- country: China
- origin.country: CHN
- continent: Asia
- latitude: 6.0122
- longitude: 113.481
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_4663.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_230;96_2318;97_2816;98_3498;99_4663&stattab=map
- Last taxonomy: Sinomicrobium
- 16S sequence: JQ352762
- Sequence Identity:
- Total samples: 1411
- soil counts: 159
- aquatic counts: 649
- animal counts: 575
- plant counts: 28
Safety information
risk assessment
- @ref: 21245
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 21245
- description: Sinomicrobium oceani strain SCSIO 03483 16S ribosomal RNA gene, partial sequence
- accession: JQ352762
- length: 1371
- database: ena
- NCBI tax ID: 1150368
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Sinomicrobium oceani CGMCC 1.12145 | GCA_900119185 | scaffold | ncbi | 1150368 |
66792 | Sinomicrobium oceani strain CGMCC 1.12145 | 1150368.4 | wgs | patric | 1150368 |
66792 | Sinomicrobium oceani CGMCC 1.12145 | 2596583572 | draft | img | 1150368 |
GC content
@ref | GC-content | method |
---|---|---|
21245 | 38.4 | high performance liquid chromatography (HPLC) |
30680 | 38.4 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 85.118 | yes |
flagellated | no | 96.273 | no |
gram-positive | no | 97.699 | no |
anaerobic | no | 99.345 | yes |
aerobic | yes | 86.844 | yes |
halophile | no | 75.472 | no |
spore-forming | no | 96.624 | yes |
glucose-ferment | no | 83.425 | no |
thermophile | no | 98.609 | no |
glucose-util | yes | 92.055 | yes |
External links
@ref: 21245
culture collection no.: DSM 25598, CGMCC 1.12145, KCTC 23994, SCSIO 03483
straininfo link
- @ref: 88022
- straininfo: 399374
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 22707529 | Sinomicrobium oceani gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from marine sediment. | Xu Y, Tian XP, Liu YJ, Li J, Kim CJ, Yin H, Li WJ, Zhang S | Int J Syst Evol Microbiol | 10.1099/ijs.0.041889-0 | 2012 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification, Geologic Sediments/*microbiology, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis | Genetics |
Phylogeny | 23416571 | Pustulibacterium marinum gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from the Bashi Channel. | Wang G, Zhou D, Dai S, Tian X, Li J, Chen W, Xiang W, Li X | Int J Syst Evol Microbiol | 10.1099/ijs.0.048413-0 | 2013 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis, Water Microbiology | Genetics |
Phylogeny | 24912822 | Sinomicrobium pectinilyticum sp. nov., a pectinase-producing bacterium isolated from alkaline and saline soil, and emended description of the genus Sinomicrobium. | Cheng B, Li C, Lai Q, Du M, Shao Z, Xu P, Yang C | Int J Syst Evol Microbiol | 10.1099/ijs.0.061671-0 | 2014 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Phosphatidylethanolamines/chemistry, *Phylogeny, Polygalacturonase/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry, alpha-Amylases/metabolism | Genetics |
Phylogeny | 35442876 | Sinomicrobium weinanense sp. nov., a halophilic bacterium isolated from saline-alkali soil. | Wu P, Ren H, Zhu Q, Mei Y, Liang Y, Chen Z | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005282 | 2022 | *Alkalies, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil, Vitamin K 2/chemistry | Transcriptome |
Reference
@id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
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 | ||||
21245 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25598 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25598) | ||||
30680 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 27011 | 28776041 | ||
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 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
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 | ||||
88022 | 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-ID399374.1 |