Strain identifier
BacDive ID: 24008
Type strain: 
Species: Ferrimonas sediminum
Strain Designation: JYr13
Strain history: X.-H. Zhang <-- R. Zhao JYr13.
NCBI tax ID(s): 718193 (species)
version 8.1 (current version)
General
@ref: 20561
BacDive-ID: 24008
DSM-Number: 23317
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, psychrophilic, Gram-negative, motile, rod-shaped
description: Ferrimonas sediminum JYr13 is a facultative anaerobe, psychrophilic, Gram-negative bacterium that was isolated from coastal sediment of an amphioxus breeding zone.
NCBI tax id
- NCBI tax id: 718193
- Matching level: species
strain history
| @ref | history |
|---|---|
| 20561 | <- X.-H. Zhang, Ocean Univ. China, Qingdao, P. R. China; JYr13 <- R. Zhao |
| 67770 | X.-H. Zhang <-- R. Zhao JYr13. |
doi: 10.13145/bacdive24008.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Alteromonadales
- family: Ferrimonadaceae
- genus: Ferrimonas
- species: Ferrimonas sediminum
- full scientific name: Ferrimonas sediminum Ji et al. 2013
@ref: 20561
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Alteromonadales
family: Ferrimonadaceae
genus: Ferrimonas
species: Ferrimonas sediminum
full scientific name: Ferrimonas sediminum Ji et al. 2013
strain designation: JYr13
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 30700 | negative | 1.35 µm | 0.5 µm | rod-shaped | yes | |
| 69480 | yes | 98.584 | ||||
| 69480 | negative | 99.997 |
pigmentation
- @ref: 30700
- production: yes
Culture and growth conditions
culture medium
- @ref: 20561
- 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 |
|---|---|---|---|---|
| 20561 | positive | growth | 16 | psychrophilic |
| 30700 | positive | growth | 16-42 | |
| 30700 | positive | optimum | 26.5 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 30700 | positive | growth | 07-10 | alkaliphile |
| 30700 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 30700
- oxygen tolerance: facultative anaerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.995 |
halophily
- @ref: 30700
- salt: NaCl
- growth: positive
- tested relation: optimum
- concentration: 3 %
observation
- @ref: 67770
- observation: quinones: MK-7, Q-7, Q-8
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30700 | 16449 | alanine | + | carbon source |
| 30700 | 29987 | glutamate | + | carbon source |
| 30700 | 17596 | inosine | + | carbon source |
| 30700 | 24996 | lactate | + | carbon source |
| 30700 | 17748 | thymidine | + | carbon source |
| 30700 | 53423 | tween 40 | + | carbon source |
| 30700 | 53426 | tween 80 | + | carbon source |
| 30700 | 16704 | uridine | + | carbon source |
| 30700 | 4853 | esculin | + | hydrolysis |
| 30700 | 17632 | nitrate | + | reduction |
metabolite production
- @ref: 30700
- Chebi-ID: 16136
- metabolite: hydrogen sulfide
- production: yes
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 30700 | catalase | + | 1.11.1.6 |
| 30700 | gelatinase | + | |
| 30700 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 20561 | coastal sediment of an amphioxus breeding zone | Qingdao, China (36° 5' N 120° 32' E) | China | CHN | Asia | 36.0833 | 120.533 |
| 67770 | Coastal sediment of an amphioxus breeding zone in Qingdao | China | CHN | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Sediment
taxonmaps
- @ref: 69479
- File name: preview.99_99282.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_59;96_7003;97_39030;98_50762;99_99282&stattab=map
- Last taxonomy: Ferrimonas
- 16S sequence: GU391222
- Sequence Identity:
- Total samples: 309
- soil counts: 6
- aquatic counts: 279
- animal counts: 24
Safety information
risk assessment
- @ref: 20561
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20561
- description: Ferrimonas sediminum strain JYr13 16S ribosomal RNA gene, partial sequence
- accession: GU391222
- length: 1416
- database: ena
- NCBI tax ID: 718193
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Ferrimonas sediminum DSM 23317 | GCA_900100175 | scaffold | ncbi | 718193 |
| 66792 | Ferrimonas sediminum strain DSM 23317 | 718193.3 | wgs | patric | 718193 |
| 66792 | Ferrimonas sediminum DSM 23317 | 2634166324 | draft | img | 718193 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 20561 | 59 | high performance liquid chromatography (HPLC) |
| 30700 | 59 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 93.841 | yes |
| flagellated | yes | 88.466 | no |
| gram-positive | no | 99.043 | yes |
| anaerobic | no | 94.167 | yes |
| aerobic | no | 55.732 | no |
| halophile | yes | 55.918 | no |
| spore-forming | no | 95.56 | no |
| glucose-ferment | no | 55.275 | no |
| thermophile | no | 99.298 | no |
| glucose-util | yes | 77.416 | no |
External links
@ref: 20561
culture collection no.: DSM 23317, LMG 25564, JCM 17552
straininfo link
- @ref: 87982
- straininfo: 369498
literature
- topic: Phylogeny
- Pubmed-ID: 22685103
- title: Ferrimonas sediminum sp. nov., isolated from coastal sediment of an amphioxus breeding zone.
- authors: Ji S, Zhao R, Li Z, Li B, Shi X, Zhang XH
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.042408-0
- year: 2012
- mesh: Animals, Bacterial Typing Techniques, Base Composition, China, Chordata, DNA, Bacterial/genetics, Fatty Acids/analysis, Ferric Compounds/metabolism, Gammaproteobacteria/*classification/genetics/isolation & purification, Geologic Sediments/*microbiology, Molecular Sequence Data, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA
- topic2: Genetics
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 | ||||
| 20561 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23317 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23317) | ||||
| 30700 | 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 | 27031 | 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 | ||
| 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 | ||||
| 87982 | 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-ID369498.1 |