Strain identifier
BacDive ID: 5717
Type strain: 
Species: Christiangramia echinicola
Strain history: <- SB Kim <- OI Nedashkovskaya, KMM, Russia
NCBI tax ID(s): 1121931 (strain), 279359 (species)
version 8.1 (current version)
General
@ref: 8271
BacDive-ID: 5717
DSM-Number: 19838
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile, rod-shaped
description: Christiangramia echinicola DSM 19838 is an aerobe, mesophilic, motile bacterium that was isolated from sea urchin Strongylocentrotus intermedius.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 279359 | species |
| 1121931 | strain |
strain history
| @ref | history |
|---|---|
| 8271 | <- O. I. Nedashkovskaya, Pacific Inst. Bioorg. Chem., RAS, Vladivostok; KMM 6050 |
| 67770 | KMM 6050 <-- O. I. Nedashkovskaya. |
| 67771 | <- SB Kim <- OI Nedashkovskaya, KMM, Russia |
doi: 10.13145/bacdive5717.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Flavobacteriia
- order: Flavobacteriales
- family: Flavobacteriaceae
- genus: Christiangramia
- species: Christiangramia echinicola
- full scientific name: Christiangramia echinicola (Nedashkovskaya et al. 2005) Deshmukh and Oren 2023
synonyms
- @ref: 20215
- synonym: Gramella echinicola
@ref: 8271
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Gramella
species: Gramella echinicola
full scientific name: Gramella echinicola Nedashkovskaya et al. 2005 emend. Jeong et al. 2013 emend. Shahina et al. 2014 emend. Panschin et al. 2016
type strain: yes
Morphology
cell morphology
| @ref | cell shape | motility | flagellum arrangement | gram stain |
|---|---|---|---|---|
| 67771 | rod-shaped | yes | gliding | |
| 67771 | negative |
multimedia
| @ref | multimedia content | caption | intellectual property rights |
|---|---|---|---|
| 66793 | EM_DSM_19838_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_19838_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_19838_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_19838_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_19838_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_19838_6.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
- @ref: 8271
- 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 |
|---|---|---|---|---|
| 8271 | positive | growth | 25 | mesophilic |
| 67770 | positive | growth | 25 | mesophilic |
| 67771 | positive | growth | 25 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
observation
| @ref | observation |
|---|---|
| 67770 | quinones: MK-6 |
| 67771 | quinones: MK-6 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | host species | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|---|
| 8271 | sea urchin Strongylocentrotus intermedius | Strongylocentrotus intermedius | Sea of Japan, Gulf of Peter the Great, Troitsa Bay | Russia | RUS | Asia |
| 67770 | Sea urchin Strongylocentrotus intermedius | Strongylocentrotus intermedius | Troitsa Bay, Gulf of Peter the Great | |||
| 67771 | From sea urchin `Strongylocentrotus intermedius` | Troitsa Bay, Gulf of Peter the Great, Sea of Japan, Pacific Ocean | Russia | RUS | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Invertebrates (Other) | #Echinodermata |
| #Environmental | #Aquatic | #Marine |
taxonmaps
- @ref: 69479
- File name: preview.99_86171.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_52;96_1604;97_1915;98_6856;99_86171&stattab=map
- Last taxonomy: Gramella
- 16S sequence: AY608409
- Sequence Identity:
- Total samples: 139
- soil counts: 7
- aquatic counts: 117
- animal counts: 15
Safety information
risk assessment
- @ref: 8271
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Gramella echinicola gene for 16S rRNA, partial sequence, strain: NBRC 100593 | AB681204 | 1455 | ena | 279359 |
| 8271 | Gramella echinicola strain KMM 6050 16S ribosomal RNA gene, partial sequence | AY608409 | 1438 | ena | 1121931 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Gramella echinicola DSM 19838 | 1121931.6 | wgs | patric | 1121931 |
| 66792 | Gramella echinicola DSM 19838 | 2524614734 | draft | img | 1121931 |
| 67770 | Christiangramia echinicola DSM 19838 | GCA_000423065 | scaffold | ncbi | 1121931 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 8271 | 39.6 | |
| 67770 | 39.6 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 85.326 | no |
| flagellated | no | 94.622 | yes |
| gram-positive | no | 97.78 | no |
| anaerobic | no | 99.049 | yes |
| halophile | yes | 56.167 | no |
| spore-forming | no | 95.943 | no |
| thermophile | no | 99.514 | no |
| glucose-util | yes | 88.745 | no |
| aerobic | yes | 91.228 | yes |
| glucose-ferment | no | 87.92 | no |
External links
@ref: 8271
culture collection no.: DSM 19838, JCM 13510, KCTC 12278, KMM 6050, LMG 22585, NBRC 100593, IAM 15331
straininfo link
- @ref: 75199
- straininfo: 277605
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 15653906 | Gramella echinicola gen. nov., sp. nov., a novel halophilic bacterium of the family Flavobacteriaceae isolated from the sea urchin Strongylocentrotus intermedius. | Nedashkovskaya OI, Kim SB, Lysenko AM, Frolova GM, Mikhailov VV, Bae KS, Lee DH, Kim IS | Int J Syst Evol Microbiol | 10.1099/ijs.0.63314-0 | 2005 | Animals, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Flavobacteriaceae/chemistry/*classification/genetics/isolation & purification, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sea Urchins/*microbiology, Sequence Analysis, DNA, *Sodium Chloride | Genetics |
| Phylogeny | 16280516 | Gramella portivictoriae sp. nov., a novel member of the family Flavobacteriaceae isolated from marine sediment. | Lau SCK, Tsoi MMY, Li X, Plakhotnikova I, Dobretsov S, Wong PK, Qian PY | Int J Syst Evol Microbiol | 10.1099/ijs.0.63824-0 | 2005 | DNA, Bacterial/analysis, Fatty Acids/analysis, Flavobacteriaceae/chemistry/classification/genetics/*isolation & purification, Geologic Sediments/*microbiology, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/analysis/genetics, Seawater/*microbiology, Sequence Analysis, DNA, *Water Microbiology | Genetics |
| Phylogeny | 24522286 | Gramella planctonica sp. nov., a zeaxanthin-producing bacterium isolated from surface seawater, and emended descriptions of Gramella aestuarii and Gramella echinicola. | Shahina M, Hameed A, Lin SY, Lee RJ, Lee MR, Young CC | Antonie Van Leeuwenhoek | 10.1007/s10482-014-0133-4 | 2014 | Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification/*metabolism, Locomotion, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Taiwan, Xanthophylls/*metabolism, Zeaxanthins | Metabolism |
| Phylogeny | 24835164 | Gramella oceani sp. nov., a zeaxanthin-producing bacterium of the family Flavobacteriaceae isolated from marine sediment. | Hameed A, Shahina M, Lin SY, Liu YC, Lai WA, Young CC | Int J Syst Evol Microbiol | 10.1099/ijs.0.059881-0 | 2014 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Geologic Sediments/*microbiology, Molecular Sequence Data, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Taiwan, Vitamin K 2/analogs & derivatives/chemistry, Xanthophylls/*biosynthesis, Zeaxanthins | Genetics |
| 27274783 | Comparing polysaccharide decomposition between the type strains Gramella echinicola KMM 6050(T) (DSM 19838(T)) and Gramella portivictoriae UST040801-001(T) (DSM 23547(T)), and emended description of Gramella echinicola Nedashkovskaya et al. 2005 emend. Shahina et al. 2014 and Gramella portivictoriae Lau et al. 2005. | Panschin I, Huang S, Meier-Kolthoff JP, Tindall BJ, Rohde M, Verbarg S, Lapidus A, Han J, Trong S, Haynes M, Reddy TB, Huntemann M, Pati A, Ivanova NN, Mavromatis K, Markowitz V, Woyke T, Goker M, Klenk HP, Kyrpides NC, Hahnke RL | Stand Genomic Sci | 10.1186/s40793-016-0163-9 | 2016 | |||
| Phylogeny | 27902319 | Description of Gramella forsetii sp. nov., a marine Flavobacteriaceae isolated from North Sea water, and emended description of Gramella gaetbulicola Cho et al. 2011. | Panschin I, Becher M, Verbarg S, Sproer C, Rohde M, Schuler M, Amann RI, Harder J, Tindall BJ, Hahnke RL | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001700 | 2017 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Germany, North Sea, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 8271 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19838) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19838 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
| 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 75199 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID277605.1 | StrainInfo: A central database for resolving microbial strain identifiers |