Strain identifier
BacDive ID: 5855
Type strain: 
Species: Endozoicomonas elysicola
Strain history: IAM 15107 <-- M. Kurahashi MKT110.
NCBI tax ID(s): 1121862 (strain), 305900 (species)
version 8.1 (current version)
General
@ref: 16315
BacDive-ID: 5855
DSM-Number: 22380
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Endozoicomonas elysicola DSM 22380 is a mesophilic, Gram-negative bacterium that was isolated from gastrointestinal tract of the mollusk sea slug Elysia ornata.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 305900 | species |
| 1121862 | strain |
strain history
| @ref | history |
|---|---|
| 16315 | <- KCTC <- M. Kurahashi, Inst. Molecular and Cellular Biosci., Univ. Tokyo, Japan |
| 67770 | IAM 15107 <-- M. Kurahashi MKT110. |
doi: 10.13145/bacdive5855.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Oceanospirillales
- family: Endozoicomonadaceae
- genus: Endozoicomonas
- species: Endozoicomonas elysicola
- full scientific name: Endozoicomonas elysicola Kurahashi and Yokota 2007
@ref: 16315
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Oceanospirillales
family: Endozoicomonadaceae
genus: Endozoicomonas
species: Endozoicomonas elysicola
full scientific name: Endozoicomonas elysicola Kurahashi and Yokota 2007
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.988
multimedia
| @ref | multimedia content | caption | intellectual property rights |
|---|---|---|---|
| 66793 | EM_DSM_22380_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_22380_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_22380_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_22380_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_22380_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
- @ref: 16315
- 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 |
|---|---|---|---|---|
| 16315 | positive | growth | 28 | mesophilic |
| 67770 | positive | growth | 25 | mesophilic |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.998 |
observation
- @ref: 67770
- observation: quinones: Q-8
Isolation, sampling and environmental information
isolation
| @ref | sample type | host species | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|---|
| 16315 | gastrointestinal tract of the mollusk sea slug Elysia ornata | Elysia ornata | Tokyo, seawater off the coast of Izu-Miyake Island (at a depth of 15 m) | Japan | JPN | Asia |
| 67770 | Sea slug Elysia ornata collected in seawater off the coast of Izu-Miyake Island | Elysia ornata | Japan | JPN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Invertebrates (Other) | #Mollusca |
| #Host Body-Site | #Gastrointestinal tract |
taxonmaps
- @ref: 69479
- File name: preview.99_4854.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_202;96_2395;97_2914;98_3634;99_4854&stattab=map
- Last taxonomy: Endozoicomonas elysicola subclade
- 16S sequence: AB196667
- Sequence Identity:
- Total samples: 375
- soil counts: 54
- aquatic counts: 279
- animal counts: 42
Safety information
risk assessment
- @ref: 16315
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16315
- description: Endozoicimonas elysicola gene for 16S ribosomal RNA, partial sequence
- accession: AB196667
- length: 1437
- database: ena
- NCBI tax ID: 1091502
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Endozoicomonas elysicola DSM 22380 | 1121862.3 | wgs | patric | 1121862 |
| 66792 | Endozoicomonas elysicola strain DSM 22380 | 305900.3 | wgs | patric | 305900 |
| 66792 | Endozoicomonas elysicola MKT110, DSM 22380 | 2515154160 | draft | img | 1121862 |
| 67770 | Endozoicomonas elysicola DSM 22380 | GCA_000373945 | scaffold | ncbi | 1121862 |
| 67770 | Endozoicomonas elysicola DSM 22380 | GCA_000710775 | scaffold | ncbi | 305900 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 16315 | 50.4 | |
| 67770 | 50.4 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 53.343 | no |
| flagellated | yes | 52.902 | no |
| gram-positive | no | 98.143 | no |
| anaerobic | no | 98.476 | no |
| halophile | yes | 69.729 | no |
| spore-forming | no | 95.239 | no |
| thermophile | no | 98.678 | yes |
| glucose-util | yes | 92.574 | no |
| aerobic | yes | 83.856 | no |
| glucose-ferment | no | 58.172 | no |
External links
@ref: 16315
culture collection no.: DSM 22380, IAM 15107, JCM 21568, KCTC 12372, MKT 110, BCRC 17936, KCTC 23743
straininfo link
- @ref: 75336
- straininfo: 232853
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 16904280 | Endozoicomonas elysicola gen. nov., sp. nov., a gamma-proteobacterium isolated from the sea slug Elysia ornata. | Kurahashi M, Yokota A | Syst Appl Microbiol | 10.1016/j.syapm.2006.07.003 | 2006 | Animals, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Gammaproteobacteria/*classification/genetics, Gastropoda/*microbiology, Japan, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology | Genetics |
| Phylogeny | 19666790 | Endozoicomonas montiporae sp. nov., isolated from the encrusting pore coral Montipora aequituberculata. | Yang CS, Chen MH, Arun AB, Chen CA, Wang JT, Chen WM | Int J Syst Evol Microbiol | 10.1099/ijs.0.014357-0 | 2009 | Animals, Anthozoa/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Gammaproteobacteria/*classification/genetics/*isolation & purification/physiology, Genes, rRNA, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Taiwan | Genetics |
| Phylogeny | 22544802 | Endozoicomonas numazuensis sp. nov., a gammaproteobacterium isolated from marine sponges, and emended description of the genus Endozoicomonas Kurahashi and Yokota 2007. | Nishijima M, Adachi K, Katsuta A, Shizuri Y, Yamasato K | Int J Syst Evol Microbiol | 10.1099/ijs.0.042077-0 | 2012 | Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Gammaproteobacteria/*classification/genetics/isolation & purification, Japan, Molecular Sequence Data, *Phylogeny, Porifera/*microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
| Phylogeny | 24733175 | Endozoicomonas atrinae sp. nov., isolated from the intestine of a comb pen shell Atrina pectinata. | Hyun DW, Shin NR, Kim MS, Oh SJ, Kim PS, Whon TW, Bae JW | Int J Syst Evol Microbiol | 10.1099/ijs.0.060780-0 | 2014 | Animals, Bacterial Typing Techniques, Base Composition, Bivalvia/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/genetics/isolation & purification, Gastrointestinal Tract/microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/chemistry | Genetics |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 16315 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22380) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22380 | |||
| 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 | |||
| 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 | |
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 75336 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID232853.1 | StrainInfo: A central database for resolving microbial strain identifiers |