Strain identifier
BacDive ID: 110
Type strain: 
Species: Ilumatobacter fluminis
Strain Designation: YM22-133
Strain history: DSM 18936 <-- MBIC 08263 <-- Y. Matsuo YM22-133.
NCBI tax ID(s): 467091 (species)
version 8.1 (current version)
General
@ref: 7794
BacDive-ID: 110
DSM-Number: 18936
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Ilumatobacter fluminis YM22-133 is a mesophilic bacterium that was isolated from sediment.
NCBI tax id
- NCBI tax id: 467091
- Matching level: species
strain history
| @ref | history |
|---|---|
| 7794 | <- H. Kasai <- Y. Matsuo, Marine Biotechnol. Inst., Kamaishi, Japan; YM22-133 |
| 67770 | DSM 18936 <-- MBIC 08263 <-- Y. Matsuo YM22-133. |
doi: 10.13145/bacdive110.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Acidimicrobiia
- order: Acidimicrobiales
- family: Ilumatobacteraceae
- genus: Ilumatobacter
- species: Ilumatobacter fluminis
- full scientific name: Ilumatobacter fluminis Matsumoto et al. 2009
@ref: 7794
domain: Bacteria
phylum: Actinobacteria
class: Acidimicrobiia
order: Acidimicrobiales
family: Ilumatobacteraceae
genus: Ilumatobacter
species: Ilumatobacter fluminis
full scientific name: Ilumatobacter fluminis Matsumoto et al. 2009
strain designation: YM22-133
type strain: yes
Culture and growth conditions
culture medium
- @ref: 7794
- 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; with strain-specific modifications) Composition: NaCl 19.45 g/l Agar 15.0 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 |
|---|---|---|---|---|
| 7794 | positive | growth | 28 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
observation
- @ref: 67770
- observation: quinones: MK-9(H8)
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 7794 | sediment | Okinawa Prefecture, Iriomote, mouth of Kuiragawa River (N 24°19'23.9", E 123°44'44.7") | Japan | JPN | Asia | 24.3233 | 123.746 |
| 67770 | Sediment at the mouth of the Kuiragawa River | Iriomote, Okinawa Pref. | Japan | JPN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Sediment |
| #Environmental | #Terrestrial | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_165704.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15782;96_4873;97_21794;98_64927;99_165704&stattab=map
- Last taxonomy: Ilumatobacter fluminis subclade
- 16S sequence: AB360343
- Sequence Identity:
- Total samples: 948
- soil counts: 14
- aquatic counts: 927
- animal counts: 5
- plant counts: 2
Safety information
risk assessment
- @ref: 7794
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7794
- description: Ilumatobacter fluminis gene for 16S rRNA, partial sequence
- accession: AB360343
- length: 1439
- database: ena
- NCBI tax ID: 1331058
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Ilumatobacter fluminis strain DSM 18936 | 467091.3 | wgs | patric | 467091 |
| 66792 | Ilumatobacter fluminis DSM 18936 | 2772190982 | draft | img | 467091 |
| 67770 | Ilumatobacter fluminis DSM 18936 | GCA_004364865 | contig | ncbi | 467091 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 7794 | 68 | |
| 67770 | 68 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| gram-positive | yes | 69.725 | no |
| anaerobic | no | 98.788 | no |
| halophile | no | 86.44 | no |
| spore-forming | no | 85.361 | no |
| glucose-util | yes | 82.702 | no |
| aerobic | yes | 91.041 | no |
| flagellated | no | 98.314 | no |
| thermophile | no | 98.225 | no |
| motile | no | 93.995 | no |
| glucose-ferment | no | 93.168 | no |
External links
@ref: 7794
culture collection no.: DSM 18936, JCM 17811, MBIC 08263
straininfo link
- @ref: 69793
- straininfo: 404734
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19590147 | Ilumatobacter fluminis gen. nov., sp. nov., a novel actinobacterium isolated from the sediment of an estuary. | Matsumoto A, Kasai H, Matsuo Y, Omura S, Shizuri Y, Takahashi Y | J Gen Appl Microbiol | 10.2323/jgam.55.201 | 2009 | Actinobacteria/*classification/*cytology/physiology, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Geologic Sediments/*microbiology, Phylogeny, Rivers/*microbiology, Sequence Homology, *Water Microbiology | |
| Phylogeny | 23524358 | Ilumatobacter nonamiense sp. nov. and Ilumatobacter coccineum sp. nov., isolated from seashore sand. | Matsumoto A, Kasai H, Matsuo Y, Shizuri Y, Ichikawa N, Fujita N, Omura S, Takahashi Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.047316-0 | 2013 | Actinobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, *Silicon Dioxide, Vitamin K 2/analogs & derivatives/analysis | Genetics |
| Genetics | 24501628 | Complete genome sequence of Ilumatobacter coccineum YM16-304(T.). | Fujinami S, Takarada H, Kasai H, Sekine M, Omata S, Harada T, Fukai R, Hosoyama A, Horikawa H, Kato Y, Nakazawa H, Fujita N | Stand Genomic Sci | 10.4056/sigs.4007734 | 2013 |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 7794 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18936) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18936 | |
| 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) | |
| 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 | |
| 69793 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID404734.1 | StrainInfo: A central database for resolving microbial strain identifiers |