Strain identifier
BacDive ID: 131337
Type strain: 
Species: Algibacter amylolyticus
Strain Designation: RU-4-M-4
Strain history: <- R. Margesin, Inst. Microbiology, Univ. Innsbruck, Austria; RU-4-M-4 <- D.-C. Zhang, CAS, Inst. of Oceanologoy
NCBI tax ID(s): 1608400 (species)
version 8.1 (current version)
General
@ref: 22564
BacDive-ID: 131337
DSM-Number: 29199
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Algibacter amylolyticus RU-4-M-4 is a mesophilic, Gram-negative bacterium that was isolated from intertidal sediment.
NCBI tax id
- NCBI tax id: 1608400
- Matching level: species
strain history
- @ref: 22564
- history: <- R. Margesin, Inst. Microbiology, Univ. Innsbruck, Austria; RU-4-M-4 <- D.-C. Zhang, CAS, Inst. of Oceanologoy
doi: 10.13145/bacdive131337.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Flavobacteriia
- order: Flavobacteriales
- family: Flavobacteriaceae
- genus: Algibacter
- species: Algibacter amylolyticus
- full scientific name: Algibacter amylolyticus Zhang et al. 2015
@ref: 22564
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Algibacter
species: Algibacter amylolyticus
full scientific name: Algibacter amylolyticus Zhang et al. 2015
strain designation: RU-4-M-4
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.909
Culture and growth conditions
culture medium
- @ref: 22564
- 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: 22564
- growth: positive
- type: growth
- temperature: 25
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.997 |
Isolation, sampling and environmental information
isolation
- @ref: 22564
- sample type: intertidal sediment
- geographic location: Sakhalin Island (48° 00' N 142° 82' E)
- country: Russia
- origin.country: RUS
- continent: Asia
- latitude: 48
- longitude: 143.367
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Sediment |
| #Environmental | #Terrestrial | #Tidal flat |
taxonmaps
- @ref: 69479
- File name: preview.99_166718.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_107;96_7999;97_9621;98_109441;99_166718&stattab=map
- Last taxonomy: Algibacter amylolyticus subclade
- 16S sequence: KP136798
- Sequence Identity:
- Total samples: 88
- soil counts: 1
- aquatic counts: 82
- animal counts: 5
Safety information
risk assessment
- @ref: 22564
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22564
- description: Algibacter amylolyticus strain RU-4-M-4 16S ribosomal RNA gene, partial sequence
- accession: KP136798
- length: 1373
- database: ena
- NCBI tax ID: 1608400
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Algibacter amylolyticus DSM 29199 | GCA_014202225 | scaffold | ncbi | 1608400 |
| 66792 | Algibacter amylolyticus RU-4-M-4 | GCA_007559325 | contig | ncbi | 1608400 |
| 66792 | Algibacter amylolyticus RU-4-M-4 | GCA_008630605 | contig | ncbi | 1608400 |
| 66792 | Algibacter amylolyticus strain DSM 29199 | 1608400.5 | wgs | patric | 1608400 |
| 66792 | Algibacter amylolyticus DSM 29199 | 2861381790 | draft | img | 1608400 |
GC content
- @ref: 22564
- GC-content: 36.4
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| flagellated | no | 94.287 | no |
| gram-positive | no | 97.91 | no |
| anaerobic | no | 99.754 | no |
| aerobic | yes | 94.108 | no |
| halophile | no | 76.747 | no |
| spore-forming | no | 96.77 | no |
| glucose-util | yes | 84.187 | no |
| thermophile | no | 99.553 | yes |
| glucose-ferment | no | 89.536 | no |
| motile | no | 88.475 | no |
External links
@ref: 22564
culture collection no.: DSM 29199, LMG 28383
straininfo link
- @ref: 89778
- straininfo: 402105
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 25713044 | Algibacter amylolyticus sp. nov., isolated from intertidal sediment. | Zhang DC, Wu J, Neuner K, Yao J, Margesin R | Int J Syst Evol Microbiol | 10.1099/ijs.0.000134 | 2015 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Geologic Sediments/*microbiology, Islands, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Russia, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
| Phylogeny | 32783808 | Algibacter marinivivus sp. nov., isolated from the surface of a marine red alga. | Zhong XC, Xu W, Zhang Y, Zhang QQ, Du ZJ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004375 | 2020 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/isolation & purification, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodophyta/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 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 | |
| 22564 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-29199 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29199) | |
| 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 | |
| 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 | |
| 89778 | 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-ID402105.1 |