Strain identifier
BacDive ID: 500
Type strain: 
Species: Catenovulum agarivorans
Strain history: X.-H. Zhang YM01 <-- Y. Wang YM01.
NCBI tax ID(s): 1172192 (species)
version 8.1 (current version)
General
@ref: 16702
BacDive-ID: 500
DSM-Number: 23111
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Catenovulum agarivorans DSM 23111 is a mesophilic bacterium that was isolated from seawater.
NCBI tax id
- NCBI tax id: 1172192
- Matching level: species
strain history
| @ref | history |
|---|---|
| 16702 | <- X.-H. Zhang, Ocean Univ. China, Qingdao, P. R. China; YM01 <- Y. Wang |
| 67770 | X.-H. Zhang YM01 <-- Y. Wang YM01. |
doi: 10.13145/bacdive500.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Alteromonadales
- family: Alteromonadaceae
- genus: Catenovulum
- species: Catenovulum agarivorans
- full scientific name: Catenovulum agarivorans Yan et al. 2011
@ref: 16702
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Alteromonadales
family: Alteromonadaceae
genus: Catenovulum
species: Catenovulum agarivorans
full scientific name: Catenovulum agarivorans Yan et al. 2011
type strain: yes
Culture and growth conditions
culture medium
- @ref: 16702
- 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 MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l Agar 2.0 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 |
|---|---|---|---|---|
| 16702 | positive | growth | 28 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
observation
- @ref: 67770
- observation: quinones: MK-7
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 16702 | seawater | Yellow Sea, coastal region of Qingdao (36° 04' N 120° 19' E) | China | CHN | Asia | 36.0667 | 120.317 |
| 67770 | Seawater of Yellow Sea | China | CHN | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
taxonmaps
- @ref: 69479
- File name: preview.99_1784.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_255;96_1014;97_1180;98_1410;99_1784&stattab=map
- Last taxonomy: Alteromonadaceae
- 16S sequence: GQ262000
- Sequence Identity:
- Total samples: 523
- soil counts: 20
- aquatic counts: 432
- animal counts: 70
- plant counts: 1
Safety information
risk assessment
- @ref: 16702
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16702
- description: Catenovulum agarivorans YM01 16S ribosomal RNA gene, partial sequence
- accession: GQ262000
- length: 1379
- database: ena
- NCBI tax ID: 659495
Genome sequences
- @ref: 67770
- description: Catenovulum agarivorans YM01
- accession: GCA_000281085
- assembly level: scaffold
- database: ncbi
- NCBI tax ID: 659495
GC content
| @ref | GC-content | method |
|---|---|---|
| 16702 | 44.8 | high performance liquid chromatography (HPLC) |
| 67770 | 44.8 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | yes | 86.569 | no |
| flagellated | yes | 80.506 | no |
| gram-positive | no | 99.206 | no |
| anaerobic | no | 99.098 | no |
| aerobic | yes | 83.537 | no |
| halophile | no | 64.976 | no |
| spore-forming | no | 94.127 | no |
| thermophile | no | 98.391 | yes |
| glucose-util | yes | 88.681 | no |
| glucose-ferment | no | 73.601 | no |
External links
@ref: 16702
culture collection no.: DSM 23111, CGMCC 1.10245, JCM 16580, YM 01
straininfo link
- @ref: 70179
- straininfo: 408154
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 21257691 | Catenovulum agarivorans gen. nov., sp. nov., a peritrichously flagellated, chain-forming, agar-hydrolysing gammaproteobacterium from seawater. | Yan S, Yu M, Wang Y, Shen C, Zhang XH | Int J Syst Evol Microbiol | 10.1099/ijs.0.027565-0 | 2011 | Agar/*metabolism, Base Composition, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Gammaproteobacteria/*classification/genetics/*isolation & purification/metabolism, Hydrolysis, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sodium Chloride/metabolism | Metabolism |
| Genetics | 22965101 | Genome sequence of the thermostable-agarase-producing marine bacterium Catenovulum agarivorans YM01(T), which reveals the presence of a series of agarase-encoding genes. | Shi X, Yu M, Yan S, Dong S, Zhang XH | J Bacteriol | 10.1128/JB.01283-12 | 2012 | Alteromonadaceae/*classification/*genetics, Gene Expression Regulation, Bacterial/*physiology, Gene Expression Regulation, Enzymologic/*physiology, *Genome, Bacterial, Glycoside Hydrolases/genetics/*metabolism, Hot Temperature, Molecular Sequence Data, Oceans and Seas | Stress |
| Phylogeny | 23966020 | Isolation and characterization of a novel agar-degrading marine bacterium, Gayadomonas joobiniege gen, nov, sp. nov., from the Southern Sea, Korea. | Chi WJ, Park JS, Kwak MJ, Kim JF, Chang YK, Hong SK | J Microbiol Biotechnol | 10.4014/jmb.1308.08007 | 2013 | Agar/*metabolism, Alteromonadaceae/*classification/genetics/isolation & purification/*metabolism, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrolysis, Microbial Sensitivity Tests, Microscopy, Electron, Transmission, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA | Metabolism |
| Genetics | 24824021 | Overexpression and characterization of a novel thermostable beta-agarase YM01-3, from marine bacterium Catenovulum agarivorans YM01(T). | Cui F, Dong S, Shi X, Zhao X, Zhang XH | Mar Drugs | 10.3390/md12052731 | 2014 | Agar/chemistry, Alteromonadaceae/*chemistry/genetics, Amino Acid Sequence, Cloning, Molecular, Escherichia coli/metabolism, Genome, Bacterial, Glycoside Hydrolases/*chemistry, Molecular Sequence Data, Open Reading Frames/genetics, Phylogeny, Recombinant Proteins/chemistry/genetics/pharmacology | Enzymology |
| Phylogeny | 26036673 | Catenovulum maritimus sp. nov., a novel agarolytic gammaproteobacterium isolated from the marine alga Porphyra yezoensis Ueda (AST58-103), and emended description of the genus Catenovulum. | Li DQ, Zhou YX, Liu T, Chen GJ, Du ZJ | Antonie Van Leeuwenhoek | 10.1007/s10482-015-0495-2 | 2015 | Aerobiosis, Alteromonadaceae/*classification/genetics/*isolation & purification/physiology, Anaerobiosis, Aquatic Organisms/microbiology, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genome, Bacterial, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Pigments, Biological/analysis, Porphyra/*microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature | Genetics |
| Phylogeny | 28895510 | Catenovulum sediminis sp. nov., isolated from coastal sediment. | Shi MJ, Du WJ, Wang C, Chen GJ, Du ZJ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002219 | 2017 | Alteromonadaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
| Enzymology | 28986239 | Characterization and overexpression of a glycosyl hydrolase family 16 beta-agarase YM01-1 from marine bacterium Catenovulum agarivorans YM01(T). | An K, Shi X, Cui F, Cheng J, Liu N, Zhao X, Zhang XH | Protein Expr Purif | 10.1016/j.pep.2017.10.002 | 2017 | Alteromonadaceae/*enzymology/genetics, Bacterial Proteins/chemistry/genetics/*metabolism, Escherichia coli/genetics, Glycoside Hydrolases/chemistry/genetics/*metabolism, Hydrogen-Ion Concentration, Kinetics, Recombinant Proteins/chemistry/genetics/*metabolism, Temperature | Metabolism |
| Phylogeny | 33332262 | Algibacillus agarilyticus gen. nov., sp. nov., isolated from the surface of the red algae Gelidium amansii. | Meng X, Chang YQ, Wang H, Du ZJ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004558 | 2020 | Alteromonadaceae/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodophyta/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
| Phylogeny | 34752210 | Saccharobesus litoralis gen. nov., sp. nov., a novel alginate-degrading bacterium isolated from the surface of intertidal algal turf. | Amrina RA, Furusawa G, Lau NS | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005087 | 2021 | *Alginates, Alteromonadaceae/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Malaysia, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 16702 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23111) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23111 | |
| 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 | |
| 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 | |
| 70179 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID408154.1 | StrainInfo: A central database for resolving microbial strain identifiers |