Strain identifier
BacDive ID: 5673
Type strain: 
Species: Chryseobacterium scophthalmum
Strain Designation: MM1
Strain history: CIP <- 1994, J.F. Bernardet, INRA, Jouy-en-Josas, France: strain MM1, Flavobacterium scophthalmum <- CCM <- B. Austin, Herriot-Watt Univ., Edinburg, UK
NCBI tax ID(s): 59733 (species)
version 8.1 (current version)
General
@ref: 6582
BacDive-ID: 5673
DSM-Number: 16779
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, animal pathogen
description: Chryseobacterium scophthalmum MM1 is a mesophilic animal pathogen that was isolated from turbot, gill.
NCBI tax id
- NCBI tax id: 59733
- Matching level: species
strain history
| @ref | history |
|---|---|
| 6582 | <- CIP <- J. F. Bernadet, INRA, Jouy-en-Josas, France; MM1 <- CCM <- B. Austin, Herriot-Watt Univ., Edinburg, UK |
| 122526 | CIP <- 1994, J.F. Bernardet, INRA, Jouy-en-Josas, France: strain MM1, Flavobacterium scophthalmum <- CCM <- B. Austin, Herriot-Watt Univ., Edinburg, UK |
doi: 10.13145/bacdive5673.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Flavobacteriia
- order: Flavobacteriales
- family: Weeksellaceae
- genus: Chryseobacterium
- species: Chryseobacterium scophthalmum
- full scientific name: Chryseobacterium scophthalmum (Mudarris et al. 1994) Vandamme et al. 1994
synonyms
- @ref: 20215
- synonym: Flavobacterium scophthalmum
@ref: 6582
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Weeksellaceae
genus: Chryseobacterium
species: Chryseobacterium scophthalmum
full scientific name: Chryseobacterium scophthalmum (Mudarris et al. 1994) Vandamme et al. 1994
strain designation: MM1
type strain: yes
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 6582 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | https://mediadive.dsmz.de/medium/92 | Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water |
| 37164 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
| 122526 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 6582 | positive | growth | 30 | mesophilic |
| 37164 | positive | growth | 30 | mesophilic |
| 51528 | positive | growth | 18-24 | psychrophilic |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | isolation date |
|---|---|---|---|---|---|---|
| 6582 | turbot, gill | Scotland | United Kingdom | GBR | Europe | |
| 51528 | Turbot (Scophthalmus maximus),gills | United Kingdom | GBR | Europe | ||
| 122526 | Turbot, gill | Scotland | United Kingdom | GBR | Europe | 1987 |
isolation source categories
| Cat1 | Cat2 |
|---|---|
| #Host | #Fishes |
| #Host Body-Site | #Oral cavity and airways |
taxonmaps
- @ref: 69479
- File name: preview.99_2837.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_206;97_225;98_254;99_2837&stattab=map
- Last taxonomy: Chryseobacterium scophthalmum
- 16S sequence: AJ271009
- Sequence Identity:
- Total samples: 471
- soil counts: 35
- aquatic counts: 104
- animal counts: 160
- plant counts: 172
Safety information
risk assessment
| @ref | pathogenicity animal | biosafety level | biosafety level comment |
|---|---|---|---|
| 6582 | yes | 2 | Risk group (German classification) |
| 122526 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 6582
- description: Chryseobacterium scophthalmum 16S rRNA gene, strain LMG 13028
- accession: AJ271009
- length: 1458
- database: ena
- NCBI tax ID: 59733
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Chryseobacterium scophthalmum DSM 16779 | GCA_900143185 | contig | ncbi | 59733 |
| 66792 | Chryseobacterium scophthalmum strain DSM 16779 | 59733.4 | wgs | patric | 59733 |
| 66792 | Chryseobacterium scophthalmum DSM 16779 | 2690315624 | draft | img | 59733 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| gram-positive | no | 98.304 | no |
| anaerobic | no | 99.352 | no |
| halophile | no | 94.368 | no |
| spore-forming | no | 95.398 | no |
| glucose-util | yes | 87.158 | no |
| thermophile | no | 99.67 | no |
| flagellated | no | 95.517 | no |
| aerobic | yes | 91.813 | no |
| motile | no | 90.783 | no |
| glucose-ferment | no | 92.076 | no |
External links
@ref: 6582
culture collection no.: DSM 16779, ATCC 700039, CCM 4109, CCUG 33454, CIP 104199, LMG 13028
straininfo link
- @ref: 75155
- straininfo: 9865
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 8068540 | Flavobacterium scophthalmum sp. nov., a pathogen of turbot (Scophthalmus maximus L.). | Mudarris M, Austin B, Segers P, Vancanneyt M, Hoste B, Bernardet JF | Int J Syst Bacteriol | 10.1099/00207713-44-3-447 | 1994 | Animals, Base Composition, DNA, Bacterial/chemistry/genetics, Flatfishes/*microbiology, Flavobacterium/genetics/*isolation & purification/pathogenicity, Microscopy, Electron, Nucleic Acid Hybridization, Phenotype, Scotland, Species Specificity, Terminology as Topic, Water Microbiology | Phenotype |
| Phylogeny | 15545478 | Kaistella koreensis gen. nov., sp. nov., a novel member of the Chryseobacterium-Bergeyella-Riemerella branch. | Kim MK, Im WT, Shin YK, Lim JH, Kim SH, Lee BC, Park MY, Lee KY, Lee ST | Int J Syst Evol Microbiol | 10.1099/ijs.0.02998-0 | 2004 | Bacterial Typing Techniques, Base Composition, Chryseobacterium/genetics, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Flavobacteriaceae/*classification/cytology/*isolation & purification/physiology, Fresh Water/*microbiology, Genes, rRNA, Gentian Violet, Korea, Molecular Sequence Data, Phenazines, Phylogeny, Pigments, Biological, Quinones/analysis/isolation & purification, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spores, Bacterial, Water Microbiology | Enzymology |
| Phylogeny | 18319450 | Chryseobacterium aquaticum sp. nov., isolated from a water reservoir. | Kim KK, Lee KC, Oh HM, Lee JS | Int J Syst Evol Microbiol | 10.1099/ijs.0.65491-0 | 2008 | Bacterial Typing Techniques, Chryseobacterium/*classification/genetics/isolation & purification/physiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Fresh Water/*microbiology, Genes, rRNA, Genotype, Korea, Molecular Sequence Data, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity | Genetics |
| Phylogeny | 19819990 | Soonwooa buanensis gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from seawater. | Joung Y, Song J, Lee K, Oh HM, Joh K, Cho JC | Int J Syst Evol Microbiol | 10.1099/ijs.0.017707-0 | 2009 | DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Flavobacteriaceae/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology | Metabolism |
| Phylogeny | 23378110 | Chryseobacterium ginsengisoli sp. nov., isolated from the rhizosphere of ginseng and emended description of Chryseobacterium gleum. | Nguyen NL, Kim YJ, Hoang VA, Yang DC | Int J Syst Evol Microbiol | 10.1099/ijs.0.045427-0 | 2013 | Bacterial Typing Techniques, Base Composition, Chryseobacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Molecular Sequence Data, Nucleic Acid Hybridization, Panax/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, Soil Microbiology, Vitamin K 2/analogs & derivatives/analysis | Genetics |
| Phylogeny | 31424383 | Chryseobacterium mulctrae sp. nov., isolated from raw cow's milk. | Yoon SH, Lee JE, Han RH, Kwon M, Kim GB | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003647 | 2019 | Animals, Bacterial Typing Techniques, Base Composition, Cattle, Chryseobacterium/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Female, Milk/*microbiology, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
| Phylogeny | 34040129 | Chryseobacterium schmidteae sp. nov. a novel bacterial species isolated from planarian Schmidtea mediterranea. | Kangale LJ, Raoult D, Ghigo E, Fournier PE | Sci Rep | 10.1038/s41598-021-90562-3 | 2021 | *Chryseobacterium, Mediterranea, Phylogeny, RNA, Ribosomal, 16S |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 6582 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16779) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16779 | |
| 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 | |
| 37164 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/16081 | ||
| 51528 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 33454) | https://www.ccug.se/strain?id=33454 | |
| 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) | |
| 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 | |
| 75155 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID9865.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
| 122526 | Curators of the CIP | Collection of Institut Pasteur (CIP 104199) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104199 |