Strain identifier
BacDive ID: 5507
Type strain:
Species: Elizabethkingia miricola
Strain Designation: W3-B1
Strain history: CIP <- 2004, JCM <- 2001, T. Ezaki: strain W3-B1
NCBI tax ID(s): 172045 (species)
General
@ref: 5389
BacDive-ID: 5507
DSM-Number: 14571
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped, human pathogen
description: Elizabethkingia miricola W3-B1 is an aerobe, mesophilic, Gram-negative human pathogen that was isolated from condensation water.
NCBI tax id
- NCBI tax id: 172045
- Matching level: species
strain history
@ref | history |
---|---|
5389 | <- T. Ezaki; W3-B1 |
67770 | T. Ezaki W3-B1. |
120972 | CIP <- 2004, JCM <- 2001, T. Ezaki: strain W3-B1 |
doi: 10.13145/bacdive5507.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Flavobacteriia
- order: Flavobacteriales
- family: Weeksellaceae
- genus: Elizabethkingia
- species: Elizabethkingia miricola
- full scientific name: Elizabethkingia miricola (Li et al. 2004) Kim et al. 2005
synonyms
- @ref: 20215
- synonym: Chryseobacterium miricola
@ref: 5389
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Weeksellaceae
genus: Elizabethkingia
species: Elizabethkingia miricola
full scientific name: Elizabethkingia miricola (Li et al. 2004) Kim et al. 2005 emend. Nicholson et al. 2018
strain designation: W3-B1
type strain: yes
Morphology
cell morphology
- @ref: 120972
- gram stain: negative
- cell shape: rod-shaped
- motility: no
colony morphology
- @ref: 120972
pigmentation
- @ref: 120972
- production: no
- name: Flexirubin
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
5389 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
5389 | BHI MEDIUM (DSMZ Medium 215) | yes | https://mediadive.dsmz.de/medium/215 | Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water |
41929 | MEDIUM 112 - for Janibacter | yes | Distilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (1.000 g);Agar (20.000 g);Yeast extract (5.000 g);Peptone (10.000 g);Tween 80 (50.000 mg);Glycerol (2.000 g);Malt extract (5.000 g);Beef extract (2.000 g);Casamino acids (5.000 g);Ca | |
120972 | CIP Medium 112 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=112 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
5389 | positive | growth | 30 | mesophilic |
41929 | positive | growth | 30 | mesophilic |
61683 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
120972 | positive | growth | 15-37 | |
120972 | no | growth | 5 | psychrophilic |
120972 | no | growth | 41 | thermophilic |
120972 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
61683 | aerobe |
120972 | obligate aerobe |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
120972 | NaCl | positive | growth | 0-6 % |
120972 | NaCl | no | growth | 8 % |
120972 | NaCl | no | growth | 10 % |
observation
- @ref: 67770
- observation: quinones: MK-6
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
120972 | 16947 | citrate | - | carbon source |
120972 | 4853 | esculin | + | hydrolysis |
120972 | 606565 | hippurate | + | hydrolysis |
120972 | 17632 | nitrate | - | builds gas from |
120972 | 17632 | nitrate | - | reduction |
120972 | 16301 | nitrite | - | builds gas from |
120972 | 16301 | nitrite | + | reduction |
120972 | 35020 | tributyrin | + | hydrolysis |
120972 | 15792 | malonate | - | assimilation |
120972 | 17632 | nitrate | - | respiration |
metabolite production
- @ref: 120972
- Chebi-ID: 35581
- metabolite: indole
- production: yes
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
120972 | 15688 | acetoin | - | |
120972 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | + | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | + | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | + | |
68382 | leucine arylamidase | - | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | - | |
68382 | esterase (C 4) | - | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
120972 | oxidase | + | |
120972 | beta-galactosidase | + | 3.2.1.23 |
120972 | alcohol dehydrogenase | - | 1.1.1.1 |
120972 | gelatinase | + | |
120972 | amylase | - | |
120972 | DNase | + | |
120972 | caseinase | + | 3.4.21.50 |
120972 | catalase | + | 1.11.1.6 |
120972 | tween esterase | - | |
120972 | gamma-glutamyltransferase | + | 2.3.2.2 |
120972 | lecithinase | + | |
120972 | lipase | - | |
120972 | lysine decarboxylase | - | 4.1.1.18 |
120972 | ornithine decarboxylase | - | 4.1.1.17 |
120972 | phenylalanine ammonia-lyase | + | 4.3.1.24 |
120972 | tryptophan deaminase | - | |
120972 | urease | - | 3.5.1.5 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120972 | - | + | - | - | - | - | + | - | + | - | + | + | - | - | - | + | - | + | - | + |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120972 | + | + | - | + | + | - | - | - | - | + | + | + | - | - | - | - | + | - | + | - | - | - | - | - | + | - | - | - | - | - | - | + | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | - | - | - | - | + | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | + | + | + | - | + | + | - | - | + | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
5389 | condensation water | Russian Space station Mir | |||
61683 | Water,condensation | Russion space laboratory Mir | Space | ||
67770 | Condensation water in the Russian space laboratory Mir | ||||
120972 | Environment, Water | Mir space laboratory | Russian Federation | RUS | Europe |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
Safety information
risk assessment
@ref | pathogenicity human | pathogenicity animal | biosafety level | biosafety level comment |
---|---|---|---|---|
5389 | yes | yes | 2 | Risk group (German classification) |
120972 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 20218
- description: Elizabethkingia miricola gene for 16S rRNA, partial sequence
- accession: AB071953
- length: 1312
- database: ena
- NCBI tax ID: 172045
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Elizabethkingia miricola Elizabethkingia miricola KCTC 12492 | GCA_900092045 | contig | ncbi | 172045 |
66792 | Elizabethkingia miricola strain DSM 14571 | 172045.68 | wgs | patric | 172045 |
66792 | Elizabethkingia miricola strain Elizabethkingia miricola KCTC 12492 | 172045.52 | wgs | patric | 172045 |
66792 | Elizabethkingia miricola DSM 14571 | 2593339301 | draft | img | 172045 |
67770 | Elizabethkingia miricola DSM 14571 | GCA_008124555 | scaffold | ncbi | 172045 |
GC content
@ref | GC-content | method |
---|---|---|
67770 | 35 | high performance liquid chromatography (HPLC) |
67770 | 34.6 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 89.993 | no |
gram-positive | no | 98.026 | no |
anaerobic | no | 99.717 | yes |
aerobic | yes | 91.393 | no |
halophile | no | 95.394 | no |
spore-forming | no | 94.592 | no |
glucose-util | yes | 87.273 | no |
thermophile | no | 99.485 | yes |
flagellated | no | 94.785 | no |
glucose-ferment | no | 91.664 | no |
External links
@ref: 5389
culture collection no.: CCUG 58416, JCM 11413, DSM 14571, CIP 108250, GTC 862, KCTC 12492, BCRC 17371
straininfo link
- @ref: 74992
- straininfo: 131416
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 14666980 | Chryseobacterium miricola sp. nov., a novel species isolated from condensation water of space station Mir. | Li Y, Kawamura Y, Fujiwara N, Naka T, Liu H, Huang X, Kobayashi K, Ezaki T | Syst Appl Microbiol | 10.1078/072320203770865828 | 2003 | Base Composition, Chryseobacterium/*classification/cytology/*isolation & purification/physiology, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/chemistry, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Phenotype, Phylogeny, Pigments, Biological/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Spacecraft, Spores, Bacterial, Vitamin K 2/analysis/chemistry, *Water Microbiology | Enzymology |
Phylogeny | 15879269 | Transfer of Chryseobacterium meningosepticum and Chryseobacterium miricola to Elizabethkingia gen. nov. as Elizabethkingia meningoseptica comb. nov. and Elizabethkingia miricola comb. nov. | Kim KK, Kim MK, Lim JH, Park HY, Lee ST | Int J Syst Evol Microbiol | 10.1099/ijs.0.63541-0 | 2005 | Bacterial Typing Techniques, Base Composition, Chryseobacterium/*classification/cytology/physiology, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Flavobacteriaceae/*classification/cytology/physiology, Genes, Bacterial, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Enzymology |
Phylogeny | 21169462 | Elizabethkingia anophelis sp. nov., isolated from the midgut of the mosquito Anopheles gambiae. | Kampfer P, Matthews H, Glaeser SP, Martin K, Lodders N, Faye I | Int J Syst Evol Microbiol | 10.1099/ijs.0.026393-0 | 2010 | Animals, Anopheles/*microbiology, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Flavobacteriaceae/*classification/genetics/*isolation & purification/metabolism, Gastrointestinal Tract/microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics | Metabolism |
Phylogeny | 25858248 | Elizabethkingia endophytica sp. nov., isolated from Zea mays and emended description of Elizabethkingia anophelisKampfer et al. 2011. | Kampfer P, Busse HJ, McInroy JA, Glaeser SP | Int J Syst Evol Microbiol | 10.1099/ijs.0.000236 | 2015 | Alabama, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, Plant Stems/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/analogs & derivatives/chemistry, Vitamin K 2/analogs & derivatives/chemistry, Zea mays/*microbiology | Genetics |
Phylogeny | 33835912 | Elizabethkingia argenteiflava sp. nov., isolated from the pod of soybean, Glycine max. | Hwang JH, Kim J, Kim JH, Mo S | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004767 | 2021 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/isolation & purification, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Soybeans/*microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
5389 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14571) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-14571 | |||
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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
41929 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5852 | ||||
61683 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 58416) | https://www.ccug.se/strain?id=58416 | |||
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/ | ||||
68382 | Automatically annotated from API zym | |||||
74992 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID131416.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
120972 | Curators of the CIP | Collection of Institut Pasteur (CIP 108250) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108250 |