Strain identifier
BacDive ID: 5542
Type strain:
Species: Flavobacterium xanthum
Strain Designation: 5-O-C
Strain history: CIP <- 2002, J. Bowman, Tasmania Univ., Tasmania, Australia: strain ACAM 81 <- NCIMB 2069
NCBI tax ID(s): 69322 (species)
General
@ref: 1445
BacDive-ID: 5542
DSM-Number: 3661
keywords: genome sequence, 16S sequence, Bacteria, psychrophilic, Gram-negative
description: Flavobacterium xanthum 5-O-C is a psychrophilic, Gram-negative bacterium that was isolated from soil.
NCBI tax id
- NCBI tax id: 69322
- Matching level: species
strain history
@ref | history |
---|---|
1445 | <- H. Reichenbach <- NCMB <- K. Yamasoto <- K. Inoue, 5-O-C (Cytophaga xantha) |
67770 | IAM 12026 <-- K. Inoue and K. Komagata 5-O-c. |
123969 | CIP <- 2002, J. Bowman, Tasmania Univ., Tasmania, Australia: strain ACAM 81 <- NCIMB 2069 |
doi: 10.13145/bacdive5542.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Flavobacteriia
- order: Flavobacteriales
- family: Flavobacteriaceae
- genus: Flavobacterium
- species: Flavobacterium xanthum
- full scientific name: Flavobacterium xanthum (ex Inoue and Komagata 1976) McCammon and Bowman 2000
@ref: 1445
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Flavobacterium
species: Flavobacterium xanthum
full scientific name: Flavobacterium xanthum (ex Inoue and Komagata 1976) McCammon and Bowman 2000
strain designation: 5-O-C
type strain: yes
Morphology
cell morphology
@ref | gram stain | confidence | cell shape | motility |
---|---|---|---|---|
69480 | negative | 99.997 | ||
123969 | negative | rod-shaped | no |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
1445 | CY-AGAR (DSMZ Medium 67) | yes | https://mediadive.dsmz.de/medium/67 | Name: CY-AGAR (DSMZ Medium 67) Composition: Agar 15.0 g/l Casitone 3.0 g/l CaCl2 x 2 H2O 1.36 g/l Yeast extract 1.0 g/l Distilled water |
34273 | Marine agar (MA) | yes | Distilled water make up to (1000.000 ml);Marine agar (55.100 g) | |
123969 | CIP Medium 13 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13 | |
123969 | CIP Medium 566 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
1445 | positive | growth | 10-20 | psychrophilic |
34273 | positive | growth | 20 | psychrophilic |
67770 | positive | growth | 10 | psychrophilic |
123969 | positive | growth | 5-25 | psychrophilic |
123969 | no | growth | 30 | mesophilic |
123969 | no | growth | 37 | mesophilic |
123969 | no | growth | 41 | thermophilic |
123969 | no | growth | 45 | thermophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.997 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
123969 | NaCl | no | growth | 0 % |
123969 | NaCl | no | growth | 2 % |
123969 | NaCl | no | growth | 4 % |
123969 | NaCl | no | growth | 6 % |
123969 | NaCl | no | growth | 8 % |
123969 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
123969 | 4853 | esculin | - | hydrolysis |
123969 | 17632 | nitrate | - | builds gas from |
123969 | 17632 | nitrate | + | reduction |
123969 | 16301 | nitrite | - | builds gas from |
123969 | 16301 | nitrite | - | reduction |
123969 | 15792 | malonate | - | assimilation |
metabolite production
- @ref: 123969
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
123969 | 15688 | acetoin | - | |
123969 | 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 |
123969 | oxidase | + | |
123969 | beta-galactosidase | - | 3.2.1.23 |
123969 | alcohol dehydrogenase | - | 1.1.1.1 |
123969 | gelatinase | - | |
123969 | amylase | - | |
123969 | DNase | - | |
123969 | caseinase | + | 3.4.21.50 |
123969 | catalase | + | 1.11.1.6 |
123969 | tween esterase | + | |
123969 | gamma-glutamyltransferase | - | 2.3.2.2 |
123969 | lecithinase | - | |
123969 | lipase | - | |
123969 | lysine decarboxylase | - | 4.1.1.18 |
123969 | ornithine decarboxylase | - | 4.1.1.17 |
123969 | protease | + | |
123969 | tryptophan deaminase | - | |
123969 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123969 | - | + | + | + | - | + | + | - | - | - | + | + | - | - | - | + | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | continent | country | origin.country | isolation date |
---|---|---|---|---|---|
1445 | soil | Australia and Oceania | |||
67770 | Soil at Showa Station | Antarctica | Antarctica | ATA | |
123969 | Environment, Pond, mud | Antarctica | Antarctica | ATA | 1975 |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
1445 | 1 | Risk group (German classification) |
123969 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Flavobacterium xanthum 16S ribosomal RNA gene, partial sequence | AF030380 | 1454 | ena | 69322 |
20218 | Flavobacterium xanthum O31 16S ribosomal RNA gene, partial sequence | AF312005 | 472 | ena | 69322 |
20218 | Flavobacterium xanthum axD2 16S ribosomal RNA gene, partial sequence | AF312006 | 459 | ena | 69322 |
20218 | Flavobacterium xanthum gene for 16S rRNA, partial sequence, strain: NBRC 14972 | AB680727 | 1439 | ena | 69322 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Flavobacterium xanthum strain DSM 3661 | 69322.3 | wgs | patric | 69322 |
66792 | Flavobacterium xanthum DSM 3661 | 2700988712 | draft | img | 69322 |
67770 | Flavobacterium xanthum DSM 3661 | GCA_900142695 | contig | ncbi | 69322 |
GC content
- @ref: 67770
- GC-content: 39
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | no | 98.507 | no |
anaerobic | no | 99.313 | no |
halophile | no | 92.869 | no |
spore-forming | no | 93.883 | no |
glucose-util | yes | 82.283 | no |
thermophile | no | 99.794 | yes |
flagellated | no | 94.253 | no |
motile | no | 91.464 | no |
aerobic | yes | 91.808 | no |
glucose-ferment | no | 94.687 | no |
External links
@ref: 1445
culture collection no.: DSM 3661, ACAM 81, IAM 12026, NCMB 2069, JCM 20358, DSM 3312, IFO 14972, LMG 8372, NBRC 14972, NCIMB 2069, CIP 107448
straininfo link
- @ref: 75025
- straininfo: 10830
literature
- topic: Enzymology
- Pubmed-ID: 17369961
- title: A novel, intracellular antifreeze protein in an antarctic bacterium, Flavobacterium xanthum.
- authors: Kawahara H, Iwanaka Y, Higa S, Muryoi N, Sato M, Honda M, Omura H, Obata H
- journal: Cryo Letters
- year: 2007
- mesh: Acclimatization/physiology, Antarctic Regions, Antifreeze Proteins/chemistry/*isolation & purification/*metabolism, Bacterial Proteins/chemistry/isolation & purification/metabolism, Cold Temperature, Electrophoresis, Polyacrylamide Gel, Flavobacterium/classification/*metabolism, Microbiological Techniques, Molecular Weight
- topic2: Phylogeny
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
1445 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3661) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-3661 | |||
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 | |
34273 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/4885 | ||||
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 | |||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
75025 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID10830.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
123969 | Curators of the CIP | Collection of Institut Pasteur (CIP 107448) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107448 |