Strain identifier
BacDive ID: 5602
Type strain: 
Species: Leeuwenhoekiella marinoflava
Strain history: LMG 1345 <-- NCIMB 397 <-- R. Spencer SW1 (Flavobacterium sp.).
NCBI tax ID(s): 1122159 (strain), 988 (species)
version 8.1 (current version)
General
@ref: 1437
BacDive-ID: 5602
DSM-Number: 3653
keywords: genome sequence, 16S sequence, Bacteria, psychrophilic, Gram-negative
description: Leeuwenhoekiella marinoflava DSM 3653 is a psychrophilic, Gram-negative bacterium that was isolated from seawater.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1122159 | strain |
| 988 | species |
strain history
| @ref | history |
|---|---|
| 1437 | <- H. Reichenbach <- NCMB <- R. Spencer (Flavobacterium sp.) |
| 67770 | LMG 1345 <-- NCIMB 397 <-- R. Spencer SW1 (Flavobacterium sp.). |
doi: 10.13145/bacdive5602.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Flavobacteriia
- order: Flavobacteriales
- family: Flavobacteriaceae
- genus: Leeuwenhoekiella
- species: Leeuwenhoekiella marinoflava
- full scientific name: Leeuwenhoekiella marinoflava (Reichenbach 1989 ex Colwell et al. 1966) Nedashkovskaya et al. 2005
synonyms
- @ref: 20215
- synonym: Cytophaga marinoflava
@ref: 1437
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Leeuwenhoekiella
species: Leeuwenhoekiella marinoflava
full scientific name: Leeuwenhoekiella marinoflava (Reichenbach 1989) Nedashkovskaya et al. 2005 emend. Nedashkovskaya et al. 2014
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.984
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 1437 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | yes | https://mediadive.dsmz.de/medium/514 | 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 |
| 1437 | CYTOPHAGA (marine) MEDIUM (DSMZ Medium 172) | yes | https://mediadive.dsmz.de/medium/172 | Name: CYTOPHAGA (marine) MEDIUM (DSMZ Medium 172) Composition: NaCl 24.7 g/l Agar 15.0 g/l MgSO4 x 7 H2O 6.3 g/l MgCl2 x 6 H2O 4.6 g/l CaCl2 x 2 H2O 1.2 g/l Yeast extract 1.0 g/l Tryptone 1.0 g/l KCl 0.7 g/l NaHCO3 0.2 g/l Distilled water |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 1437 | positive | growth | 20 | psychrophilic |
| 1437 | positive | growth | 20-25 | |
| 67770 | positive | growth | 25 | mesophilic |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.998 |
observation
- @ref: 67770
- observation: quinones: MK-6
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 1437 | seawater | Scotland, Aberdeen | United Kingdom | GBR | Europe |
| 67770 | Seawater in the North Sea off Aberdeen | Scotland | United Kingdom | GBR | Europe |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
taxonmaps
- @ref: 69479
- File name: preview.99_147004.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_74;96_712;97_2762;98_37726;99_147004&stattab=map
- Last taxonomy: Leeuwenhoekiella
- 16S sequence: AB680577
- Sequence Identity:
- Total samples: 2
- aquatic counts: 1
- animal counts: 1
Safety information
risk assessment
- @ref: 1437
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Cytophaga marinoflava 16S ribosomal RNA gene, partial sequence | AF203475 | 1445 | ena | 988 |
| 20218 | Leeuwenhoekiella marinoflava gene for 16S rRNA, partial sequence, strain: NBRC 14170 | AB680577 | 1453 | ena | 988 |
| 20218 | Leeuwenhoekiella marinoflava gene for 16S ribosomal RNA, partial sequence, strain: NCIMB 397 | D12668 | 1257 | ena | 988 |
| 1437 | Cytophaga marinoflava 16S ribosomal RNA gene, partial sequence | M58770 | 1478 | ena | 988 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Leeuwenhoekiella marinoflava DSM 3653 | 1122159.4 | wgs | patric | 1122159 |
| 66792 | Leeuwenhoekiella marinoflava strain LMG 1345 | 988.5 | wgs | patric | 988 |
| 66792 | Leeuwenhoekiella marinoflava DSM 3653 | 2582581269 | draft | img | 1122159 |
| 66792 | Leeuwenhoekiella marinoflava LMG 1345 | 2772190910 | draft | img | 988 |
| 67770 | Leeuwenhoekiella marinoflava DSM 3653 | GCA_900129005 | scaffold | ncbi | 1122159 |
| 67770 | Leeuwenhoekiella marinoflava LMG 1345 | GCA_004104035 | contig | ncbi | 988 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 1437 | 37.0 | |
| 67770 | 37 | Buoyant density centrifugation (BD) |
| 67770 | 38 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 84.959 | no |
| flagellated | no | 93.896 | no |
| gram-positive | no | 97.69 | no |
| anaerobic | no | 99.672 | no |
| aerobic | yes | 90.356 | no |
| halophile | no | 62.571 | no |
| spore-forming | no | 95.364 | no |
| thermophile | no | 99.526 | no |
| glucose-util | yes | 88.921 | no |
| glucose-ferment | no | 87.841 | no |
External links
@ref: 1437
culture collection no.: DSM 3653, ATCC 19326, IAM 14116, NCMB 397, JCM 31008, IFO 14170, IFO 15939, JCM 8517, KCTC 2915, LMG 1345, NBRC 14170, NBRC 15939, NCIMB 397
straininfo link
- @ref: 75084
- straininfo: 2152
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Enzymology | 8984902 | Purification of a marine bacterial glucose dehydrogenase from Cytophaga marinoflava and its application for measurement of 1,5-anhydro-D-glucitol. | Tsugawa W, Horiuchi S, Tanaka M, Wake H, Sode K | Appl Biochem Biotechnol | 10.1007/BF02786960 | 1996 | Chromatography/methods, Cytophaga/*enzymology, Deoxyglucose/*analysis, Glucose 1-Dehydrogenase, Glucose Dehydrogenases/*isolation & purification | Phylogeny |
| Phylogeny | 25736409 | Leeuwenhoekiella polynyae sp. nov., isolated from a polynya in western Antarctica. | Si OJ, Kim SJ, Jung MY, Choi SB, Kim JG, Kim SG, Roh SW, Lee S, Rhee SK | Int J Syst Evol Microbiol | 10.1099/ijs.0.000160 | 2015 | Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
| Phylogeny | 28920849 | Flavimarina flava sp. nov., isolated from Salicornia herbacea. | Cho ES, Cha IT, Park JM, Choi HJ, Lee JH, Roh SW, Cho EA, Kweon MH, Nam YD, Seo MJ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002292 | 2017 | Bacterial Typing Techniques, Base Composition, Chenopodiaceae/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 1437 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3653) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-3653 | |||
| 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 | |
| 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/ | ||||
| 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 | |||
| 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 | |||
| 75084 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID2152.1 | StrainInfo: A central database for resolving microbial strain identifiers |