Strain identifier
BacDive ID: 24026
Type strain: 
Species: Flavobacterium urocaniciphilum
Strain history: D. Fujii strain 95 (=YIT 12746).
NCBI tax ID(s): 1299341 (species)
version 9.3 (current version)
General
@ref: 20573
BacDive-ID: 24026
DSM-Number: 27078
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Flavobacterium urocaniciphilum DSM 27078 is a mesophilic bacterium that was isolated from sludge from wastewater treatment plant associated with a facility, that produces a fermented milk drink.
NCBI tax id
- NCBI tax id: 1299341
- Matching level: species
strain history
| @ref | history |
|---|---|
| 20573 | <- D. Fujii, Yakult Central Inst. Microbiol. Res., Kunitachi, Japan; YIT 12746 <- F. Nagai |
| 67770 | D. Fujii strain 95 (=YIT 12746). |
doi: 10.13145/bacdive24026.20250331.9.3
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 urocaniciphilum
- full scientific name: Flavobacterium urocaniciphilum Fujii et al. 2014
@ref: 20573
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Flavobacterium
species: Flavobacterium urocaniciphilum
full scientific name: Flavobacterium urocaniciphilum Fujii et al. 2014
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 125438 | no | 93 | |
| 125438 | 98.413 | negative | |
| 125439 | 99.8 | negative |
Culture and growth conditions
culture medium
- @ref: 20573
- name: R2A MEDIUM (DSMZ Medium 830)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830
- composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 20573 | positive | growth | 25 |
| 67770 | positive | growth | 25 |
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: obligate aerobe
- confidence: 97.6
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 125438 | no | 92.785 |
| 125439 | no | 98.6 |
observation
- @ref: 67770
- observation: quinones: MK-6
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 20573 | sludge from wastewater treatment plant associated with a facility, that produces a fermented milk drink | Saga Prefecture, Yakult Honsha Co., Ltd. | Japan | JPN | Asia |
| 67770 | Sludge from a wastewater treatment plant in Saga Pref. | Japan | JPN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Food production | |
| #Engineered | #Waste | #Water treatment plant |
| #Environmental | #Terrestrial | #Mud (Sludge) |
| #Host Body Product | #Fluids | #Milk |
taxonmaps
- @ref: 69479
- File name: preview.99_27208.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_13493;97_16430;98_20384;99_27208&stattab=map
- Last taxonomy: Flavobacterium urocaniciphilum subclade
- 16S sequence: AB795015
- Sequence Identity:
- Total samples: 2083
- soil counts: 418
- aquatic counts: 1375
- animal counts: 211
- plant counts: 79
Safety information
risk assessment
- @ref: 20573
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20573
- description: Flavobacterium urocaniciphilum gene for 16S ribosomal RNA, partial sequence
- accession: AB795015
- length: 1468
- database: nuccore
- NCBI tax ID: 1299341
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Flavobacterium urocaniciphilum strain DSM 27078 | 1299341.3 | wgs | patric | 1299341 |
| 66792 | Flavobacterium urocaniciphilum DSM 27078 | 2693429864 | draft | img | 1299341 |
| 67770 | Flavobacterium urocaniciphilum DSM 27078 | GCA_900110615 | contig | ncbi | 1299341 |
GC content
- @ref: 20573
- GC-content: 30.9
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 98.413 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 98.748 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 92.785 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 85.808 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 96.339 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 93 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 98.6 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 74.1 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 99.8 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 97.6 |
External links
@ref: 20573
culture collection no.: DSM 27078, JCM 19142, YIT 12746, BCRC 81228, NRIC 0940
straininfo link
- @ref: 88000
- straininfo: 407649
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 24453232 | Flavobacterium longum sp. nov. and Flavobacterium urocaniciphilum sp. nov., isolated from a wastewater treatment plant, and emended descriptions of Flavobacterium caeni and Flavobacterium terrigena. | Fujii D, Nagai F, Watanabe Y, Shirasawa Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.054312-0 | 2014 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Japan, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Vitamin K 2/analogs & derivatives/chemistry, Waste Water/*microbiology | Genetics |
| Phylogeny | 26118784 | Flavobacterium maris sp. nov. isolated from shallow sediments of the Sea of Japan. | Romanenko LA, Tanaka N, Svetashev VI, Kurilenko VV, Mikhailov VV | Arch Microbiol | 10.1007/s00203-015-1128-x | 2015 | Bacterial Typing Techniques, Base Composition, Fatty Acids/analysis, Flavobacterium/*classification/*genetics/isolation & purification, Geologic Sediments/*microbiology, Japan, *Phylogeny, RNA, Ribosomal, 16S/genetics, Species Specificity, Vitamin K 2/analysis | Enzymology |
| Phylogeny | 30355396 | Flavobacterium sediminis sp. nov., a starch-degrading bacterium isolated from tidal flat sediment. | Bae SS, Kim MR, Jung Y, Yang SH, Kwon KK, Baek K | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003081 | 2018 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | title | doi/url | catalogue | journal | pubmed |
|---|---|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |||
| 20573 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-27078 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27078) | |||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
| 88000 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID407649.1 | |||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 | |||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |