Strain identifier
BacDive ID: 132986
Type strain:
Species: Flavobacterium aquicola
Strain Designation: TMd3a3
Strain history: K. Hatayama; Sagami Chem. Res. Inst., Japan; TMd3a3.
NCBI tax ID(s): 1682742 (species)
General
@ref: 24774
BacDive-ID: 132986
DSM-Number: 100880
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, motile, rod-shaped, colony-forming
description: Flavobacterium aquicola TMd3a3 is a facultative anaerobe, mesophilic, Gram-negative bacterium that forms irregular colonies and was isolated from fresh water from a river.
NCBI tax id
- NCBI tax id: 1682742
- Matching level: species
strain history
@ref | history |
---|---|
24774 | <- K. Hatayama, Sagami Chemical Research Institute, Kanagawa, Japan; TMd3a3 <- K. Hatayama and T. Kuno |
67770 | K. Hatayama; Sagami Chem. Res. Inst., Japan; TMd3a3. |
doi: 10.13145/bacdive132986.20230509.8.1
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 aquicola
- full scientific name: Flavobacterium aquicola Hatayama et al. 2016
@ref: 24774
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Flavobacterium
species: Flavobacterium aquicola
full scientific name: Flavobacterium aquicola Hatayama et al. 2016
strain designation: TMd3a3
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | flagellum arrangement | confidence |
---|---|---|---|---|---|---|---|
43092 | negative | 4-11 µm | 0.5-0.6 µm | rod-shaped | yes | gliding | |
69480 | negative | 99.992 |
colony morphology
- @ref: 43092
- colony color: light yellow
- colony shape: irregular
- incubation period: 3 days
- medium used: R2A
pigmentation
- @ref: 43092
- production: yes
- name: Flexirubin-type pigment
Culture and growth conditions
culture medium
@ref | name | growth | composition | link |
---|---|---|---|---|
43092 | Reasoner's 2A agar (R2A) | yes | ||
43092 | IPM | yes | 0.5 g/l yeast extract, 0.5 g/l proteose peptone no. 3, 0.5 g/l tryptone, 0.5 g/l sucrose, 0.3 g/l sodium pyruvate, 0.3 g/l K2HPO4, 0.3 g/l MgSO4x7H2O, 0.3 g/l CaCl2x2H2O, 15 g/l gellan gum, pH 6.6 | |
43092 | trypticase soy agar (TSA) | yes | ||
43092 | nutritient agar (NA) | yes | ||
43092 | Marine agar (MA) | no | ||
24774 | R2A MEDIUM (DSMZ Medium 830) | yes | 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 | https://mediadive.dsmz.de/medium/830 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
43092 | positive | optimum | 25 | mesophilic |
43092 | positive | growth | 4-30 | |
24774 | positive | growth | 25 | mesophilic |
67770 | positive | growth | 25 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
43092 | positive | growth | 6.0-8.0 |
43092 | positive | optimum | 6.0-7.0 |
Physiology and metabolism
oxygen tolerance
- @ref: 43092
- oxygen tolerance: facultative anaerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
43092 | no | |
69481 | no | 100 |
69480 | no | 99.987 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
43092 | NaCl | positive | growth | 0-1 %(w/v) |
43092 | NaCl | positive | optimum | 0 %(w/v) |
observation
- @ref: 67770
- observation: quinones: MK-6
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
43092 | casein | + | hydrolysis | |
43092 | starch | + | hydrolysis | 28017 |
43092 | carboxymethylcellulose | - | hydrolysis | 85146 |
43092 | chitin | - | hydrolysis | 17029 |
43092 | pectin | - | hydrolysis | 17309 |
43092 | L-tyrosine | - | hydrolysis | 17895 |
43092 | dna | - | hydrolysis | 16991 |
43092 | egg yolk | - | hydrolysis | |
43092 | gelatin | - | hydrolysis | 5291 |
43092 | nitrate | + | reduction | 17632 |
43092 | D-glucose | + | assimilation | 17634 |
43092 | L-arabinose | + | assimilation | 30849 |
43092 | D-mannose | + | assimilation | 16024 |
43092 | maltose | + | assimilation | 17306 |
43092 | D-mannitol | - | assimilation | 16899 |
43092 | N-acetylglucosamine | - | assimilation | 506227 |
43092 | potassium gluconate | - | assimilation | 32032 |
43092 | decanoate | - | assimilation | 27689 |
43092 | adipate | - | assimilation | 17128 |
43092 | malate | - | assimilation | 25115 |
43092 | sodium citrate | - | assimilation | 53258 |
43092 | phenylacetate | - | assimilation | 18401 |
43092 | glucose | - | fermentation | 17234 |
43092 | citrate | - | assimilation | 16947 |
43092 | D-mannitol | - | fermentation | 16899 |
43092 | myo-inositol | - | fermentation | 17268 |
43092 | D-sorbitol | - | fermentation | 17924 |
43092 | L-rhamnose | - | fermentation | 62345 |
43092 | sucrose | - | fermentation | 17992 |
43092 | melibiose | - | fermentation | 28053 |
43092 | amygdalin | - | fermentation | 27613 |
43092 | L-arabinose | - | fermentation | 30849 |
43092 | alpha-cyclodextrin | + | oxidation | 40585 |
43092 | dextrin | + | oxidation | 23652 |
43092 | glycogen | + | oxidation | 28087 |
43092 | L-arabinose | + | oxidation | 30849 |
43092 | cellobiose | + | oxidation | 17057 |
43092 | D-galactose | + | oxidation | 12936 |
43092 | gentiobiose | + | oxidation | 28066 |
43092 | alpha-D-glucose | + | oxidation | 17925 |
43092 | alpha-lactose | + | oxidation | 36219 |
43092 | maltose | + | oxidation | 17306 |
43092 | D-mannose | + | oxidation | 16024 |
43092 | L-glutamate | + | oxidation | 29985 |
43092 | glycyl L-aspartic acid | + | oxidation | 73804 |
43092 | glycyl-l-glutamate | + | oxidation | 73784 |
43092 | tween 40 | - | oxidation | 53423 |
43092 | tween 80 | - | oxidation | 53426 |
43092 | N-acetylgalactosamine | - | oxidation | 28037 |
43092 | N-acetylglucosamine | - | oxidation | 506227 |
43092 | ribitol | - | oxidation | 15963 |
43092 | D-arabitol | - | oxidation | 18333 |
43092 | erythritol | - | oxidation | 17113 |
43092 | D-fructose | - | oxidation | 15824 |
43092 | L-fucose | - | oxidation | 18287 |
43092 | myo-inositol | - | oxidation | 17268 |
43092 | lactulose | - | oxidation | 6359 |
43092 | D-mannitol | - | oxidation | 16899 |
43092 | melibiose | - | oxidation | 28053 |
43092 | methyl beta-D-glucopyranoside | - | oxidation | 320055 |
43092 | D-psicose | - | oxidation | 27605 |
43092 | raffinose | - | oxidation | 16634 |
43092 | L-rhamnose | - | oxidation | 62345 |
43092 | D-sorbitol | - | oxidation | 17924 |
43092 | sucrose | - | oxidation | 17992 |
43092 | trehalose | - | oxidation | 27082 |
43092 | turanose | - | oxidation | 32528 |
43092 | xylitol | - | oxidation | 17151 |
43092 | methyl pyruvate | - | oxidation | 51850 |
43092 | monomethyl succinate | - | oxidation | 75146 |
43092 | acetate | - | oxidation | 30089 |
43092 | cis-aconitate | - | oxidation | 16383 |
43092 | citrate | - | oxidation | 16947 |
43092 | formate | - | oxidation | 15740 |
43092 | D-galactonic acid lactone | - | oxidation | 15895 |
43092 | D-galacturonic acid | - | oxidation | 18024 |
43092 | D-gluconate | - | oxidation | 8391 |
43092 | D-glucosaminic acid | - | oxidation | 17784 |
43092 | D-glucuronate | - | oxidation | 15748 |
43092 | 2-hydroxybutyrate | - | oxidation | 64552 |
43092 | beta-hydroxybutyrate | - | oxidation | 8295 |
43092 | 4-hydroxybutyrate | - | oxidation | 16724 |
43092 | 4-hydroxyphenylacetic acid | - | oxidation | 18101 |
43092 | itaconate | - | oxidation | 17240 |
43092 | 2-oxobutanoate | - | oxidation | 16763 |
43092 | 2-oxoglutarate | - | oxidation | 30916 |
43092 | 2-oxopentanoate | - | oxidation | 28644 |
43092 | lactate | - | oxidation | 24996 |
43092 | malonate | - | oxidation | 15792 |
43092 | propionate | - | oxidation | 17272 |
43092 | quinate | - | oxidation | 26490 |
43092 | D-saccharate | - | oxidation | 33801 |
43092 | sebacic acid | - | oxidation | 41865 |
43092 | succinate | - | oxidation | 30031 |
43092 | bromosuccinate | - | oxidation | 73706 |
43092 | succinamate | - | oxidation | 143136 |
43092 | glucuronamide | - | oxidation | 32323 |
43092 | L-alaninamide | - | oxidation | 21217 |
43092 | D-alanine | - | oxidation | 15570 |
43092 | L-alanine | - | oxidation | 16977 |
43092 | L-alanylglycine | - | oxidation | 73786 |
43092 | L-asparagine | - | oxidation | 17196 |
43092 | L-aspartate | - | oxidation | 29991 |
43092 | L-histidine | - | oxidation | 15971 |
43092 | 4-hydroxy-L-proline | - | oxidation | 18240 |
43092 | L-leucine | - | oxidation | 15603 |
43092 | L-ornithine | - | oxidation | 15729 |
43092 | L-phenylalanine | - | oxidation | 17295 |
43092 | L-proline | - | oxidation | 17203 |
43092 | L-pyroglutamic acid | - | oxidation | 18183 |
43092 | D-serine | - | oxidation | 16523 |
43092 | L-serine | - | oxidation | 17115 |
43092 | L-threonine | - | oxidation | 16857 |
43092 | DL-carnitine | - | oxidation | 17126 |
43092 | gamma-aminobutyric acid | - | oxidation | 16865 |
43092 | urocanic acid | - | oxidation | 27248 |
43092 | inosine | - | oxidation | 17596 |
43092 | uridine | - | oxidation | 16704 |
43092 | thymidine | - | oxidation | 17748 |
43092 | phenylethylamine | - | oxidation | 50048 |
43092 | putrescine | - | oxidation | 17148 |
43092 | ethanolamine | - | oxidation | 16000 |
43092 | 2,3-butanediol | - | oxidation | 62064 |
43092 | glycerol | - | oxidation | 17754 |
43092 | glucose 1-phosphate | - | oxidation | 29042 |
43092 | D-glucose 6-phosphate | - | oxidation | 14314 |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
43092 | 35581 | indole | no |
43092 | 16136 | hydrogen sulfide | no |
43092 | 15688 | acetoin | no |
metabolite tests
- @ref: 43092
- Chebi-ID: 15688
- metabolite: acetoin
- voges-proskauer-test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
43092 | catalase | + | 1.11.1.6 |
43092 | cytochrome oxidase | + | 1.9.3.1 |
43092 | arginine dihydrolase | - | 3.5.3.6 |
43092 | urease | - | 3.5.1.5 |
43092 | beta-glucosidase | + | 3.2.1.21 |
43092 | beta-galactosidase | + | 3.2.1.23 |
43092 | lysine decarboxylase | - | 4.1.1.18 |
43092 | ornithine decarboxylase | - | 4.1.1.17 |
43092 | tryptophan deaminase | - | 4.1.99.1 |
fatty acid profile
fatty acids
@ref fatty acid percentage 43092 C13:0 iso 2.9 43092 C14:0 iso 2.7 43092 iso C15:1 G 5.8 43092 C15:0 iso 23.3 43092 C15:0 anteiso 5.7 43092 C15:1ω6c 5 43092 C16:1 iso H 1.2 43092 C16:0 iso 2.4 43092 C16:0 1.5 43092 C15:0 iso 3OH 3.8 43092 C15:0 3OH 1.1 43092 C17:1ω6c 1.9 43092 C16:0 iso 3OH 6.8 43092 C16:0 3OH 2.2 43092 C17:0 iso 3OH 7.6 43092 C16:1ω6c / C16:1ω7c 17.7 43092 C17:1 iso ω9c / C16:0 10-methyl 2.4 - type of FA analysis: whole cell analysis
- incubation medium: R2A
- agar/liquid: liquid
- incubation temperature: 25
- incubation time: 1
- software version: Sherlock 6.0
- system: MIS MIDI
- cutoff value:
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | enrichment culture | enrichment culture duration | enrichment culture temperature |
---|---|---|---|---|---|---|---|---|
24774 | fresh water from a river | Kanagawa, Atsugi, Tamagawa River | Japan | JPN | Asia | |||
43092 | freshwater sample | Tamagawa River, Atsugi, Kanagawa | Japan | JPN | Asia | IPM plates | 2-7 days | 25 |
67770 | Freshwater sample collected from the Tamagawa River | Japan | JPN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Freshwater |
#Environmental | #Aquatic | #River (Creek) |
Safety information
risk assessment
- @ref: 24774
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
24774 | Flavobacterium aquicola gene for 16S ribosomal RNA, partial sequence | LC065662 | 1436 | ena | 1682742 |
24774 | Flavobacterium aquicola gene for 16S ribosomal RNA, partial sequence, clone: C1 | LC120818 | 1436 | ena | 1682742 |
24774 | Flavobacterium aquicola gene for 16S ribosomal RNA, partial sequence, clone: C2 | LC120819 | 1436 | ena | 1682742 |
24774 | Flavobacterium aquicola gene for 16S ribosomal RNA, partial sequence, clone: C3 | LC120820 | 1436 | ena | 1682742 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Flavobacterium aquicola DSM 100880 | GCA_003385115 | scaffold | ncbi | 1682742 |
66792 | Flavobacterium aquicola strain DSM 100880 | 1682742.3 | wgs | patric | 1682742 |
66792 | Flavobacterium aquicola DSM 100880 (v2) | 2739367662 | draft | img | 1682742 |
GC content
- @ref: 24774
- GC-content: 36.5
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 90.273 | no |
flagellated | no | 95.001 | yes |
gram-positive | no | 97.839 | yes |
anaerobic | no | 99.625 | no |
aerobic | yes | 90.336 | no |
halophile | no | 96.835 | yes |
spore-forming | no | 94.376 | yes |
glucose-util | yes | 87.658 | no |
thermophile | no | 99.659 | yes |
glucose-ferment | no | 90.195 | yes |
External links
@ref: 24774
culture collection no.: DSM 100880, JCM 30987, BCRC 81042
straininfo link
- @ref: 91262
- straininfo: 406973
literature
- topic: Phylogeny
- Pubmed-ID: 27045592
- title: Flavobacterium aquicola sp. nov., isolated from river water.
- authors: Hatayama K, Ushida A, Kuno T
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.001057
- year: 2016
- mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Japan, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
- topic2: 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 | |||
24774 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-100880 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100880) | |||
43092 | Kouta Hatayama, Ayako Ushida, Teruaki Kuno | Flavobacterium aquicola sp. nov., isolated from river water | 10.1099/ijsem.0.001057 | IJSEM 66: 2789-2796 2016 | 27045592 | |
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 | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
91262 | 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-ID406973.1 |