Strain identifier
BacDive ID: 24024
Type strain:
Species: Flavobacterium akiainvivens
Strain Designation: IK-1
Strain history: <- S. P. Donachie, Dept. Microbiology, Univ. Hawaii; IK-1 <- I. Kuo
NCBI tax ID(s): 1202724 (species)
General
@ref: 20571
BacDive-ID: 24024
DSM-Number: 25510
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Flavobacterium akiainvivens IK-1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from decaying wood of Wikstroemia oahuensis.
NCBI tax id
- NCBI tax id: 1202724
- Matching level: species
strain history: <- S. P. Donachie, Dept. Microbiology, Univ. Hawaii; IK-1 <- I. Kuo
doi: 10.13145/bacdive24024.20221219.7.1
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 akiainvivens
- full scientific name: Flavobacterium akiainvivens Kuo et al. 2013
@ref: 20571
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Flavobacterium
species: Flavobacterium akiainvivens
full scientific name: Flavobacterium akiainvivens Kuo et al. 2013
strain designation: IK-1
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
30907 | negative | 2 µm | 0.4 µm | rod-shaped | no | |
27237 | negative | 2 µm | 0.4 µm | rod-shaped | no | |
69480 | negative | 99.367 |
colony morphology
@ref | colony size | colony color | incubation period | medium used |
---|---|---|---|---|
27237 | 2-3 mm | cream to off-white, translucent | 2 days | R2A agar |
27237 | 2 mm | pale beige | CY | |
27237 | 2 mm | pale beige | TSA |
pigmentation
- @ref: 30907
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | composition | link |
---|---|---|---|---|
32791 | MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati | yes | Distilled water make up to (1000.000 ml);R2A agar (18.200 g) | |
27237 | Reasoner's 2A agar (R2A) | yes | ||
27237 | CY | yes | ||
27237 | Trypticase Soy Agar (TSA) | yes | ||
27237 | Marine agar (MA) | no | ||
20571 | 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 |
---|---|---|---|---|
20571 | positive | growth | 28 | mesophilic |
32791 | positive | growth | 25 | mesophilic |
27237 | positive | maximum | 35 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
30907 | aerobe |
27237 | aerobe |
27237 | microaerophile |
spore formation
- @ref: 69480
- spore formation: no
- confidence: 98.28
halophily
- @ref: 69480
- halophily level: non-halophilic
- confidence: 99.544
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
27237 | 16763 | 2-oxobutanoate | + | respiration |
27237 | 28644 | 2-oxopentanoate | +/- | respiration |
27237 | 30089 | acetate | + | respiration |
27237 | 40585 | alpha-cyclodextrin | + | respiration |
27237 | 17925 | alpha-D-glucose | + | respiration |
27237 | 17057 | cellobiose | + | respiration |
27237 | 62968 | cellulose | - | hydrolysis |
27237 | 15824 | D-fructose | + | respiration |
27237 | 14314 | D-glucose 6-phosphate | - | respiration |
27237 | 15748 | D-glucuronate | +/- | respiration |
27237 | 16024 | D-mannose | + | respiration |
27237 | 16991 | dna | - | hydrolysis |
27237 | 28066 | gentiobiose | + | respiration |
27237 | 29042 | glucose 1-phosphate | - | respiration |
27237 | 73804 | glycyl L-aspartic acid | + | respiration |
27237 | 24741 | hydroxyproline | +/- | respiration |
27237 | 16977 | L-alanine | + | respiration |
27237 | 73786 | L-alanylglycine | + | respiration |
27237 | 30849 | L-arabinose | + | respiration |
27237 | 17196 | L-asparagine | + | respiration |
27237 | 29991 | L-aspartate | + | respiration |
27237 | 18287 | L-fucose | +/- | respiration |
27237 | 15603 | L-leucine | +/- | respiration |
27237 | 15729 | L-ornithine | + | respiration |
27237 | 17203 | L-proline | +/- | respiration |
27237 | 17115 | L-serine | + | respiration |
27237 | 16857 | L-threonine | + | respiration |
27237 | 24996 | lactate | + | respiration |
27237 | 17716 | lactose | + | respiration |
27237 | 6359 | lactulose | + | respiration |
27237 | 28053 | melibiose | + | respiration |
27237 | 37657 | methyl D-glucoside | + | respiration |
27237 | 51850 | methyl pyruvate | +/- | respiration |
27237 | 75146 | monomethyl succinate | - | respiration |
27237 | 506227 | N-acetylglucosamine | - | respiration |
27237 | 73784 | glycyl-l-glutamate | + | respiration |
27237 | 17632 | nitrate | - | reduction |
27237 | 17992 | sucrose | +/- | respiration |
27237 | 17748 | thymidine | +/- | respiration |
27237 | 27082 | trehalose | + | respiration |
27237 | 32528 | turanose | +/- | respiration |
27237 | 53423 | tween 40 | - | respiration |
27237 | 16704 | uridine | +/- | respiration |
enzymes
@ref | value | activity | ec |
---|---|---|---|
30907 | catalase | + | 1.11.1.6 |
27237 | acid phosphatase | +/- | 3.1.3.2 |
27237 | alkaline phosphatase | +/- | 3.1.3.1 |
27237 | alpha-chymotrypsin | - | 3.4.21.1 |
27237 | cystine arylamidase | +/- | 3.4.11.3 |
27237 | esterase (C 4) | +/- | |
27237 | esterase Lipase (C 8) | +/- | |
27237 | alpha-galactosidase | +/- | 3.2.1.22 |
27237 | beta-galactosidase | +/- | 3.2.1.23 |
27237 | alpha-glucosidase | +/- | 3.2.1.20 |
27237 | leucine arylamidase | +/- | 3.4.11.1 |
27237 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
27237 | naphthol-AS-BI-phosphohydrolase | +/- | |
27237 | trypsin | +/- | 3.4.21.4 |
27237 | valine arylamidase | +/- | |
27237 | beta-glucosidase | +/- | 3.2.1.21 |
27237 | catalase | + | 1.11.1.6 |
27237 | cytochrome oxidase | - | 1.9.3.1 |
27237 | amylase | + | |
27237 | caseinase | + | 3.4.21.50 |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | geographic location | country | origin.country | continent | latitude | longitude |
---|---|---|---|---|---|---|---|---|
20571 | decaying wood of Wikstroemia oahuensis | Wikstroemia oahuensis | Hawai'i, O'ahu, Lulumahu trail (21° 20' 52.67'' N 157° 47' 54.36'' W, at a height of ~615–620 m) | USA | USA | Australia and Oceania | 21.348 | -157.798 |
27237 | decaying wood of Wikstroemia oahuensis | Island of Oahu, Hawaii | USA | USA | Australia and Oceania | 21 | -157 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Plants | #Decomposing plant |
#Host | #Plants | #Shrub (Scrub) |
#Host Body Product | #Plant | #Timber |
taxonmaps
- @ref: 69479
- File name: preview.99_413.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_280;97_309;98_343;99_413&stattab=map
- Last taxonomy: Flavobacterium akiainvivens subclade
- 16S sequence: JQ228532
- Sequence Identity:
- Total samples: 4825
- soil counts: 1185
- aquatic counts: 1666
- animal counts: 1442
- plant counts: 532
Safety information
risk assessment
- @ref: 20571
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20571
- description: Flavobacterium akiainvivens strain IK-1 16S ribosomal RNA gene, partial sequence
- accession: JQ228532
- length: 1346
- database: ena
- NCBI tax ID: 1202724
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Flavobacterium akiainvivens IK-1 | GCA_001278115 | scaffold | ncbi | 1202724 |
66792 | Flavobacterium akiainvivens DSM 25510 | GCA_900115875 | contig | ncbi | 1202724 |
66792 | Flavobacterium akiainvivens strain DSM 25510 | 1202724.5 | wgs | patric | 1202724 |
66792 | Flavobacterium akiainvivens DSM 25510 | 2693429907 | draft | img | 1202724 |
66792 | Flavobacterium akiainvivens IK-1 | 2648501255 | draft | img | 1202724 |
66792 | uncultured Firmicutes bacterium SRR12081298_bin.5_metaWRAP_v1.3_MAG | GCA_946412265 | contig | patric | 344338 |
GC content
@ref | GC-content | method |
---|---|---|
20571 | 44.2 | high performance liquid chromatography (HPLC) |
30907 | 44.2 |
External links
@ref: 20571
culture collection no.: DSM 25510, ATCC BAA 2412, CIP 110358
straininfo link
@ref | passport |
---|---|
20218 | http://www.straininfo.net/strains/890977 |
20218 | http://www.straininfo.net/strains/890978 |
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 23475344 | Flavobacterium akiainvivens sp. nov., from decaying wood of Wikstroemia oahuensis, Hawai'i, and emended description of the genus Flavobacterium. | Kuo I, Saw J, Kapan DD, Christensen S, Kaneshiro KY, Donachie SP | Int J Syst Evol Microbiol | 10.1099/ijs.0.047217-0 | 2013 | Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacterium/*classification/genetics/isolation & purification, Hawaii, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Wikstroemia/*microbiology, Wood/*microbiology, Xanthophylls/analysis, Zeaxanthins | Genetics |
Phylogeny | 25726422 | Flavobacterium shanxiense sp. nov., isolated from soil. | Yang F, Liu HM, Zhang R, Chen DB, Wang X, Yan X, Hong Q, Li SP | Curr Microbiol | 10.1007/s00284-015-0792-z | 2015 | Bacterial Typing Techniques, China, Cities, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flavobacterium/*classification/genetics/*isolation & purification/physiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Pigments, Biological/analysis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, *Soil Microbiology, Temperature | Genetics |
Genetics | 26494668 | Genome Sequence of Flavobacterium akiainvivens IK-1T, Isolated from Decaying Wikstroemia oahuensis, an Endemic Hawaiian Shrub. | Wan X, Hou S, Saito JA, Kaneshiro KY, Donachie SP | Genome Announc | 10.1128/genomeA.01222-15 | 2015 | Phylogeny | |
Phylogeny | 30499767 | Flavobacterium niveum sp. nov., isolated from a freshwater creek. | Chen WM, Chen WT, Young CC, Sheu SY | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003150 | 2018 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/isolation & purification, Fresh Water/*microbiology, Phospholipids/chemistry, *Phylogeny, Polyamines/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Taiwan, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Genetics | 31623351 | Comparative Genome Analyses Reveal the Genomic Traits and Host Plant Adaptations of Flavobacterium akiainvivens IK-1(T). | Wan X | Int J Mol Sci | 10.3390/ijms20194910 | 2019 | *Adaptation, Physiological, Bacterial Physiological Phenomena, Biological Evolution, Computational Biology/methods, Flavobacterium/classification/*physiology, *Genome, Bacterial, *Genomics/methods, *Host-Pathogen Interactions, Plant Diseases/microbiology, Plants/*microbiology, Quorum Sensing, Synteny | Pathogenicity |
Reference
@id | authors | title | doi/url | journal | pubmed | catalogue | ID_cross_reference |
---|---|---|---|---|---|---|---|
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 | ||||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | StrainInfo introduces electronic passports for microorganisms. | 10.1016/j.syapm.2013.11.002 | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | ||
20571 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25510 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25510) | ||||
27237 | 10.1099/ijs.0.047217-0 | 23475344 | |||||
30907 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 28776041 | 27237 | ||
32791 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/8208 | |||||
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 | ||
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/ | ||||
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 |