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Strain identifier

BacDive ID: 24024

Type strain: Yes

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)

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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

@refgram staincell lengthcell widthcell shapemotilityconfidence
30907negative2 µm0.4 µmrod-shapedno
27237negative2 µm0.4 µmrod-shapedno
69480negative99.367

colony morphology

@refcolony sizecolony colorincubation periodmedium used
272372-3 mmcream to off-white, translucent2 daysR2A agar
272372 mmpale beigeCY
272372 mmpale beigeTSA

pigmentation

  • @ref: 30907
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
32791MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
27237Reasoner's 2A agar (R2A)yes
27237CYyes
27237Trypticase Soy Agar (TSA)yes
27237Marine agar (MA)no
20571R2A MEDIUM (DSMZ Medium 830)yesName: 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 waterhttps://mediadive.dsmz.de/medium/830

culture temp

@refgrowthtypetemperaturerange
20571positivegrowth28mesophilic
32791positivegrowth25mesophilic
27237positivemaximum35mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30907aerobe
27237aerobe
27237microaerophile

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 98.28

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 99.544

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
27237167632-oxobutanoate+respiration
27237286442-oxopentanoate+/-respiration
2723730089acetate+respiration
2723740585alpha-cyclodextrin+respiration
2723717925alpha-D-glucose+respiration
2723717057cellobiose+respiration
2723762968cellulose-hydrolysis
2723715824D-fructose+respiration
2723714314D-glucose 6-phosphate-respiration
2723715748D-glucuronate+/-respiration
2723716024D-mannose+respiration
2723716991dna-hydrolysis
2723728066gentiobiose+respiration
2723729042glucose 1-phosphate-respiration
2723773804glycyl L-aspartic acid+respiration
2723724741hydroxyproline+/-respiration
2723716977L-alanine+respiration
2723773786L-alanylglycine+respiration
2723730849L-arabinose+respiration
2723717196L-asparagine+respiration
2723729991L-aspartate+respiration
2723718287L-fucose+/-respiration
2723715603L-leucine+/-respiration
2723715729L-ornithine+respiration
2723717203L-proline+/-respiration
2723717115L-serine+respiration
2723716857L-threonine+respiration
2723724996lactate+respiration
2723717716lactose+respiration
272376359lactulose+respiration
2723728053melibiose+respiration
2723737657methyl D-glucoside+respiration
2723751850methyl pyruvate+/-respiration
2723775146monomethyl succinate-respiration
27237506227N-acetylglucosamine-respiration
2723773784glycyl-l-glutamate+respiration
2723717632nitrate-reduction
2723717992sucrose+/-respiration
2723717748thymidine+/-respiration
2723727082trehalose+respiration
2723732528turanose+/-respiration
2723753423tween 40-respiration
2723716704uridine+/-respiration

enzymes

@refvalueactivityec
30907catalase+1.11.1.6
27237acid phosphatase+/-3.1.3.2
27237alkaline phosphatase+/-3.1.3.1
27237alpha-chymotrypsin-3.4.21.1
27237cystine arylamidase+/-3.4.11.3
27237esterase (C 4)+/-
27237esterase Lipase (C 8)+/-
27237alpha-galactosidase+/-3.2.1.22
27237beta-galactosidase+/-3.2.1.23
27237alpha-glucosidase+/-3.2.1.20
27237leucine arylamidase+/-3.4.11.1
27237N-acetyl-beta-glucosaminidase-3.2.1.52
27237naphthol-AS-BI-phosphohydrolase+/-
27237trypsin+/-3.4.21.4
27237valine arylamidase+/-
27237beta-glucosidase+/-3.2.1.21
27237catalase+1.11.1.6
27237cytochrome oxidase-1.9.3.1
27237amylase+
27237caseinase+3.4.21.50

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentlatitudelongitude
20571decaying wood of Wikstroemia oahuensisWikstroemia oahuensisHawai'i, O'ahu, Lulumahu trail (21° 20' 52.67'' N 157° 47' 54.36'' W, at a height of ~615–620 m)USAUSAAustralia and Oceania21.348-157.798
27237decaying wood of Wikstroemia oahuensisIsland of Oahu, HawaiiUSAUSAAustralia and Oceania21-157

isolation source categories

Cat1Cat2Cat3
#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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium akiainvivens IK-1GCA_001278115scaffoldncbi1202724
66792Flavobacterium akiainvivens DSM 25510GCA_900115875contigncbi1202724
66792Flavobacterium akiainvivens strain DSM 255101202724.5wgspatric1202724
66792Flavobacterium akiainvivens DSM 255102693429907draftimg1202724
66792Flavobacterium akiainvivens IK-12648501255draftimg1202724
66792uncultured Firmicutes bacterium SRR12081298_bin.5_metaWRAP_v1.3_MAGGCA_946412265contigpatric344338

GC content

@refGC-contentmethod
2057144.2high performance liquid chromatography (HPLC)
3090744.2

External links

@ref: 20571

culture collection no.: DSM 25510, ATCC BAA 2412, CIP 110358

straininfo link

@refpassport
20218http://www.straininfo.net/strains/890977
20218http://www.straininfo.net/strains/890978

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23475344Flavobacterium 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 SPInt J Syst Evol Microbiol10.1099/ijs.0.047217-02013Base 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, ZeaxanthinsGenetics
Phylogeny25726422Flavobacterium shanxiense sp. nov., isolated from soil.Yang F, Liu HM, Zhang R, Chen DB, Wang X, Yan X, Hong Q, Li SPCurr Microbiol10.1007/s00284-015-0792-z2015Bacterial 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, TemperatureGenetics
Genetics26494668Genome Sequence of Flavobacterium akiainvivens IK-1T, Isolated from Decaying Wikstroemia oahuensis, an Endemic Hawaiian Shrub.Wan X, Hou S, Saito JA, Kaneshiro KY, Donachie SPGenome Announc10.1128/genomeA.01222-152015Phylogeny
Phylogeny30499767Flavobacterium niveum sp. nov., isolated from a freshwater creek.Chen WM, Chen WT, Young CC, Sheu SYInt J Syst Evol Microbiol10.1099/ijsem.0.0031502018Bacterial 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/chemistryTranscriptome
Genetics31623351Comparative Genome Analyses Reveal the Genomic Traits and Host Plant Adaptations of Flavobacterium akiainvivens IK-1(T).Wan XInt J Mol Sci10.3390/ijms201949102019*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, SyntenyPathogenicity

Reference

@idauthorstitledoi/urljournalpubmedcatalogueID_cross_reference
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.StrainInfo introduces electronic passports for microorganisms.10.1016/j.syapm.2013.11.002Syst Appl Microbiol. 37: 42-50 201424321274
20571Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-25510Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25510)
2723710.1099/ijs.0.047217-023475344
30907Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172877604127237
32791Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8208
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
69479João 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 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions 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