Strain identifier

BacDive ID: 159829

Type strain: Yes

Species: Ottowia oryzae

Strain Designation: KADR8-3

NCBI tax ID(s): 2109914 (species)

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General

@ref: 66664

BacDive-ID: 159829

keywords: genome sequence, 16S sequence, Bacteria, Gram-negative, rod-shaped

description: Ottowia oryzae KADR8-3 is a Gram-negative, rod-shaped bacterium that was isolated from Sikhye from Andongsi.

NCBI tax id

  • NCBI tax id: 2109914
  • Matching level: species

doi: 10.13145/bacdive159829.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Ottowia
  • species: Ottowia oryzae
  • full scientific name: Ottowia oryzae Heo et al. 2018

@ref: 66664

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Ottowia

species: Ottowia oryzae

strain designation: KADR8-3

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
66664negative1.4-1.8 µm0.9 µmrod-shapedno
125439negative97.4
125438negative98

Culture and growth conditions

culture medium

@refnamegrowth
66664Reasoner's 2A agar (R2A)yes
66664R2A brothyes

culture temp

@refgrowthtypetemperature
66664positivegrowth10-37
66664positiveoptimum28-37

culture pH

@refabilitytypepHPH range
66664positivegrowth5-10alkaliphile
66664positiveoptimum7.0-8.0

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: obligate aerobe
  • confidence: 95.5

spore formation

@refspore formationconfidence
66664no
125439no96.7
125438no91.187

halophily

  • @ref: 66664
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-3 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6666415971L-histidine-assimilation
66664161933-hydroxybenzoate-assimilation
6666416899D-mannitol-assimilation
6666416988D-ribose-assimilation
6666417115L-serine-assimilation
6666417240itaconate-assimilation
6666417268myo-inositol-assimilation
6666417306maltose-assimilation
6666417634D-glucose-assimilation
6666417814salicin-assimilation
6666417924D-sorbitol-assimilation
6666417992sucrose-assimilation
6666418287L-fucose-assimilation
6666427689decanoate-assimilation
6666428053melibiose-assimilation
6666428087glycogen-assimilation
6666430849L-arabinose-assimilation
6666459640N-acetylglucosamine-assimilation
6666462345L-rhamnose-assimilation
6666462983sodium malonate-assimilation
66664potassium 2-dehydro-D-gluconate-assimilation
66664potassium 5-dehydro-D-gluconate-assimilation
666649300suberic acid+assimilation
6666416977L-alanine+assimilation
6666417203L-proline+assimilation
6666417272propionate+assimilation
66664178794-hydroxybenzoate+assimilation
6666424996lactate+assimilation
6666431011valerate+assimilation
6666432954sodium acetate+assimilation
66664370543-hydroxybutyrate+assimilation
6666453258sodium citrate+assimilation
6666415318xanthine-hydrolysis
6666416991dna-hydrolysis
6666417368hypoxanthine-hydrolysis
6666428017starch-hydrolysis
6666485146carboxymethylcellulose-hydrolysis
666644853esculin+hydrolysis
666645291gelatin+hydrolysis
6666418186tyrosine+hydrolysis
6666453426tween 80+hydrolysis
66664casein+hydrolysis
6666417632nitrate+reduction

metabolite production

  • @ref: 66664
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
66664alpha-chymotrypsin-3.4.21.1
66664alpha-fucosidase-3.2.1.51
66664alpha-galactosidase-3.2.1.22
66664alpha-glucosidase-3.2.1.20
66664alpha-mannosidase-3.2.1.24
66664arginine dihydrolase-3.5.3.6
66664beta-galactosidase-3.2.1.23
66664beta-glucosidase-3.2.1.21
66664beta-glucuronidase-3.2.1.31
66664cystine arylamidase-3.4.11.3
66664lipase-
66664N-acetyl-beta-glucosaminidase-3.2.1.52
66664trypsin-3.4.21.4
66664valine arylamidase-
66664acid phosphatase+3.1.3.2
66664alkaline phosphatase+3.1.3.1
66664catalase+1.11.1.6
66664cytochrome oxidase+1.9.3.1
66664esterase (C 4)+
66664esterase Lipase (C 8)+
66664leucine arylamidase+3.4.11.1
66664naphthol-AS-BI-phosphohydrolase+
66664urease+3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    66664C12:03
    66664C14:0 2OH0.9
    66664C12:0 3OH1.6
    66664C18:1 w6c / C18:1 w7c19.2
    66664C10:0 3OH2.3
    66664C16:029.7
    66664C14:03.5
    66664C16:1 w6c / C16:1 w7c30.6
    66664C17:0 cyclo7.8
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A agar
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 2
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA6.1
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

  • @ref: 66664
  • sample type: Sikhye from Andongsi
  • geographic location: Andongsi, Gyeongsangbuk-do
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia
  • enrichment culture: Reasoner's 2A agar
  • enrichment culture composition: supplemented with cycloheximide (200 µg ml-1)
  • enrichment culture duration: 3 days
  • enrichment culture temperature: 28
  • isolation procedure: The sikhye sample was transferred into sterile homogenization bag, and the homogenate was serial diluted, and spread on Reasoner's 2A agar and incubated for 3days at 28°C.

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Food production
  • Cat3: #Beverage

taxonmaps

  • @ref: 69479
  • File name: preview.99_174167.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_44601;97_84106;98_114027;99_174167&stattab=map
  • Last taxonomy: Ottowia oryzae subclade
  • 16S sequence: MH031704
  • Sequence Identity:
  • Total samples: 3960
  • soil counts: 2514
  • aquatic counts: 691
  • animal counts: 260
  • plant counts: 495

Sequence information

16S sequences

  • @ref: 66664
  • description: Ottowia oryzae strain KADR8-3 16S ribosomal RNA gene, partial sequence
  • accession: MH031704
  • length: 1525
  • database: nuccore
  • NCBI tax ID: 2109914

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ottowia oryzae KADR8-3GCA_003008535completencbi2109914
66792Ottowia sp. KADR8-32109914.3completepatric2109914

GC content

  • @ref: 66664
  • GC-content: 66.8
  • method: genome sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno98yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.753no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes84.839no
125438spore-formingspore-formingAbility to form endo- or exosporesno91.187yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95.219no
125438motile2+flagellatedAbility to perform flagellated movementyes58.852no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno96.7
125439BacteriaNetmotilityAbility to perform movementyes79.7
125439BacteriaNetgram_stainReaction to gram-stainingnegative97.4
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe95.5

External links

@ref: 66664

culture collection no.: KACC 19325, NBRC 113109

literature

  • topic: Phylogeny
  • Pubmed-ID: 30102146
  • title: Ottowia oryzae sp. nov., isolated from Andong sikhye, a Korean traditional rice beverage.
  • authors: Heo J, Cho H, Hong SB, Kim JS, Kwon SW, Kim SJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002935
  • year: 2018
  • mesh: Bacterial Typing Techniques, Base Composition, Beverages/*microbiology, Comamonadaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Food Microbiology, Oryza, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/chemistry
  • topic2: Biotechnology

Reference

@idauthorstitledoi/urljournalpubmed
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
66664Jun Heo, Hayoung Cho, Seung-Beom Hong, Jeong-Seon Kim, Soon-Wo Kwon, Soo-Jin KimOttowia oryzae sp. nov., isolated from Andong sikhye, a Korean traditional rice beverage10.1099/ijsem.0.002935IJSEM 68: 3096-3100 201830102146
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
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/
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG