Strain identifier

BacDive ID: 140815

Type strain: Yes

Species: Tsuneonella rigui

Strain Designation: WW3

Strain history: <- C.N. Seong, Sunchon National Univ..

NCBI tax ID(s): 1708790 (species)

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General

@ref: 43603

BacDive-ID: 140815

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

description: Tsuneonella rigui WW3 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from freshwater of Woopo wetland.

NCBI tax id

  • NCBI tax id: 1708790
  • Matching level: species

strain history

@refhistory
67770C. N. Seong; Sunchon Natl. Univ., South Korea; WW3.
67771<- C.N. Seong, Sunchon National Univ..

doi: 10.13145/bacdive140815.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Erythrobacteraceae
  • genus: Tsuneonella
  • species: Tsuneonella rigui
  • full scientific name: Tsuneonella rigui (Kang et al. 2016) Xu et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Altererythrobacter rigui

@ref: 43603

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Erythrobacteraceae

genus: Altererythrobacter

species: Altererythrobacter rigui

strain designation: WW3

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43603negative0.58-0.63 µm0.42-0.58 µmrod-shapedno
125439negative97.9
125438negative96.81

colony morphology

  • @ref: 43603
  • colony size: 1-2 mm
  • colony color: Yellow
  • colony shape: circular
  • incubation period: 3 days
  • medium used: R2A agar

Culture and growth conditions

culture medium

@refnamegrowth
43603Marine agar (MA)no
43603Nutrient agar (NA)yes
43603PCAyes
43603Reasoner's 2A agar (R2A)yes
43603Trypticase Soy Agar (TSA)yes

culture temp

@refgrowthtypetemperature
43603positivegrowth4-37
43603positiveoptimum25
67770positivegrowth25
67771positivegrowth25

culture pH

@refabilitytypepHPH range
43603positivegrowth6-9alkaliphile
43603positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
43603aerobe
67771aerobe
125439obligate aerobe99.7

spore formation

@refspore formationconfidence
125439no93.8
125438no94.68

halophily

@refsaltgrowthtested relationconcentrationhalophily level
43603NaClpositivegrowth0-3 %(w/v)
43603NaClpositiveoptimum0 %(w/v)non-halophilic

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4360327689decanoate-assimilation
4360316947citrate-assimilation
4360324265gluconate-assimilation
4360317234glucose-assimilation
4360329864mannitol-assimilation
4360337684mannose-assimilation
43603506227N-acetylglucosamine-assimilation
4360318401phenylacetate-assimilation
4360328757fructose-builds acid from
4360328260galactose-builds acid from
4360317234glucose-builds acid from
4360317306maltose-builds acid from
4360329864mannitol-builds acid from
4360337684mannose-builds acid from
4360326546rhamnose-builds acid from
4360317992sucrose-builds acid from
4360327082trehalose-builds acid from
4360318222xylose-builds acid from
4360358187alginate-hydrolysis
4360385146carboxymethylcellulose-hydrolysis
43603casein-hydrolysis
4360317029chitin-hydrolysis
436035291gelatin-hydrolysis
4360317368hypoxanthine-hydrolysis
4360353311sodium alginate-hydrolysis
4360328017starch-hydrolysis
4360353424tween 20-hydrolysis
4360318186tyrosine-hydrolysis
4360316199urea-hydrolysis
4360315318xanthine-hydrolysis
4360337166xylan-hydrolysis
4360317128adipate+assimilation
4360322599arabinose+assimilation
4360325115malate+assimilation
4360332032potassium gluconate+assimilation
4360317716lactose+builds acid from
4360353426tween 80+hydrolysis

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
4360328971ampicillinyesyes10 µg (disc)
436032637amikacinyesyes30 µg (disc)
4360317698chloramphenicolyesyes30 µg (disc)
4360317833gentamicinyesyes10 µg (disc)
436036104kanamycinyesyes30 µg (disc)
4360327902tetracyclineyesyes30 µg (disc)
4360328001vancomycinyesyes30 µg (disc)
4360317334penicillinyesyes10 Unit (disc)
4360348923erythromycinyesyes15 µg (disc)
43603100147nalidixic acidyesyes30 µg (disc)
4360317076streptomycinyesyes10 µg (disc)
436038309polymyxin byesyes300 Unit (disc)

metabolite production

@refChebi-IDmetaboliteproduction
4360316136hydrogen sulfideno
4360335581indoleno
4360317632nitrateyes

enzymes

@refvalueactivityec
43603catalase+1.11.1.6
43603acid phosphatase+3.1.3.2
43603alkaline phosphatase+3.1.3.1
43603esterase (C 4)+
43603esterase Lipase (C 8)+
43603leucine arylamidase+3.4.11.1
43603valine arylamidase+
43603naphthol-AS-BI-phosphohydrolase+
43603alpha-chymotrypsin+3.4.21.1
43603cytochrome oxidase-1.9.3.1
43603cystine arylamidase-3.4.11.3
43603alpha-galactosidase-3.2.1.22
43603beta-galactosidase-3.2.1.23
43603alpha-glucosidase-3.2.1.20
43603beta-glucosidase-3.2.1.21
43603beta-glucuronidase-3.2.1.31
43603lipase (C 14)-
43603alpha-mannosidase-3.2.1.24
43603N-acetyl-beta-glucosaminidase-3.2.1.52
43603trypsin-3.4.21.4
43603alpha-fucosidase-3.2.1.51

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
43603freshwater of Woopo wetlandWoopo wetland, Changnyeong countyRepublic of KoreaKORAsia35.55128.416
67770Freshwater of Woopo wetlandRepublic of KoreaKORAsia
67771From freshwaterRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Freshwater
#Environmental#Terrestrial#Wetland (Swamp)

taxonmaps

  • @ref: 69479
  • File name: preview.99_21384.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_543;97_13101;98_16124;99_21384&stattab=map
  • Last taxonomy: Erythrobacteraceae
  • 16S sequence: KP997219
  • Sequence Identity:
  • Total samples: 1706
  • soil counts: 456
  • aquatic counts: 834
  • animal counts: 152
  • plant counts: 264

Sequence information

16S sequences

  • @ref: 43603
  • description: Tsuneonella rigui strain WW3 16S ribosomal RNA gene, partial sequence
  • accession: KP997219
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Altererythrobacter rigui strain KCTC 426201708790.3wgspatric1708790
66792Tsuneonella rigui KCTC 426202880984762draftimg1708790
67770Tsuneonella rigui KCTC 42620GCA_003958625contigncbi1708790

GC content

@refGC-contentmethod
6777063thermal denaturation, midpoint method (Tm)
6777066.7genome sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno96.81yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.017yes
125438spore-formingspore-formingAbility to form endo- or exosporesno94.68no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes87.174yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno91.8yes
125438motile2+flagellatedAbility to perform flagellated movementno62.021no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno93.8
125439BacteriaNetmotilityAbility to perform movementyes53.5
125439BacteriaNetgram_stainReaction to gram-stainingnegative97.9
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.7

External links

@ref: 43603

culture collection no.: KCTC 42620, JCM 30975

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
43603Joo Won Kang, Mi Sun Kim, Ji Hee Lee, Keun Sik Baik, Chi Nam SeongAltererythrobacter rigui sp. nov., isolated from wetland freshwater10.1099/ijsem.0.001078IJSEM 66: 2491-2496 201627073894
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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