Strain identifier

BacDive ID: 140607

Type strain: Yes

Species: Pseudothioclava arenosa

Strain history: <- Wonyong Kim, Chung-Ang Univ..

NCBI tax ID(s): 1795308 (species)

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General

@ref: 64856

BacDive-ID: 140607

DSM-Number: 108277

keywords: 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, rod-shaped, colony-forming

description: Pseudothioclava arenosa KCTC 52190 is a facultative anaerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from sea sand sample.

NCBI tax id

  • NCBI tax id: 1795308
  • Matching level: species

strain history

@refhistory
64856<- Y. Muramatsu, NBRC; NBRC 111989 <- W. Kim, Chung-Ang Univ., Seoul, Republic of Korea; CAU 1312
67771<- Wonyong Kim, Chung-Ang Univ..

doi: 10.13145/bacdive140607.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Paracoccaceae
  • genus: Pseudothioclava
  • species: Pseudothioclava arenosa
  • full scientific name: Pseudothioclava arenosa (Thongphrom et al. 2017) Kim and Lee 2020

  • synonyms

    • @ref: 20215
    • synonym: Thioclava arenosa

@ref: 64856

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Pseudothioclava

species: Pseudothioclava arenosa

full scientific name: Pseudothioclava arenosa (Thongphrom et al. 2017) Kim and Lee 2020

type strain: yes

Morphology

cell morphology

  • @ref: 43257
  • gram stain: negative
  • cell length: 1.5-3.1 µm
  • cell width: 0.1-0.4 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 43257
  • colony color: pale pinkish
  • colony shape: circular
  • incubation period: 5 days
  • medium used: MA

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43257Marine agar (MA)yes
64856BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
43257positiveoptimum30mesophilic
43257positivegrowth20-40
64856positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
43257positivegrowth6.0-9.0alkaliphile
43257positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43257facultative anaerobe
67771aerobe

spore formation

  • @ref: 43257
  • type of spore: spore
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
43257NaClpositivegrowth1-4 %(w/v)
43257NaClpositiveoptimum2 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
43257casein-hydrolysis
43257gelatin-hydrolysis5291
43257citrate-hydrolysis16947
43257nitrate-reduction17632
43257D-glucose+fermentation17634
43257D-glucose+assimilation17634
43257D-mannitol-assimilation16899
43257L-arabinose-assimilation30849
43257D-mannose-assimilation16024
43257N-acetylglucosamine-assimilation506227
43257maltose-assimilation17306
43257potassium gluconate-assimilation32032
43257L-arabinose+builds acid from30849
43257potassium 5-dehydro-D-gluconate+builds acid from
43257glycerol-builds acid from17754
43257erythritol-builds acid from17113
43257D-arabinose-builds acid from17108
43257ribose-builds acid from33942
43257xylose-builds acid from18222
43257ribitol-builds acid from15963
43257methyl beta-D-xylopyranoside-builds acid from74863
43257D-galactose-builds acid from12936
43257D-glucose-builds acid from17634
43257D-fructose-builds acid from15824
43257D-mannose-builds acid from16024
43257L-sorbose-builds acid from17266
43257L-rhamnose-builds acid from62345
43257galactitol-builds acid from16813
43257myo-inositol-builds acid from17268
43257D-mannitol-builds acid from16899
43257D-sorbitol-builds acid from17924
43257N-acetylglucosamine-builds acid from506227
43257esculin ferric citrate-builds acid from
43257salicin-builds acid from17814
43257cellobiose-builds acid from17057
43257maltose-builds acid from17306
43257lactose-builds acid from17716
43257melibiose-builds acid from28053
43257sucrose-builds acid from17992
43257trehalose-builds acid from27082
43257inulin-builds acid from15443
43257starch-builds acid from28017
43257potassium 2-dehydro-D-gluconate-builds acid from
43257esculin-hydrolysis4853
43257decanoate-assimilation27689
43257adipate-assimilation17128
43257malate-assimilation25115
43257turanose-builds acid from32528
43257D-fucose-builds acid from28847
43257L-fucose-builds acid from18287
43257D-arabitol-builds acid from18333
68369malate+assimilation25115
68369adipate-assimilation17128
68369decanoate-assimilation27689
68369maltose-assimilation17306
68369N-acetylglucosamine-assimilation59640
68369D-mannitol-assimilation16899
68369D-mannose-assimilation16024
68369L-arabinose-assimilation30849
68369D-glucose-assimilation17634
68369gelatin+hydrolysis5291
68369esculin-hydrolysis4853
68369urea-hydrolysis16199
68369arginine-hydrolysis29016
68369D-glucose-fermentation17634
68369tryptophan-energy source27897
68369nitrate-reduction17632

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.group ID
432572676amoxicillinyesyes20 µg (disc)
4325728971ampicillinyesyes10 µg (disc)
432573393carbenicillinyesyes100 µg (disc)
43257209807cefoxitinyesyes30 µg (disc)
432573542cephalothinyesyes30 µg (disc)
4325717698chloramphenicolyesyes30 µg (disc)
4325748923erythromycinyesyes15 µg (disc)
4325717833gentamicinyesyes10 µg (disc)
432576104kanamycinyesyes30 µg (disc)
43257100147nalidixic acidyesyes30 µg (disc)
4325717334penicillinyesyes10 Unit
432578309polymyxin byesyes300 Unit
4325728077rifampicinyesyes5 µg (disc)
4325717076streptomycinyesyes10 µg (disc)
432579332sulfamethoxazoleyesyes23.75 µg (disc)26
4325727902tetracyclineyesyes30 µg (disc)
4325728864tobramycinyesyes10 µg (disc)
4325745924trimethoprimyesyes1.25 µg (disc)26

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
43257cytochrome oxidase+1.9.3.1
43257catalase+1.11.1.6
43257arginine dihydrolase-3.5.3.6
43257beta-galactosidase-3.2.1.23
43257esterase (C 4)+
43257esterase Lipase (C 8)+
43257leucine arylamidase+3.4.11.1
43257valine arylamidase+
43257cystine arylamidase+3.4.11.3
43257acid phosphatase+3.1.3.2
43257naphthol-AS-BI-phosphohydrolase+/-
43257trypsin+/-3.4.21.4
43257urease-3.5.1.5
43257alkaline phosphatase-3.1.3.1
43257alpha-galactosidase-3.2.1.22
43257alpha-glucosidase-3.2.1.20
43257beta-glucosidase-3.2.1.21
68369gelatinase+
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43257C16:06.4
    43257C17:04.6
    43257C18:05.9
    43257C10:0 3OH2.9
    43257C16:1ω6c / C16:1ω7c14
    43257C18:1ω6c / C18:1ω7c65.1
  • type of FA analysis: whole cell analysis
  • incubation medium: MA
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 3
  • incubation pH: 6.00
  • software version: Sherlock 6.1
  • system: MIS MIDI
  • cutoff value:

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
64856-----+/---------------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
64856------+-------+/---++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
43257sea sand sampleEurwangri beach in Incheon, Republic of KoreaRepublic of KoreaKORAsia37126
64856Sea sandEurwangri beach, Incheon (37° 26' 55.8'' N, 126° 22' 15.7'' E)Republic of KoreaKORAsia37.4488126.371
67771From sea soil of Eurwangri beachIncheonRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Terrestrial#Sandy

taxonmaps

  • @ref: 69479
  • File name: preview.99_27236.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_849;97_16445;98_20401;99_27236&stattab=map
  • Last taxonomy: Thioclava arenosa subclade
  • 16S sequence: KU671051
  • Sequence Identity:
  • Total samples: 121
  • soil counts: 12
  • aquatic counts: 85
  • animal counts: 17
  • plant counts: 7

Safety information

risk assessment

  • @ref: 64856
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 64856
  • description: Thioclava arenosa strain CAU 1312 16S ribosomal RNA gene, partial sequence
  • accession: KU671051
  • length: 1442
  • database: ena
  • NCBI tax ID: 1795308

GC content

  • @ref: 43257
  • GC-content: 64.7
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 64856

culture collection no.: KCTC 52190, NBRC 111989, DSM 108277, CAU 1312

straininfo link

  • @ref: 96754
  • straininfo: 405933

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28598314Thioclava arenosa sp. nov., isolated from sea sand.Thongphrom C, Kim JH, Bora N, Kim WInt J Syst Evol Microbiol10.1099/ijsem.0.0018532017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/isolation & purification, Salinity, Seawater/*microbiology, Sequence Analysis, DNA, *Silicon Dioxide, Ubiquinone/analogs & derivatives/chemistryTranscriptome
Phylogeny32239456Erratum to: Hahyoungchilella caricis gen. nov., sp. nov., isolated from a rhizosphere mudflat of a halophyte (Carex scabrifolia), transfer of Thioclava arenosa Thongphrom et al. 2017 to Pseudothioclava as Pseudothioclava arenosa gen. nov., comb. nov. and proposal of Thioclava electrotropha Chang et al. 2018 as a later heterosynonym of Thioclava sediminum.Kim YJ, Lee SDJ Microbiol10.1007/s12275-020-9725-z2020

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
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
43257Chutimon Thongphrom, Jong-Hwa Kim, Nagamani Bora and Wonyong KimThioclava arenosa sp. nov., isolated from sea sand10.1099/ijsem.0.001853IJSEM 67: 1735-1739 201728598314
64856Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-108277Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 108277)
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
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/
96754Reimer, 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 identifiers10.60712/SI-ID405933.1