Strain identifier

BacDive ID: 133320

Type strain: Yes

Species: Formosimonas limnophila

Strain Designation: AHQ-12

Strain history: <- Wen-Ming Chen (Nat. Kaohsiung Univ., Taiwan)

NCBI tax ID(s): 1384487 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 8.1 (current version)

General

@ref: 64838

BacDive-ID: 133320

DSM-Number: 109231

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

description: Formosimonas limnophila AHQ-12 is an aerobe, chemolithotroph, Gram-negative bacterium that forms circular colonies and was isolated from freshwater sample.

NCBI tax id

  • NCBI tax id: 1384487
  • Matching level: species

strain history

@refhistory
64838<- KCTC; KCTC 32501 <- W.-M. Chen, Nat. Kaohsiung Univ., Taiwan; AHQ-12
67771<- Wen-Ming Chen (Nat. Kaohsiung Univ., Taiwan)

doi: 10.13145/bacdive133320.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Burkholderiaceae
  • genus: Formosimonas
  • species: Formosimonas limnophila
  • full scientific name: Formosimonas limnophila Chen et al. 2017

@ref: 64838

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Formosimonas

species: Formosimonas limnophila

full scientific name: Formosimonas limnophila Chen et al. 2017

strain designation: AHQ-12

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
25149negative0.6-1.2 µm0.3-0.4 µmrod-shapedno
69480negative99.966

colony morphology

  • @ref: 25149
  • colony size: 0.5-0.9 mm
  • colony color: translucent white
  • colony shape: circular
  • incubation period: 2 days
  • medium used: R2A agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
25149tryptic soy agar (TSA)no
25149LB (Luria-Bertani) MEDIUMno
25149Reasoner's 2A agar (R2A)yes
64838R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: 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

culture temp

@refgrowthtypetemperaturerange
25149positivegrowth10.0-37.0
25149positiveoptimum20psychrophilic
64838positivegrowth28mesophilic
67771positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
25149positivegrowth5.0-9.0alkaliphile
25149positiveoptimum6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
25149aerobe
67771aerobe

nutrition type

  • @ref: 25149
  • type: chemolithotroph

spore formation

@refspore formationconfidence
25149no
69481no100
69480no99.999

halophily

@refsalttested relationconcentration
25149NaCloptimum0 %
25149NaClmaximum1 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2514917521(-)-quinic acid-carbon source
25149167632-oxobutanoate-carbon source
25149286442-oxopentanoate-carbon source
25149620642,3-butanediol-carbon source
25149182404-hydroxy-L-proline-carbon source
25149167244-hydroxybutyrate-carbon source
25149181014-hydroxyphenylacetic acid-carbon source
2514930089acetate-carbon source
2514915963ribitol-carbon source
2514940585alpha-cyclodextrin-carbon source
2514936219alpha-lactose-carbon source
2514922599arabinose-assimilation
2514973706bromosuccinate-carbon source
2514917968butyrate-assimilation
2514985146carboxymethylcellulose-hydrolysis
2514917126carnitine-carbon source
25149casein-hydrolysis
2514917029chitin-hydrolysis
2514916383cis-aconitate-carbon source
2514916947citrate-assimilation
2514916947citrate-carbon source
25149corn oil-hydrolysis
2514915570D-alanine-carbon source
2514912936D-galactose-carbon source
2514930612D-glucarate-carbon source
2514914314D-glucose 6-phosphate-carbon source
2514916523D-serine-carbon source
2514923652dextrin-carbon source
2514917113erythritol-carbon source
251494853esculin-hydrolysis
2514916000ethanolamine-carbon source
2514915740formate-carbon source
251495291gelatin-hydrolysis
2514928066gentiobiose-carbon source
2514924265gluconate-assimilation
2514917234glucose-fermentation
2514929042glucose 1-phosphate-carbon source
2514932323glucuronamide-carbon source
2514917754glycerol-carbon source
2514914336glycerol 1-phosphate-carbon source
2514928087glycogen-carbon source
2514917268myo-inositol-carbon source
2514917240itaconate-carbon source
2514921217L-alaninamide-carbon source
2514930849L-arabinose-carbon source
2514917196L-asparagine-carbon source
2514929991L-aspartate-carbon source
2514918287L-fucose-carbon source
2514915971L-histidine-carbon source
2514915603L-leucine-carbon source
2514915729L-ornithine-carbon source
2514917295L-phenylalanine-carbon source
2514918183L-pyroglutamic acid-carbon source
2514962345L-rhamnose-carbon source
2514917115L-serine-carbon source
2514916857L-threonine-carbon source
251496359lactulose-carbon source
2514925115malate-assimilation
2514915792malonate-carbon source
2514917306maltose-assimilation
2514917306maltose-carbon source
2514928053melibiose-carbon source
25149320055methyl beta-D-glucopyranoside-carbon source
2514928037N-acetylgalactosamine-carbon source
25149506227N-acetylglucosamine-assimilation
25149506227N-acetylglucosamine-carbon source
2514917632nitrate-reduction
2514918401phenylacetate-assimilation
2514950048phenylethylamine-carbon source
2514917272propionate-carbon source
2514917148putrescine-carbon source
2514916634raffinose-carbon source
25149143136succinamate-carbon source
2514917992sucrose-carbon source
2514917748thymidine-carbon source
2514927897tryptophan-energy source
2514932528turanose-carbon source
2514953424tween 20-hydrolysis
2514953423tween 40-hydrolysis
2514953423tween 40-carbon source
2514953425tween 60-hydrolysis
2514953426tween 80-hydrolysis
2514927248urocanic acid-carbon source
2514917151xylitol-carbon source
25149645522-hydroxybutyrate+carbon source
25149309162-oxoglutarate+carbon source
25149370543-hydroxybutyrate+carbon source
2514917128adipate+assimilation
2514917925alpha-D-glucose+carbon source
2514917057cellobiose+carbon source
2514918333D-arabitol+carbon source
2514915824D-fructose+carbon source
2514915895D-galactonic acid lactone+carbon source
2514918024D-galacturonic acid+carbon source
251498391D-gluconate+carbon source
2514917784D-glucosaminic acid+carbon source
2514915748D-glucuronate+carbon source
2514916899D-mannitol+carbon source
2514916024D-mannose+carbon source
2514927605D-psicose+carbon source
2514917924D-sorbitol+carbon source
2514916991dna+hydrolysis
2514916865gamma-aminobutyric acid+carbon source
2514917234glucose+assimilation
2514928087glycogen+carbon source
2514973804glycyl L-aspartic acid+carbon source
2514917596inosine+carbon source
2514916977L-alanine+carbon source
2514973786L-alanylglycine+carbon source
2514929985L-glutamate+carbon source
2514917203L-proline+carbon source
2514924996lactate+carbon source
2514929864mannitol+assimilation
2514937684mannose+assimilation
2514951850methyl pyruvate+carbon source
2514975146monomethyl succinate+carbon source
2514973784glycyl-l-glutamate+carbon source
2514941865sebacic acid+carbon source
2514928017starch+hydrolysis
2514930031succinate+carbon source
2514927082trehalose+carbon source
2514953426tween 80+carbon source
2514916704uridine+carbon source
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantresistance conc.is sensitivesensitivity conc.group ID
2514918208penicillin gyesyes10 Unit
2514928971ampicillinyesyes10 µg
2514917698chloramphenicolyesyes30 µg
2514917833gentamicinyesyes10 µg
2514928077rifampicinyesyes5 µg
251496104kanamycinyesyes30 µg
2514927902tetracyclineyesyes30 µg
2514928368novobiocinyesyes30 µg
2514917076streptomycinyesyes10 µg
25149100147nalidixic acidyesyes30 µg
2514945924trimethoprimyesyes1.25 µg26
251499332sulfamethoxazoleyesyes23.75 µg26

metabolite production

@refChebi-IDmetaboliteproduction
2514935581indoleno
6836935581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
2514935581indole-
6836935581indole-

enzymes

@refvalueactivityec
25149acid phosphatase+3.1.3.2
25149alkaline phosphatase+3.1.3.1
25149alpha-chymotrypsin-3.4.21.1
25149alpha-fucosidase-3.2.1.51
25149alpha-galactosidase-3.2.1.22
25149alpha-glucosidase+3.2.1.20
25149alpha-mannosidase-3.2.1.24
25149arginine dihydrolase-3.5.3.6
25149beta-galactosidase-3.2.1.23
25149beta-glucosidase-3.2.1.21
25149beta-glucuronidase-3.2.1.31
25149catalase+1.11.1.6
25149cystine arylamidase-3.4.11.3
25149cytochrome oxidase+1.9.3.1
25149esterase (C 4)+
25149esterase Lipase (C 8)+
25149leucine arylamidase+3.4.11.1
25149lipase (C 14)+
25149N-acetyl-beta-glucosaminidase-3.2.1.52
25149naphthol-AS-BI-phosphohydrolase+
25149trypsin-3.4.21.4
25149tryptophan deaminase-4.1.99.1
25149urease-3.5.1.5
25149valine arylamidase+
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    25149C12:02.8
    25149C14:01.6
    25149C14:0 3OH2.5
    25149C16:019.9
    25149C16:1ω7c / C16:1ω6c36.3
    25149C18:01
    25149C18:1ω7c6.7
    25149C11:0 iso4
    25149C13:0 iso 3OH3.6
    25149C15:0 iso3.7
    25149C15:0 iso 3OH5.1
    25149C17:0 iso7.1
    25149C17:1 iso ω9c3.4
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: agar
  • incubation temperature: 25
  • incubation time: 2
  • software version: Sherlock 6.0
  • library/peak naming table: RTSBA 6
  • system: MIS MIDI
  • cutoff value:

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
64838-----------+--------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperature
25149freshwater sampleLotus Lake in Sun Yat-sen University,Kaoshiung CountyTaiwanTWNAsia22.682120.295R2A agar (BD Difco)2-3 days25
64838freshwaterLotus Lake (22° 37' 46'' N, 120° 15' 46'' E)
67771From a freshwater lake in TaiwanTaiwanTWNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Freshwater

taxonmaps

  • @ref: 69479
  • File name: preview.99_91637.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_28536;97_48159;98_63149;99_91637&stattab=map
  • Last taxonomy: Formosimonas limnophila subclade
  • 16S sequence: HG421033
  • Sequence Identity:
  • Total samples: 6128
  • soil counts: 163
  • aquatic counts: 5570
  • animal counts: 351
  • plant counts: 44

Safety information

risk assessment

  • @ref: 64838
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 64838
  • description: Beta proteobacterium AHQ-12 partial 16S rRNA gene, strain AHQ-12
  • accession: HG421033
  • length: 1427
  • database: ena
  • NCBI tax ID: 1384487

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Formosimonas limnophila KCTC 32501GCA_014652675contigncbi1384487
66792Formosimonas limnophila strain KCTC 325011384487.3wgspatric1384487
66792Formosimonas limnophila KCTC 325012923739291draftimg1384487

GC content

  • @ref: 64838
  • GC-content: 50.4
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.456no
gram-positiveno97.538yes
anaerobicno99.161no
halophileno94.44no
spore-formingno97.072yes
glucose-utilyes67.907no
thermophileno97.828yes
aerobicyes83.972yes
flagellatedno95.555no
glucose-fermentno87.792yes

External links

@ref: 64838

culture collection no.: BCRC 80690, LMG 27847, KCTC 32501, DSM 109231

straininfo link

  • @ref: 91409
  • straininfo: 406900

literature

  • topic: Phylogeny
  • Pubmed-ID: 27902193
  • title: Formosimonas limnophila gen. nov., sp. nov., a new member of the family Burkholderiaceae isolated from a freshwater lake.
  • authors: Chen WM, Xie PB, Young CC, Sheu SY
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001561
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, Burkholderiaceae/*classification/genetics/isolation & purification, Cadaverine/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lakes/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Taiwan, Ubiquinone/chemistry
  • topic2: Transcriptome

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
25149W. M. X. Chen, P. B.,Young, C. C.,Sheu, S. Y.Formosimonas limnophila gen. nov., sp. nov., a new member of the family Burkholderiaceae isolated from a freshwater lake10.1099/ijsem.0.001561IJSEM 67: 17-24 201727902193
64838Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-109231Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 109231)
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
91409Reimer, 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-ID406900.1