Strain identifier

BacDive ID: 158808

Type strain: Yes

Species: Acidovorax kalamii

Strain Designation: KNDSW-TSA6

NCBI tax ID(s): 2004485 (species)

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General

@ref: 65571

BacDive-ID: 158808

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

description: Acidovorax kalamii KNDSW-TSA6 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from water sample from the river Ganges.

NCBI tax id

  • NCBI tax id: 2004485
  • Matching level: species

doi: 10.13145/bacdive158808.20230509.8.1

Name and taxonomic classification

LPSN

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

@ref: 65571

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Acidovorax

species: Acidovorax kalamii

strain designation: KNDSW-TSA6

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
65571negative2.0-2.8 µm0.71-0.76 µmrod-shapedyespolar
69480yes91.353
69480negative99.999

colony morphology

  • @ref: 65571
  • colony color: straw yellow
  • colony shape: circular
  • medium used: TSA

Culture and growth conditions

culture medium

  • @ref: 65571
  • name: Trypticase Soy Agar (TSA)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
65571positivegrowth20-37
65571positiveoptimum30mesophilic

culture pH

@refabilitytypepH
65571positivegrowth6.0-8.0
65571positiveoptimum7.0

Physiology and metabolism

oxygen tolerance

  • @ref: 65571
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
65571no
69480no99.997
69481no100

halophily

@refsaltgrowthtested relationconcentrationhalophily level
65571NaClpositivegrowth0-0.5 %
65571NaClpositiveoptimum0 %non-halophilic

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6557116651(S)-lactate+growth
655711 % sodium lactate+growth
65571645522-hydroxybutyrate+growth
65571167632-oxobutanoate+growth
65571309162-oxoglutarate+growth
65571370543-hydroxybutyrate+growth
6557130089acetate+growth
6557113705acetoacetate+growth
6557115963ribitol-builds acid from
6557117925alpha-D-glucose+growth
6557122599arabinose+builds acid from
65571161680aztreonam+growth
6557173706bromosuccinate+growth
65571casein-hydrolysis
6557117057cellobiose-builds acid from
6557117057cellobiose+growth
6557116947citrate-growth
6557116947citrate+growth
6557118333D-arabitol+growth
6557129990D-aspartate+growth
6557115824D-fructose+growth
6557178697D-fructose 6-phosphate+growth
6557128847D-fucose+growth
655718391D-gluconate+growth
6557114314D-glucose 6-phosphate+growth
6557115748D-glucuronate+growth
6557115588D-malate+growth
6557133801D-saccharate+growth
6557116523D-serine-oxidation
6557117924D-sorbitol+growth
6557123652dextrin+growth
6557116813galactitol-builds acid from
6557115740formate-oxidation
6557128757fructose+builds acid from
6557171321fusidate-oxidation
6557116537galactarate+growth
6557128260galactose+builds acid from
6557116865gamma-aminobutyric acid-oxidation
655715291gelatin+growth
6557128066gentiobiose-oxidation
6557117234glucose-fermentation
6557117234glucose+builds acid from
6557117754glycerol+growth
6557132735guanidinium chloride+growth
6557117268myo-inositol-builds acid from
6557115443inulin-builds acid from
6557116977L-alanine+growth
6557129991L-aspartate+growth
6557118287L-fucose+growth
6557117464L-galactonic acid gamma-lactone+growth
6557129985L-glutamate+growth
6557115589L-malate+growth
6557118183L-pyroglutamic acid+growth
6557117115L-serine+growth
6557117716lactose-builds acid from
6557117716lactose-oxidation
655716472lincomycin+growth
6557148607lithium chloride-oxidation
6557117306maltose-builds acid from
6557129864mannitol+builds acid from
6557137684mannose+builds acid from
6557128053melibiose-builds acid from
6557174611methyl (R)-lactate+growth
65571320055methyl beta-D-glucopyranoside+growth
6557151850methyl pyruvate-oxidation
6557150694minocycline-oxidation
6557117268myo-inositol+growth
6557163154N-acetyl-beta-D-mannosamine+growth
6557128037N-acetylgalactosamine+growth
65571506227N-acetylglucosamine+growth
65571100147nalidixic acid-oxidation
6557175273niaproof-oxidation
6557117632nitrate+reduction
6557117309pectin-oxidation
6557175248potassium tellurite+growth
6557117272propionate-oxidation
6557126490quinate+growth
6557116634raffinose-builds acid from
6557116634raffinose-oxidation
6557126546rhamnose-builds acid from
6557129673rifamycin sv+growth
6557117814salicin-builds acid from
6557175229sodium bromate-oxidation
6557164103sodium butyrate-oxidation
6557117164stachyose+growth
6557128017starch-hydrolysis
6557117992sucrose-builds acid from
6557117992sucrose+growth
6557175198tetrazolium blue+growth
6557127082trehalose-builds acid from
6557127082trehalose-oxidation
6557145735troleandomycin-oxidation
6557132528turanose+growth
6557153423tween 40+growth
6557128001vancomycin-oxidation
6557118222xylose-builds acid from

metabolite production

@refChebi-IDmetaboliteproduction
6557115688acetoinno
6557135581indoleno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-test
6557117234glucose-
6557115688acetoin-

enzymes

@refvalueactivityec
65571catalase-1.11.1.6
65571cytochrome oxidase+1.9.3.1

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    65571C12:05.9
    65571C14:04.5
    65571C16:023.2
    65571C16:0 N alcohol2.4
    65571C10:0 3OH1.3
    65571C18:1ω7c / C18:1ω6c11.6
    65571C16:1ω7c / C16:1ω6c49.5
    65571C18:3ω6c (6,9,12)0.9
  • type of FA analysis: whole cell analysis
  • incubation medium: TSA
  • incubation temperature: 30
  • incubation time: 1.5
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA 5.0
  • system: MIS MIDI
  • method/protocol: Sasser, 1990

Isolation, sampling and environmental information

isolation

  • @ref: 65571
  • sample type: water sample from the river Ganges
  • geographic location: Kanpur
  • country: India
  • origin.country: IND
  • continent: Asia
  • latitude: 26.4153
  • longitude: 80.4517
  • enrichment culture: TSA
  • enrichment culture duration: 7 days
  • enrichment culture temperature: 30

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #River (Creek)

taxonmaps

  • @ref: 69479
  • File name: preview.99_2459.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_491;97_560;98_1918;99_2459&stattab=map
  • Last taxonomy: Acidovorax
  • 16S sequence: KY425604
  • Sequence Identity:
  • Total samples: 612
  • soil counts: 88
  • aquatic counts: 321
  • animal counts: 170
  • plant counts: 33

Sequence information

16S sequences

  • @ref: 65571
  • description: 16S rRNA gene sequence
  • accession: KY425604
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Acidovorax kalamii KNDSW-TSA6GCA_002245625scaffoldncbi2004485
66792Acidovorax kalamii KNDSW-TSA62839292028draftimg2004485

GC content

  • @ref: 65571
  • GC-content: 65.7
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes84.939yes
gram-positiveno98.936yes
anaerobicno99.091yes
aerobicyes96.147no
halophileno95.662yes
spore-formingno95.175yes
glucose-utilyes64.514no
thermophileno97.871yes
glucose-fermentno88.444no
motileyes90.803yes

External links

@ref: 65571

culture collection no.: MTCC 12652, KCTC 52819, VTCC B-910010

literature

  • topic: Phylogeny
  • Pubmed-ID: 29616893
  • title: Acidovorax kalamii sp. nov., isolated from a water sample of the river Ganges.
  • authors: Pal D, Kaur N, Sudan SK, Bisht B, Krishnamurthi S, Mayilraj S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002736
  • year: 2018
  • mesh: Bacterial Typing Techniques, Base Composition, Comamonadaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, India, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA
  • topic2: Transcriptome

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
65571Deepika Pal, Navjot Kaur, Sarabjeet Kour Sudan, Bhawana Bisht, Srinivasan Krishnamurthi and Shanmugam MayilrajAcidovorax kalamii sp. nov., isolated from a water sample of the river Ganges10.1099/ijsem.0.002736IJSEM 68: 1719-1724 201829616893
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/
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