Strain identifier

BacDive ID: 132374

Type strain: Yes

Species: Parviterribacter kavangonensis

Strain Designation: D16/0/H6

Strain history: <- B. Fösel, DSMZ GmbH, Braunschweig, Germany; D16_0_H6

NCBI tax ID(s): 1640865 (species)

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General

@ref: 24163

BacDive-ID: 132374

DSM-Number: 25205

keywords: 16S sequence, Bacteria, obligate aerobe, chemoorganotroph, Gram-positive, motile, pleomorphic-shaped, colony-forming

description: Parviterribacter kavangonensis D16/0/H6 is an obligate aerobe, chemoorganotroph, Gram-positive bacterium that forms circular colonies and was isolated from loamy subtropical savannah soil.

NCBI tax id

  • NCBI tax id: 1640865
  • Matching level: species

strain history

  • @ref: 24163
  • history: <- B. Fösel, DSMZ GmbH, Braunschweig, Germany; D16_0_H6

doi: 10.13145/bacdive132374.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Thermoleophilia
  • order: Solirubrobacterales
  • family: Parviterribacteraceae
  • genus: Parviterribacter
  • species: Parviterribacter kavangonensis
  • full scientific name: Parviterribacter kavangonensis Foesel et al. 2016

@ref: 24163

domain: Bacteria

phylum: Actinobacteria

class: Thermoleophilia

order: Solirubrobacterales

family: Parviterribacteraceae

genus: Parviterribacter

species: Parviterribacter kavangonensis

full scientific name: Parviterribacter kavangonensis Foesel et al. 2016

strain designation: D16/0/H6

type strain: yes

Morphology

cell morphology

  • @ref: 43815
  • gram stain: positive
  • cell length: 1-1.5 µm
  • cell width: 0.6-0.7 µm
  • cell shape: pleomorphic-shaped
  • motility: yes

colony morphology

  • @ref: 43815
  • colony size: 0.1 mm
  • colony color: Light pink
  • colony shape: circular
  • medium used: Agar-solidified SSE/HD 1 : 10 medium

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43815Agar-solidified SSE/HD 1 : 10 mediumyes
24163SSE/HD1:10 (DSMZ Medium 1426)yeshttps://mediadive.dsmz.de/medium/1426Name: SSE/HD 1:10 MEDIUM (DSMZ Medium 1426) Composition: MES 1.95 g/l Peptone 0.5 g/l CaSO4 x 2 H2O 0.4303 g/l MgSO4 x 7 H2O 0.3695 g/l Yeast extract 0.25 g/l Na NO3 0.212 g/l CaCl2 x 2 H2O 0.1469 g/l Ca(NO3)2 x 4 H2O 0.118 g/l MgCl2 x 6 H2O 0.1018 g/l Glucose 0.1 g/l (NH4)2SO4 0.09915 g/l NH4Cl 0.05345 g/l K2SO4 0.0435 g/l FeSO4 x 7 H2O 0.00555 g/l KH2PO4 0.00340213 g/l HCl 0.0025 g/l FeCl2 x 4 H2O 0.0015 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 4 H2O 0.0001 g/l ZnCl2 7e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l Pyridoxine hydrochloride 1e-05 g/l H3BO3 6e-06 g/l Lipoic acid 5e-06 g/l D-Calcium pantothenate 5e-06 g/l Nicotinic acid 5e-06 g/l Riboflavin 5e-06 g/l Thiamine-HCl x 2 H2O 5e-06 g/l p-Aminobenzoic acid 5e-06 g/l Folic acid 2e-06 g/l Biotin 2e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Vitamin B12 1e-07 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
43815positivegrowth13-43
43815positiveoptimum35-43
24163positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
43815positivegrowth4.5-8.5alkaliphile
43815positiveoptimum5-8

Physiology and metabolism

oxygen tolerance

  • @ref: 43815
  • oxygen tolerance: obligate aerobe

nutrition type

  • @ref: 43815
  • type: chemoorganotroph

spore formation

  • @ref: 43815
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentrationhalophily level
43815NaClpositivegrowth0-0.5 %(w/v)
43815NaClpositiveoptimum0 %(w/v)non-halophilic

observation

  • @ref: 43815
  • observation: Capsule forming

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
43815526821,2-butandiol-growth
43815169971,2-propandiol-growth
438152-oxogluconate-growth
43815309162-oxoglutarate-growth
43815286442-oxopentanoate-growth
43815620642,3-butanediol-growth
4381515688acetoin-growth
4381517128adipate-growth
4381515963ribitol-growth
4381516449alanine-growth
43815645522-hydroxybutyrate-growth
4381522599arabinose-growth
4381522605arabinitol-growth
4381529016arginine-growth
4381522651ascorbate-growth
4381516150benzoate-growth
4381528885butanol-growth
4381527689decanoate-growth
4381525646octanoate-growth
4381517057cellobiose-growth
4381562968cellulose-growth
4381517029chitin-growth
4381516947citrate-growth
4381535899crotonate-growth
4381515356cysteine-growth
4381516813galactitol-growth
4381533946erythrose-growth
4381523958erythrulose-growth
4381516236ethanol-growth
4381530742ethylene glycol-growth
43815fermented rumen extract-growth
4381515740formate-growth
4381528757fructose-growth
4381533984fucose-growth
4381529806fumarate-growth
4381528260galactose-growth
43815167244-hydroxybutyrate-growth
4381524265gluconate-growth
438155417glucosamine-growth
4381524297glucuronate-growth
4381529987glutamate-growth
4381517754glycerol-growth
4381515428glycine-growth
4381529805glycolate-growth
4381536655glyoxylate-growth
4381532362heptanoate-growth
4381527570histidine-growth
4381548944isobutyrate-growth
4381516087isocitrate-growth
4381524898isoleucine-growth
4381548942isovalerate-growth
4381524996lactate-growth
4381517716lactose-growth
43815391504-oxopentanoate-growth
438156364laminarin-growth
4381525017leucine-growth
4381525097lyxose-growth
4381525115malate-growth
4381515792malonate-growth
4381517306maltose-growth
4381529864mannitol-growth
438156731melezitose-growth
4381517790methanol-growth
4381516811methionine-growth
4381517268myo-inositol-growth
4381528037N-acetylgalactosamine-growth
43815506227N-acetylglucosamine-growth
4381532544nicotinate-growth
4381518257ornithine-growth
4381516452oxaloacetate-growth
4381528044phenylalanine-growth
4381526271proline-growth
4381528831propanol-growth
4381516634raffinose-growth
4381526546rhamnose-growth
4381536208shikimate-growth
4381530911sorbitol-growth
4381527922sorbose-growth
4381528017starch-growth
4381517992sucrose-growth
4381530929tartrate-growth
4381526986threonine-growth
4381527082trehalose-growth
43815trimethoxybenzoate-growth
4381527897tryptophan-growth
4381553426tween 80-growth
4381518186tyrosine-growth
4381527266valine-growth
4381517151xylitol-growth
4381518222xylose-growth
4381515379dioxygen+electron acceptor
4381530089acetate+growth
4381535391aspartate+growth
438158295beta-hydroxybutyrate+growth
4381517968butyrate+growth
43815casamino acids+growth
43815casein hydrolysate+growth
4381517234glucose+growth
4381524741hydroxyproline+growth
4381525094lysine+growth
4381522605arabinitol+growth
4381537684mannose+growth
43815peptone+growth
4381517272propionate+growth
4381536241protocatechuate+growth
4381515361pyruvate+growth
4381530031succinate+growth
43815yeast extract+growth
438154853esculin+hydrolysis
438155291gelatin+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
4381515688acetoinno
4381535581indoleno

enzymes

@refvalueactivityec
43815acid phosphatase+3.1.3.2
43815alkaline phosphatase+3.1.3.1
43815naphthol-AS-BI-phosphohydrolase+
43815esterase (C 4)+
43815esterase Lipase (C 8)+
43815leucine arylamidase+3.4.11.1
43815cystine arylamidase+/-3.4.11.3
43815beta-glucuronidase+3.2.1.31
43815alpha-mannosidase+3.2.1.24
43815alpha-fucosidase+/-3.2.1.51
43815urease-3.5.1.5
43815arginine dihydrolase-3.5.3.6
43815lipase (C 14)-
43815valine arylamidase-
43815trypsin-3.4.21.4
43815alpha-chymotrypsin-3.4.21.1
43815alpha-galactosidase-3.2.1.22
43815beta-galactosidase-3.2.1.23
43815alpha-glucosidase-3.2.1.20
43815beta-glucosidase-3.2.1.21
43815N-acetyl-beta-glucosaminidase-3.2.1.52
43815catalase+1.11.1.6
43815cytochrome oxidase+/-1.9.3.1

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43815C15:0 anteiso0.31
    43815C17:0 anteiso3.7
    43815C14:00.25
    43815C15:00.33
    43815C15:0 3OH0.49
    43815C15:1ω6c0.25
    43815C16:00.47
    43815C16:1ω7c / C15:0 iso 2OH3.86
    4381510-methyl C17:035.97
    43815C17:1ω6c2.86
    43815C17:1ω8c3.89
    4381510-methyl C18:01.29
    43815C18:1ω9c9.99
    43815C18:3ω6,9,12c0.27
    4381510-methyl C19:00.84
    43815C19:0ω10c-cyclo / C19:1ω6c0.26
    43815C19:1ω9c / C19:1ω11c2.46
    43815C14:0 iso1.21
    43815C15:0 iso0.38
    43815C16:0 iso21.58
    43815C16:1 iso H1.07
    43815C17:0 iso1.66
    43815C17:1 iso I / C17:1 anteiso B0.49
    43815C17:1 iso ω9c1.65
    43815C18:0 iso3.47
    43815iso-C18:1H0.65
    43815C20:0 iso0.36
  • type of FA analysis: whole cell analysis
  • incubation medium: SSE/HD 1 : 10 agar plates
  • agar/liquid: agar
  • incubation time: 18
  • incubation pH: 5.5
  • incubation_oxygen: aerobic
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA40
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeisolation date
24163loamy subtropical savannah soilKavango, Mile46/Mutompo (18° 17' 14.0'' S 19° 15' 32.3'' E)NamibiaNAMAfrica-18.287219.259
43815Loamy subtropical savannah soil at Mile 46Mile 46, Kavango regionNamibiaNAMAfrica-18.28719.2582008

isolation source categories

Cat1Cat2Cat3
#Climate#Hot#Tropical
#Climate#Temperate#Subtropical
#Environmental#Terrestrial#Desert
#Environmental#Terrestrial#Soil

Safety information

risk assessment

  • @ref: 24163
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24163
  • description: Parviterribacter kavangonensis strain D16/0/H6 16S ribosomal RNA gene, partial sequence
  • accession: KP981370
  • length: 1456
  • database: ena
  • NCBI tax ID: 1640865

GC content

@refGC-contentmethod
4381572.8high performance liquid chromatography (HPLC)
2416372.8

External links

@ref: 24163

culture collection no.: DSM 25205, LMG 26950

straininfo link

  • @ref: 90718
  • straininfo: 397550

literature

  • topic: Phylogeny
  • Pubmed-ID: 26582010
  • title: Parviterribacter kavangonensis gen. nov., sp. nov. and Parviterribacter multiflagellatus sp. nov., novel members of Parviterribacteraceae fam. nov. within the order Solirubrobacterales, and emended descriptions of the classes Thermoleophilia and Rubrobacteria and their orders and families.
  • authors: Foesel BU, Geppert A, Rohde M, Overmann J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000770
  • year: 2015

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
24163Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-25205Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25205)
43815Bärbel U. Foesel, Alicia Geppert, Manfred Rohde, Jörg OvermannParviterribacter kavangonensis gen. nov., sp. nov. and Parviterribacter multiflagellatus sp. nov., novel members of Parviterribacteraceae fam. nov. within the order Solirubrobacterales, and emended descriptions of the classes Thermoleophilia and Rubrobacteria and their orders and families10.1099/ijsem.0.000770IJSEM 66: 652-655 201626582010
90718Reimer, 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-ID397550.1