Strain identifier

BacDive ID: 132354

Type strain: Yes

Species: Silvibacterium dinghuense

Strain Designation: DHOF10

Strain history: <- KCTC; KCTC 42631

NCBI tax ID(s): 1560006 (species)

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General

@ref: 24143

BacDive-ID: 132354

DSM-Number: 103429

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

description: Silvibacterium dinghuense DHOF10 is an aerobe, chemoheterotroph, Gram-negative bacterium that forms circular colonies and was isolated from forest soil.

NCBI tax id

  • NCBI tax id: 1560006
  • Matching level: species

strain history

  • @ref: 24143
  • history: <- KCTC; KCTC 42631

doi: 10.13145/bacdive132354.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/acidobacteriota
  • domain: Bacteria
  • phylum: Acidobacteriota
  • class: Terriglobia
  • order: Terriglobales
  • family: Acidobacteriaceae
  • genus: Silvibacterium
  • species: Silvibacterium dinghuense
  • full scientific name: Silvibacterium dinghuense (Jiang et al. 2016) Zhang et al. 2022

  • synonyms

    • @ref: 20215
    • synonym: Acidipila dinghuensis

@ref: 24143

domain: Bacteria

phylum: Acidobacteria

class: Acidobacteriia

order: Acidobacteriales

family: Acidobacteriaceae

genus: Acidipila

species: Acidipila dinghuensis

full scientific name: Acidipila dinghuensis Jiang et al. 2016

strain designation: DHOF10

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43829negative1-1.4 µm0.6-1.1 µmcoccus-shapedno
69480negative99.989

colony morphology

  • @ref: 43829
  • colony size: 1.9-2.6 mm
  • colony color: White to light beige
  • colony shape: circular
  • incubation period: 14 days
  • medium used: GYS agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43829GYS agaryes
24143SSE/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
43829positivegrowth10-37
43829positiveoptimum28-37mesophilic
24143positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
43829positivegrowth3.5-8acidophile
43829positiveoptimum4-4.5

Physiology and metabolism

oxygen tolerance

  • @ref: 43829
  • oxygen tolerance: aerobe

nutrition type

  • @ref: 43829
  • type: chemoheterotroph

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.984

halophily

  • @ref: 43829
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-1 %(w/v)

observation

  • @ref: 43829
  • observation: Capsule forming

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
43829168082-dehydro-D-gluconate-carbon source
43829581435-dehydro-D-gluconate-carbon source
4382930089acetate-carbon source
4382917128adipate-carbon source
4382935391aspartate-carbon source
4382916150benzoate-carbon source
4382916947citrate-carbon source
4382915963ribitol-carbon source
4382917108D-arabinose-carbon source
4382918333D-arabitol-carbon source
4382928847D-fucose-carbon source
4382915748D-glucuronate-carbon source
4382962318D-lyxose-carbon source
4382916988D-ribose-carbon source
4382917924D-sorbitol-carbon source
4382925115malate-carbon source
4382916813galactitol-carbon source
4382917113erythritol-carbon source
4382916236ethanol-carbon source
4382916977L-alanine-carbon source
4382918403L-arabitol-carbon source
4382929985L-glutamate-carbon source
4382915971L-histidine-carbon source
4382917266L-sorbose-carbon source
4382924996lactate-carbon source
4382917790methanol-carbon source
4382930623oxalate-carbon source
4382918401phenylacetate-carbon source
4382917234glucose-fermentation
4382917632nitrate-reduction
4382927613amygdalin+carbon source
4382918305arbutin+carbon source
4382927689decanoate+carbon source
43829casamino acids+carbon source
4382917057cellobiose+carbon source
4382915824D-fructose+carbon source
4382912936D-galactose+carbon source
4382917634D-glucose+carbon source
4382916899D-mannitol+carbon source
4382916024D-mannose+carbon source
4382965327D-xylose+carbon source
438294853esculin+carbon source
4382928066gentiobiose+carbon source
4382924265gluconate+carbon source
4382917754glycerol+carbon source
4382928087glycogen+carbon source
4382917268myo-inositol+carbon source
4382915443inulin+carbon source
4382930849L-arabinose+carbon source
4382918287L-fucose+carbon source
4382962345L-rhamnose+carbon source
4382917115L-serine+carbon source
4382965328L-xylose+carbon source
4382917716lactose+carbon source
4382917306maltose+carbon source
438296731melezitose+carbon source
4382928053melibiose+carbon source
43829320061methyl alpha-D-glucopyranoside+carbon source
4382943943methyl alpha-D-mannoside+carbon source
4382974863methyl beta-D-xylopyranoside+carbon source
43829506227N-acetylglucosamine+carbon source
4382918257ornithine+carbon source
4382915361pyruvate+carbon source
4382916634raffinose+carbon source
4382917814salicin+carbon source
4382928017starch+carbon source
4382930031succinate+carbon source
4382917992sucrose+carbon source
4382930929tartrate+carbon source
4382927082trehalose+carbon source
43829tryptone+carbon source
4382932528turanose+carbon source
4382917151xylitol+carbon source
43829yeast extract+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

metabolite production

@refChebi-IDmetaboliteproduction
4382935581indoleno
6836935581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
43829acid phosphatase+3.1.3.2
43829alkaline phosphatase+3.1.3.1
43829naphthol-AS-BI-phosphohydrolase+
43829alpha-glucosidase+3.2.1.20
43829beta-glucosidase+3.2.1.21
43829alpha-galactosidase+3.2.1.22
43829beta-galactosidase+3.2.1.23
43829alpha-fucosidase+3.2.1.51
43829N-acetyl-beta-glucosaminidase+3.2.1.52
43829leucine arylamidase+3.4.11.1
43829cystine arylamidase+3.4.11.3
43829valine arylamidase+
43829trypsin+3.4.21.4
43829esterase (C 4)+
43829esterase Lipase (C 8)+
43829alpha-mannosidase-3.2.1.24
43829beta-glucuronidase-3.2.1.31
43829alpha-chymotrypsin-3.4.21.1
43829lipase (C 14)-
43829arginine dihydrolase-3.5.3.6
43829urease-3.5.1.5
43829protease-
43829catalase-1.11.1.6
43829cytochrome oxidase-1.9.3.1
68369cytochrome oxidase-1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
68382alkaline phosphatase+3.1.3.1
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
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+
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
    43829C14:01.7
    43829C16:08.6
    43829C16:1ω7c / C16:1ω6c11.5
    43829C17:02.7
    43829C17:1ω8c1.5
    43829C18:03.7
    43829C18:1ω9c17
    43829C15:0 iso48.6
    43829C15:1H iso / C13:0 3OH1.1
    43829C17:1 iso ω9c / C16:0 10-methyl2.3
  • type of FA analysis: whole cell analysis
  • incubation medium: GYS agar
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation pH: 4.5
  • incubation_oxygen: aerobic
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • method/protocol: Sasser, 1990
  • 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
24143-++/-+/--++-+-+++/-+--++-+

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
24143-----+-+-------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeisolation date
24143forest soilDinghushan biosphere reserve (DHSBR), Guangdong ProvinceChinaCHNAsia23.1667112.517
43829An acidic soil sample collected from the forest of Dinghushan Biosphere ReserveGuangdong ProvinceChinaCHNAsia23.1667112.5172013-09

isolation source categories

Cat1Cat2Cat3
#Condition#Acidic
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil

Safety information

risk assessment

  • @ref: 24143
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24143
  • description: Acidipila dinghuensis 16S ribosomal RNA gene, partial sequence
  • accession: KM083127
  • length: 1461
  • database: ena
  • NCBI tax ID: 1560006

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Silvibacterium dinghuense DHOF10GCA_004123295contigncbi1560006
66792Silvibacterium dinghuense CGMCC 1.13007GCA_014640355contigncbi1560006
66792Acidipila dinghuensis strain CGMCC 1.130071560006.5wgspatric1560006
66792Acidipila dinghuensis DHOF102882000052draftimg1560006

GC content

  • @ref: 43829
  • GC-content: 56.3
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno71no
motileno60.18yes
gram-positiveno97.71yes
anaerobicno98.49yes
aerobicyes83.979yes
halophileno96.007yes
spore-formingno88.035no
thermophileno92.977no
glucose-utilyes75.201no
flagellatedno88.891yes
glucose-fermentno89.537no

External links

@ref: 24143

culture collection no.: DSM 103429, CGMCC 1.13007, KCTC 42631

straininfo link

  • @ref: 90700
  • straininfo: 397526

literature

  • topic: Phylogeny
  • Pubmed-ID: 26475169
  • title: Acidipila dinghuensis sp. nov., an acidobacterium isolated from forest soil.
  • authors: Jiang YW, Wang J, Chen MH, Lv YY, Qiu LH
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000676
  • year: 2015
  • mesh: Acidobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Genetics

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
24143Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103429Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103429)
43829Ya-wen Jiang, Jia Wang, Mei-hong Chen, Ying-ying Lv, Li-hong QiuAcidipila dinghuensis sp. nov., an acidobacterium isolated from forest soil10.1099/ijsem.0.000676IJSEM 66: 76-83 201626475169
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
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
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
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
90700Reimer, 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-ID397526.1