Strain identifier

BacDive ID: 159867

Type strain: Yes

Species: Ahniella affigens

Strain Designation: D13

Strain history: T.-Y. Ahn; Dept. of Microbiol., Coll. of Nat. Sci., Dankook Univ., South Korea; D13.

NCBI tax ID(s): 2021234 (species)

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General

@ref: 66605

BacDive-ID: 159867

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

description: Ahniella affigens D13 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from sandy soil from a stream.

NCBI tax id

  • NCBI tax id: 2021234
  • Matching level: species

strain history

  • @ref: 67770
  • history: T.-Y. Ahn; Dept. of Microbiol., Coll. of Nat. Sci., Dankook Univ., South Korea; D13.

doi: 10.13145/bacdive159867.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Lysobacterales
  • family: Rhodanobacteraceae
  • genus: Ahniella
  • species: Ahniella affigens
  • full scientific name: Ahniella affigens Hwang et al. 2018

@ref: 66605

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Lysobacterales

family: Rhodanobacteraceae

genus: Ahniella

species: Ahniella affigens

strain designation: D13

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
66605negativerod-shapedno
69480negative98

colony morphology

  • @ref: 66605
  • colony color: yellow
  • incubation period: 3 days
  • medium used: R2A medium

Culture and growth conditions

culture medium

@refnamegrowth
66605Nutrient agar (NA)yes
66605Reasoner's 2A agar (R2A)yes
66605tryptic soy agar (TSA)yes

culture temp

@refgrowthtypetemperature
66605positiveoptimum30
66605nogrowth40
66605positivegrowth15-35
67770positivegrowth30

culture pH

@refabilitytypepH
66605positiveoptimum7
66605positivegrowth6.5-8.0

Physiology and metabolism

oxygen tolerance

  • @ref: 66605
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69480no91.262
69481no100

halophily

  • @ref: 66605
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0.5 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6660527689decanoate+/-assimilation
6660517234glucose-builds acid from
6660517306maltose-builds acid from
6660517992sucrose-builds acid from
6660518222xylose-builds acid from
6660528757fructose-builds acid from
6660529864mannitol-builds acid from
6660530911sorbitol-builds acid from
666054853esculin-hydrolysis
6660518186tyrosine-hydrolysis
666055291gelatin+hydrolysis
6660528017starch+hydrolysis
6660553426tween 80+hydrolysis
6660585146carboxymethylcellulose+hydrolysis
66605casein+hydrolysis
6660517632nitrate-reduction

metabolite production

  • @ref: 66605
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: no

enzymes

@refvalueactivityec
66605acid phosphatase-3.1.3.2
66605alpha-fucosidase-3.2.1.51
66605alpha-galactosidase-3.2.1.22
66605alpha-glucosidase-3.2.1.20
66605alpha-mannosidase-3.2.1.24
66605beta-galactosidase-3.2.1.23
66605beta-glucosidase-3.2.1.21
66605beta-glucuronidase-3.2.1.31
66605catalase-1.11.1.6
66605cystine arylamidase-3.4.11.3
66605esterase (C 4)-
66605lipase (C 14)-
66605alanine arylamidase+3.4.11.2
66605alkaline phosphatase+3.1.3.1
66605alpha-chymotrypsin+3.4.21.1
66605cytochrome oxidase+1.9.3.1
66605leucine arylamidase+3.4.11.1
66605naphthol-AS-BI-phosphohydrolase+
66605phenylalanine arylamidase+
66605proline-arylamidase+3.4.11.5
66605trypsin+3.4.21.4
66605esterase Lipase (C 8)+/-
66605N-acetyl-beta-glucosaminidase+/-3.2.1.52
66605valine arylamidase+/-

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    66605C16:0 iso35
    66605C18:1 w7c / C18:1 w6c0.5
    66605C12:0 iso0.5
    66605C10:0 iso0.6
    66605C18:0 iso0.7
    66605C17:1 iso w9c / C16:0 10-methyl12.9
    66605C15:0 iso16.5
    66605C16:1 w6c / C16:1 w7c2.6
    66605C17:0 iso2.6
    66605C14:0 iso3.2
    66605C11:0 iso3.5
    66605C11:0 iso 3OH3.9
    66605C16:1 iso H5.6
    66605C15:1 iso H / C13:0 3OH8.2
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • incubation temperature: 30
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • method/protocol: Sasser, 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperature
66605sandy soil from a streamSinan-gunRepublic of KoreaKORAsia34.95126.133R2A agar5 days30
67770Sandy soil from a stream in Sinan-gunRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Sandy
#Environmental#Terrestrial#Soil

Sequence information

16S sequences

  • @ref: 66605
  • description: Ahniella affigens strain D13 16S ribosomal RNA gene, partial sequence
  • accession: KY649437
  • length: 1476
  • database: nuccore
  • NCBI tax ID: 2021234

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ahniella affigens D13GCA_003015185completencbi2021234
66792Xanthomonadales bacterium D132021234.3completepatric2021234
66792Ahniella affigens D132833611726completeimg2021234

GC content

  • @ref: 66605
  • GC-content: 57.70
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno98yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.206yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes84.509no
69480spore-formingspore-formingAbility to form endo- or exosporesno91.262no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno97.399yes
69480flagellatedmotile2+Ability to perform flagellated movementno61.426no

External links

@ref: 66605

culture collection no.: KACC 19270, JCM 31634

literature

  • topic: Phylogeny
  • Pubmed-ID: 29923816
  • title: Ahniella affigens gen. nov., sp. nov., a gammaproteobacterium isolated from sandy soil near a stream.
  • authors: Hwang WM, Ko Y, Kim JH, Kang K
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002859
  • year: 2018
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rivers, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry
  • 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
66605Woon Mo Hwang, Yongseok Ko, Jae-Heon Kim and Keunsoo KangAhniella affigens gen. nov., sp. nov., a gammaproteobacterium isolated from sandy soil near a stream10.1099/ijsem.0.002859IJSEM 68: 2478-2484 201829923816
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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