Strain identifier

BacDive ID: 132587

Type strain: Yes

Species: Ammoniphilus resinae

Strain Designation: CC-RT-E

Strain history: <- C. C. Young, Dept. Soil and Environmental Sci., Natl. Chung Hsing Univ., Taichung, Taiwan; CC-RT-E <- Y.-H. Wu

NCBI tax ID(s): 861532 (species)

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General

@ref: 24376

BacDive-ID: 132587

DSM-Number: 24738

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, spore-forming, Gram-variable, rod-shaped, colony-forming

description: Ammoniphilus resinae CC-RT-E is a facultative anaerobe, spore-forming, Gram-variable bacterium that forms circular colonies and was isolated from aged resin.

NCBI tax id

  • NCBI tax id: 861532
  • Matching level: species

strain history

  • @ref: 24376
  • history: <- C. C. Young, Dept. Soil and Environmental Sci., Natl. Chung Hsing Univ., Taichung, Taiwan; CC-RT-E <- Y.-H. Wu

doi: 10.13145/bacdive132587.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Paenibacillaceae
  • genus: Ammoniphilus
  • species: Ammoniphilus resinae
  • full scientific name: Ammoniphilus resinae Lin et al. 2016

@ref: 24376

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Ammoniphilus

species: Ammoniphilus resinae

full scientific name: Ammoniphilus resinae Lin et al. 2016

strain designation: CC-RT-E

type strain: yes

Morphology

cell morphology

  • @ref: 43085
  • gram stain: variable
  • cell length: 2.8-3.4 µm
  • cell width: 0.5-0.6 µm
  • cell shape: rod-shaped

colony morphology

  • @ref: 43085
  • colony color: white
  • colony shape: circular
  • incubation period: 2 days
  • medium used: nutritient agar (NA)

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43085nutritient agar (NA)yes
43085ammonium-based medium (OM-2)no
24376R2A 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

@refgrowthtypetemperature
43085positiveoptimum30
43085positivegrowth20-37
24376positivegrowth28

culture pH

@refabilitytypepHPH range
43085positivegrowth6.0-9.0alkaliphile
43085positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 43085
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
43085ellipsoidal spores at terminal positionendosporeyes
69480yes91.119
69481yes100

halophily

@refsaltgrowthtested relationconcentration
43085NaClpositivegrowth0-2 %(w/v)
43085NaClpositiveoptimum1 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4308530849L-arabinose+carbon source
430858295beta-hydroxybutyrate+carbon source
43085167244-hydroxybutyrate+carbon source
43085143136succinamate+carbon source
4308517632nitrate+reduction
4308516301nitrite+reduction
4308517634D-glucose+assimilation
4308516024D-mannose+assimilation
4308532032potassium gluconate+assimilation
4308525115malate+assimilation
430854853esculin+hydrolysis
4308528017starch+hydrolysis
43085casein-hydrolysis
430855291gelatin-hydrolysis
4308553424tween 20-hydrolysis
4308553423tween 40-hydrolysis
4308553425tween 60-hydrolysis
4308553426tween 80-hydrolysis
4308517108D-arabinose+builds acid from
4308530849L-arabinose+builds acid from
4308516988D-ribose+builds acid from
4308565327D-xylose+builds acid from
4308512936D-galactose+builds acid from
4308515903beta-d-glucose+builds acid from
4308562345L-rhamnose+builds acid from
4308516899D-mannitol+builds acid from
4308517924D-sorbitol+builds acid from
4308517306maltose+builds acid from
4308517716lactose+builds acid from
4308527082trehalose+builds acid from
43085(+)-D-glycogen+builds acid from
4308517151xylitol+builds acid from
4308518287L-fucose+builds acid from
4308518333D-arabitol+builds acid from
4308517306maltose-assimilation
4308516899D-mannitol-assimilation
4308553258sodium citrate-assimilation

metabolite production

@refChebi-IDmetaboliteproduction
4308535581indoleno
4308515688acetoinyes
4308516136hydrogen sulfideyes

metabolite tests

  • @ref: 43085
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: +

enzymes

@refvalueactivityec
43085cytochrome oxidase+1.9.3.1
43085catalase+1.11.1.6
43085alkaline phosphatase+3.1.3.1
43085esterase (C 4)+
43085esterase Lipase (C 8)+
43085leucine arylamidase+3.4.11.1
43085cystine arylamidase+3.4.11.3
43085alpha-chymotrypsin+3.4.21.1
43085naphthol-AS-BI-phosphohydrolase+
43085beta-galactosidase-3.2.1.23
43085beta-glucuronidase-3.2.1.31
43085DNase-
43085beta-glucosidase+3.2.1.21

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43085C14:012.3
    43085C16:06.4
    43085C13:0 iso1
    43085C14:0 iso2.8
    43085C15:0 iso18
    43085C15:0 anteiso33.3
    43085C16:0 iso1
    43085C17:0 cyclo2.8
    43085C15:1ω6c1.6
    43085C16:1ω5c1.4
    43085C13:0 3-OH / iso-C15:1H1
    43085C16:1ω7c / C16:1ω6c13.5
  • type of FA analysis: whole cell analysis
  • incubation medium: nutritient agar (NA)
  • agar/liquid: agar
  • software version: Sherlock 6.0
  • system: MIS MIDI
  • instrument: Agilent 7890A
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture durationenrichment culture temperatureisolation procedure
24376aged resintropical rainforestIndonesiaIDNAsia
43085resin sample from tropical forestIndonesiaIDNAsianutrient agar (NA; Hi-Media)3 days30standard serial dilution-plating technique

isolation source categories

  • Cat1: #Host Body-Site
  • Cat2: #Plant

taxonmaps

  • @ref: 69479
  • File name: preview.99_95703.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_943;96_4456;97_5423;98_14661;99_95703&stattab=map
  • Last taxonomy: Ammoniphilus resinae subclade
  • 16S sequence: HM193518
  • Sequence Identity:
  • Total samples: 779
  • soil counts: 565
  • aquatic counts: 60
  • animal counts: 117
  • plant counts: 37

Safety information

risk assessment

  • @ref: 24376
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24376
  • description: Ammoniphilus resinae strain CC-RT-E 16S ribosomal RNA gene, partial sequence
  • accession: HM193518
  • length: 1497
  • database: nuccore
  • NCBI tax ID: 861532

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ammoniphilus resinae DSM 24738GCA_017873965contigncbi861532
66792Ammoniphilus resinae strain DSM 24738861532.3wgspatric861532
66792Ammoniphilus resinae DSM 247382913422633draftimg861532

GC content

  • @ref: 24376
  • GC-content: 39.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesyes100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno53.522yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no90.136yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes65.128no
69480spore-formingspore-formingAbility to form endo- or exosporesyes91.119yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno82.101no
69480flagellatedmotile2+Ability to perform flagellated movementyes80.878no

External links

@ref: 24376

culture collection no.: DSM 24738, BCRC 80314

straininfo link

  • @ref: 90904
  • straininfo: 405331

literature

  • topic: Phylogeny
  • Pubmed-ID: 27151144
  • title: Ammoniphilus resinae sp. nov., an endospore-forming bacterium isolated from resin fragments.
  • authors: Lin SY, Wu YH, Hameed A, Liu YC, Young CC
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001137
  • year: 2016
  • mesh: Bacillales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Indonesia, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Resins, Plant, Sequence Analysis, DNA, Spermidine/analogs & derivatives/chemistry, Spores, Bacterial, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

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
24376Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-24738Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24738)
43085Shih-Yao Lin, Yun-Hsuan Wu, Asif Hameed, You-Cheng Liu, Chiu-Chung YoungAmmoniphilus resinae sp. nov., an endospore-forming bacterium isolated from resin fragments10.1099/ijsem.0.001137IJSEM 66: 3010-3016 201627151144
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
90904Reimer, 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-ID405331.1