Strain identifier

BacDive ID: 140730

Type strain: Yes

Species: Amylibacter cionae

Strain Designation: H-12

NCBI tax ID(s): 2035344 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 8.1 (current version)

General

@ref: 43509

BacDive-ID: 140730

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

description: Amylibacter cionae H-12 is an aerobe, chemoautolithotroph, Gram-negative bacterium that forms circular colonies and was isolated from inner content of a sea squirt.

NCBI tax id

  • NCBI tax id: 2035344
  • Matching level: species

doi: 10.13145/bacdive140730.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Amylibacter
  • species: Amylibacter cionae
  • full scientific name: Amylibacter cionae Wang et al. 2017

@ref: 43509

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Amylibacter

species: Amylibacter cionae

strain designation: H-12

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43509negative1.5-2.2 µm0.6-1.1 µmrod-shapedno
69480negative99.996

colony morphology

  • @ref: 43509
  • colony color: light yellow
  • colony shape: circular
  • incubation period: 4 days
  • medium used: MA agar

Culture and growth conditions

culture medium

  • @ref: 43509
  • name: Marine agar (MA)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
43509positivegrowth10-35
43509positiveoptimum25-30mesophilic

culture pH

@refabilitytypepHPH range
43509positivegrowth6-9alkaliphile
43509positiveoptimum7-8

Physiology and metabolism

oxygen tolerance

  • @ref: 43509
  • oxygen tolerance: aerobe

nutrition type

  • @ref: 43509
  • type: chemoautolithotroph

spore formation

@refspore formationconfidence
69481no100
69480no99.997

halophily

@refsaltgrowthtested relationconcentration
43509NaClpositivegrowth1-6 %(w/v)
43509NaClpositiveoptimum3-4 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4350917128adipate-assimilation
4350927689decanoate-assimilation
4350916899D-mannitol-assimilation
4350916024D-mannose-assimilation
4350925115malate-assimilation
4350917234glucose-assimilation
4350930849L-arabinose-assimilation
4350917306maltose-assimilation
43509506227N-acetylglucosamine-assimilation
4350918401phenylacetate-assimilation
4350932032potassium gluconate-assimilation
4350953258sodium citrate-assimilation
43509167632-oxobutanoate-carbon source
43509739183-O-methyl-D-glucose-carbon source
43509181014-hydroxyphenylacetic acid-carbon source
4350930089acetate-carbon source
4350913705acetoacetate-carbon source
4350917925alpha-D-glucose-carbon source
4350936219alpha-lactose-carbon source
4350973706bromosuccinate-carbon source
4350917057cellobiose-carbon source
4350918333D-arabitol-carbon source
4350929990D-aspartate-carbon source
4350915824D-fructose-carbon source
4350928847D-fucose-carbon source
4350912936D-galactose-carbon source
4350918024D-galacturonic acid-carbon source
435098391D-gluconate-carbon source
4350914314D-glucose 6-phosphate-carbon source
4350915748D-glucuronate-carbon source
4350916899D-mannitol-carbon source
4350916024D-mannose-carbon source
4350933801D-saccharate-carbon source
4350916523D-serine-carbon source
4350917924D-sorbitol-carbon source
4350923652dextrin-carbon source
4350915740formate-carbon source
4350916537galactarate-carbon source
4350916865gamma-aminobutyric acid-carbon source
435095291gelatin-carbon source
4350928066gentiobiose-carbon source
4350917754glycerol-carbon source
4350970744glycine-proline-carbon source
4350917596inosine-carbon source
4350916467L-arginine-carbon source
4350929991L-aspartate-carbon source
4350918287L-fucose-carbon source
4350917464L-galactonic acid gamma-lactone-carbon source
4350918183L-pyroglutamic acid-carbon source
4350962345L-rhamnose-carbon source
4350917115L-serine-carbon source
4350925115malate-carbon source
4350917306maltose-carbon source
4350928053melibiose-carbon source
4350974611methyl (R)-lactate-carbon source
4350937657methyl D-glucoside-carbon source
4350951850methyl pyruvate-carbon source
4350917268myo-inositol-carbon source
4350963154N-acetyl-beta-D-mannosamine-carbon source
4350928037N-acetylgalactosamine-carbon source
43509506227N-acetylglucosamine-carbon source
4350935418n-acetylneuraminate-carbon source
4350917309pectin-carbon source
4350917272propionate-carbon source
4350926490quinate-carbon source
4350916634raffinose-carbon source
4350917814salicin-carbon source
4350917164stachyose-carbon source
4350917992sucrose-carbon source
4350927082trehalose-carbon source
4350932528turanose-carbon source
4350953423tween 40-carbon source
43509167632-oxobutanoate-energy source
43509739183-O-methyl-D-glucose-energy source
43509181014-hydroxyphenylacetic acid-energy source
4350930089acetate-energy source
4350913705acetoacetate-energy source
4350917925alpha-D-glucose-energy source
4350936219alpha-lactose-energy source
4350973706bromosuccinate-energy source
4350917057cellobiose-energy source
4350918333D-arabitol-energy source
4350929990D-aspartate-energy source
4350915824D-fructose-energy source
4350928847D-fucose-energy source
4350912936D-galactose-energy source
4350918024D-galacturonic acid-energy source
435098391D-gluconate-energy source
4350914314D-glucose 6-phosphate-energy source
4350915748D-glucuronate-energy source
4350916899D-mannitol-energy source
4350916024D-mannose-energy source
4350933801D-saccharate-energy source
4350916523D-serine-energy source
4350917924D-sorbitol-energy source
4350923652dextrin-energy source
4350915740formate-energy source
4350916537galactarate-energy source
4350916865gamma-aminobutyric acid-energy source
435095291gelatin-energy source
4350928066gentiobiose-energy source
4350917754glycerol-energy source
4350970744glycine-proline-energy source
4350917596inosine-energy source
4350916467L-arginine-energy source
4350929991L-aspartate-energy source
4350918287L-fucose-energy source
4350917464L-galactonic acid gamma-lactone-energy source
4350918183L-pyroglutamic acid-energy source
4350962345L-rhamnose-energy source
4350917115L-serine-energy source
4350925115malate-energy source
4350917306maltose-energy source
4350928053melibiose-energy source
4350974611methyl (R)-lactate-energy source
4350937657methyl D-glucoside-energy source
4350951850methyl pyruvate-energy source
4350917268myo-inositol-energy source
4350963154N-acetyl-beta-D-mannosamine-energy source
4350928037N-acetylgalactosamine-energy source
43509506227N-acetylglucosamine-energy source
4350935418n-acetylneuraminate-energy source
4350917309pectin-energy source
4350917272propionate-energy source
4350926490quinate-energy source
4350916634raffinose-energy source
4350917814salicin-energy source
4350917164stachyose-energy source
4350917992sucrose-energy source
4350927082trehalose-energy source
4350932528turanose-energy source
4350953423tween 40-energy source
4350917234glucose-fermentation
43509casein-hydrolysis
4350916991dna-hydrolysis
4350917895L-tyrosine-hydrolysis
4350928017starch-hydrolysis
4350953426tween 80-hydrolysis
4350916199urea-hydrolysis
4350917632nitrate-reduction
43509645522-hydroxybutyrate+carbon source
43509309162-oxoglutarate+carbon source
43509370543-hydroxybutyrate+carbon source
4350916947citrate+carbon source
4350978697D-fructose 6-phosphate+carbon source
4350932323glucuronamide+carbon source
4350915971L-histidine+carbon source
4350924996lactate+carbon source
4350925115malate+carbon source
43509645522-hydroxybutyrate+energy source
43509309162-oxoglutarate+energy source
43509370543-hydroxybutyrate+energy source
4350916947citrate+energy source
4350978697D-fructose 6-phosphate+energy source
4350932323glucuronamide+energy source
4350915971L-histidine+energy source
4350924996lactate+energy source
4350925115malate+energy source
435095291gelatin+hydrolysis
4350953424tween 20+hydrolysis

enzymes

@refvalueactivityec
43509catalase+1.11.1.6
43509cytochrome oxidase+1.9.3.1
43509arginine dihydrolase-3.5.3.6
43509urease-3.5.1.5
43509gelatinase-
43509alkaline phosphatase+/-3.1.3.1
43509esterase (C 4)+
43509esterase Lipase (C 8)+
43509lipase (C 14)+/-
43509leucine arylamidase+3.4.11.1
43509valine arylamidase+/-
43509acid phosphatase+3.1.3.2
43509cystine arylamidase-3.4.11.3
43509trypsin-3.4.21.4
43509alpha-chymotrypsin-3.4.21.1
43509naphthol-AS-BI-phosphohydrolase-
43509alpha-galactosidase-3.2.1.22
43509beta-galactosidase-3.2.1.23
43509beta-glucuronidase-3.2.1.31
43509alpha-glucosidase-3.2.1.20
43509beta-glucosidase-3.2.1.21
43509N-acetyl-beta-glucosaminidase-3.2.1.52
43509alpha-mannosidase-3.2.1.24
43509alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    4350911-methyl-C18:1ω7c1.3
    43509C12:1 3OH3.7
    43509C16:01.8
    43509C18:02.2
    43509C18:1ω7c90.3
  • type of FA analysis: whole cell analysis
  • incubation medium: MA plates
  • agar/liquid: agar
  • incubation temperature: 25
  • incubation time: 3
  • incubation_oxygen: aerobic
  • software version: Sherlock 6.0
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

  • @ref: 43509
  • sample type: inner content of a sea squirt
  • geographic location: Tsingtao Port, Jiaozhou Bay
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Host#Invertebrates (Other)#Tunicata

taxonmaps

  • @ref: 69479
  • File name: preview.99_65988.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_3523;97_4322;98_46572;99_65988&stattab=map
  • Last taxonomy: Amylibacter cionae subclade
  • 16S sequence: KX790330
  • Sequence Identity:
  • Total samples: 373
  • soil counts: 8
  • aquatic counts: 279
  • animal counts: 86

Sequence information

16S sequences

  • @ref: 43509
  • description: 16S rRNA gene sequence
  • accession: KX790330
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Amylibacter cionae CGMCC 1.15880GCA_014643735contigncbi2035344
66792Amylibacter cionae strain CGMCC 1.158802035344.4wgspatric2035344

GC content

  • @ref: 43509
  • GC-content: 53.7
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.624yes
gram-positiveno97.085yes
anaerobicno99.076yes
aerobicyes95.321yes
halophileyes85.35no
spore-formingno97.373no
glucose-utilno55.614yes
flagellatedno98.375no
thermophileno97.732yes
glucose-fermentno89.866yes

External links

@ref: 43509

culture collection no.: KCTC 52581, CGMCC 1.15880

literature

  • topic: Phylogeny
  • Pubmed-ID: 28866998
  • title: Amylibacter cionae sp. nov., isolated from the sea squirt Ciona savignyi.
  • authors: Wang D, Wei Y, Cui Q, Li W
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002140
  • year: 2017
  • mesh: Animals, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Ubiquinone/chemistry, Urochordata/*microbiology
  • 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
43509Dandan Wang, Yuxi Wei, Qiu Cui, Wenli LiAmylibacter cionae sp. nov., isolated from the sea squirt Ciona savignyi10.1099/ijsem.0.002140IJSEM 67: 3462-3466 201728866998
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
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