Strain identifier

BacDive ID: 141146

Type strain: Yes

Species: Actibacterium pelagium

Strain Designation: JN33

Strain history: <- Lili Guo, Second Institute of Oceanography

NCBI tax ID(s): 2029103 (species)

« back to strain detail view
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: 64969

BacDive-ID: 141146

DSM-Number: 109121

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

description: Actibacterium pelagium JN33 is an aerobe, chemoorganotroph, Gram-negative bacterium that forms circular colonies and was isolated from seawater.

NCBI tax id

  • NCBI tax id: 2029103
  • Matching level: species

strain history

@refhistory
64969<- J.-S. Lee, KCTC; KCTC 52653 <- L. Guo, Zhejiang Univ., Hangzhou, China; JN33
67771<- Lili Guo, Second Institute of Oceanography

doi: 10.13145/bacdive141146.20230509.8.1

Name and taxonomic classification

LPSN

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

@ref: 64969

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Actibacterium

species: Actibacterium pelagium

full scientific name: Actibacterium pelagium Guo et al. 2017

strain designation: JN33

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
44067negative1.5-2.5 µm0.6-1.2 µmrod-shapedno
69480no93.178
69480negative99.999

colony morphology

  • @ref: 44067
  • colony size: 2 mm
  • colony color: cream
  • colony shape: circular
  • incubation period: 3 days
  • medium used: MA agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
44067Marine agar (MA)yes
64969BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
44067positivegrowth10-35
44067positiveoptimum30mesophilic
64969positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
44067positivegrowth6.5-8.5alkaliphile
44067positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
44067aerobe
67771aerobe

nutrition type

  • @ref: 44067
  • type: chemoorganotroph

spore formation

@refspore formationconfidence
44067no
69481no100
69480no99.991

halophily

@refsaltgrowthtested relationconcentration
44067NaClnogrowth0 %(w/v)
44067Marine saltsnogrowth0 %(w/v)
44067NaClpositivegrowth0.5-5.0 %(w/v)
44067NaClpositiveoptimum3 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4406717057cellobiose-builds acid from
4406712936D-galactose-builds acid from
4406716988D-ribose-builds acid from
4406716236ethanol-builds acid from
4406762345L-rhamnose-builds acid from
4406717266L-sorbose-builds acid from
4406717716lactose-builds acid from
4406717306maltose-builds acid from
440676731melezitose-builds acid from
4406716634raffinose-builds acid from
4406715963ribitol-builds acid from
4406727082trehalose-builds acid from
4406791260disodium malate-carbon source
4406717561L-cysteine-carbon source
4406717716lactose-carbon source
4406727082trehalose-carbon source
4406791260disodium malate-energy source
4406717561L-cysteine-energy source
4406717716lactose-energy source
4406727082trehalose-energy source
4406728017starch-hydrolysis
4406753424tween 20-hydrolysis
4406753423tween 40-hydrolysis
4406753426tween 80-hydrolysis
4406717632nitrate-reduction
4406716899D-mannitol+builds acid from
4406717924D-sorbitol+builds acid from
4406765327D-xylose+builds acid from
4406717234glucose+builds acid from
4406717057cellobiose+carbon source
4406716024D-mannose+carbon source
4406717234glucose+carbon source
4406717754glycerol+carbon source
4406724898isoleucine+carbon source
4406716977L-alanine+carbon source
4406730849L-arabinose+carbon source
4406729864mannitol+carbon source
4406732954sodium acetate+carbon source
4406784997sodium gluconate+carbon source
4406717992sucrose+carbon source
4406717057cellobiose+energy source
4406716024D-mannose+energy source
4406717234glucose+energy source
4406717754glycerol+energy source
4406724898isoleucine+energy source
4406716977L-alanine+energy source
4406730849L-arabinose+energy source
4406729864mannitol+energy source
4406732954sodium acetate+energy source
4406784997sodium gluconate+energy source
4406717992sucrose+energy source
440674853esculin+hydrolysis
440675291gelatin+hydrolysis
4406717268myo-inositol+/-builds acid from
4406716236ethanol+/-carbon source
4406762345L-rhamnose+/-carbon source
4406717266L-sorbose+/-carbon source
4406717306maltose+/-carbon source
4406716634raffinose+/-carbon source
4406716236ethanol+/-energy source
4406762345L-rhamnose+/-energy source
4406717266L-sorbose+/-energy source
4406717306maltose+/-energy source
4406716634raffinose+/-energy 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
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
4406728971ampicillinyesyes10 µg (disc)
440672676amoxicillinyesyes20 µg (disc)
440673393carbenicillinyesyes100 µg (disc)
44067209807cefoxitinyesyes30 µg (disc)
4406717698chloramphenicolyesyes30 µg (disc)
4406748923erythromycinyesyes15 µg (disc)
440676104kanamycinyesyes30 µg (disc)
4406771415nitrofurantoinyesyes300 µg (disc)
4406728368novobiocinyesyes30 µg (disc)
4406717334penicillinyesyes10 µg (disc)
440678309polymyxin byesyes300 Unit (disc)
4406728077rifampicinyesyes5 µg (disc)
4406727902tetracyclineyesyes30 µg (disc)
4406728864tobramycinyesyes10 µg (disc)
4406728001vancomycinyesyes30 µg (disc)
4406728669bacitracinyesyes0.04 Unit (disc)
4406717833gentamicinyesyes10 µg (disc)
440677660nystatinyesyes100 µg (disc)
4406717076streptomycinyesyes10 µg (disc)

metabolite production

@refChebi-IDmetaboliteproduction
4406735581indoleno
6836935581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
44067cytochrome oxidase+1.9.3.1
44067catalase+/-1.11.1.6
44067arginine dihydrolase-3.5.3.6
44067urease-3.5.1.5
44067acid phosphatase+3.1.3.2
44067alkaline phosphatase+3.1.3.1
44067esterase (C 4)+
44067esterase Lipase (C 8)+
44067naphthol-AS-BI-phosphohydrolase+
44067N-acetyl-beta-glucosaminidase-3.2.1.52
44067cystine arylamidase-3.4.11.3
44067alpha-chymotrypsin-3.4.21.1
44067alpha-fucosidase-3.2.1.51
44067alpha-galactosidase-3.2.1.22
44067beta-glucosidase-3.2.1.21
44067beta-galactosidase-3.2.1.23
44067alpha-glucosidase-3.2.1.20
44067beta-glucuronidase-3.2.1.31
44067lipase (C 14)-
44067alpha-mannosidase-3.2.1.24
44067valine arylamidase-
44067trypsin-3.4.21.4
68369gelatinase-
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
68382alkaline phosphatase-3.1.3.1
68382esterase lipase (C 8)-
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-
68382alpha-galactosidase-3.2.1.22
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
    4406711-Methyl C18:1ω7c4.8
    44067C10:0 3OH4.6
    44067C16:011.3
    44067C16:1ω7c / C16:1ω6c0.7
    44067C18:04.6
    44067C18:1ω7c / C18:1ω6c66.9
    44067C20:1ω7c0.5
    44067C18:0 iso5.8
  • type of FA analysis: whole cell analysis
  • incubation medium: MA
  • incubation temperature: 30
  • incubation time: 3
  • library/peak naming table: RTSBA6
  • system: MIS MIDI
  • 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
64969--+/---+--------------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
64969-----+/---------------

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperaturecountryorigin.countrycontinentlatitudelongitude
44067seawater2015-12western Pacific Oceannatural seawater agarsupplemented with 0.05% peptone, 0.01% yeast extract, 1.5% agar, pH 7.2-7.430 days25
64969seawater samplewestern Pacific Ocean (3° N, 130 ° E)International waters
67771From seawaterwestern PacificChinaCHNAsia3130

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

Safety information

risk assessment

  • @ref: 64969
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 64969
  • description: Actibacterium pelagium strain JN33 16S ribosomal RNA gene, partial sequence
  • accession: KY273602
  • length: 1456
  • database: ena
  • NCBI tax ID: 2029103

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actibacterium pelagium JN33GCA_002285415scaffoldncbi2029103
66792Actibacterium pelagium CGMCC 1.16012GCA_014644355contigncbi2029103
66792Actibacterium pelagium strain CGMCC 1.160122029103.7wgspatric2029103
66792Actibacterium pelagium JN332832254508draftimg2029103

GC content

  • @ref: 44067
  • GC-content: 57.8
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno94.845no
gram-positiveno98.398yes
anaerobicno97.768yes
aerobicyes87.979no
halophileyes82.076no
spore-formingno97.253yes
glucose-utilyes65.411no
thermophileno90.147yes
motileno94.675yes
glucose-fermentno91.191yes

External links

@ref: 64969

culture collection no.: CGMCC 1.16012, KCTC 52653, DSM 109121

straininfo link

  • @ref: 96868
  • straininfo: 404323

literature

  • topic: Phylogeny
  • Pubmed-ID: 29039308
  • title: Actibacterium pelagium sp. nov., a novel alphaproteobacterium, and emended description of the genus Actibacterium.
  • authors: Guo LL, Wu YH, Xu XW, Huang CJ, Xu YY, Cheng H, Wang CS, Wu M, Xu XW
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002417
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
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
44067Li-Li Guo, Yue-Hong Wu, Xiao-Wu Xu, Chao-Jie Huang, Yun-Yun Xu, Hong Cheng, Chun-Sheng Wang, Min Wu and Xue-Wei XuActibacterium pelagium sp. nov., a novel alphaproteobacterium, and emended description of the genus Actibacterium10.1099/ijsem.0.002417IJSEM 67: 5080-5086 201729039308
64969Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-109121Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 109121)
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
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
96868Reimer, 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-ID404323.1