Strain identifier

BacDive ID: 23231

Type strain: Yes

Species: Alloyangia pacifica

Strain Designation: DX5-10

Strain history: CIP <- 2006, JCM

NCBI tax ID(s): 311180 (species)

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General

@ref: 19043

BacDive-ID: 23231

DSM-Number: 26894

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

description: Alloyangia pacifica DX5-10 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from coastal sediment.

NCBI tax id

  • NCBI tax id: 311180
  • Matching level: species

strain history

@refhistory
19043<- JCM <- D. Xin; DX5-10
400252006, JCM
67770AS 1.3455 <-- D. Xin DX5-10.
121501CIP <- 2006, JCM

doi: 10.13145/bacdive23231.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Alloyangia
  • species: Alloyangia pacifica
  • full scientific name: Alloyangia pacifica (Dai et al. 2006) Deshmukh and Oren 2023

  • synonyms

    @refsynonym
    20215Salipiger pacificus
    20215Yangia pacifica

@ref: 19043

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Salipiger

species: Salipiger pacificus

full scientific name: Salipiger pacificus (Dai et al. 2006) Hördt et al. 2020

strain designation: DX5-10

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31669negative1-1.5 µm0.8 µmrod-shapedyes
69480negative99.993
121501negativerod-shapedyes

colony morphology

  • @ref: 19043
  • incubation period: 1-2 days

pigmentation

  • @ref: 31669
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
19043BACTO 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
40025Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
121501CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
19043positivegrowth30mesophilic
31669positivegrowth22-40
31669positiveoptimum37mesophilic
40025positivegrowth30mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31669positivegrowth05-10alkaliphile
31669positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31669aerobe
121501obligate aerobe

spore formation

@refspore formationconfidence
31669no
69481no100
69480no99.996

halophily

@refsaltgrowthtested relationconcentration
31669NaClpositivegrowth01-10 %
31669NaClpositiveoptimum5 %

observation

@refobservation
31669aggregates in chains
67770quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3166929016arginine+carbon source
3166924996lactate+carbon source
3166925115malate+carbon source
3166917306maltose+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
6836916199urea+hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
12150117632nitrate-reduction
12150116301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12150135581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
19043catalase+1.11.1.6
19043cytochrome-c oxidase+1.9.3.1
31669catalase+1.11.1.6
31669cytochrome oxidase+1.9.3.1
31669urease+3.5.1.5
68369gelatinase-
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6
121501oxidase+
121501catalase+1.11.1.6
121501urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
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

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121501-+++-++---++---+++--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
19043----++/--+/-+++++++--+++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
19043coastal sedimentEast China Sea
67770Coastal sediment of the East China Sea
121501Environment, Coastal sedimentEast SeaChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Coast

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
190431Risk group (German classification)
1215011Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
19043Yangia pacifica partial 16S rRNA gene, type strain DX5-10TAJ8772651351ena311180
67770Yangia pacifica gene for 16S ribosomal RNA, partial sequence, strain: JCM 12573LC0767581384ena311180

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Yangia pacifica strain CGMCC 1.3455311180.10wgspatric311180
66792Yangia pacifica strain DSM 26894311180.11wgspatric311180
66792Salipiger pacificus CGMCC 1.34552617270881draftimg311180
66792Salipiger pacificus DSM 268942619618962draftimg311180
67770Alloyangia pacifica CGMCC 1.3455GCA_900100725contigncbi311180
67770Alloyangia pacifica DSM 26894GCA_900116195scaffoldncbi311180

GC content

@refGC-contentmethod
1904363.3thermal denaturation, midpoint method (Tm)
3166963.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.882yes
anaerobicno97.739yes
halophileyes60.378no
spore-formingno96.53yes
glucose-utilyes95.714yes
motileyes69.788no
flagellatedno72.461no
aerobicyes93.109yes
thermophileno99.368yes
glucose-fermentno88.549yes

External links

@ref: 19043

culture collection no.: DSM 26894, CGMCC 1.3455, JCM 12573, CIP 109187, NCIMB 14310

straininfo link

  • @ref: 87457
  • straininfo: 291017

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16514022Yangia pacifica gen. nov., sp. nov., a novel member of the Roseobacter clade from coastal sediment of the East China Sea.Dai X, Wang BJ, Yang QX, Jiao NZ, Liu SJInt J Syst Evol Microbiol10.1099/ijs.0.64013-02006Bacteriochlorophyll A/analysis, DNA, Ribosomal/chemistry, Geologic Sediments/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Roseobacter/*classification/genetics/isolation & purification/physiologyEnzymology
Phylogeny34550069Yangia mangrovi sp. nov., a novel member of the Roseobacter clade isolated from mangrove soil and emended description of Yangia pacifica Dai et al. 2006.Verma A, Sundharam SS, Pal Y, Bisht B, Yadav P, Krishnamurthi SInt J Syst Evol Microbiol10.1099/ijsem.0.0050212021Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae, *Roseobacter, Sequence Analysis, DNA, Soil, UbiquinoneTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
19043Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26894)https://www.dsmz.de/collection/catalogue/details/culture/DSM-26894
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
31669Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2794828776041
40025Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6900
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
87457Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID291017.1StrainInfo: A central database for resolving microbial strain identifiers
121501Curators of the CIPCollection of Institut Pasteur (CIP 109187)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109187