Strain identifier

BacDive ID: 13657

Type strain: Yes

Species: Gemmobacter caeni

Strain Designation: DCA-1

Strain history: <- S.-P. Li, Nanjing Agric. Univ., China <- J. Zeng

NCBI tax ID(s): 589035 (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 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 15972

BacDive-ID: 13657

DSM-Number: 21823

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, rod-shaped

description: Gemmobacter caeni DCA-1 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from activated sludge of butachlor waste water treatment system.

NCBI tax id

  • NCBI tax id: 589035
  • Matching level: species

strain history

  • @ref: 15972
  • history: <- S.-P. Li, Nanjing Agric. Univ., China <- J. Zeng

doi: 10.13145/bacdive13657.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Paracoccaceae
  • genus: Gemmobacter
  • species: Gemmobacter caeni
  • full scientific name: Gemmobacter caeni (Zheng et al. 2011) Chen et al. 2013

  • synonyms

    • @ref: 20215
    • synonym: Catellibacterium caeni

@ref: 15972

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Gemmobacter

species: Gemmobacter caeni

full scientific name: Gemmobacter caeni (Zheng et al. 2011) Chen et al. 2013

strain designation: DCA-1

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
30689negativerod-shapedno
69480negative99.998

pigmentation

  • @ref: 30689
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 15972
  • name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/381
  • composition: Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
15972positivegrowth30mesophilic
30689positivegrowth15-40
30689positiveoptimum32.5mesophilic

culture pH

@refabilitytypepHPH range
30689positivegrowth04-08acidophile
30689positiveoptimum5

Physiology and metabolism

oxygen tolerance

  • @ref: 30689
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
30689no
69481no100
69480no99.98

halophily

@refsaltgrowthtested relationconcentration
30689NaClpositivegrowth0-5 %
30689NaClpositiveoptimum1.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3068922599arabinose+carbon source
3068916947citrate+carbon source
3068924265gluconate+carbon source
3068917234glucose+carbon source
3068925115malate+carbon source
3068917306maltose+carbon source
3068929864mannitol+carbon source
3068937684mannose+carbon source
306894853esculin+hydrolysis

enzymes

@refvalueactivityec
30689alkaline phosphatase+3.1.3.1
30689alpha-galactosidase+3.2.1.22

Isolation, sampling and environmental information

isolation

  • @ref: 15972
  • sample type: activated sludge of butachlor waste water treatment system
  • geographic location: Nantong, Jiangsu province
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste#Activated sludge
#Engineered#Waste#Wastewater

taxonmaps

  • @ref: 69479
  • File name: preview.99_6187.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_926;97_3623;98_4586;99_6187&stattab=map
  • Last taxonomy: Gemmobacter
  • 16S sequence: FJ386516
  • Sequence Identity:
  • Total samples: 3663
  • soil counts: 396
  • aquatic counts: 2562
  • animal counts: 599
  • plant counts: 106

Sequence information

16S sequences

  • @ref: 15972
  • description: Gemmobacter caeni strain DCA-1 16S ribosomal RNA gene, partial sequence
  • accession: FJ386516
  • length: 1435
  • database: ena
  • NCBI tax ID: 589035

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gemmobacter caeni DSM 21823GCA_003054195scaffoldncbi589035
66792Gemmobacter caeni CGMCC 1.7745GCA_007830625scaffoldncbi589035
66792Gemmobacter caeni strain CGMCC 1.7745589035.6wgspatric589035
66792Gemmobacter caeni strain DSM 21823589035.3wgspatric589035
66792Gemmobacter caeni DSM 21823 (v2)2739367660draftimg589035
66792Gemmobacter caeni CGMCC 1.77452596583642draftimg589035

GC content

@refGC-contentmethod
1597262.5thermal denaturation, midpoint method (Tm)
3068962.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno82.888no
gram-positiveno98.836no
anaerobicno96.658no
halophileno86.26yes
spore-formingno96.345no
glucose-utilyes87.335yes
aerobicyes60.809yes
thermophileno98.24yes
motileno61.947yes
glucose-fermentno85.775no

External links

@ref: 15972

culture collection no.: DSM 21823, CGMCC 1.7745

straininfo link

  • @ref: 82840
  • straininfo: 399761

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20833880Description of Catellibacterium caeni sp. nov., reclassification of Rhodobacter changlensis Anil Kumar et al. 2007 as Catellibacterium changlense comb. nov. and emended description of the genus Catellibacterium.Zheng JW, Chen YG, Zhang J, Ni YY, Li WJ, He J, Li SPInt J Syst Evol Microbiol10.1099/ijs.0.025494-02010DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacter/*classification/genetics/*isolation & purification/metabolism, Rhodobacteraceae/*classification/genetics/*isolation & purification/metabolismMetabolism
Phylogeny21478399Catellibacterium nanjingense sp. nov., a propanil-degrading bacterium isolated from activated sludge, and emended description of the genus Catellibacterium.Zhang J, Chen SA, Zheng JW, Cai S, Hang BJ, He J, Li SPInt J Syst Evol Microbiol10.1099/ijs.0.029819-02011Aerobiosis, Anaerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Microscopy, Electron, Transmission, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Propanil/*metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Sequence Analysis, DNA, Sewage/*microbiology, Sodium Chloride/metabolism, TemperatureGenetics
Phylogeny22493172Description of Gemmobacter fontiphilus sp. nov., isolated from a freshwater spring, reclassification of Catellibacterium nectariphilum as Gemmobacter nectariphilus comb. nov., Catellibacterium changlense as Gemmobacter changlensis comb. nov., Catellibacterium aquatile as Gemmobacter aquaticus nom. nov., Catellibacterium caeni as Gemmobacter caeni comb. nov., Catellibacterium nanjingense as Gemmobacter nanjingensis comb. nov., and emended description of the genus Gemmobacter and of Gemmobacter aquatilis.Chen WM, Cho NT, Huang WC, Young CC, Sheu SYInt J Syst Evol Microbiol10.1099/ijs.0.042051-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Fresh Water/*microbiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Natural Springs/*microbiology, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, TaiwanGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
15972Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21823)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21823
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
30689Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2702028776041
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
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
82840Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID399761.1StrainInfo: A central database for resolving microbial strain identifiers