Strain identifier

BacDive ID: 13655

Type strain: Yes

Species: Gemmobacter nectariphilus

Strain history: Y. Tanaka AST4.

NCBI tax ID(s): 1121271 (strain), 220343 (species)

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General

@ref: 5913

BacDive-ID: 13655

DSM-Number: 15620

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

description: Gemmobacter nectariphilus DSM 15620 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from activated sludge.

NCBI tax id

NCBI tax idMatching level
1121271strain
220343species

strain history

@refhistory
5913<- Y. Tanaka; AST4
67770Y. Tanaka AST4.

doi: 10.13145/bacdive13655.20230509.8.1

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 nectariphilus
  • full scientific name: Gemmobacter nectariphilus (Tanaka et al. 2004) Chen et al. 2013

  • synonyms

    @refsynonym
    20215Wagnerdoeblera nectariphila
    20215Catellibacterium nectariphilum

@ref: 5913

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Gemmobacter

species: Gemmobacter nectariphilus

full scientific name: Gemmobacter nectariphilus (Tanaka et al. 2004) Chen et al. 2013

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilitycell lengthcell widthconfidence
30689negativerod-shapedno
29963negativerod-shapedno1.65 µm0.7 µm
69480negative99.999

pigmentation

@refproduction
29963no
30689yes

Culture and growth conditions

culture medium

  • @ref: 5913
  • name: NPB MEDIUM (DSMZ Medium 995)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/995
  • composition: Name: NPB MEDIUM (DSMZ Medium 995) Composition: Agar 15.0 g/l Tryptone peptone 10.0 g/l D-Glucose 5.0 g/l Yeast extract 2.0 g/l K2HPO4 1.0 g/l MgSO4 x 7 H2O 1.0 g/l KH2PO4 0.5 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
5913positivegrowth30mesophilic
30689positivegrowth15-40
29963positivegrowth20-37
30689positiveoptimum30mesophilic
29963positiveoptimum30mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepH
29963positivegrowth06-08
30689positivegrowth06-08
29963positiveoptimum7
30689positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29963aerobe
30689aerobe

spore formation

@refspore formationconfidence
30689no
69481no90
69480no99.995

halophily

@refsaltgrowthtested relationconcentration
30689NaClpositivegrowth0-2 %
30689NaClpositiveoptimum1 %
29963NaClpositiveoptimum<3 %

observation

@refobservation
29963aggregates in chains
67770quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2996321217L-alaninamide+carbon source
2996329987glutamate+carbon source
2996328087glycogen+carbon source
2996324996lactate+carbon source
2996351850methyl pyruvate+carbon source
2996317822serine+carbon source
2996330031succinate+carbon source
2996353426tween 80+carbon source

enzymes

@refvalueactivityec
29963catalase+1.11.1.6
29963cytochrome oxidase+1.9.3.1
30689alkaline phosphatase+3.1.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5913activated sludgeKawasaki plant of Ajinomoto Co.JapanJPNAsia
67770Activated sludgeJapanJPNAsia

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Activated sludge

taxonmaps

  • @ref: 69479
  • File name: preview.99_1629.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_926;97_1078;98_1287;99_1629&stattab=map
  • Last taxonomy: Gemmobacter nectariphilus subclade
  • 16S sequence: AB101543
  • Sequence Identity:
  • Total samples: 7825
  • soil counts: 639
  • aquatic counts: 5101
  • animal counts: 1734
  • plant counts: 351

Safety information

risk assessment

  • @ref: 5913
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 5913
  • description: Catellibacterium nectariphilum gene for 16S ribosomal RNA, partial sequence
  • accession: AB101543
  • length: 1386
  • database: ena
  • NCBI tax ID: 1121271

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Catellibacterium nectariphilum DSM 156201121271.3wgspatric1121271
66792Gemmobacter nectariphilus DSM 156202524614723draftimg1121271
67770Gemmobacter nectariphilus DSM 15620GCA_000429765scaffoldncbi1121271

GC content

@refGC-contentmethod
591364.5
6777064.5high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno90no
motileno68.043no
flagellatedno92.52no
gram-positiveno98.217yes
anaerobicno98.401no
aerobicyes84.759no
halophileno65.349yes
spore-formingno96.429no
thermophileno94.529yes
glucose-utilyes58.236no
glucose-fermentno88.778no

External links

@ref: 5913

culture collection no.: DSM 15620, JCM 11959, NBRC 100046, AST 4, CGMCC 1.8899, CGMCC 1.8904

straininfo link

  • @ref: 82838
  • straininfo: 132013

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15143049Catellibacterium nectariphilum gen. nov., sp. nov., which requires a diffusible compound from a strain related to the genus Sphingomonas for vigorous growth.Tanaka Y, Hanada S, Manome A, Tsuchida T, Kurane R, Nakamura K, Kamagata YInt J Syst Evol Microbiol10.1099/ijs.0.02750-02004Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Microscopy, Electron, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/growth & development/*metabolism, Sewage/microbiology, Sphingomonas/*metabolismGenetics
Phylogeny19820000Catellibacterium aquatile sp. nov., isolated from fresh water, and emended description of the genus Catellibacterium Tanaka et al. 2004.Liu Y, Xu CJ, Jiang JT, Liu YH, Song XF, Li H, Liu ZPInt J Syst Evol Microbiol10.1099/ijs.0.017632-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fresh Water/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/metabolism, Sodium Chloride/metabolismGenetics
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
Phylogeny24014623Gemmobacter megaterium sp. nov., isolated from coastal planktonic seaweeds.Liu JJ, Zhang XQ, Chi FT, Pan J, Sun C, Wu MInt J Syst Evol Microbiol10.1099/ijs.0.050955-02013Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater, Seaweed/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryGenetics
Phylogeny29022543Gemmobacter straminiformis sp. nov., isolated from an artificial fountain.Kang JY, Kim MJ, Chun J, Son KP, Jahng KYInt J Syst Evol Microbiol10.1099/ijsem.0.0024032017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Ubiquinone/chemistry, *Water MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
5913Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15620)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15620
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
29963Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2633228776041
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
82838Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID132013.1StrainInfo: A central database for resolving microbial strain identifiers