Strain identifier

BacDive ID: 63

Type strain: Yes

Species: Saccharibacter floricola

Strain Designation: S-877

Strain history: R. Fudou S-877.

NCBI tax ID(s): 1123227 (strain), 231053 (species)

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General

@ref: 6023

BacDive-ID: 63

DSM-Number: 15669

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

description: Saccharibacter floricola S-877 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from pollen.

NCBI tax id

NCBI tax idMatching level
1123227strain
231053species

strain history

@refhistory
6023<- R. Fudou <- S. Suzuki; S-877
67770R. Fudou S-877.

doi: 10.13145/bacdive63.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodospirillales
  • family: Acetobacteraceae
  • genus: Saccharibacter
  • species: Saccharibacter floricola
  • full scientific name: Saccharibacter floricola Jojima et al. 2004

@ref: 6023

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Acetobacteraceae

genus: Saccharibacter

species: Saccharibacter floricola

full scientific name: Saccharibacter floricola Jojima et al. 2004

strain designation: S-877

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
23247negative2.5-4.0 µm0.8-1.0 µmrod-shapedno
69480negative99.996

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_15669_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15669_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15669_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15669_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15669_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6023YPG MEDIUM (DSMZ Medium 1017)yeshttps://mediadive.dsmz.de/medium/1017Name: YPG MEDIUM (DSMZ Medium 1017) Composition: Glucose 70.0 g/l Agar 15.0 g/l Peptone 10.0 g/l Yeast extract 10.0 g/l Distilled water
23247YPG mediumyes1 % (w/v) yeast extract (Difco), 1 % (w/v) peptone (Difco) and 7% (w/v) glucose, adjusted to pH 6.0 with HCl
23247YUG mediumyes1.0 % (w/v) yeast extract (Difco), 0.1 % (w/v) urea and 20 % (w/v) glucose

culture temp

@refgrowthtypetemperaturerange
6023positivegrowth28mesophilic
23247positivegrowth28mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
23247positiveoptimum5.0-7.0
23247positivegrowth4.0-8.0acidophile
23247positiveminimum4
23247positivemaximum8

Physiology and metabolism

tolerance

  • @ref: 23247
  • compound: D-Glucose
  • percentage: 30

oxygen tolerance

  • @ref: 23247
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
23247no
69481no100
69480no99.997

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2324717790methanol-assimilation
2324717108D-arabinose-builds acid from
2324717924D-sorbitol-builds acid from
2324716813galactitol-builds acid from
2324716236ethanol-builds acid from
2324717754glycerol-builds acid from
2324762345L-rhamnose-builds acid from
2324717266L-sorbose-builds acid from
2324716634raffinose-builds acid from
2324730089acetate-oxidation
2324712936D-galactose+builds acid from
2324717634D-glucose+builds acid from
2324716899D-mannitol+builds acid from
2324716024D-mannose+builds acid from
2324765327D-xylose+builds acid from
2324730849L-arabinose+builds acid from
2324728053melibiose+builds acid from
2324717992sucrose+builds acid from
2324715824D-fructose+/-builds acid from
2324724996lactate+/-oxidation

metabolite production

@refChebi-IDmetaboliteproduction
2324716016dihydroxyacetoneno
2324762968celluloseno
2324730089acetateyes
23247174265-dehydro-D-gluconateyes
23247168082-dehydro-D-gluconateyes

enzymes

@refvalueactivityec
23247catalase+1.11.1.6
23247cytochrome oxidase-1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6023pollenKanagawaJapanJPNAsia
67770Pollen collected in Kanagawa Pref.JapanJPNAsia

isolation source categories

  • Cat1: #Host Body-Site
  • Cat2: #Plant
  • Cat3: #Fruit (Seed)

taxonmaps

  • @ref: 69479
  • File name: preview.99_6726.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_29;96_3179;97_3897;98_4955;99_6726&stattab=map
  • Last taxonomy: Saccharibacter floricola subclade
  • 16S sequence: AB110421
  • Sequence Identity:
  • Total samples: 4430
  • soil counts: 690
  • aquatic counts: 590
  • animal counts: 2893
  • plant counts: 257

Safety information

risk assessment

  • @ref: 6023
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Saccharibacter floricola DNA, 16S-23S rRNA ITS region. strain: JCM 12116AB210092680ena231053
6023Saccharibacter floricola gene for 16S ribosomal RNA, partial sequenceAB1104211436ena231053

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Saccharibacter floricola DSM 156691123227.4wgspatric1123227
66792Saccharibacter floricola DSM 156692518645607draftimg1123227
67770Saccharibacter floricola DSM 15669GCA_000378165scaffoldncbi1123227

GC content

  • @ref: 67770
  • GC-content: 52.3
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes67.837no
flagellatedno83.482yes
gram-positiveno97.902yes
anaerobicno98.665no
aerobicyes63.457no
halophileno79.695no
spore-formingno96.318yes
thermophileno91.226no
glucose-utilyes79.496no
glucose-fermentno85.956no

External links

@ref: 6023

culture collection no.: DSM 15669, AJ 13480, JCM 12116

straininfo link

  • @ref: 69747
  • straininfo: 134459

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15545468Saccharibacter floricola gen. nov., sp. nov., a novel osmophilic acetic acid bacterium isolated from pollen.Jojima Y, Mihara Y, Suzuki S, Yokozeki K, Yamanaka S, Fudou RInt J Syst Evol Microbiol10.1099/ijs.0.02911-02004Acetic Acid/metabolism, Acetobacteraceae/*classification/cytology/*isolation & purification/physiology, Aerobiosis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Ethanol/metabolism, Fatty Acids/analysis/isolation & purification, Genes, rRNA, Gentian Violet, Japan, Molecular Sequence Data, Osmolar Concentration, Phenazines, Phylogeny, Pollen/*microbiology, Quinones/analysis/isolation & purification, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Xylitol/metabolismEnzymology
Phylogeny25336723Bombella intestini gen. nov., sp. nov., an acetic acid bacterium isolated from bumble bee crop.Li L, Praet J, Borremans W, Nunes OC, Manaia CM, Cleenwerck I, Meeus I, Smagghe G, De Vuyst L, Vandamme PInt J Syst Evol Microbiol10.1099/ijs.0.068049-02014Acetic Acid, Acetobacteraceae/*classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, Bees/*microbiology, Belgium, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6023Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15669)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15669
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
23247Yasuko Jojima, Yasuhiro Mihara, Sonoko Suzuki, Kenzo Yokozeki, Shigeru Yamanaka, Ryosuke Fudou10.1099/ijs.0.02911-0Saccharibacter floricola gen. nov., sp. nov., a novel osmophilic acetic acid bacterium isolated from pollenIJSEM 54: 2263-2267 200415545468
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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
69747Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134459.1StrainInfo: A central database for resolving microbial strain identifiers