Strain identifier

BacDive ID: 6698

Type strain: Yes

Species: Holzapfeliella floricola

Strain Designation: Ryu1-2

Strain history: S. Kawasaki Ryu1-2.

NCBI tax ID(s): 679249 (species)

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General

@ref: 16663

BacDive-ID: 6698

DSM-Number: 23037

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Holzapfeliella floricola Ryu1-2 is a mesophilic bacterium that was isolated from flower of Caltha palustris.

NCBI tax id

  • NCBI tax id: 679249
  • Matching level: species

strain history

@refhistory
16663<- S. Kawasaki, Dept. Bio-Science, Tokyo Univ. Agriculture, Japan; NRIC 0774
67770S. Kawasaki Ryu1-2.

doi: 10.13145/bacdive6698.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Holzapfeliella
  • species: Holzapfeliella floricola
  • full scientific name: Holzapfeliella floricola (Kawasaki et al. 2011) Deshmukh and Oren 2023

  • synonyms

    @refsynonym
    20215Lactobacillus floricola
    20215Holzapfelia floricola

@ref: 16663

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Holzapfeliella

species: Holzapfeliella floricola

full scientific name: Holzapfeliella floricola (Kawasaki et al. 2011) Deshmukh and Oren 2023

strain designation: Ryu1-2

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
125438no94
12543892.982positive

Culture and growth conditions

culture medium

  • @ref: 16663
  • name: MRS MEDIUM (DSMZ Medium 11)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/11
  • composition: Name: MRS MEDIUM (DSMZ Medium 11) Composition: Glucose 20.0 g/l Casein peptone 10.0 g/l Meat extract 10.0 g/l Na-acetate 5.0 g/l Yeast extract 5.0 g/l (NH4)3 citrate 2.0 g/l K2HPO4 2.0 g/l Tween 80 1.0 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperature
16663positivegrowth30
67770positivegrowth30

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: obligate aerobe
  • confidence: 98.1

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose+builds acid from17716
68371maltose+builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
16663----------+/-++---------------++--+-----------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
16663flower of Caltha palustrisCaltha palustrisOze National ParkJapanJPNAsia
67770Flower, buttercup (Caltha palustris)Caltha palustrisOze National ParkJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Flower

taxonmaps

  • @ref: 69479
  • File name: preview.99_7131.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_3344;97_4101;98_5246;99_7131&stattab=map
  • Last taxonomy: Holzapfelia floricola subclade
  • 16S sequence: LC519858
  • Sequence Identity:
  • Total samples: 2442
  • soil counts: 88
  • aquatic counts: 112
  • animal counts: 2097
  • plant counts: 145

Safety information

risk assessment

  • @ref: 16663
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
16663Lactobacillus floricola gene for 16S rRNA, partial sequence, strain: Ryu1-2AB5237801566nuccore1423744
67770Lactobacillus floricola JCM 16512 gene for 16S rRNA, partial sequenceLC5198581514nuccore679249

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus floricola DSM 23037 = JCM 165121423744.4wgspatric1423744
66792Lactobacillus floricola DSM 23037 = JCM 165121423744.3wgspatric1423744
66792Lactobacillus floricola JCM 165122728369687draftimg1423744
66792Lactobacillus floricola DSM 230372667527860draftimg1423744
67770Holzapfeliella floricola DSM 23037 = JCM 16512GCA_001436605scaffoldncbi1423744
67770Holzapfeliella floricola DSM 23037 = JCM 16512GCA_001311465contigncbi1423744

GC content

@refGC-contentmethod
1666348.0high performance liquid chromatography (HPLC)
6777034.5genome sequence analysis
6777048high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes92.982no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no82.14no
125438spore-formingspore-formingAbility to form endo- or exosporesno89.291no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no89.925no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno98yes
125438motile2+flagellatedAbility to perform flagellated movementno94no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno85.7
125439BacteriaNetmotilityAbility to perform movementno64.8
125439BacteriaNetgram_stainReaction to gram-stainingpositive80.7
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe98.1

External links

@ref: 16663

culture collection no.: DSM 23037, JCM 16512, NRIC 0774, KCTC 21006

straininfo link

  • @ref: 76172
  • straininfo: 406305

literature

  • topic: Phylogeny
  • Pubmed-ID: 20601482
  • title: Lactobacillus floricola sp. nov., lactic acid bacteria isolated from mountain flowers.
  • authors: Kawasaki S, Kurosawa K, Miyazaki M, Yagi C, Kitajima Y, Tanaka S, Irisawa T, Okada S, Sakamoto M, Ohkuma M, Niimura Y
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.022988-0
  • year: 2010
  • mesh: Bacterial Typing Techniques, Carbohydrate Metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA-Directed RNA Polymerases/genetics, Flowers/*microbiology, Japan, Lactobacillus/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16663Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23037)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23037
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
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
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
76172Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID406305.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1