Name: Rhizocola hellebori K12-0602
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 24218

Type strain:

Species: Rhizocola hellebori

Strain Designation: K12-0602

Culture col. no.: DSM 45988, NBRC 109834

Strain history: <- A. Matsumoto, Kitasato Univ., Tokyo, Japan; K12-0602 <- Y. Kawaguchi

NCBI tax ID(s): 1392758 (species)

SI-ID 398233

DSM 45988

Special Collections

DSMZ

Section

Rhizocola hellebori K12-0602 is a spore-forming bacterium that was isolated from root of Helleborus orientalis .

spore-forming
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micromonosporales*
	Family	*Micromonosporaceae*
	Genus	*Rhizocola*
	Species	**Rhizocola hellebori**
	Full Scientific Name (LPSN)	Rhizocola hellebori Matsumoto et al. 2014

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	positive Confidence in %90.344

Multimedia content

[Ref.: #21345]

Caption:

Medium 554 28°C

[Ref.: #21345]

Intellectual property rights:

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]

Ability of spore formation

yes Confidence in %92

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #21345]	Sample type/isolated from	root of Helleborus orientalis
[Ref.: #21345]	Host species	Helleborus orientalis
[Ref.: #21345]	Geographic location (country and/or sea, region)	Kanagawa Prefecture, Medicinal Plant Garden of Kitasato University
[Ref.: #21345]	Country	Japan
[Ref.: #21345]	Country ISO 3 Code	JPN
[Ref.: #21345]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root (Rhizome)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB848707 (>99% sequence identity) for Rhizocola hellebori subclade from Microbeatlas

Aquatic Samples	28
Soil Samples	852
Animal Samples	16
Plant Samples	40
Total Samples	936

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #21345]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #21345]	Rhizocola hellebori gene for 16S ribosomal RNA, partial sequence	AB848707	1451	GenBank ENA	1392758 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rhizocola hellebori NBRC 109834	GCA_016862955	contig	GenBank ENA	1392758 tax ID	*
[Ref.: #66792]	Rhizocola hellebori strain NBRC 109834	1392758.3	wgs	PATRIC	1392758 tax ID	*

[Ref.: #21345]

GC-content

67 mol%

high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Rhizocola hellebori strain NBRC 109834 PATRIC: 1392758.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	92	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhizocola hellebori strain NBRC 109834 PATRIC: 1392758.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	90.344	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	95.253	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	86	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	88.139	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	91.278	no
[Ref.: #69480]	flagellated	motile2+ⓘ	no	86.5	no

Availability in culture collections External links

[Ref.: #21345]

Culture collection no.

DSM 45988, NBRC 109834

[Ref.: #88161]

SI-ID 398233

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Allorhizocola rhizosphaerae gen. nov., sp. nov., a new member of Micromonosporaceae isolated from rhizosphere soil of the plant Calligonum mongolicum.	Sun Y, Jiang ZM, Zhao LL, Su J, Yu LY, Tian YQ, Zhang YQ	Int J Syst Evol Microbiol	10.1099/ijsem.0.003114	2018	*
Phylogeny	Rhizocola hellebori gen. nov., sp. nov., an actinomycete of the family Micromonosporaceae containing 3,4-dihydroxydiaminopimelic acid in the cell-wall peptidoglycan.	Matsumoto A, Kawaguchi Y, Nakashima T, Iwatsuki M, Omura S, Takahashi Y	Int J Syst Evol Microbiol	10.1099/ijs.0.060293-0	2014	*

References

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#21345

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45988

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69479

João 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.: MicrobeAtlas 1.0 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#88161

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID398233.1 )

* These data were automatically processed and therefore are not curated

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Rhizocola hellebori strain NBRC 109834

Rhizocola hellebori strain NBRC 109834

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