Name: Phytohabitans rumicis K11-0047
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 23125

Type strain:

Species: Phytohabitans rumicis

Strain Designation: K11-0047

Culture col. no.: DSM 45865, BCC 48146, JCM 17829, NBRC 108638

Strain history: A. Matsumoto K11-0047.

NCBI tax ID(s): 1076125 (species)

SI-ID 404075

DSM 45865

Section

Phytohabitans rumicis K11-0047 is an aerobe, spore-forming, mesophilic bacterium that was isolated from roots of Rumex acetosa.

Gram-positive
spore-forming
aerobe
mesophilic
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	*Phytohabitans*
	Species	**Phytohabitans rumicis**
	Full Scientific Name (LPSN)	Phytohabitans rumicis Inahashi et al. 2012

Information on morphological and physiological properties Morphology

[Ref.: #30512]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #30512]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #19190]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

[Ref.: #19190]

Culture medium growth

[Ref.: #19190]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #19190]

Culture medium

N-Z-AMINE-MEDIUM (DSMZ Medium 554)

[Ref.: #19190]

Culture medium growth

[Ref.: #19190]

Culture medium link

Medium recipe at MediaDive

[Ref.: #19190]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #19190]	growth	28 °C
[Ref.: #30512]	growth	20-34 °C
[Ref.: #30512]	optimum	27 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #19190]	Temperature range	mesophilic
[Ref.: #30512]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30512]			optimum	8
[Ref.: #30512]			growth	07-11

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30512]

Oxygen tolerance

aerobe

[Ref.: #30512]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %99.999

[Ref.: #67770]

Observation

quinones: MK-10(H₈), MK-10(H₆)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30512]	arabinose ChEBI	+	carbon source
[Ref.: #30512]	fructose ChEBI	+	carbon source
[Ref.: #30512]	glucose ChEBI	+	carbon source
[Ref.: #30512]	maltose ChEBI	+	carbon source
[Ref.: #30512]	mannitol ChEBI	+	carbon source
[Ref.: #30512]	nitrate ChEBI	+	reduction
[Ref.: #30512]	sorbitol ChEBI	+	carbon source
[Ref.: #30512]	sucrose ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #30512]	acid phosphatase	+	3.1.3.2
[Ref.: #30512]	alkaline phosphatase	+	3.1.3.1
[Ref.: #30512]	gelatinase	+

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

[Ref.: #19190]	Sample type/isolated from	roots of Rumex acetosa
[Ref.: #19190]	Geographic location (country and/or sea, region)	Kanagawa Pref.
[Ref.: #19190]	Country	Japan
[Ref.: #19190]	Country ISO 3 Code	JPN
[Ref.: #19190]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Roots of Rumex acetosa
[Ref.: #67770]	Host species	Rumex acetosa
[Ref.: #67770]	Geographic location (country and/or sea, region)	Kanagawa Pref.
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	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?

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

[Ref.: #19190]

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.: #19190]	Phytohabitans rumicis gene for 16S rRNA, partial sequence	AB663559	1470	ENA	1076125 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Phytohabitans rumicis NBRC 108638	GCA_011764445	contig	GenBank	1076125 tax ID	*
[Ref.: #66792]	Phytohabitans rumicis strain NBRC 108638	1076125.3	wgs	PATRIC	1076125 tax ID	*

[Ref.: #19190]	GC-content	72 mol%
[Ref.: #67770]	GC-content	72 mol%	high performance liquid chromatography (HPLC)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Phytohabitans rumicis strain NBRC 108638 PATRIC: 1076125.3
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Phytohabitans rumicis strain NBRC 108638 PATRIC: 1076125.3
[Ref.: #69480]	motile	no	93.623	no
[Ref.: #69480]	flagellated	no	97.675	no
[Ref.: #69480]	gram-positive	yes	87.546	yes
[Ref.: #69480]	anaerobic	no	98.962	yes
[Ref.: #69480]	aerobic	yes	92.25	yes
[Ref.: #69480]	halophile	no	96.204	no
[Ref.: #69480]	spore-forming	yes	92.669	no
[Ref.: #69480]	thermophile	no	97.988	yes
[Ref.: #69480]	glucose-util	yes	86.552	yes
[Ref.: #69480]	glucose-ferment	no	90.501	no

Availability in culture collections External links

[Ref.: #19190]

Culture collection no.

DSM 45865, BCC 48146, JCM 17829, NBRC 108638

[Ref.: #87361]

SI-ID 404075

Literature:

	Title	Authors	Journal	DOI	Year
Phylogeny	Phytohabitans flavus sp. nov., Phytohabitans rumicis sp. nov. and Phytohabitans houttuyneae sp. nov., isolated from plant roots, and emended description of the genus Phytohabitans.	Inahashi Y, Matsumoto A, Omura S, Takahashi Y	Int J Syst Evol Microbiol	10.1099/ijs.0.037747-0	2012	*
	Polyketide Synthase and Nonribosomal Peptide Synthetase Gene Clusters in Type Strains of the Genus Phytohabitans.	Komaki H, Tamura T	Life (Basel)	10.3390/life10110257	2020	*

References

#19190

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45865

#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 )

#30512

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26844 (see below)

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 )

#87361

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-ID404075.1 )

#26844

IJSEM 2717 2012 ( DOI 10.1099/ijs.0.037747-0 , PubMed 22228668 )

* These data were automatically processed and therefore are not curated

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Phytohabitans rumicis strain NBRC 108638

Phytohabitans rumicis strain NBRC 108638

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