Name: Phytohabitans houttuyneae K11-0057
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 23124

Type strain:

Species: Phytohabitans houttuyneae

Strain Designation: K11-0057

Culture col. no.: DSM 45864, BCC 48147, JCM 17830, NBRC 108639

Strain history: A. Matsumoto K11-0057.

NCBI tax ID(s): 1076126 (species)

SI-ID 404222

DSM 45864

Section

Phytohabitans houttuyneae K11-0057 is an aerobe, spore-forming, mesophilic bacterium that was isolated from roots of Houttuynia cordata.

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 houttuyneae**
	Full Scientific Name (LPSN)	Phytohabitans houttuyneae 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

Multimedia content

[Ref.: #19189]

Caption:

Medium 65 28°C

[Ref.: #19189]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #19189]

Culture medium

GPHF-MEDIUM (DSMZ Medium 553)

[Ref.: #19189]

Culture medium growth

[Ref.: #19189]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #19189]

Culture medium

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

[Ref.: #19189]

Culture medium growth

[Ref.: #19189]

Culture medium link

Medium recipe at MediaDive

[Ref.: #19189]

Culture medium composition

expand / minimize

[Ref.: #19189]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

[Ref.: #19189]

Culture medium growth

[Ref.: #19189]

Culture medium link

Medium recipe at MediaDive

[Ref.: #19189]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #19189]	growth	28 °C
[Ref.: #30512]	growth	20-42 °C
[Ref.: #30512]	optimum	30 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #19189]	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	06-11

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 %98
[Ref.: #69480]	Ability of spore formation	yes Confidence in %100

[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]	rhamnose ChEBI	+	carbon source
[Ref.: #30512]	sucrose ChEBI	+	carbon source
[Ref.: #30512]	xylose 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]	alpha-galactosidase	+	3.2.1.22
[Ref.: #30512]	gelatinase	+

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

[Ref.: #19189]	Sample type/isolated from	roots of Houttuynia cordata
[Ref.: #19189]	Geographic location (country and/or sea, region)	Kanagawa Pref.
[Ref.: #19189]	Country	Japan
[Ref.: #19189]	Country ISO 3 Code	JPN
[Ref.: #19189]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Roots of Houttuynia cordata
[Ref.: #67770]	Host species	Houttuynia cordata
[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.: #19189]

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.: #19189]	Phytohabitans houttuyneae gene for 16S rRNA, partial sequence	AB663560	1468	ENA	1076126 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Phytohabitans houttuyneae NBRC 108639	GCA_011764425	contig	GenBank	1076126 tax ID	*
[Ref.: #66792]	Phytohabitans houttuyneae strain NBRC 108639	1076126.3	wgs	PATRIC	1076126 tax ID	*

[Ref.: #19189]	GC-content	73 mol%
[Ref.: #67770]	GC-content	73 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 houttuyneae strain NBRC 108639 PATRIC: 1076126.3
[Ref.: #69481]	spore-forming	yes	98	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Phytohabitans houttuyneae strain NBRC 108639 PATRIC: 1076126.3
[Ref.: #69480]	motile	no	90.231	no
[Ref.: #69480]	flagellated	no	97.555	no
[Ref.: #69480]	gram-positive	yes	84.674	no
[Ref.: #69480]	anaerobic	no	98.946	yes
[Ref.: #69480]	aerobic	yes	91.875	yes
[Ref.: #69480]	halophile	no	94.115	no
[Ref.: #69480]	spore-forming	yes	90.54	no
[Ref.: #69480]	thermophile	no	97.614	yes
[Ref.: #69480]	glucose-util	yes	88.28	yes
[Ref.: #69480]	glucose-ferment	no	90.31	no

Availability in culture collections External links

[Ref.: #19189]

Culture collection no.

DSM 45864, BCC 48147, JCM 17830, NBRC 108639

[Ref.: #87360]

SI-ID 404222

Literature:

	Title	Authors	Journal	DOI	Year
Phylogeny	Phytohabitans kaempferiae sp. nov., an endophytic actinomycete isolated from the leaf of Kaempferia larsenii.	Niemhom N, Chutrakul C, Suriyachadkun C, Thawai C	Int J Syst Evol Microbiol	10.1099/ijsem.0.001121	2016	*
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

#19189

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45864

#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 )

#87360

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-ID404222.1 )

#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 houttuyneae strain NBRC 108639

Phytohabitans houttuyneae strain NBRC 108639

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