Phytohabitans flavus (DSM 45551, JCM 17387, NBRC 107702)

Name: Phytohabitans flavus (DSM 45551, JCM 17387, NBRC 107702)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 23123

Type strain

Strain Designation K09-0627

Culture col. no. DSM 45551 JCM 17387 NBRC 107702 K09-0627

NCBI tax ID(s) 1076124

Special Collections DSMZ JCM Literature strains

History <- Y. Takahashi, Kitasato Univ., Tokyo, Japan; K09-0627 <- Y. Inahashi A. Matsumoto K09-0627.

Links

Phytohabitans flavus K09-0627 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from orchid root.

spore-forming Gram-positive aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 398319

NBRC 107702,JCM 17387,DSM 45551

@ref 20215

Last LPSN update 2026-02-09 11:23:40

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micromonosporales

Family Micromonosporaceae

Genus Phytohabitans

Species Phytohabitans flavus

Full scientific name Phytohabitans flavus Inahashi et al. 2012

Morphology

Cell morphology

@ref	Confidence	Gram stain
30512		positive
125439	90.1
125439	99.7	positive

Pigmentation

30512

Productionyes

Multimedia

@ref:	19188
multimedia content:	DSM_45551.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_45551.jpg
caption:	Medium 554 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
19188	GPHF-MEDIUM (DSMZ Medium 553)	Medium recipe at MediaDive	Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
19188	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
19188	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)	Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
19188	N-Z-AMINE-MEDIUM (DSMZ Medium 554)	Medium recipe at MediaDive	Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
19188	positive	growth	28
30512	positive	growth	20-35
30512	positive	optimum	28
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
30512	positive	optimum	8
30512	positive	growth	07-11	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30512	aerobe
125438	aerobe	91.838
125439	obligate aerobe	98.7

Spore formation

@ref	Spore formation	Confidence
30512
125438		92.229

Observation

67770

Observationquinones: MK-9(H₈), MK-9(H₆), MK-10(H₈), MK-10(H₆)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30512	22599 ChEBI	arabinose	+	carbon source
30512	28757 ChEBI	fructose	+	carbon source
30512	17234 ChEBI	glucose	+	carbon source
30512	29864 ChEBI	mannitol	+	carbon source
30512	26546 ChEBI	rhamnose	+	carbon source
30512	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30512	alkaline phosphatase	+	3.1.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root (Rhizome)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
19188	orchid root	Okinawa Prefecture	Japan	JPN	Asia
67770	Roots of an orchid	Okinawa Pref.	Japan	JPN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
19188	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1176454v1 assembly for Phytohabitans flavus NBRC 107702	complete	GCA_011764545	1076124.3	2993845517	1076124	81.38
124043	ASM3953748v1 assembly for Phytohabitans flavus JCM 17387	scaffold	GCA_039537485			1076124	52.48
124043	ASM4267654v1 assembly for Phytohabitans flavus JCM 17387	contig	GCA_042676545			1076124	31.9

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
19188	Phytohabitans flavus gene for 16S rRNA, partial sequence	AB663558	1466		1076124

GC content

@ref	GC-content (mol%)	Method
19188	71	high performance liquid chromatography (HPLC)
30512	71

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Phytohabitans flavus strain NBRC 107702
PATRIC: 1076124.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.70	no
125439	gram_stain	BacteriaNetⓘ	positive	99.70	no
125439	motility	BacteriaNetⓘ	no	90.10	no
125439	spore_formation	BacteriaNetⓘ	yes	84.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Phytohabitans flavus NBRC 107702
NCBI: GCA_011764545.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	86.64	yes
125438	anaerobic	anaerobicⓘ	no	92.90	no
125438	aerobic	aerobicⓘ	yes	91.84	yes
125438	spore-forming	spore-formingⓘ	yes	92.23	yes
125438	thermophilic	thermophileⓘ	no	91.00	yes
125438	flagellated	motile2+ⓘ	no	89.07	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	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
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

References

#19188	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45551
#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 )
#26844	IJSEM 2717 2012 ( DOI 10.1099/ijs.0.037747-0 , PubMed 22228668 )
#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
#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;
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Phytohabitans flavus (DSM 45551, JCM 17387, NBRC 107702)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_011764545

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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