Patulibacter minatonensis (DSM 18081, CIP 109166, JCM 12834)

Name: Patulibacter minatonensis (DSM 18081, CIP 109166, JCM 12834)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17628

Type strain

Strain Designation KV-614

Culture col. no. DSM 18081 CIP 109166 JCM 12834 NBRC 100761 NRRL B-24346 3 more

NCBI tax ID(s) 929712 298163

Special Collections DSMZ JCM KCTC CIP Wink compendium Literature strains

Links

Patulibacter minatonensis KV-614 is an aerobe, mesophilic, Gram-positive prokaryote that was isolated from soil.

Gram-positive motile rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 289981

JCM 12834,NBRC 100761,NRRL B-24346,DSM 18081,CIP 109166

@ref 20215

Last LPSN update 2025-12-16 09:51:08

Domain Bacillati

Phylum Actinomycetota

Class Thermoleophilia

Order Solirubrobacterales

Family Patulibacteraceae

Genus Patulibacter

Species Patulibacter minatonensis

Full scientific name Patulibacter minatonensis Takahashi et al. 2006

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31552	positive	1.2-1.5 µm	0.6-0.7 µm	rod-shaped
125439	positive				99.3
120957	positive			rod-shaped

Colony morphology

@ref	Colony color	Incubation period	Medium used
18411	Colorless	10-14 days	ISP 2
18411	Colorless	10-14 days	ISP 3
18411	Colorless	10-14 days	ISP 4
18411	Colorless	10-14 days	ISP 5
18411	Colorless	10-14 days	ISP 7

Multicellular morphology

@ref	Forms multicellular complex	Medium name
18411		ISP 2
18411		ISP 3
18411		ISP 4
18411		ISP 5
18411		ISP 7

Pigmentation

31552

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7382	R2A MEDIUM (DSMZ Medium 830)	Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
18411	ISP 2		Name: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
18411	ISP 3		Name: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
18411	ISP 4		Name: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
18411	ISP 5		Name: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
18411	ISP 7		Name: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
37470	MEDIUM 112 - for Janibacter		Distilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (1.000 g);Agar (20.000 g);Yeast extract (5.000 g);Peptone (10.000 g);Tween 80 (50.000 mg);Glycerol (2.000 g);Malt extract (5.000 g);Beef extract (2.000 g);Casamino acids (5.000 g);Ca
120957	CIP Medium 112	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7382	positive	growth	25	mesophilic
18411	positive	optimum	28	mesophilic
31552	positive	growth	16-28
31552	positive	optimum	24-27
37470	positive	growth	25	mesophilic
67770	positive	growth	25	mesophilic

Culture pH

@ref	Ability	Type	PH
31552	positive	optimum	7
31552	positive	growth	06-08

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31552	aerobe
120957	obligate aerobe
125439	obligate aerobe	99

Spore formation

31552

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31552	NaCl	positive	growth	0-1 %
31552	NaCl	positive	optimum	0-1 %

Observation

@ref	Observation
31552	aggregates in chains
67770	quinones: DMK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31552	22599 ChEBI	arabinose	+	carbon source
31552	17057 ChEBI	cellobiose	+	carbon source
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
31552	23652 ChEBI	dextrin	+	carbon source
68379	4853 ChEBI	esculin	-	hydrolysis	from API Coryne
31552	28757 ChEBI	fructose	+	carbon source
31552	33984 ChEBI	fucose	+	carbon source
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
31552	17234 ChEBI	glucose	+	carbon source
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
31552	18403 ChEBI	L-arabitol	+	carbon source
31552	24996 ChEBI	lactate	+	carbon source
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
31552	17306 ChEBI	maltose	+	carbon source
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
31552	37684 ChEBI	mannose	+	carbon source
31552	17632 ChEBI	nitrate	+	reduction
120957	17632 ChEBI	nitrate	-	reduction
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
120957	16301 ChEBI	nitrite	-	reduction
31552	26546 ChEBI	rhamnose	+	carbon source
31552	17814 ChEBI	salicin	+	carbon source
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne

Metabolite production

@ref	Chebi-ID	Metabolite	Production
120957	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68379	alkaline phosphatase	+	3.1.3.1	from API Coryne
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68379	alpha-glucosidase	-	3.2.1.20	from API Coryne
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68379	beta-galactosidase	-	3.2.1.23	from API Coryne
68382	beta-glucosidase	-	3.2.1.21	from API zym
68379	beta-glucosidase	-	3.2.1.21	from API Coryne
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
31552	catalase	+	1.11.1.6
120957	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68379	gelatinase	-		from API Coryne
68382	leucine arylamidase	-	3.4.11.1	from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68379	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API Coryne
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
120957	oxidase	-
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	-	3.4.19.3	from API Coryne
68382	trypsin	-	3.4.21.4	from API zym
120957	urease	+	3.5.1.5
68379	urease	-	3.5.1.5	from API Coryne

API coryne

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
18411	-	-	-	+	-	-	-	-	-	-	-	not determinedn.d.	-	-	-	-	-	-	-	-	not determinedn.d.

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
18411	not determinedn.d.	-	+	+	+	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-
120957	-	+	+	+	-	-	+	-	-	-	+	+	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7382	soil	Tokyo, Minatu-ku	Japan	JPN	Asia
67770	Soil	Minato-ku, Tokyo	Japan	JPN	Asia
120957	Environment, Soil sample	Minato, Tokyo	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB193261 (>99% sequence identity) for Patulibacter from Microbeatlas

Aquatic Samples	3344
Soil Samples	6270
Animal Samples	6085
Plant Samples	2710
Total Samples	18409

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7382	1	Risk group (German classification) According to TRBA 466
18411	1	German classification According to TRBA 466
120957	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM51932v1 assembly for Patulibacter minatonensis DSM 18081	scaffold	GCA_000519325	929712.6	2510065083	929712	60.54
66792	Patulibacter minatonensis DSM 18081	contig		929712.3		929712	25.5

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7382	Patulibacter minatonensis gene for 16S rRNA, partial sequence	AB193261	1528		929712

GC content

@ref	GC-content (mol%)	Method
7382	72
67770	72	high performance liquid chromatography (HPLC)
67770	74.1	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Patulibacter minatonensis DSM 18081
NCBI: GCA_000519325

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	52.60	no
125439	motility	BacteriaNetⓘ	no	66.10	no
125439	gram_stain	BacteriaNetⓘ	positive	99.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Patulibacter minatonensis DSM 18081
PATRIC: 929712.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	70.59	no
125438	anaerobic	anaerobicⓘ	no	91.29	yes
125438	aerobic	aerobicⓘ	yes	84.12	yes
125438	spore-forming	spore-formingⓘ	no	60.76	yes
125438	thermophilic	thermophileⓘ	no	93.00	yes
125438	flagellated	motile2+ⓘ	no	56.79	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Immobilization of high temperature-resistant GH3 beta-glucosidase on a magnetic particle Fe₃O₄-SiO₂-NH₂-Cellu-ZIF8/zeolitic imidazolate framework.	Shi X, Xu J, Lu C, Wang Z, Xiao W, Zhao L.	Enzyme Microb Technol	10.1016/j.enzmictec.2019.05.004	2019
Metabolism	Structural investigation of the lipopolysaccharide O-chain isolated from Burkholderia fungorum strain DSM 17061.	De Felice A, Di Lorenzo F, Scherlach K, Ross C, Silipo A, Hertweck C, Molinaro A.	Carbohydr Res	10.1016/j.carres.2016.07.008	2016
Phylogeny	ezTree: an automated pipeline for identifying phylogenetic marker genes and inferring evolutionary relationships among uncultivated prokaryotic draft genomes.	Wu YW.	BMC Genomics	10.1186/s12864-017-4327-9	2018
	The Effects of Freeze-Thaw and UVC Radiation on Microbial Survivability in a Selected Mars-like Environment.	Keaney D, Lucey B, Quinn N, Finn K.	Microorganisms	10.3390/microorganisms10030576	2022
	Two new siderophores produced by Pseudomonas sp. NCIMB 10586: The anti-oomycete non-ribosomal peptide synthetase-dependent mupirochelin and the NRPS-independent triabactin.	Grosse C, Brandt N, Van Antwerpen P, Wintjens R, Matthijs S.	Front Microbiol	10.3389/fmicb.2023.1143861	2023
Phylogeny	Complete Genome of the Starch-Degrading Myxobacteria Sandaracinus amylolyticus DSM 53668T.	Sharma G, Khatri I, Subramanian S.	Genome Biol Evol	10.1093/gbe/evw151	2016
Metabolism	Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities.	Acinas SG, Sanchez P, Salazar G, Cornejo-Castillo FM, Sebastian M, Logares R, Royo-Llonch M, Paoli L, Sunagawa S, Hingamp P, Ogata H, Lima-Mendez G, Roux S, Gonzalez JM, Arrieta JM, Alam IS, Kamau A, Bowler C, Raes J, Pesant S, Bork P, Agusti S, Gojobori T, Vaque D, Sullivan MB, Pedros-Alio C, Massana R, Duarte CM, Gasol JM.	Commun Biol	10.1038/s42003-021-02112-2	2021
Phylogeny	Comparative Genomics of Myxobacterial Chemosensory Systems.	Sharma G, Khatri I, Subramanian S.	J Bacteriol	10.1128/jb.00620-17	2018
Metabolism	Genome Analysis of the Fruiting Body-Forming Myxobacterium Chondromyces crocatus Reveals High Potential for Natural Product Biosynthesis.	Zaburannyi N, Bunk B, Maier J, Overmann J, Muller R.	Appl Environ Microbiol	10.1128/aem.03011-15	2016
Phylogeny	Baekduia soli gen. nov., sp. nov., a novel bacterium isolated from the soil of Baekdu Mountain and proposal of a novel family name, Baekduiaceae fam. nov.	An DS, Siddiqi MZ, Kim KH, Yu HS, Im WT	J Microbiol	10.1007/s12275-018-7107-6	2018
Phylogeny	Solirubrobacter soli sp. nov., isolated from soil of a ginseng field.	Kim MK, Na JR, Lee TH, Im WT, Soung NK, Yang DC	Int J Syst Evol Microbiol	10.1099/ijs.0.64715-0	2007
Phylogeny	Patulibacter minatonensis gen. nov., sp. nov., a novel actinobacterium isolated using an agar medium supplemented with superoxide dismutase, and proposal of Patulibacteraceae fam. nov.	Takahashi Y, Matsumoto A, Morisaki K, Omura S	Int J Syst Evol Microbiol	10.1099/ijs.0.63796-0	2006
Phylogeny	Patulibacter brassicae sp. nov., isolated from rhizosphere soil of Chinese cabbage (Brassica campestris).	Jin D, Kong X, Li H, Luo L, Zhuang X, Zhuang G, Deng Y, Bai Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.001469	2016
Phylogeny	Patulibacter medicamentivorans sp. nov., isolated from activated sludge of a wastewater treatment plant.	Almeida B, Vaz-Moreira I, Schumann P, Nunes OC, Carvalho G, Crespo MTB	Int J Syst Evol Microbiol	10.1099/ijs.0.047522-0	2012
Phylogeny	Patulibacter ginsengiterrae sp. nov., isolated from soil of a ginseng field, and an emended description of the genus Patulibacter.	Kim KK, Lee KC, Lee JS	Int J Syst Evol Microbiol	10.1099/ijs.0.032052-0	2011

References

#7382	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18081
#18411	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#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 )
#31552	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 #27843 (see below)
#37470	; Curators of the CIP;
#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;
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#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 .
#120957	Collection of Institut Pasteur ; Curators of the CIP; CIP 109166
#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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Patulibacter minatonensis (DSM 18081, CIP 109166, JCM 12834)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

API coryne

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000519325

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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