Paenibacillus oryzae (1DrF-4, ACCC 19927, JCM 30486)

Name: Paenibacillus oryzae (1DrF-4, ACCC 19927, JCM 30486)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133265

Type strain

Strain Designation 1DrF-4

Culture col. no. 1DrF-4 ACCC 19927 JCM 30486

NCBI tax ID(s) 1844972

Special Collections JCM Literature strains

History JCM <-- X. Zhang; ACCC, China; 1DrF-4.

Links

Paenibacillus oryzae 1DrF-4 is a facultative anaerobe, spore-forming, Gram-positive bacterium that forms circular colonies and was isolated from rice roots.

spore-forming Gram-positive motile rod-shaped colony-forming facultative anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 359513

JCM 30486

@ref 20215

Last LPSN update 2026-05-29 08:38:03

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Paenibacillaceae

Genus Paenibacillus

Species Paenibacillus oryzae

Full scientific name Paenibacillus oryzae Zhang et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
25128	positive	1.0-2.5 µm	0.5-0.75 µm	rod-shaped

Colony morphology

@ref	Colony color	Colony shape	Medium used
25128	greyish	circular	TSA

Culture and growth conditions

Culture medium

@ref	Name	Growth
25128	Trypticase Soy Agar (TSA)

Culture temp

@ref	Growth	Type	Temperature (°C)
25128	positive	growth	15-40
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
25128	positive	growth	6.0-11.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
25128	facultative anaerobe
125439	facultative anaerobe	92.748

Spore formation

@ref	Type of spore	Confidence
25128	endospore
125439		92.365
125438		94.188

Halophily

@ref	Salt	Growth	Tested relation	Concentration
25128	NaCl	positive	growth	0-3.0 %

Observation

67770

Observationquinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
25128	17128 ChEBI	adipate	-	carbon source
25128	2509 ChEBI	agar	-	hydrolysis
25128	28938 ChEBI	ammonium	+	nitrogen source
25128	27613 ChEBI	amygdalin	+	carbon source
25128	27613 ChEBI	amygdalin	+	builds acid from
25128		casein	-	hydrolysis
25128	16947 ChEBI	citrate	+	carbon source
25128	17634 ChEBI	D-glucose	-	carbon source
25128	17634 ChEBI	D-glucose	-	builds acid from
25128	17634 ChEBI	D-glucose	-	assimilation
25128	16899 ChEBI	D-mannitol	-	carbon source
25128	16899 ChEBI	D-mannitol	-	builds acid from
25128	16899 ChEBI	D-mannitol	-	assimilation
25128	16024 ChEBI	D-mannose	+	carbon source
25128	16024 ChEBI	D-mannose	+	assimilation
25128	17924 ChEBI	D-sorbitol	-	carbon source
25128	27689 ChEBI	decanoate	-	carbon source
25128	4853 ChEBI	esculin	+	hydrolysis
25128	5291 ChEBI	gelatin	-	hydrolysis
25128	30849 ChEBI	L-arabinose	-	builds acid from
25128	30849 ChEBI	L-arabinose	+	carbon source
25128	30849 ChEBI	L-arabinose	+	assimilation
25128	62345 ChEBI	L-rhamnose	-	carbon source
25128	25115 ChEBI	malate	-	carbon source
25128	17306 ChEBI	maltose	+	carbon source
25128	28053 ChEBI	melibiose	+	carbon source
25128	28053 ChEBI	melibiose	+	builds acid from
25128	506227 ChEBI	N-acetylglucosamine	-	carbon source
25128	506227 ChEBI	N-acetylglucosamine	-	assimilation
25128	17632 ChEBI	nitrate	+	reduction
25128	18401 ChEBI	phenylacetate	-	carbon source
25128	32032 ChEBI	potassium gluconate	-	carbon source
25128	32032 ChEBI	potassium gluconate	-	assimilation
25128	53258 ChEBI	sodium citrate	-	carbon source
25128	28017 ChEBI	starch	+	hydrolysis
25128	17992 ChEBI	sucrose	+	carbon source
25128	17992 ChEBI	sucrose	+	builds acid from
25128	27897 ChEBI	tryptophan	-	energy source
25128	53426 ChEBI	tween 80	+	hydrolysis

Metabolite production

@ref	Chebi-ID	Metabolite	Production
25128	15688 ChEBI	acetoin
25128	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Citrate test	Indole test
25128	15688 ChEBI	acetoin	+
25128	16947 ChEBI	citrate		+
25128	35581 ChEBI	indole			-

Enzymes

@ref	Value	Activity	Ec
25128	arginine dihydrolase	-	3.5.3.6
25128	beta-galactosidase	+	3.2.1.23
25128	catalase	-	1.11.1.6
25128	cytochrome oxidase	+	1.9.3.1
25128	lysine decarboxylase	-	4.1.1.18
25128	ornithine decarboxylase	-	4.1.1.17
25128	tryptophan deaminase	-	4.1.99.1
25128	urease	-	3.5.1.5

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	adipate degradation	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	pentose phosphate pathway	100	11 of 11
66794	coenzyme A metabolism	100	4 of 4
66794	ppGpp biosynthesis	100	4 of 4
66794	suberin monomers biosynthesis	100	2 of 2
66794	ceramide biosynthesis	100	1 of 1
66794	teichoic acid biosynthesis	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	ribulose monophosphate pathway	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	cardiolipin biosynthesis	100	7 of 7
66794	tetrahydrofolate metabolism	100	14 of 14
66794	palmitate biosynthesis	95.45	21 of 22
66794	NAD metabolism	94.44	17 of 18
66794	vitamin B1 metabolism	92.31	12 of 13
66794	Entner Doudoroff pathway	90	9 of 10
66794	starch degradation	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	d-mannose degradation	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	methionine metabolism	88.46	23 of 26
66794	ketogluconate metabolism	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	heme metabolism	85.71	12 of 14
66794	phenylalanine metabolism	84.62	11 of 13
66794	1,4-dihydroxy-6-naphthoate biosynthesis	83.33	5 of 6
66794	degradation of aromatic, nitrogen containing compounds	83.33	10 of 12
66794	degradation of sugar alcohols	81.25	13 of 16
66794	glycine betaine biosynthesis	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	peptidoglycan biosynthesis	80	12 of 15
66794	lipoate biosynthesis	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	4-hydroxyphenylacetate degradation	80	8 of 10
66794	threonine metabolism	80	8 of 10
66794	allantoin degradation	77.78	7 of 9
66794	pyrimidine metabolism	77.78	35 of 45
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	purine metabolism	77.66	73 of 94
66794	acetate fermentation	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	butanoate fermentation	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	gluconeogenesis	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	vitamin B6 metabolism	72.73	8 of 11
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	glutamate and glutamine metabolism	71.43	20 of 28
66794	propanol degradation	71.43	5 of 7
66794	non-pathway related	71.05	27 of 38
66794	glycolysis	70.59	12 of 17
66794	oxidative phosphorylation	70.33	64 of 91
66794	urea cycle	69.23	9 of 13
66794	alanine metabolism	68.97	20 of 29
66794	degradation of hexoses	66.67	12 of 18
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	glutathione metabolism	64.29	9 of 14
66794	metabolism of disaccharids	63.64	7 of 11
66794	d-xylose degradation	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	histidine metabolism	62.07	18 of 29
66794	cysteine metabolism	61.11	11 of 18
66794	degradation of pentoses	60.71	17 of 28
66794	tryptophan metabolism	60.53	23 of 38
66794	factor 420 biosynthesis	60	3 of 5
66794	myo-inositol biosynthesis	60	6 of 10
66794	3-chlorocatechol degradation	60	3 of 5
66794	methylglyoxal degradation	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	phenol degradation	60	12 of 20
66794	gallate degradation	60	3 of 5
66794	degradation of sugar acids	60	15 of 25
66794	arginine metabolism	58.33	14 of 24
66794	citric acid cycle	57.14	8 of 14
66794	lipid metabolism	54.84	17 of 31
66794	leucine metabolism	53.85	7 of 13
66794	lysine metabolism	52.38	22 of 42
66794	polyamine pathway	52.17	12 of 23
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	kanosamine biosynthesis II	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	androgen and estrogen metabolism	50	8 of 16
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	biotin biosynthesis	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	quinate degradation	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	CMP-KDO biosynthesis	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	proline metabolism	45.45	5 of 11
66794	ascorbate metabolism	45.45	10 of 22
66794	propionate fermentation	40	4 of 10
66794	coenzyme M biosynthesis	40	4 of 10
66794	bacilysin biosynthesis	40	2 of 5
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	sulfate reduction	38.46	5 of 13
66794	tyrosine metabolism	35.71	5 of 14
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	lipid A biosynthesis	33.33	3 of 9
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	mevalonate metabolism	28.57	2 of 7
66794	cholesterol biosynthesis	27.27	3 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	carotenoid biosynthesis	27.27	6 of 22
66794	vitamin B12 metabolism	26.47	9 of 34
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	chlorophyll metabolism	22.22	4 of 18
66794	nitrate assimilation	22.22	2 of 9
66794	4-hydroxymandelate degradation	22.22	2 of 9

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
25128	rice roots	Qiyang County of Hunan Province	China	CHN	Asia
67770	Rice roots from Qiyang County of Hunan Province		China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence KX196453 (>99% sequence identity) for Paenibacillus oryzae subclade from Microbeatlas

Aquatic Samples	11
Soil Samples	76
Animal Samples	10
Plant Samples	63
Total Samples	160

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM167504v1 assembly for Paenibacillus oryzae 1DrF-4	scaffold	GCA_001675045	1844972.5	2791355222	1844972	57.38

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
25128	Paenibacillus oryzae strain 1DrF-4 16S ribosomal RNA gene, partial sequence	KX196453	1423		1844972

GC content

@ref	GC-content (mol%)	Method
25128	50.16	Thermal denaturation, fluorometry
67770	50.16	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM167504v1 assembly for Paenibacillus oryzae 1DrF-4
NCBI: GCA_001675045

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	92.75	no
125439	gram_stain	BacteriaNetⓘ	variable	75.97	no
125439	motility	BacteriaNetⓘ	yes	83.49	no
125439	spore_formation	BacteriaNetⓘ	yes	92.37	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paenibacillus oryzae strain 1DrF-4
PATRIC: 1844972.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	72.95	yes
125438	anaerobic	anaerobicⓘ	no	89.83	no
125438	spore-forming	spore-formingⓘ	yes	94.19	no
125438	aerobic	aerobicⓘ	no	52.49	yes
125438	thermophilic	thermophileⓘ	no	91.98	yes
125438	flagellated	motile2+ⓘ	yes	85.95	no

Literature

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 )
#25128	J. M. Zhang, X. T.,Gao, J. S.,Zhao, J. J.,Yin, H. Q.,Zhang, C. W.,Zhang, R. J.,Zhang, X. X.: Paenibacillus oryzae sp. nov., isolated from rice roots. IJSEM 66: 5000 - 5004 2016 ( DOI 10.1099/ijsem.0.001459 , PubMed 27565704 )
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#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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