Clostridium oryzae (DSM 28571, NBRC 110163, KC3)

Name: Clostridium oryzae (DSM 28571, NBRC 110163, KC3)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130250

Type strain

Strain Designation KC3

Culture col. no. DSM 28571 NBRC 110163 KC3

NCBI tax ID(s) 1450648

Special Collections DSMZ

History <- A. Tonouchi, Faculty Agriculture and Life Sci., Hirosaki Univ., Japan; KC3 <- A. Tonouchi {2011}

Links

Clostridium oryzae KC3 is an anaerobe bacterium that was isolated from rice field soil.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 407839

NBRC 110163,DSM 28571

@ref 20215

Last LPSN update 2026-02-09 11:31:10

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Clostridiaceae

Genus Clostridium

Species Clostridium oryzae

Full scientific name Clostridium oryzae Horino et al. 2015

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
21884	PY + X MEDIUM (DSMZ Medium 104b)		Medium recipe at MediaDive	Name: PY + X MEDIUM (DSMZ Medium 104b; with strain-specific modifications) Composition: Yeast extract 10.0 g/l Trypticase peptone 5.0 g/l Meat peptone 5.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Sodium resazurin 0.0005 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
21884	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
21884	anaerobe
125439	anaerobe	90.5

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	teichoic acid biosynthesis	100	1 of 1
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	cardiolipin biosynthesis	100	7 of 7
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	L-lactaldehyde degradation	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	vitamin B1 metabolism	92.31	12 of 13
66794	threonine metabolism	90	9 of 10
66794	starch degradation	90	9 of 10
66794	d-mannose degradation	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	pyrimidine metabolism	84.44	38 of 45
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	cellulose degradation	80	4 of 5
66794	hydrogen production	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	Entner Doudoroff pathway	80	8 of 10
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	valine metabolism	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	glycogen biosynthesis	75	3 of 4
66794	ppGpp biosynthesis	75	3 of 4
66794	vitamin E metabolism	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	peptidoglycan biosynthesis	73.33	11 of 15
66794	pentose phosphate pathway	72.73	8 of 11
66794	alanine metabolism	72.41	21 of 29
66794	degradation of hexoses	72.22	13 of 18
66794	NAD metabolism	72.22	13 of 18
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	purine metabolism	71.28	67 of 94
66794	methionine metabolism	69.23	18 of 26
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	cyanate degradation	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	methane metabolism	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	histidine metabolism	65.52	19 of 29
66794	oxidative phosphorylation	64.84	59 of 91
66794	glycolysis	64.71	11 of 17
66794	photosynthesis	64.29	9 of 14
66794	degradation of pentoses	64.29	18 of 28
66794	d-xylose degradation	63.64	7 of 11
66794	non-pathway related	63.16	24 of 38
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	gluconeogenesis	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	ketogluconate metabolism	62.5	5 of 8
66794	lysine metabolism	61.9	26 of 42
66794	urea cycle	61.54	8 of 13
66794	methylglyoxal degradation	60	3 of 5
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	flavin biosynthesis	60	9 of 15
66794	lipid metabolism	58.06	18 of 31
66794	tryptophan metabolism	57.89	22 of 38
66794	glutathione metabolism	57.14	8 of 14
66794	propanol degradation	57.14	4 of 7
66794	cysteine metabolism	55.56	10 of 18
66794	metabolism of disaccharids	54.55	6 of 11
66794	phosphatidylethanolamine bioynthesis	53.85	7 of 13
66794	CMP-KDO biosynthesis	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	biotin biosynthesis	50	2 of 4
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	degradation of sugar acids	48	12 of 25
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	leucine metabolism	46.15	6 of 13
66794	proline metabolism	45.45	5 of 11
66794	lipid A biosynthesis	44.44	4 of 9
66794	polyamine pathway	43.48	10 of 23
66794	tetrahydrofolate metabolism	42.86	6 of 14
66794	tyrosine metabolism	42.86	6 of 14
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	citric acid cycle	42.86	6 of 14
66794	aclacinomycin biosynthesis	42.86	3 of 7
66794	isoprenoid biosynthesis	42.31	11 of 26
66794	arginine metabolism	41.67	10 of 24
66794	propionate fermentation	40	4 of 10
66794	myo-inositol biosynthesis	40	4 of 10
66794	3-chlorocatechol degradation	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	vitamin B12 metabolism	38.24	13 of 34
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	nitrate assimilation	33.33	3 of 9
66794	sulfoquinovose degradation	33.33	1 of 3
66794	degradation of sugar alcohols	31.25	5 of 16
66794	sulfate reduction	30.77	4 of 13
66794	coenzyme M biosynthesis	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	arachidonic acid metabolism	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	ascorbate metabolism	27.27	6 of 22
66794	vitamin B6 metabolism	27.27	3 of 11
66794	cholesterol biosynthesis	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	androgen and estrogen metabolism	25	4 of 16
66794	alginate biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	4-hydroxymandelate degradation	22.22	2 of 9
66794	chlorophyll metabolism	22.22	4 of 18

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
21884	rice field soil	Aomori Prefecture, Goshogawara city, Kanagi	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB904755 (>99% sequence identity) for Clostridium oryzae subclade from Microbeatlas

Aquatic Samples	1863
Soil Samples	3427
Animal Samples	1263
Plant Samples	290
Total Samples	6843

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21884	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score	IMG accession
66792	Clostridium oryzae DSM 28571	complete			1450648	56.68	2711768656
66792	ASM202923v1 assembly for Clostridium oryzae DSM 28571	contig	GCA_002029235	1450648.3	1450648	38.52

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
21884	Clostridium oryzae gene for 16S ribosomal RNA, partial sequence	AB904755	1458		1450648

GC content

@ref	GC-content (mol%)	Method
21884	37.5	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Clostridium oryzae DSM 28571
NCBI: GCA_002029235

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	84.70	no
125439	motility	BacteriaNetⓘ	yes	84.40	no
125439	gram_stain	BacteriaNetⓘ	variable	76.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	90.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Clostridium oryzae strain DSM 28571
PATRIC: 1450648.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	62.51	no
125438	anaerobic	anaerobicⓘ	yes	87.23	yes
125438	spore-forming	spore-formingⓘ	yes	73.03	no
125438	aerobic	aerobicⓘ	no	95.31	yes
125438	thermophilic	thermophileⓘ	no	84.02	no
125438	flagellated	motile2+ⓘ	yes	78.58	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	First Insights into the Genome Sequence of Clostridium oryzae DSM 28571, Isolated from the Soil of a Japanese Rice Field.	Poehlein A, Gippert AL, Bierenbroodspot MJ, Daniel R	Genome Announc	10.1128/genomeA.00539-17	2017
Phylogeny	Clostridium composti sp. nov., a new anaerobic bacteria isolated from compost.	Shin Y, Paek J, Son AY, Kim H, Kook JK, Paek WK, Chang YH	Int J Syst Evol Microbiol	10.1099/ijsem.0.003074	2018
Phylogeny	Clostridium oryzae sp. nov., from soil of a Japanese rice field.	Horino H, Ito M, Tonouchi A	Int J Syst Evol Microbiol	10.1099/ijs.0.000042	2015

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 )
#21884	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28571
#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) .
#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 )
#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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Clostridium oryzae (DSM 28571, NBRC 110163, KC3)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002029235

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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