Mucilaginibacter oryzae (DSM 19975, B9)

Name: Mucilaginibacter oryzae (DSM 19975, B9)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14135

Type strain

Strain Designation B9

Culture col. no. DSM 19975 B9

NCBI tax ID(s) 468058

Special Collections DSMZ Literature strains

History DSMZ <- C. O. Jeon, Gyeongsang Natl. Univ. (GNU), Jinju, Korea; B9

Links

Mucilaginibacter oryzae B9 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from paddy rhizosphere soil from a rice plant.

Gram-negative rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 402556

DSM 19975

@ref 20215

Last LPSN update 2026-05-29 08:28:12

Domain Bacteria

Phylum Bacteroidota

Class Sphingobacteriia

Order Sphingobacteriales

Family Sphingobacteriaceae

Genus Mucilaginibacter

Species Mucilaginibacter oryzae

Full scientific name Mucilaginibacter oryzae Jeon et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29137	negative	2.15 µm	0.65 µm	rod-shaped
125439	negative				99.66
125438	negative				94.097

Pigmentation

29137

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
8349	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

Culture temp

@ref	Growth	Type	Temperature (°C)
8349	positive	growth	28
29137	positive	growth	15-35
29137	positive	optimum	27.5

Culture pH

@ref	Ability	Type	PH
29137	positive	optimum	6
29137	positive	growth	5.0-8.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29137	aerobe
125439	obligate aerobe	93.079

Spore formation

@ref	Spore formation	Confidence
29137
125439		99.918

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29137	30089 ChEBI	acetate	+	carbon source
29137	16449 ChEBI	alanine	+	carbon source
29137	22599 ChEBI	arabinose	+	carbon source
29137	35391 ChEBI	aspartate	+	carbon source
29137	17057 ChEBI	cellobiose	+	carbon source
29137	23652 ChEBI	dextrin	+	carbon source
29137	4853 ChEBI	esculin	+	hydrolysis
29137	28757 ChEBI	fructose	+	carbon source
29137	28260 ChEBI	galactose	+	carbon source
29137	24265 ChEBI	gluconate	+	carbon source
29137	28087 ChEBI	glycogen	+	carbon source
29137	21217 ChEBI	L-alaninamide	+	carbon source
29137	17716 ChEBI	lactose	+	carbon source
29137	17306 ChEBI	maltose	+	carbon source
29137	29864 ChEBI	mannitol	+	carbon source
29137	37684 ChEBI	mannose	+	carbon source
29137	28053 ChEBI	melibiose	+	carbon source
29137	37657 ChEBI	methyl D-glucoside	+	carbon source
29137	18257 ChEBI	ornithine	+	carbon source
29137	26271 ChEBI	proline	+	carbon source
29137	16634 ChEBI	raffinose	+	carbon source
29137	17814 ChEBI	salicin	+	carbon source
29137	17822 ChEBI	serine	+	carbon source
29137	17992 ChEBI	sucrose	+	carbon source
29137	26986 ChEBI	threonine	+	carbon source
29137	27082 ChEBI	trehalose	+	carbon source
29137	16199 ChEBI	urea	+	carbon source

Enzymes

@ref	Value	Activity	Ec
29137	acid phosphatase	+	3.1.3.2
29137	alkaline phosphatase	+	3.1.3.1
29137	alpha-galactosidase	+	3.2.1.22
29137	catalase	+	1.11.1.6
29137	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizosphere

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
8349	paddy rhizosphere soil from a rice plant	Jinju	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence EU109722 (>99% sequence identity) for Mucilaginibacter oryzae from Microbeatlas

Aquatic Samples	38
Soil Samples	205
Animal Samples	68
Plant Samples	24
Total Samples	335

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8349	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	ASM314884v1 assembly for Mucilaginibacter oryzae DSM 19975	scaffold	GCA_003148845	468058.3	2595698252	468058	69.51

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
8349	Mucilaginibacter oryzae strain B9 16S ribosomal RNA gene, partial sequence	EU109722	1484		468058

GC content

@ref	GC-content (mol%)	Method
8349	44.4	high performance liquid chromatography (HPLC)
29137	44.4

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM314884v1 assembly for Mucilaginibacter oryzae DSM 19975
NCBI: GCA_003148845

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	93.08	no
125439	motility	BacteriaNetⓘ	no	76.16	no
125439	gram_stain	BacteriaNetⓘ	negative	99.66	no
125439	spore_formation	BacteriaNetⓘ	no	99.92	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Mucilaginibacter oryzae DSM 19975
NCBI: GCA_003148845.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	94.10	no
125438	anaerobic	anaerobicⓘ	no	96.86	yes
125438	aerobic	aerobicⓘ	yes	84.94	yes
125438	spore-forming	spore-formingⓘ	no	87.06	no
125438	thermophilic	thermophileⓘ	no	97.74	no
125438	flagellated	motile2+ⓘ	no	85.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Mucilaginibacter endophyticus sp. nov., an endophytic polysaccharide-producing bacterium isolated from a stem of Miscanthus sinensis.	Zhang Z, Sun F, Chen Y, Yao L, Chen Z, Tian W	Antonie Van Leeuwenhoek	10.1007/s10482-019-01242-2	2019
Phylogeny	Mucilaginibacter oryzae sp. nov., isolated from soil of a rice paddy.	Jeon Y, Lee SS, Chung BS, Kim JM, Bae JW, Park SK, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijs.0.007138-0	2009

References

#8349	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19975
#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 )
#25562	IJSEM 1451 2009 ( DOI 10.1099/ijs.0.007138-0 , PubMed 19502333 )
#29137	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 #25562
#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) .
#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 )

Content

About us

Mucilaginibacter oryzae (DSM 19975, B9)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003148845

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media