Methylobacterium phyllosphaerae (DSM 19779, KACC 11716, LMG 24361)

Name: Methylobacterium phyllosphaerae (DSM 19779, KACC 11716, LMG 24361)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7192

Type strain

Strain Designation CBMB27, EF 126746

Culture col. no. DSM 19779 KACC 11716 LMG 24361 CBMB27 EF 126746 1 more

NCBI tax ID(s) 1295137 418223

Special Collections DSMZ JCM Literature strains

History DSMZ <- T. Sa, Chungbuk Natl. Univ., Republic of Korea; CBMB27 <- M. Madhaiyan JCM <-- KACC 11716 <-- T.-M. Sa CBMB27.

Links

Methylobacterium phyllosphaerae CBMB27 is an aerobe, Gram-negative, motile bacterium that was isolated from leaf of the rice Oryza sativa L. cv. Dong-Jin.

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

Name and taxonomic classification

SI-ID 360511

DSM 19779,KACC 11716,LMG 24361,JCM 16408

@ref 20215

Last LPSN update 2026-05-29 08:26:35

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Methylobacteriaceae

Genus Methylobacterium

Species Methylobacterium phyllosphaerae

Full scientific name Methylobacterium phyllosphaerae Madhaiyan et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
28925	negative	2.25 µm	0.64 µm	rod-shaped
125438	negative					97.802

Pigmentation

28925

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
8312	NUTRIENT AGAR (DSMZ Medium 1)		Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: Agar 15.0 g/l Methanol 10.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
8312	positive	growth	28
28925	positive	growth	20-30
28925	positive	optimum	28
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
28925	positive	optimum	6.8
28925	positive	growth	05-09	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
28925	aerobe
125439	obligate aerobe	92.211

Spore formation

@ref	Spore formation	Confidence
28925
125439		99.086

Halophily

@ref	Salt	Growth	Tested relation	Concentration
28925	NaCl	positive	growth	<2.0 %

Observation

28925

Observationaggregates in clumps

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
28925	16808 ChEBI	2-dehydro-D-gluconate	+	carbon source
28925	28644 ChEBI	2-oxopentanoate	+	carbon source
28925	37054 ChEBI	3-hydroxybutyrate	+	carbon source
28925	17879 ChEBI	4-hydroxybenzoate	+	carbon source
28925	58143 ChEBI	5-dehydro-D-gluconate	+	carbon source
28925	30089 ChEBI	acetate	+	carbon source
28925	17128 ChEBI	adipate	+	carbon source
28925	16449 ChEBI	alanine	+	carbon source
28925	22599 ChEBI	arabinose	+	carbon source
28925	22653 ChEBI	asparagine	+	carbon source
28925	35391 ChEBI	aspartate	+	carbon source
28925	16947 ChEBI	citrate	+	carbon source
28925	16236 ChEBI	ethanol	+	carbon source
28925	16000 ChEBI	ethanolamine	+	carbon source
28925	15740 ChEBI	formate	+	carbon source
28925	28757 ChEBI	fructose	+	carbon source
28925	33984 ChEBI	fucose	+	carbon source
28925	24148 ChEBI	galactonate	+	carbon source
28925	24175 ChEBI	galacturonate	+	carbon source
28925	24265 ChEBI	gluconate	+	carbon source
28925	17234 ChEBI	glucose	+	carbon source
28925	29987 ChEBI	glutamate	+	carbon source
28925	17754 ChEBI	glycerol	+	carbon source
28925	28087 ChEBI	glycogen	+	carbon source
28925	17240 ChEBI	itaconate	+	carbon source
28925	21217 ChEBI	L-alaninamide	+	carbon source
28925	24996 ChEBI	lactate	+	carbon source
28925	25115 ChEBI	malate	+	carbon source
28925	28053 ChEBI	melibiose	+	carbon source
28925	51850 ChEBI	methyl pyruvate	+	carbon source
28925	26271 ChEBI	proline	+	carbon source
28925	17272 ChEBI	propionate	+	carbon source
28925	26546 ChEBI	rhamnose	+	carbon source
28925	33942 ChEBI	ribose	+	carbon source
28925	17814 ChEBI	salicin	+	carbon source
28925	17822 ChEBI	serine	+	carbon source
28925	30911 ChEBI	sorbitol	+	carbon source
28925	30031 ChEBI	succinate	+	carbon source
28925	17992 ChEBI	sucrose	+	carbon source
28925	53426 ChEBI	tween 80	+	carbon source
28925	16199 ChEBI	urea	+	carbon source
28925	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
28925	acid phosphatase	+	3.1.3.2
28925	catalase	+	1.11.1.6
28925	cytochrome oxidase	+	1.9.3.1
28925	urease	+	3.5.1.5

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
8312	leaf of the rice Oryza sativa L. cv. Dong-Jin	Oryza sativa	Iksan, Ho-nam	Republic of Korea	KOR	Asia
67770	Leaf tissues of rice (Oryza sativa L. 'Dong-Jin')	Oryza sativa

Taxonmaps

69479

Global distribution of 16S sequence EF126746 (>99% sequence identity) for Methylobacterium from Microbeatlas

Aquatic Samples	1020
Soil Samples	439
Animal Samples	1696
Plant Samples	535
Total Samples	3690

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8312	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	ASM193617v1 assembly for Methylobacterium phyllosphaerae CBMB27	complete	GCA_001936175		2721755615	418223	98.61
66792	IMG-taxon 2651870129 annotated assembly for Methylobacterium phyllosphaerae CBMB27	scaffold	GCA_900113465	418223.10	2651870129	418223	62.79
66792	ASM131228v1 assembly for Methylobacterium phyllosphaerae JCM 16408	contig	GCA_001312285	1295137.3	2728369718	1295137	0

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
8312	Methylobacterium phyllosphaerae strain CBMB27 16S ribosomal RNA gene, partial sequence	EF126746	1367		418223

GC content

@ref	GC-content (mol%)	Method
8312	66.8
67770	66.8	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: ASM193617v1 assembly for Methylobacterium phyllosphaerae CBMB27
NCBI: GCA_001936175

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	92.21	no
125439	gram_stain	BacteriaNetⓘ	negative	89.39	no
125439	motility	BacteriaNetⓘ	yes	48.19	no
125439	spore_formation	BacteriaNetⓘ	no	99.09	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Methylobacterium phyllosphaerae CBMB27
NCBI: GCA_001936175.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.80	yes
125438	anaerobic	anaerobicⓘ	no	96.46	no
125438	aerobic	aerobicⓘ	yes	88.73	yes
125438	spore-forming	spore-formingⓘ	no	88.92	yes
125438	thermophilic	thermophileⓘ	no	96.50	yes
125438	flagellated	motile2+ⓘ	yes	69.61	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Production of Glycolipid Biosurfactants, cellobiose lipids, by Cryptococcus humicola JCM 1461 and their interfacial properties.	Morita T, Ishibashi Y, Fukuoka T, Imura T, Sakai H, Abe M, Kitamoto D.	Biosci Biotechnol Biochem	10.1271/bbb.110036	2011
	Intimate relationships among actinomycetes and mycolic acid-containing bacteria.	Kato M, Asamizu S, Onaka H.	Sci Rep	10.1038/s41598-022-11406-2	2022
	Aerobic Methoxydotrophy: Growth on Methoxylated Aromatic Compounds by Methylobacteriaceae.	Lee JA, Stolyar S, Marx CJ.	Front Microbiol	10.3389/fmicb.2022.849573	2022
Phylogeny	Methylobacterium radiodurans sp. nov., a novel radiation-resistant Methylobacterium.	Maeng S, Kim DU, Lim S, Lee BH, Lee KE, Kim M, Srinivasan S, Bai J	Arch Microbiol	10.1007/s00203-021-02293-8	2021
Phylogeny	Methylobacterium trifolii sp. nov. and Methylobacterium thuringiense sp. nov., methanol-utilizing, pink-pigmented bacteria isolated from leaf surfaces.	Wellner S, Lodders N, Glaeser SP, Kampfer P	Int J Syst Evol Microbiol	10.1099/ijs.0.047787-0	2013
Phylogeny	Methylobacterium dankookense sp. nov., isolated from drinking water.	Lee SW, Oh HW, Lee KH, Ahn TY	J Microbiol	10.1007/s12275-009-0126-6	2010
Phylogeny	Methylobacterium phyllosphaerae sp. nov., a pink-pigmented, facultative methylotroph from the phyllosphere of rice.	Madhaiyan M, Poonguzhali S, Kwon SW, Sa TM	Int J Syst Evol Microbiol	10.1099/ijs.0.001693-0	2009

References

#8312	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19779
#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 )
#25364	IJSEM 22 2009 ( DOI 10.1099/ijs.0.001693-0 , PubMed 19126717 )
#28925	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 #25364
#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;
#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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Methylobacterium phyllosphaerae (DSM 19779, KACC 11716, LMG 24361)

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

Halophily

Observation

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_001936175

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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