Methylobacterium mesophilicum (DSM 1708, ATCC 29983, ICPB 4095)

Name: Methylobacterium mesophilicum (DSM 1708, ATCC 29983, ICPB 4095)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7149

Type strain

Strain Designation A 47

Culture col. no. DSM 1708 ATCC 29983 ICPB 4095 CCUG 16482 A 47 8 more

NCBI tax ID(s) 39956

Special Collections DSMZ CCUG JCM CIP

History <- B. Austin, A 47 T. Urakami TK 0034 <-- ATCC 29983 <-- B. Austin A47. CIP <- 1984, NCIB <- B. Austin: strain A47, Pseudomonas mesophila

Links

Methylobacterium mesophilicum A 47 is a mesophilic, Gram-negative, motile prokaryote that was isolated from phylloplane of Lolium perenne.

Gram-negative motile rod-shaped mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 3560

LMG 5275,ATCC 29983,CCUG 16482,DSM 1708,NCIB 11561,CIP 101129,JCM 2829,IFO 15688,NCIMB 11561,NBRC 15688,NRRL B-14246,VTT E-981080

@ref 20215

Last LPSN update 2025-12-16 09:48:30

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Methylobacteriaceae

Genus Methylobacterium

Species Methylobacterium mesophilicum

Full scientific name Methylobacterium mesophilicum (Austin and Goodfellow 1979) Green and Bousfield 1983

Synonyms (1)

Pseudomonas mesophilica

BacDive ID	Other strains from **Methylobacterium mesophilicum** (7)	Type strain
100158	M. mesophilicum STI09576(IMET), JCM 3323, INA 1671, IMET ...
151707	M. mesophilicum CCUG 44687
151708	M. mesophilicum CCUG 44688
151711	M. mesophilicum CCUG 44695
152109	M. mesophilicum CCUG 45817
152282	M. mesophilicum CCUG 46323
153712	M. mesophilicum CCUG 50716

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
120912	negative	rod-shaped
125439	negative		93.5
125438	negative		97.333

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
865	ANCYLOBACTER - SPIROSOMA MEDIUM (DSMZ Medium 7)	Medium recipe at MediaDive	Name: ANCYLOBACTER - SPIROSOMA MEDIUM (DSMZ Medium 7) Composition: Agar 15.0 g/l Yeast extract 1.0 g/l Peptone 1.0 g/l Glucose 1.0 g/l Distilled water
865	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 Peptone 5.0 g/l Meat extract 3.0 g/l Methanol Distilled water
40315	MEDIUM 18 - for Hydrogenophaga, Vogesella and Pseudomonas genera		Distilled water make up to (1000.000 ml);Sodium chloride (3.000 g);Agar(12.000 g);Yeast extract (3.000 g);Peptone (0.600 g)
865	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
120912	CIP Medium 29	Medium recipe at CIP
120912	CIP Medium 566	Medium recipe at CIP
120912	CIP Medium 18	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
865	positive	growth	25	mesophilic
40315	positive	growth	25	mesophilic
46495	positive	growth	25-30	mesophilic
67770	positive	growth	30	mesophilic
120912	positive	growth	10-25	psychrophilic
120912	negative	growth	5
120912	negative	growth	37
120912	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	aerobe	91.8

Spore formation

@ref	Spore formation	Confidence
125439		96.4
125438		91.014

Halophily

@ref	Salt	Growth	Tested relation	Concentration
120912	NaCl	positive	growth	0 %
120912	NaCl		growth	2 %
120912	NaCl		growth	4 %
120912	NaCl		growth	6 %
120912	NaCl		growth	8 %
120912	NaCl		growth	10 %

Observation

67770

Observationquinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
120912	16947 ChEBI	citrate	-	carbon source
120912	4853 ChEBI	esculin	-	hydrolysis
120912	17632 ChEBI	nitrate	-	reduction
120912	16301 ChEBI	nitrite	-	reduction
120912	15882 ChEBI	phenol	-	degradation

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
120912	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
120912	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
120912	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	-	3.1.3.1	from API zym
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
68382	alpha-mannosidase	-	3.2.1.24	from API zym
120912	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
120912	beta-galactosidase	-	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
120912	caseinase	-	3.4.21.50
120912	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
120912	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
120912	gelatinase	-
120912	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
120912	lipase	-
68382	lipase (C 14)	-		from API zym
120912	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
120912	ornithine decarboxylase	-	4.1.1.17
68382	trypsin	+	3.4.21.4	from API zym
120912	tryptophan deaminase	-
120912	tween esterase	-
120912	urease	+	3.5.1.5
68382	valine arylamidase	-		from API zym

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
120912	-	-	+	+	-	+	-	-	+	-	+	+	-	-	-	-	-	-	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
120912	not determinedn.d.	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	+	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	+	-	+	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	+

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Host species	Country	Country ISO 3 Code	Continent
865	phylloplane of Lolium perenne	Lolium perenne	United Kingdom	GBR	Europe
46495	Lolium perenne phylloplane		United Kingdom	GBR	Europe
67770	Lolium prenne leaf	Lolium prenne
120912	Environment, Perennial rye grass		United Kingdom	GBR	Europe

Taxonmaps

69479

Global distribution of 16S sequence AB175636 (>99% sequence identity) for Methylobacterium from Microbeatlas

Aquatic Samples	142
Soil Samples	88
Animal Samples	737
Plant Samples	195
Total Samples	1162

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Biosafety level	Biosafety level comment
865	yes, in single cases	1	Risk group (German classification) According to TRBA 466
120912		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
124043	ASM4265930v1 assembly for Methylobacterium mesophilicum CCUG 16482	scaffold	GCA_042659305			39956	54.12
66792	ASM2217944v1 assembly for Methylobacterium mesophilicum NBRC 15688	scaffold	GCA_022179445	39956.9	8112588504	39956	33.09

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
865	Methylobacterium mesophilicum gene for 16S ribosomal RNA, partial sequence, strain:DSM 1708	AB175636	1433	39956
124043	Methylobacterium mesophilicum partial 16S rRNA gene, strain JCM 2829	AJ400919	1405	39956
124043	Methylobacterium mesophilicum gene for 16S rRNA, strain: JCM 2829.	D32225	1405	39956

GC content

@ref	GC-content (mol%)	Method
67770	66	thermal denaturation, midpoint method (Tm)
67770	65.8	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: Methylobacterium mesophilicum NBRC 15688
NCBI: GCA_022179445

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.40	no
125439	motility	BacteriaNetⓘ	yes	56.70	no
125439	gram_stain	BacteriaNetⓘ	negative	93.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	91.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Methylobacterium mesophilicum NBRC 15688
NCBI: GCA_022179445.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.33	no
125438	anaerobic	anaerobicⓘ	no	94.99	no
125438	aerobic	aerobicⓘ	yes	88.46	no
125438	spore-forming	spore-formingⓘ	no	91.01	no
125438	thermophilic	thermophileⓘ	no	98.43	yes
125438	flagellated	motile2+ⓘ	yes	71.23	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Specialized Metabolites from Methylotrophic Proteobacteria.	Puri AW.	Curr Issues Mol Biol	10.21775/cimb.033.211	2019
	Differentiation of gram-negative, nonfermentative bacteria isolated from biofilters on the basis of Fatty Acid composition, quinone system, and physiological reaction profiles.	Lipski A, Klatte S, Bendinger B, Altendorf K.	Appl Environ Microbiol	10.1128/aem.58.6.2053-2065.1992	1992
Enzymology	Pseudomonas mesophilica and an unnamed taxon, clinical isolates of pink-pigmented oxidative bacteria.	Gilardi GL, Faur YC	J Clin Microbiol	10.1128/jcm.20.4.626-629.1984	1984
Phylogeny	Methylobacterium soli sp. nov. a methanol-utilizing bacterium isolated from the forest soil.	Cao YR, Wang Q, Jin RX, Tang SK, Jiang Y, He WX, Lai HX, Xu LH, Jiang CL	Antonie Van Leeuwenhoek	10.1007/s10482-010-9535-0	2011
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	Bosea minatitlanensis sp. nov., a strictly aerobic bacterium isolated from an anaerobic digester.	Ouattara AS, Assih EA, Thierry S, Cayol JL, Labat M, Monroy O, Macarie H	Int J Syst Evol Microbiol	10.1099/ijs.0.02540-0	2003

References

#865	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 1708
#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 )
#40315	; Curators of the CIP;
#46495	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 16482
#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;
#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 .
#120912	Collection of Institut Pasteur ; Curators of the CIP; CIP 101129
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 mesophilicum (DSM 1708, ATCC 29983, ICPB 4095)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Enzymes

API zym

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_042659305

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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