Methylobacterium organophilum (DSM 760, XX)

Name: Methylobacterium organophilum (DSM 760, XX)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7150

Type strain

Strain Designation XX

Culture col. no. DSM 760 XX

NCBI tax ID(s) 410

Special Collections DSMZ JCM CIP

History DSMZ <- R.S. Hanson, strain XX. Strain obtained directly from the laboratory where the strain was isolated. Not identical to DSM 18172, obtained via the NCIMB JCM <-- T. Urakami TK 0047 <-- ATCC 27886 <-- R. Hanson XX.

Links

Methylobacterium organophilum XX is a bacterium that was isolated from sediment.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 3561

LMG 6083,ATCC 27886,DSM 760,JCM 2833,NCIB 11278,CIP 101049,CCRC 10934,IFO 15689,NCIMB 11278,CCM 4460,VKM B-2066,NBRC 15689,NCCB 78041,LMD 78.41,HAMBI 2263,BCRC 10934,DSM 18172,CCUG 55902

@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 organophilum

Full scientific name Methylobacterium organophilum Patt et al. 1976 (Approved Lists 1980)

BacDive ID	Other strains from **Methylobacterium organophilum** (4)	Type strain
7151	M. organophilum XX, DSM 18172, ATCC 27886, CIP 101049, IFO ... (type strain)
136034	M. organophilum 998-85, CIP 102028
138029	M. organophilum 535-86, CIP 102545
149309	M. organophilum CCUG 37468

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	97.802

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
432	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
38089	MEDIUM 54 - for Methylobacterium organophilum and M. rhodinum		Distilled water make up to (995.000 ml);Iron (II) sulphate heptahydrate (4.000 mg);Zinc sulphate heptahydrate (0.100 mg);ManganeseII chloride tetrahydrate (0.030 mg);Boric acid (0.300 mg);Magnesium sulphate heptahydrate (1.000 g);Calcium chloride dihydrat
121432	CIP Medium 72	Medium recipe at CIP
121432	CIP Medium 54	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
432	positive	growth	30
38089	positive	growth	25
67770	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	95.968

Spore formation

@ref	Spore formation	Confidence
125439		98.549

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
432	sediment	Madison, Lake Mendota	USA	USA	North America
67770	Lake Mendota	Madison, WI	USA	USA	North America

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
432	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	ASM309661v1 assembly for Methylobacterium radiotolerans DSM 760	scaffold	GCA_003096615	410.10	2756170276	410	62.15
66792	ASM2217946v1 assembly for Methylobacterium organophilum NBRC 15689	contig	GCA_022179465	410.23	8071723820	410	55.92

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
432	Methylobacterium organophilum gene for 16S ribosomal RNA, partial sequence, strain:ATCC 27886	AB175638	1433	410
432	Methylobacterium radiotolerans gene for 16S ribosomal RNA, partial sequence, strain:DSM 760	AB175637	1433	31998
67770	Methylobacterium organophilum gene for 16S ribosomal RNA, partial sequence, strain:JCM 2833	AB175639	1433	410
67770	Methylobacterium organophilum gene for 16S rRNA, strain: JCM 2833	D32226	1405	410
67770	M.organophilum 16S rRNA	M29028	1316	410

GC content

@ref	GC-content (mol%)	Method
432	66.0
67770	66	thermal denaturation, midpoint method (Tm)
67770	66.8	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: ASM309661v1 assembly for Methylobacterium radiotolerans DSM 760
NCBI: GCA_003096615

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.97	no
125439	gram_stain	BacteriaNetⓘ	negative	85.49	no
125439	motility	BacteriaNetⓘ	yes	52.23	no
125439	spore_formation	BacteriaNetⓘ	no	98.55	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Methylobacterium organophilum strain DSM 760
PATRIC: 410.10

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.80	no
125438	anaerobic	anaerobicⓘ	no	94.84	no
125438	spore-forming	spore-formingⓘ	no	86.41	no
125438	aerobic	aerobicⓘ	yes	88.94	no
125438	thermophilic	thermophileⓘ	no	98.50	no
125438	flagellated	motile2+ⓘ	yes	73.91	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Insights into the genome of Methylobacterium sp. NMS14P, a novel bacterium for growth promotion of maize, chili, and sugarcane.	Jirakkakul J, Khoiri AN, Duangfoo T, Dulsawat S, Sutheeworapong S, Petsong K, Wattanachaisaereekul S, Paenkaew P, Tachaleat A, Cheevadhanarak S, Prommeenate P.	PLoS One	10.1371/journal.pone.0281505	2023
	First historical genome of a crop bacterial pathogen from herbarium specimen: Insights into citrus canker emergence.	Campos PE, Groot Crego C, Boyer K, Gaudeul M, Baider C, Richard D, Pruvost O, Roumagnac P, Szurek B, Becker N, Gagnevin L, Rieux A.	PLoS Pathog	10.1371/journal.ppat.1009714	2021
Enzymology	PqqE from Methylobacterium extorquens AM1: a radical S-adenosyl-l-methionine enzyme with an unusual tolerance to oxygen.	Saichana N, Tanizawa K, Pechousek J, Novak P, Yakushi T, Toyama H, Frebortova J.	J Biochem	10.1093/jb/mvv073	2016
Phylogeny	Distribution of tetrahydromethanopterin-dependent enzymes in methylotrophic bacteria and phylogeny of methenyl tetrahydromethanopterin cyclohydrolases.	Vorholt JA, Chistoserdova L, Stolyar SM, Thauer RK, Lidstrom ME.	J Bacteriol	10.1128/jb.181.18.5750-5757.1999	1999
Metabolism	Identification and nucleotide sequences of mxaA, mxaC, mxaK, mxaL, and mxaD genes from Methylobacterium extorquens AM1.	Morris CJ, Kim YM, Perkins KE, Lidstrom ME.	J Bacteriol	10.1128/jb.177.23.6825-6831.1995	1995
Genetics	Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.	Hordt A, Lopez MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Goker M.	Front Microbiol	10.3389/fmicb.2020.00468	2020
Metabolism	Molecular genetics of the genus Paracoccus: metabolically versatile bacteria with bioenergetic flexibility.	Baker SC, Ferguson SJ, Ludwig B, Page MD, Richter OM, van Spanning RJ.	Microbiol Mol Biol Rev	10.1128/mmbr.62.4.1046-1078.1998	1998
Phylogeny	Genomic Metrics Applied to Rhizobiales (Hyphomicrobiales): Species Reclassification, Identification of Unauthentic Genomes and False Type Strains.	Volpiano CG, Sant'Anna FH, Ambrosini A, de Sao Jose JFB, Beneduzi A, Whitman WB, de Souza EM, Lisboa BB, Vargas LK, Passaglia LMP	Front Microbiol	10.3389/fmicb.2021.614957	2021
Metabolism	Sequence analysis of pqq genes required for biosynthesis of pyrroloquinoline quinone in Methylobacterium extorquens AM1 and the purification of a biosynthetic intermediate.	Toyama H, Chistoserdova L, Lidstrom ME	Microbiology (Reading)	10.1099/00221287-143-2-595	1997
Phylogeny	Isolation, phenotypic characterization, and complementation analysis of mutants of Methylobacterium extorquens AM1 unable to synthesize pyrroloquinoline quinone and sequences of pqqD, pqqG, and pqqC.	Morris CJ, Biville F, Turlin E, Lee E, Ellermann K, Fan WH, Ramamoorthi R, Springer AL, Lidstrom ME	J Bacteriol	10.1128/jb.176.6.1746-1755.1994	1994
Enzymology	Localization of a pyrroloquinoline quinone biosynthesis gene near the methanol dehydrogenase structural gene in Methylobacterium organophilum DSM 760.	Mazodier P, Biville F, Turlin E, Gasser F	J Gen Microbiol	10.1099/00221287-134-9-2513	1988
Phylogeny	Methylobacterium terricola sp. nov., a gamma radiation-resistant bacterium isolated from gamma ray-irradiated soil.	Kim J, Chhetri G, Kim I, Lee B, Jang W, Kim MK, Seo T	Int J Syst Evol Microbiol	10.1099/ijsem.0.004054	2020
Metabolism	Methylobacterium durans sp. nov., a radiation-resistant bacterium isolated from gamma ray-irradiated soil.	Kim J, Chhetri G, Kim I, Kim MK, Seo T	Antonie Van Leeuwenhoek	10.1007/s10482-019-01331-2	2019
Phylogeny	Methylobacterium terrae sp. nov., a radiation-resistant bacterium isolated from gamma ray-irradiated soil.	Kim J, Chhetri G, Kim I, Kim H, Kim MK, Seo T	J Microbiol	10.1007/s12275-019-9007-9	2019
Phylogeny	Psychroglaciecola arctica gen. nov., sp. nov., isolated from Arctic glacial foreland soil.	Qu Z, Jiang F, Chang X, Qiu X, Ren L, Fang C, Peng F	Int J Syst Evol Microbiol	10.1099/ijs.0.060913-0	2014
Phylogeny	Methylobacterium haplocladii sp. nov. and Methylobacterium brachythecii sp. nov., isolated from bryophytes.	Tani A, Sahin N	Int J Syst Evol Microbiol	10.1099/ijs.0.048215-0	2013
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 gnaphalii sp. nov., isolated from leaves of Gnaphalium spicatum.	Tani A, Sahin N, Kimbara K	Int J Syst Evol Microbiol	10.1099/ijs.0.037713-0	2011
Phylogeny	Methylobacterium jeotgali sp. nov., a non-pigmented, facultatively methylotrophic bacterium isolated from jeotgal, a traditional Korean fermented seafood.	Aslam Z, Lee CS, Kim KH, Im WT, Ten LN, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.64625-0	2007
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

#432	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 760
#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 )
#38089	; Curators of the CIP;
#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;
#121432	Collection of Institut Pasteur ; Curators of the CIP; CIP 101049
#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 organophilum (DSM 760, XX)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003096615

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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