Methylobacillus glycogenes (DSM 5685, ATCC 29475, DSM 46232)

Name: Methylobacillus glycogenes (DSM 5685, ATCC 29475, DSM 46232)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7232

Type strain

Strain Designation T-11

Culture col. no. DSM 5685 ATCC 29475 DSM 46232 IMET 10774 NCIMB 11375 6 more

NCBI tax ID(s) 1236959 406

Special Collections DSMZ JCM JMRC

History DSMZ <- NCIMB <- ATCC <- Yordy <- Weaver JCM <-- T. Urakami TK 0113 <-- ATCC 29475 <-- J. R. Yordy T-11 <-- T. Weaver.

Links

Methylobacillus glycogenes T-11 is a bacterium that was isolated from decaying tomato.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 3558

LMG 6082,ATCC 29475,IMET 10774,JCM 2850,LMG 6786,NCIB 11375,NCIMB 11375,DSM 5685,DSM 46232,VKM B-2060

@ref 20215

Last LPSN update 2026-05-29 08:26:36

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Spirillales

Family Methylophilaceae

Genus Methylobacillus

Species Methylobacillus glycogenes

Full scientific name Methylobacillus glycogenes Yordy and Weaver 1977 (Approved Lists 1980)

BacDive ID	Other strains from **Methylobacillus glycogenes** (21)	Type strain
24847	M. glycogenes Sanraku-Ocean Co. M1, DSM 46233, ATCC 21852, ...
24848	M. glycogenes Sanraku-Ocean Co. M8, DSM 46234, ATCC 21370, ...
163510	M. glycogenes JCM 2841, ATCC 21275, KCTC 1656
163511	M. glycogenes JCM 2842, ATCC 21452
163512	M. glycogenes JCM 2843, ATCC 21961
163513	M. glycogenes JCM 2844, ATCC 21369
163514	M. glycogenes JCM 2847, ATCC 21958
163515	M. glycogenes JCM 2848, ATCC 21963
163516	M. glycogenes JCM 2851, KCTC 1477, NRRL B-5458
163517	M. glycogenes JCM 2855, ATCC 21453
163518	M. glycogenes JCM 2856, ATCC 21962
163519	M. glycogenes JCM 2857, ATCC 21704, KCTC 2634
163520	M. glycogenes JCM 2858, ATCC 21960, KCTC 2635
163521	M. glycogenes JCM 2859, NCIMB 10508
163522	M. glycogenes JCM 2860, NCIMB 10510
163523	M. glycogenes JCM 2861, NCIMB 10512
163524	M. glycogenes JCM 2862, NCIMB 10592
163525	M. glycogenes JCM 2863, NCIMB 10594
163532	M. glycogenes JCM 2864, NCIMB 10596
163540	M. glycogenes JCM 2865
163545	M. glycogenes JCM 2866

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	97.5
125439	negative	97.404

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
2282	COLBY AND ZATHMAN MEDIUM (DSMZ Medium 606)		Medium recipe at MediaDive	Name: COLBY AND ZATHMAN MEDIUM (DSMZ Medium 606) Composition: Agar 15.0 g/l Methanol 1.584 g/l K2HPO4 1.2 g/l KH2PO4 0.62 g/l (NH4)2SO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l NaCl 0.1 g/l CaCl2 x 6 H2O 0.05 g/l FeCl3 x 6 H2O 0.001 g/l ZnSO4 x 7 H2O 7e-05 g/l Na2MoO4 x 2 H2O 1e-05 g/l H3BO3 1e-05 g/l MnSO4 x 5 H2O 1e-05 g/l CuSO4 x 5 H2O 5e-06 g/l CoCl2 x 6 H2O 5e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
2282	positive	growth	30
67770	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	facultative anaerobe	91.619

Spore formation

@ref	Spore formation	Confidence
125439		98.952

Observation

67770

Observationquinones: Q-8

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Decomposing plant
#Host	#Plants	#Shrub (Scrub)
#Host Body-Site	#Plant	#Fruit (Seed)

Isolation

@ref	Sample type
2282	decaying tomato
67770	Decaying tomato

Taxonmaps

69479

Global distribution of 16S sequence FR733701 (>99% sequence identity) for Methylobacillus from Microbeatlas

Aquatic Samples	1076
Soil Samples	589
Animal Samples	2643
Plant Samples	789
Total Samples	5097

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
2282	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	Methylobacillus glycogenes JCM 2850	contig		1236959.3		1236959	56.8
67770	ASM61792v1 assembly for Methylobacillus glycogenes JCM 2850	contig	GCA_000617925	1236959.5	2585427884	1236959	55.63

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
2282	Methylobacillus glycogenes partial 16S rRNA gene, type strain DSM5685T	FR733701	1532		406

GC content

@ref	GC-content (mol%)	Method
67770	53.2	thermal denaturation, midpoint method (Tm)
67770	54.1

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM61792v1 assembly for Methylobacillus glycogenes JCM 2850
NCBI: GCA_000617925

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	91.62	no
125439	gram_stain	BacteriaNetⓘ	negative	97.40	no
125439	motility	BacteriaNetⓘ	yes	73.71	no
125439	spore_formation	BacteriaNetⓘ	no	98.95	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Methylobacillus glycogenes JCM 2850
PATRIC: 1236959.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.50	no
125438	anaerobic	anaerobicⓘ	no	88.95	no
125438	spore-forming	spore-formingⓘ	no	88.58	no
125438	aerobic	aerobicⓘ	yes	71.34	no
125438	thermophilic	thermophileⓘ	no	96.84	no
125438	flagellated	motile2+ⓘ	yes	68.53	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Characterization of a unique mutant lysE gene, originating from Corynebacterium glutamicum, encoding a product that induces L-lysine production in Methylophilus methylotrophus.	Gunji Y, Ito H, Masaki H, Yasueda H.	Biosci Biotechnol Biochem	10.1271/bbb.60339	2006
Enzymology	Characterization of an iron- and manganese-containing superoxide dismutase from Methylobacillus sp. strain SK1 DSM 8269.	Seo SN, Lee JH, Kim YM.	Mol Cells	10.1016/s1016-8478(23)10728-x	2007
Enzymology	Purification and characterization of chaperonins 60 and 10 from Methylobacillus glycogenes.	Kawata Y, Doi K, Omoto H, Mizobata T, Nagai J.	Cell Stress Chaperones	10.1379/1466-1268(1998)003<0200:pacoca>2.3.co;2	1998
Metabolism	Effects of the amplification of the genes coding for the L-threonine biosynthetic enzymes on the L-threonine production from methanol by a gram-negative obligate methylotroph, Methylobacillus glycogenes.	Motoyama H, Yano H, Ishino S, Anazawa H, Teshiba S.	Appl Microbiol Biotechnol	10.1007/bf00170226	1994
	Amino Acid Production from Methanol by Methylobacillus glycogenes Mutants: Isolation of L-Glutamic Acid Hyper-producing Mutants from M. glycogenes Strains, and Derivation of L-Threonine and L-Lysine-producing Mutants from Them.	Motoyama H, Anazawa H, Katsumata R, Araki K, Teshiba S.	Biosci Biotechnol Biochem	10.1271/bbb.57.82	1993
	Transformation of methylotrophic bacteria by electroporation.	Gliesche CG.	Can J Microbiol	10.1139/m97-026	1997
Metabolism	Overproduction of L-Lysine from methanol by Methylobacillus glycogenes derivatives carrying a plasmid with a mutated dapA gene.	Motoyama H, Yano H, Terasaki Y, Anazawa H.	Appl Environ Microbiol	10.1128/aem.67.7.3064-3070.2001	2001
Metabolism	Impact of the lanthanide contraction on the activity of a lanthanide-dependent methanol dehydrogenase - a kinetic and DFT study.	Lumpe H, Pol A, Op den Camp HJM, Daumann LJ.	Dalton Trans	10.1039/c8dt01238e	2018
	CO₂ to succinic acid - Estimating the potential of biocatalytic routes.	Liebal UW, Blank LM, Ebert BE.	Metab Eng Commun	10.1016/j.mec.2018.e00075	2018
Metabolism	Biochemical and molecular characterization of the isocitrate dehydrogenase with dual coenzyme specificity from the obligate methylotroph Methylobacillus Flagellatus.	Romkina AY, Kiriukhin MY.	PLoS One	10.1371/journal.pone.0176056	2017
Metabolism	Analysis and manipulation of aspartate pathway genes for L-lysine overproduction from methanol by Bacillus methanolicus.	Naerdal I, Netzer R, Ellingsen TE, Brautaset T.	Appl Environ Microbiol	10.1128/aem.05093-11	2011
Enzymology	Cloning and nucleotide sequences of the homoserine dehydrogenase genes (hom) and the threonine synthase genes (thrC) of the gram-negative obligate methylotroph Methylobacillus glycogenes.	Motoyama H, Maki K, Anazawa H, Ishino S, Teshiba S.	Appl Environ Microbiol	10.1128/aem.60.1.111-119.1994	1994
Enzymology	Distribution of aldoxime dehydratase in microorganisms.	Kato Y, Ooi R, Asano Y.	Appl Environ Microbiol	10.1128/aem.66.6.2290-2296.2000	2000
Phylogeny	[Methylovorus mays--novel species of aerobic, obligatory methylotrophic bacteria associated with plants].	Doronina NV, Kudinova LV, Trotsenko IuA	Mikrobiologiia		2000
Phylogeny	[Analysis of DNA-DNA homologies in obligate methylotrophic bacteria].	Doronina NV, Govorukhina NI, Lysenko AM, Trotsenko IuA	Mikrobiologiia		1988

References

#2282	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5685
#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 )
#20216	Curators of the JMRC: Jena Microbial Resource Collection (JMRC):
#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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Methylobacillus glycogenes (DSM 5685, ATCC 29475, DSM 46232)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000617925

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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