Methylobacterium oxalidis (DSM 24028, NBRC 107715, 35a)

Name: Methylobacterium oxalidis (DSM 24028, NBRC 107715, 35a)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 23092

Type strain

Strain Designation 35a

Culture col. no. DSM 24028 NBRC 107715 35a

NCBI tax ID(s) 944322

Special Collections DSMZ Literature strains

Links

Methylobacterium oxalidis 35a is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from leaves of the sorrel Oxalis corniculata.

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

Name and taxonomic classification

SI-ID 380589

DSM 24028,NBRC 107715,LMG 28250,NCIMB 14840

@ref 20215

Last LPSN update 2025-12-16 09:52:34

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Methylobacteriaceae

Genus Methylobacterium

Species Methylobacterium oxalidis

Full scientific name Methylobacterium oxalidis Tani et al. 2012

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
30303	negative	1.8 µm	1.3 µm	rod-shaped
125439	negative				93.8
125438	negative				95.784

Colony morphology

19152

Incubation period3-7 days

Pigmentation

30303

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
19152	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)	Range
19152	positive	growth	28	mesophilic
30303	positive	growth	28-35	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30303	aerobe
125439	obligate aerobe	93.7

Spore formation

@ref	Spore formation	Confidence
30303
125439		94.5

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30303	NaCl	positive	growth	<2 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30303	30089 ChEBI	acetate	+	carbon source
30303	15740 ChEBI	formate	+	carbon source
30303	28757 ChEBI	fructose	+	carbon source
30303	29987 ChEBI	glutamate	+	carbon source
30303	24996 ChEBI	lactate	+	carbon source
30303	15792 ChEBI	malonate	+	carbon source
30303	51850 ChEBI	methyl pyruvate	+	carbon source
30303	17272 ChEBI	propionate	+	carbon source
30303	30031 ChEBI	succinate	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30303	catalase	+	1.11.1.6

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	Country	Country ISO 3 Code	Continent
19152	leaves of the sorrel Oxalis corniculata	Oxalis corniculata	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB607860 (>99% sequence identity) for Methylobacterium oxalidis subclade from Microbeatlas

Aquatic Samples	701
Soil Samples	3583
Animal Samples	1775
Plant Samples	836
Total Samples	6895

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
19152	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
124043	ASM3016099v1 assembly for Methylobacterium oxalidis NBRC 107715	scaffold	GCA_030160995	944322.5	8119296875	944322	42.13
66792	ASM2217950v1 assembly for Methylobacterium oxalidis DSM 24028	contig	GCA_022179505	944322.4	8069131891	944322	14.83
66792	ASM799219v1 assembly for Methylobacterium oxalidis NBRC 107715	contig	GCA_007992195	944322.3	8069196877	944322	6.82

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
19152	Methylobacterium oxalidis gene for 16S ribosomal RNA, partial sequence	AB607860	1446		944322

GC content

@ref	GC-content (mol%)	Method
19152	70.2	thermal denaturation, midpoint method (Tm)
30303	70.2

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Methylobacterium oxalidis NBRC 107715
NCBI: GCA_007992195

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	94.50	no
125439	motility	BacteriaNetⓘ	yes	67.60	no
125439	gram_stain	BacteriaNetⓘ	negative	93.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	93.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Methylobacterium oxalidis strain NBRC 107715
PATRIC: 944322.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.78	yes
125438	anaerobic	anaerobicⓘ	no	94.05	yes
125438	aerobic	aerobicⓘ	yes	84.66	yes
125438	spore-forming	spore-formingⓘ	no	85.05	yes
125438	thermophilic	thermophileⓘ	no	97.12	yes
125438	flagellated	motile2+ⓘ	yes	76.32	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Prerequisites for amplicon pyrosequencing of microbial methanol utilizers in the environment.	Kolb S, Stacheter A.	Front Microbiol	10.3389/fmicb.2013.00268	2013
	A conserved signaling pathway activates bacterial CBASS immune signaling in response to DNA damage.	Lau RK, Enustun E, Gu Y, Nguyen JV, Corbett KD.	EMBO J	10.15252/embj.2022111540	2022
Phylogeny	Methylobacterium nigriterrae sp. nov., isolated from black soil.	Chen LB, OuYang YT, Liu L, Jin PJ, Huang RR, Pan WY, Wang Y, Xing JY, She TT, Jiao JY, Wang S, Li WJ.	Antonie Van Leeuwenhoek	10.1007/s10482-024-01981-x	2024
Phylogeny	Methylobacterium segetis sp. nov., a novel member of the family Methylobacteriaceae isolated from soil on Jeju Island.	Ten LN, Li W, Elderiny NS, Kim MK, Lee SY, Rooney AP, Jung HY	Arch Microbiol	10.1007/s00203-019-01784-z	2019
Phylogeny	Methylobacterium oxalidis sp. nov., isolated from leaves of Oxalis corniculata.	Tani A, Sahin N, Kimbara K	Int J Syst Evol Microbiol	10.1099/ijs.0.033019-0	2011

References

#19152	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24028
#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 )
#30303	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 #26644 (see below)
#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 .
#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 oxalidis (DSM 24028, NBRC 107715, 35a)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

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_030160995

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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