Name: Methylorubrum extorquens 0355
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 7143

Type strain:

Species: Methylorubrum extorquens

Strain Designation: 0355, D355, AM1

Culture col. no.: DSM 1338, ATCC 14718, NCIB 9133, CCUG 2477, JCM 2805, IAM 12632, NCCB 78016, NCIMB 9133, VKM B-2067

Strain history: T. Urakami TK 0004 <-- NCIB 9133 <-- P. H. A. Sneath D355.

NCBI tax ID(s): 408 (species)

SI-ID 45565

ATCC 14718, NCIB 9133, CCUG 2477, DSM 1338, JCM 2805, IAM 12632, NCIMB 9133, NCIMB9276, VKM B-2067, NCCB 78016, LMD 78.16

Special Collections

Other strains from Methylorubrum extorquens

Section

When using BacDive for research please cite our paper

Methylorubrum extorquens 0355 is a mesophilic bacterium that was isolated from air.

mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Methylobacteriaceae*
	Genus	*Methylorubrum*
	Species	**Methylorubrum extorquens**
	Full Scientific Name (LPSN)	Methylorubrum extorquens (Urakami and Komagata 1984 ex Bassalik 1913) Green and Ardley 2018

	Synonym	Methylobacterium extorquens
	Synonym	Protomonas extorquens

Information on morphological and physiological properties Morphology

[Ref.: #125439]	Gram stain	negative Confidence in %91.6
[Ref.: #125438]	Gram stain	negative Confidence in %97.815

Information on culture and growth conditions Culture and growth conditions

[Ref.: #528]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #528]

Culture medium growth

[Ref.: #528]

Culture medium link

Medium recipe at MediaDive

[Ref.: #528]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #528]			growth	30 °C
[Ref.: #67770]			growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #125439]

Oxygen tolerance

aerobe Confidence in %92.8

[Ref.: #125439]

Ability of spore formation

no Confidence in %94.6

[Ref.: #528]	Name of produced compound	bacteriochlorophyll
[Ref.: #528]	Name of produced compound	glutamate dehydrogenase, NADP-dependent

[Ref.: #67770]

Observation

quinones: Q-10

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #44544]

Fatty acid	Percentage	ECL
C18:1 ω7c /12t/9t	75.4	17.824
C16:1 ω7c	11.8	15.819
C14:0 3OH/C16:1 ISO I	7.1	15.485
C13:0	3.2	13
C18:0	2.5	18

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #528]	Sample type/isolated from	air

[Ref.: #44544]	Sample type/isolated from	Air
* marker position based on {}

Isolation sources categories

#Environmental

#Air

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AF293375 (>99% sequence identity) for Methylorubrum from Microbeatlas

Aquatic Samples	23711
Soil Samples	23280
Animal Samples	47578
Plant Samples	16159
Total Samples	110728

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #528]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #20218]	Methylobacterium extorquens 16S ribosomal RNA gene, partial sequence; tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequence	AF293375	2552	GenBank ENA	408 tax ID	*
[Ref.: #124043]	Methylobacterium extorquens partial 16S rRNA gene, strain IAM 12632	AJ400916	736	GenBank ENA	408 tax ID	*
[Ref.: #20218]	Methylobacterium extorquens partial 16S rRNA gene, isolate OS-44.c3	AM237358	510	GenBank ENA	408 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Methylorubrum extorquens AM1	GCA_000022685	complete	GenBank ENA	272630 tax ID

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Methylorubrum extorquens AM1 AM1 NCBI: GCA_000022685.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	97.815	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	93.265	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	83.644	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	84.795	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	97.437	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	74.534	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Methylorubrum extorquens AM1 NCBI: GCA_000022685
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	94.6
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	54.3
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	91.6
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	aerobe	92.8

Availability in culture collections External links

[Ref.: #528]

Culture collection no.

DSM 1338, ATCC 14718, NCIB 9133, CCUG 2477, JCM 2805, IAM 12632, NCCB 78016, NCIMB 9133, VKM B-2067

[Ref.: #76597]

SI-ID 45565

Literature:

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Molecular cloning of the DNA gyrase genes from Methylovorus sp. strain SS1 and the mechanism of intrinsic quinolone resistance in methylotrophic bacteria.	Kim KS, Kim JH, Kim DY, Kim HJ, Park ST, Kim YM	Mol Cells	922	2005	*
	Enzymatic synthesis of L-[4-13C]aspartic acid.	Maeda H, Suzuki S, Ikeguchi M, Sakai T, Shibata K	J Biosci Bioeng	10.1016/s1389-1723(00)88966-5	2000	*

References

#528	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 1338

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#44544 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 2477
#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 .

#76597

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID45565.1 )

#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 .

* These data were automatically processed and therefore are not curated

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Methylorubrum extorquens AM1 AM1

Methylorubrum extorquens AM1

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