Name: Pseudomonas rhodina DSM 2163
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 7153

Type strain:

Species: Pseudomonas rhodina

Culture col. no.: DSM 2163, ATCC 14821, NCIB 9421, JCM 2811, CCM 4463, CCUG 36917, CCUG 51501, CIP 101127, IFO 15691, LMG 2275, NBRC 15691, NCIMB 9421, VKM B-2065, CCUG 2875

Strain history: CIP <- 1984, NCIB <- W. Heumann, Pseudomonas rhodos

NCBI tax ID(s): 1236969 (strain), 29428 (species)

SI-ID 3565

LMG 2275, ATCC 14821, DSM 2163, JCM 2811, LMG 6084, NCIB 9421, CCUG 36917, NCIMB 9421, CIP 101127, CCUG 2875, IFO 15691, CCM 4463, VKM B-2065, NBRC 15691, CCUG 51501, CCUG 55908

Special Collections

Section

When using BacDive for research please cite our paper

Pseudomonas rhodina DSM 2163 is a mesophilic, Gram-negative bacterium that was isolated from Alnus rhizosphere.

Gram-negative
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	*Gammaproteobacteria*
	Order	*Pseudomonadales*
	Family	*Pseudomonadaceae*
	Genus	*Pseudomonas*
	Species	Pseudomonas rhodina
	Full Scientific Name (LPSN)	Pseudomonas rhodina corrig. Heumann 1962 (Approved Lists 1980)

	Synonym	Pseudomonas rhodos
	Synonym	Methylobacterium rhodos
	Synonym	Methylobacterium rhodinum
	Synonym	**Methylorubrum rhodinum**

Information on morphological and physiological properties Morphology

[Ref.: #125438]	Gram stain	negative Confidence in %95.469
[Ref.: #125439]	Gram stain	negative Confidence in %95.9

Information on culture and growth conditions Culture and growth conditions

[Ref.: #988]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #988]

Culture medium growth

[Ref.: #988]

Culture medium link

Medium recipe at MediaDive

[Ref.: #988]

Culture medium composition

expand / minimize

[Ref.: #40314]

Culture medium

MEDIUM 54 - for Methylobacterium organophilum and M. rhodinum

[Ref.: #40314]

Culture medium growth

[Ref.: #40314]

Culture medium composition

expand / minimize

[Ref.: #122219]

Culture medium

CIP Medium 54

[Ref.: #122219]

Culture medium growth

[Ref.: #122219]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #988]	growth	30 °C
[Ref.: #40314]	growth	25 °C
[Ref.: #67770]	growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #125439]

Oxygen tolerance

obligate aerobe Confidence in %93.8

[Ref.: #125439]

Ability of spore formation

no Confidence in %96.1

[Ref.: #67770]

Observation

quinones: Q-10

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

[Ref.: #988]	Sample type/isolated from	Alnus rhizosphere
[Ref.: #988]	Host species	Alnus

[Ref.: #67770]	Sample type/isolated from	Alnus rhizosphere
[Ref.: #67770]	Host species	Alnus rhizosphere

[Ref.: #122219]	Sample type/isolated from	Environment, Alnus rhizosphere
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Rhizosphere

What are isolation sources categories?

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

[Ref.: #988]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #122219]	Biosafety level	1	Risk group (French classification)

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.: #988]	Methylobacterium rhodinum gene for 16S ribosomal RNA, partial sequence, strain:DSM 2163	AB175644	1435	GenBank ENA	29428 tax ID
[Ref.: #20218]	Methylobacterium rhodinum 16S ribosomal RNA gene, partial sequence; tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequence	AF338179	1118	GenBank ENA	29428 tax ID	*
[Ref.: #124043]	Methylobacterium rhodinum gene for 16S rRNA, strain: JCM 2811.	D32229	1407	GenBank ENA	29428 tax ID	*

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Methylorubrum rhodinum DSM 2163	GCA_014199935	scaffold	GenBank ENA	29428 tax ID	*
[Ref.: #66792]	Methylorubrum rhodinum JCM 2811	GCA_001310855	contig	GenBank ENA	1236969 tax ID	*
[Ref.: #66792]	Methylorubrum rhodinum JCM 2811	1236969.4	wgs	PATRIC	1236969 tax ID	*
[Ref.: #66792]	Methylorubrum rhodinum strain DSM 2163	29428.5	wgs	PATRIC	29428 tax ID	*
[Ref.: #66792]	Methylorubrum rhodinum DSM 2163	2829745981	draft	JGI IMG/M	29428 tax ID	*
[Ref.: #66792]	Methylorubrum rhodinum JCM 2811	2728369659	draft	JGI IMG/M	1236969 tax ID	*

[Ref.: #67770]

GC-content

65.8 mol%

thermal denaturation, midpoint method (Tm)

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 rhodinum JCM 2811 PATRIC: 1236969.4
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	95.469	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	86.946	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	87.909	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	74.532	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	96.999	no
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	56.614	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Methylorubrum rhodinum DSM 2163 NCBI: GCA_014199935
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	93.8
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	95.9
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	66.5
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	96.1

Availability in culture collections External links

[Ref.: #988]

Culture collection no.

DSM 2163, ATCC 14821, NCIB 9421, JCM 2811, CCM 4463, CCUG 36917, CCUG 51501, CIP 101127, IFO 15691, LMG 2275, NBRC 15691, NCIMB 9421, VKM B-2065, CCUG 2875

[Ref.: #76606]

SI-ID 3565

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Review of the genus Methylobacterium and closely related organisms: a proposal that some Methylobacterium species be reclassified into a new genus, Methylorubrum gen. nov.	Green PN, Ardley JK	Int J Syst Evol Microbiol	10.1099/ijsem.0.002856	2018	*

References

#988	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 2163

#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 )

#40314 ; 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;

#76606

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-ID3565.1 )

#122219 Collection of Institut Pasteur ; Curators of the CIP; CIP 101127

#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 rhodinum JCM 2811

Methylorubrum rhodinum DSM 2163

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