Name: Massilia varians R-3575
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 11333

Type strain:

Species: Massilia varians

Strain Designation: R-3575, RSTN 96/5182

Culture col. no.: DSM 21873, CCM 7478, CCUG 35299

Strain history: <- P. Kämpfer, Univ. Giessen <- CCUG <- S.-T. Thomassen, Tromsø, Norway; RSTN 96/5182

NCBI tax ID(s): 457921 (species)

SI-ID 16235

CCUG 35299, CCM 7478, DSM 21873

Other strains from Massilia varians

M. varians CCUG 24677 A, LMG 9558
M. varians CCUG 48018
M. varians CCUG 48700 A
M. varians CCUG 49054

Section

Massilia varians R-3575 is an aerobe, mesophilic, Gram-negative human pathogen that was isolated from human eye, 90-year-old man.

Gram-negative
rod-shaped
aerobe
human pathogen
mesophilic
16S sequence
Bacteria

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Oxalobacteraceae*
	Genus	*Massilia*
	Species	**Massilia varians**
	Full Scientific Name (LPSN)	Massilia varians (Kämpfer et al. 2008) Kämpfer et al. 2011

	Synonym	Naxibacter varians
	Synonym	Telluria varians

Information on morphological and physiological properties Morphology

[Ref.: #32451]	Gram stain	negative

[Ref.: #32451]	Cell length	2 µm

[Ref.: #32451]	Cell width	1 µm

[Ref.: #32451]	Cell shape	rod-shaped

[Ref.: #32451]	Motility	no

[Ref.: #32451]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16006]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #16006]

Culture medium growth

[Ref.: #16006]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16006]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16006]	growth	28 °C
[Ref.: #32451]	growth	15-37 °C
[Ref.: #32451]	optimum	25-30 °C

[Ref.: #16006]	Temperature range	mesophilic
[Ref.: #32451]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32451]			optimum	7
[Ref.: #32451]			growth	5.5-11.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32451]

Oxygen tolerance

aerobe

[Ref.: #32451]

Ability of spore formation

[Ref.: #32451]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32451]	3-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #32451]	acetate ChEBI	+	carbon source
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #32451]	esculin ChEBI	+	hydrolysis
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	L-arabinose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #32451]	pyruvate ChEBI	+	carbon source
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE
[Ref.: #32451]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #68369]	gelatinase	+		* from API 20NE
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE

API® 20NE:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #16006]	23835	-	-	-	-	-	+	+	+	+	+	-	-	+	+	-	-	-	+	-	+	+

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

[Ref.: #16006]	Sample type/isolated from	human eye, 90-year-old man
[Ref.: #16006]	Geographic location (country and/or sea, region)	Tromsø
[Ref.: #16006]	Country	Norway
[Ref.: #16006]	Country ISO 3 Code	NOR
[Ref.: #16006]	Continent	Europe

[Ref.: #52657]	Sample type/isolated from	Human eye,90-yr-old man
[Ref.: #52657]	Sampling date	1996-01-01
[Ref.: #52657]	Geographic location (country and/or sea, region)	Tromsö
[Ref.: #52657]	Country	Norway
[Ref.: #52657]	Country ISO 3 Code	NOR
[Ref.: #52657]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Host	#Human	#Male
#Host Body-Site	#Organ	#Eye

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AM774587 (>99% sequence identity) for Massilia from Microbeatlas

Aquatic Samples	118
Soil Samples	34
Animal Samples	196
Plant Samples	90
Total Samples	438

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

[Ref.: #16006]	Pathogenicity (human)	yes, in single cases
[Ref.: #16006]	Biosafety level	1	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.: #16006]	Naxibacter varians partial 16S rRNA gene, type strain CCUG 35299T	AM774587	1362	ENA	457921 tax ID

Availability in culture collections External links

[Ref.: #16006]

Culture collection no.

DSM 21873, CCM 7478, CCUG 35299

[Ref.: #80566]

SI-ID 16235

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Massilia agri sp. nov., isolated from reclaimed grassland soil.	Chaudhary DK, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.002002	2017	*
Phylogeny	Massilia tieshanensis sp. nov., isolated from mining soil.	Du Y, Yu X, Wang G	Int J Syst Evol Microbiol	10.1099/ijs.0.034306-0	2011	*
Phylogeny	Revision of the genus Massilia La Scola et al. 2000, with an emended description of the genus and inclusion of all species of the genus Naxibacter as new combinations, and proposal of Massilia consociata sp. nov.	Kampfer P, Lodders N, Martin K, Falsen E	Int J Syst Evol Microbiol	10.1099/ijs.0.025585-0	2010	*
Phylogeny	Naxibacter varians sp. nov. and Naxibacter haematophilus sp. nov., and emended description of the genus Naxibacter.	Kampfer P, Falsen E, Busse HJ	Int J Syst Evol Microbiol	10.1099/ijs.0.65516-0	2008	*

References

#16006

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21873

#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 )

#32451

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 #28673 (see below)

#52657 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 35299

#68369

Automatically annotated from API 20NE .

#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 .

#80566

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-ID16235.1 )

#28673

IJSEM 1680 2008 ( DOI 10.1099/ijs.0.65516-0 , PubMed 18599716 )

* These data were automatically processed and therefore are not curated

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