Name: Microvirga aerophila 5420S-12
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 7204

Type strain:

Species: Microvirga aerophila

Strain Designation: 5420S-12

Culture col. no.: DSM 21344, KACC 12743, NBRC 106136

Strain history: <- S.-W. Kwon, KACC; 5420S-12 <- H.-Y. Weon

NCBI tax ID(s): 670291 (species)

SI-ID 405794

DSM 21344

Section

Microvirga aerophila 5420S-12 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from air.

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

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	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Methylobacteriaceae*
	Genus	*Microvirga*
	Species	**Microvirga aerophila**
	Full Scientific Name (LPSN)	Microvirga aerophila Weon et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #29689]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.99

[Ref.: #29689]	Cell length	1.6-4.2 µm

[Ref.: #29689]	Cell width	0.8-1.1 µm

[Ref.: #29689]	Cell shape	rod-shaped

[Ref.: #29689]	Motility	no

[Ref.: #29689]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15630]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #15630]

Culture medium growth

[Ref.: #15630]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15630]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #15630]	growth	28 °C
[Ref.: #29689]	growth	10-35 °C
[Ref.: #29689]	optimum	30 °C

[Ref.: #15630]	Temperature range	mesophilic
[Ref.: #29689]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29689]			optimum	07-10
[Ref.: #29689]			growth	07-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29689]

Oxygen tolerance

aerobe

[Ref.: #29689]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.971

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29689]		NaCl		growth	0-2	%
[Ref.: #29689]		NaCl		optimum	0-2	%

[Ref.: #29689]

Observation

aggregates in chains

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #29689]		catalase	+	1.11.1.6

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	propanol degradation	100	7 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	resorcinol degradation	100	2 of 2
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	ketogluconate metabolism	100	8 of 8
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	CO2 fixation in Crenarchaeota	100	9 of 9
[Ref.: #66794]	NAD metabolism	94.44	17 of 18
[Ref.: #66794]	citric acid cycle	92.86	13 of 14
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	allantoin degradation	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	degradation of sugar acids	88	22 of 25
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	flavin biosynthesis	86.67	13 of 15
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	purine metabolism	81.91	77 of 94
[Ref.: #66794]	metabolism of disaccharids	81.82	9 of 11
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	lipid metabolism	80.65	25 of 31
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	myo-inositol biosynthesis	80	8 of 10
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	tyrosine metabolism	78.57	11 of 14
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	77.78	7 of 9
[Ref.: #66794]	methionine metabolism	76.92	20 of 26
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	histidine metabolism	75.86	22 of 29
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	cyclohexanol degradation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	lysine metabolism	73.81	31 of 42
[Ref.: #66794]	tryptophan metabolism	73.68	28 of 38
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	d-xylose degradation	72.73	8 of 11
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	oxidative phosphorylation	71.43	65 of 91
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	4-hydroxyphenylacetate degradation	70	7 of 10
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	pyrimidine metabolism	68.89	31 of 45
[Ref.: #66794]	degradation of pentoses	67.86	19 of 28
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	sulfoquinovose degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	arginine metabolism	66.67	16 of 24
[Ref.: #66794]	phenol degradation	65	13 of 20
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	androgen and estrogen metabolism	62.5	10 of 16
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	glycine metabolism	60	6 of 10
[Ref.: #66794]	3-phenylpropionate degradation	60	9 of 15
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	vitamin B1 metabolism	53.85	7 of 13
[Ref.: #66794]	ascorbate metabolism	50	11 of 22
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	heme metabolism	42.86	6 of 14
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	vitamin B12 metabolism	32.35	11 of 34
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	carotenoid biosynthesis	27.27	6 of 22
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #15630]	Sample type/isolated from	air
[Ref.: #15630]	Geographic location (country and/or sea, region)	Suwon
[Ref.: #15630]	Country	Republic of Korea
[Ref.: #15630]	Country ISO 3 Code	KOR
[Ref.: #15630]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Air

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence GQ421848 (>99% sequence identity) for Microvirga aerophila subclade from Microbeatlas

Aquatic Samples	20
Soil Samples	412
Animal Samples	21
Plant Samples	13
Total Samples	466

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

[Ref.: #15630]

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.: #15630]	Microvirga aerophila strain 5420S-12 16S ribosomal RNA gene, partial sequence	GQ421848	1439	ENA	670291 tax ID
[Ref.: #20218]	Microvirga aerophila gene for 16S rRNA, partial sequence, strain: NBRC 106136	AB682367	1412	ENA	670291 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Microvirga aerophila DSM 21344	GCA_003332305	contig	GenBank	670291 tax ID	*
[Ref.: #66792]	Microvirga aerophila NBRC 106136	GCA_007991675	contig	GenBank	670291 tax ID	*
[Ref.: #66792]	Microvirga aerophila strain DSM 21344	670291.3	wgs	PATRIC	670291 tax ID	*
[Ref.: #66792]	Microvirga aerophila strain NBRC 106136	670291.4	wgs	PATRIC	670291 tax ID	*
[Ref.: #66792]	Microvirga aerophila DSM 21344	2894369371	draft	JGI IMG/M	670291 tax ID	*

[Ref.: #15630]	GC-content	62.2 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29689]	GC-content	62.2 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Microvirga aerophila strain NBRC 106136 PATRIC: 670291.4
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Microvirga aerophila strain DSM 21344 PATRIC: 670291.3
[Ref.: #69480]	gram-positive	no	97.814	no
[Ref.: #69480]	anaerobic	no	97.995	yes
[Ref.: #69480]	halophile	no	90.697	no
[Ref.: #69480]	spore-forming	no	96.185	yes
[Ref.: #69480]	glucose-util	yes	83.805	no
[Ref.: #69480]	flagellated	no	96.61	yes
[Ref.: #69480]	thermophile	no	96.345	no
[Ref.: #69480]	motile	no	88.687	yes
[Ref.: #69480]	aerobic	yes	87.034	yes
[Ref.: #69480]	glucose-ferment	no	90.077	no

Availability in culture collections External links

[Ref.: #15630]

Culture collection no.

DSM 21344, KACC 12743, NBRC 106136

[Ref.: #76657]

SI-ID 405794

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Description and genome analysis of Microvirga antarctica sp. nov., a novel pink-pigmented psychrotolerant bacterium isolated from Antarctic soil.	Zhu L, Ping W, Zhang S, Chen Y, Zhang Y, Zhang J	Antonie Van Leeuwenhoek	10.1007/s10482-021-01674-9	2021	*
Phylogeny	Microvirga flavescens sp. nov., a novel bacterium isolated from forest soil and emended description of the genus Microvirga.	Zhang XJ, Zhang J, Yao Q, Feng GD, Zhu HH	Int J Syst Evol Microbiol	10.1099/ijsem.0.003189	2019	*
Phylogeny	Microvirga rosea sp. nov.: a nanoparticle producing bacterium isolated from soil of rose garden.	Huq MA	Arch Microbiol	10.1007/s00203-018-1558-3	2018	*
Phylogeny	Description of Microvirga aerophila sp. nov. and Microvirga aerilata sp. nov., isolated from air, reclassification of Balneimonas flocculans Takeda et al. 2004 as Microvirga flocculans comb. nov. and emended description of the genus Microvirga.	Weon HY, Kwon SW, Son JA, Jo EH, Kim SJ, Kim YS, Kim BY, Ka JO	Int J Syst Evol Microbiol	10.1099/ijs.0.018770-0	2009	*

References

#15630

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21344

#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 )

#29689

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 #26074 (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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#76657

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-ID405794.1 )

#26074

IJSEM 2596 2010 ( DOI 10.1099/ijs.0.018770-0 , PubMed 20023055 )

* These data were automatically processed and therefore are not curated

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Microvirga aerophila strain NBRC 106136

Microvirga aerophila strain DSM 21344

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