Name: Roseomonas stagni HS-69
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 75

Type strain:

Species: Roseomonas stagni

Strain Designation: HS-69

Culture col. no.: DSM 19981, JCM 15034, KCTC 22213

Strain history: <- K Furuhata, Azabu Univ., Japan

NCBI tax ID(s): 1123062 (strain), 484882 (species)

SI-ID 402956

DSM 19981

Section

Roseomonas stagni HS-69 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from pond water of Nomori no Ike.

Gram-negative
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	*Rhodospirillales*
	Family	*Acetobacteraceae*
	Genus	*Roseomonas*
	Species	**Roseomonas stagni**
	Full Scientific Name (LPSN)	Roseomonas stagni Furuhata et al. 2008

Synonym

Falsiroseomonas stagni

Information on morphological and physiological properties Morphology

[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.999

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8353]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #8353]

Culture medium growth

[Ref.: #8353]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8353]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #8353]	growth	30 °C
[Ref.: #67770]	growth	30 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #8353]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67771]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %97
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.992

[Ref.: #67770]	Observation	quinones: Q-10
[Ref.: #67771]	Observation	quinones: Q-10

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	100	8 of 8
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	ethanol fermentation	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]	gallate degradation	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	propanol degradation	100	7 of 7
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	ethylmalonyl-CoA pathway	100	5 of 5
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	citric acid cycle	92.86	13 of 14
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	91.67	11 of 12
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	flavin biosynthesis	86.67	13 of 15
[Ref.: #66794]	glutathione metabolism	85.71	12 of 14
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	alanine metabolism	82.76	24 of 29
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	80	8 of 10
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	3-phenylpropionate degradation	80	12 of 15
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	arginine metabolism	79.17	19 of 24
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	purine metabolism	77.66	73 of 94
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	degradation of sugar acids	76	19 of 25
[Ref.: #66794]	toluene degradation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	75	6 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	metabolism of disaccharids	72.73	8 of 11
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	non-pathway related	71.05	27 of 38
[Ref.: #66794]	tryptophan metabolism	71.05	27 of 38
[Ref.: #66794]	oxidative phosphorylation	70.33	64 of 91
[Ref.: #66794]	phenol degradation	70	14 of 20
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	pyrimidine metabolism	68.89	31 of 45
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	allantoin degradation	66.67	6 of 9
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	degradation of pentoses	64.29	18 of 28
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	lysine metabolism	61.9	26 of 42
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	61.54	8 of 13
[Ref.: #66794]	chlorophyll metabolism	61.11	11 of 18
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	ascorbate metabolism	59.09	13 of 22
[Ref.: #66794]	glycolysis	58.82	10 of 17
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	polyamine pathway	56.52	13 of 23
[Ref.: #66794]	degradation of hexoses	55.56	10 of 18
[Ref.: #66794]	aspartate and asparagine metabolism	55.56	5 of 9
[Ref.: #66794]	carotenoid biosynthesis	54.55	12 of 22
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	sphingosine metabolism	50	3 of 6
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	47.06	8 of 17
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	d-xylose degradation	45.45	5 of 11
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	elloramycin biosynthesis	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	daunorubicin biosynthesis	22.22	2 of 9
		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.: #8353]	Sample type/isolated from	pond water of Nomori no Ike
[Ref.: #8353]	Geographic location (country and/or sea, region)	Shizuoka
[Ref.: #8353]	Country	Japan
[Ref.: #8353]	Country ISO 3 Code	JPN
[Ref.: #8353]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Pond water of Nomori no Ike in Shizuoka
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From pond water of "Nomori No Ike"
[Ref.: #67771]	Geographic location (country and/or sea, region)	Shizuoka
[Ref.: #67771]	Country	Japan
[Ref.: #67771]	Country ISO 3 Code	JPN
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Pond (small)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB369258 (>99% sequence identity) for Roseomonas stagni subclade from Microbeatlas

Aquatic Samples	178
Soil Samples	7
Animal Samples	12
Plant Samples	2
Total Samples	199

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

[Ref.: #8353]

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.: #8353]	Roseomonas stagni gene for 16S rRNA, partial sequence	AB369258	1439	ENA	1123062 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Falsiroseomonas stagni DSM 19981	GCA_900114315	scaffold	GenBank	1123062 tax ID
[Ref.: #66792]	Roseomonas stagni DSM 19981	1123062.3	wgs	PATRIC	1123062 tax ID	*
[Ref.: #66792]	Roseomonas stagni DSM 19981	2602042029	draft	JGI IMG/M	1123062 tax ID	*

[Ref.: #8353]	GC-content	72.0 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	72 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67771]	GC-content	72.0 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: Roseomonas stagni DSM 19981 DSM 19981 NCBI: GCA_900114315.1
[Ref.: #69481]	spore-forming	no	97	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Roseomonas stagni DSM 19981 PATRIC: 1123062.3
[Ref.: #69480]	motile	yes	56.033	no
[Ref.: #69480]	flagellated	no	85.375	no
[Ref.: #69480]	gram-positive	no	98.621	no
[Ref.: #69480]	anaerobic	no	98.88	yes
[Ref.: #69480]	aerobic	yes	93.61	yes
[Ref.: #69480]	halophile	no	92.51	no
[Ref.: #69480]	spore-forming	no	94.578	no
[Ref.: #69480]	glucose-util	yes	82.523	no
[Ref.: #69480]	thermophile	no	93.274	yes
[Ref.: #69480]	glucose-ferment	no	90.123	no

Availability in culture collections External links

[Ref.: #8353]

Culture collection no.

DSM 19981, JCM 15034, KCTC 22213

[Ref.: #69759]

SI-ID 402956

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Roseomonas oleicola sp. nov., isolated from an oil production mixture in Yumen Oilfield, and emended description of Roseomonas frigidaquae.	Wu D, Liu H, Zhou Y, Wu X, Nie Y, Cai M	Int J Syst Evol Microbiol	10.1099/ijsem.0.005064	2021	*
Phylogeny	Roseomonas ponticola sp. nov., a novel bacterium isolated from Pearl River estuary.	Yin LZ, Li JL, Fang BZ, Liu ZT, Wang P, Dong L, Duan L, Luo XQ, Li SH, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.004994	2021	*
Phylogeny	Roseomonas selenitidurans sp. nov., isolated from urban soil, and emended description of Roseomonas frigidaquae.	Hou X, Liu H, Wei S, Ding Z, Sang F, Zhao Y, Dong Y, Li H, Wang Q, Zhao J, Deng H, Zhang C, Kong L, Gao Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.004496	2020	*
Phylogeny	Roseomonas algicola sp. nov., isolated from a green alga, Pediastrum duplex.	Kim HM, Khan SA, Han DM, Chun BH, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijsem.0.004454	2020	*
Phylogeny	Roseomonas bella sp. nov., isolated from lake sediment.	Zhang JY, Jiang XB, Zhu D, Wang XM, Du ZJ, Mu DS	Int J Syst Evol Microbiol	10.1099/ijsem.0.004436	2020	*
Phylogeny	Roseomonas wooponensis sp. nov., isolated from wetland freshwater.	Lee JH, Kim MS, Baik KS, Kim HM, Lee KH, Seong CN	Int J Syst Evol Microbiol	10.1099/ijsem.0.000536	2015	*
Phylogeny	Roseomonas tokyonensis sp. nov. isolated from a biofilm sample obtained from a cooling tower in Tokyo, Japan.	Furuhata K, Ishizaki N, Edagawa A, Fukuyama M	Biocontrol Sci	10.4265/bio.18.205	2013	*
Phylogeny	Roseomonas riguiloci sp. nov., isolated from wetland freshwater.	Baik KS, Park SC, Choe HN, Kim SN, Moon JH, Seong CN	Int J Syst Evol Microbiol	10.1099/ijs.0.036186-0	2012	*

References

#8353

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19981

#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 )

#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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 )

#69759

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-ID402956.1 )

* These data were automatically processed and therefore are not curated

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Roseomonas stagni DSM 19981 DSM 19981

Roseomonas stagni DSM 19981

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