Name: Umboniibacter marinipuniceus DSM 25080
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17913

Type strain:

Species: Umboniibacter marinipuniceus

Culture col. no.: DSM 25080, JCM 15738, NRIC 0753, KMM 3891, KCTC 42352

Strain history: N. Tanaka <-- L. A. Romanenko Sh24 (=KMM 3891).

NCBI tax ID(s): 569599 (species)

SI-ID 401425

DSM 25080

Section

Umboniibacter marinipuniceus DSM 25080 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from internal tissue of the sand snail Umbonium costatum.

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	*Gammaproteobacteria*
	Order	*Cellvibrionales*
	Family	*Cellvibrionaceae*
	Genus	*Umboniibacter*
	Species	**Umboniibacter marinipuniceus**
	Full Scientific Name (LPSN)	Umboniibacter marinipuniceus Romanenko et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #29313]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.977

[Ref.: #29313]	Cell length	2 µm

[Ref.: #29313]	Cell width	0.5 µm

[Ref.: #29313]	Cell shape	rod-shaped

[Ref.: #29313]	Motility	no

[Ref.: #29313]

Pigment production

yes

Multimedia content

[Ref.: #17839]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17839]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #17839]

Culture medium growth

[Ref.: #17839]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17839]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #17839]	growth	28 °C
[Ref.: #29313]	growth	05-33 °C
[Ref.: #29313]	optimum	26.5 °C
[Ref.: #67770]	growth	25 °C

[Ref.: #17839]	Temperature range	mesophilic
[Ref.: #29313]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29313]			optimum	8.25
[Ref.: #29313]			growth	6.5-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29313]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.992

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29313]		NaCl		growth	02-05	%
[Ref.: #29313]		NaCl		optimum	2.75	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29313]	alanine ChEBI	+	carbon source
[Ref.: #29313]	arginine ChEBI	+	carbon source
[Ref.: #29313]	asparagine ChEBI	+	carbon source
[Ref.: #29313]	glucose ChEBI	+	carbon source
[Ref.: #29313]	histidine ChEBI	+	carbon source
[Ref.: #29313]	leucine ChEBI	+	carbon source
[Ref.: #29313]	phenylalanine ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #29313]	acid phosphatase	+	3.1.3.2
[Ref.: #29313]	alkaline phosphatase	+	3.1.3.1
[Ref.: #29313]	catalase	+	1.11.1.6
[Ref.: #29313]	cytochrome oxidase	+	1.9.3.1
[Ref.: #29313]	gelatinase	+

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	peptidoglycan biosynthesis	73.33	11 of 15
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	purine metabolism	71.28	67 of 94
[Ref.: #66794]	starch degradation	70	7 of 10
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	arginine metabolism	66.67	16 of 24
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	tryptophan metabolism	65.79	25 of 38
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	histidine metabolism	62.07	18 of 29
[Ref.: #66794]	lipid metabolism	61.29	19 of 31
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	alanine metabolism	58.62	17 of 29
[Ref.: #66794]	photosynthesis	57.14	8 of 14
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	pyrimidine metabolism	55.56	25 of 45
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	degradation of sugar alcohols	50	8 of 16
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	3-phenylpropionate degradation	40	6 of 15
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	isoprenoid biosynthesis	38.46	10 of 26
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	oxidative phosphorylation	37.36	34 of 91
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	degradation of pentoses	32.14	9 of 28
[Ref.: #66794]	carotenoid biosynthesis	31.82	7 of 22
[Ref.: #66794]	urea cycle	30.77	4 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	vitamin B1 metabolism	30.77	4 of 13
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	25	2 of 8
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	degradation of sugar acids	24	6 of 25
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	23.53	4 of 17
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	vitamin B12 metabolism	20.59	7 of 34
		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.: #17839]	Sample type/isolated from	internal tissue of the sand snail Umbonium costatum
[Ref.: #17839]	Host species	Umbonium costatum
[Ref.: #17839]	Geographic location (country and/or sea, region)	Sea of Japan
[Ref.: #17839]	Country	Russia
[Ref.: #17839]	Country ISO 3 Code	RUS
[Ref.: #17839]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Southern coast of the Sea of Japan
[Ref.: #67770]	Country	Russia
[Ref.: #67770]	Country ISO 3 Code	RUS
* marker position based on {}

Isolation sources categories

#Host	#Invertebrates (Other)	#Mollusca
#Host Body-Site	-	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB467279 (>99% sequence identity) for Umboniibacter marinipuniceus subclade from Microbeatlas

Aquatic Samples	10973
Soil Samples	118
Animal Samples	305
Plant Samples	70
Total Samples	11466

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

[Ref.: #17839]

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.: #17839]	Umboniibacter marinipuniceus gene for 16S ribosomal RNA, partial sequence, strain: KMM 3891	AB467279	1507	ENA	569599 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Umboniibacter marinipuniceus DSM 25080	GCA_003688415	scaffold	GenBank	569599 tax ID
[Ref.: #66792]	Umboniibacter marinipuniceus strain DSM 25080	569599.3	wgs	PATRIC	569599 tax ID	*
[Ref.: #66792]	Umboniibacter marinipuniceus DSM 25080	2770939661	draft	JGI IMG/M	569599 tax ID	*

[Ref.: #17839]	GC-content	51.7 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29313]	GC-content	51.7 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: Umboniibacter marinipuniceus DSM 25080 NCBI: GCA_003688415.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Umboniibacter marinipuniceus strain DSM 25080 PATRIC: 569599.3
[Ref.: #69480]	gram-positive	no	98.687	yes
[Ref.: #69480]	anaerobic	no	98.859	no
[Ref.: #69480]	halophile	yes	66.583	no
[Ref.: #69480]	spore-forming	no	97.357	no
[Ref.: #69480]	glucose-util	yes	85.303	yes
[Ref.: #69480]	thermophile	no	98.093	no
[Ref.: #69480]	flagellated	no	87.048	yes
[Ref.: #69480]	motile	no	80.237	yes
[Ref.: #69480]	aerobic	yes	82.327	no
[Ref.: #69480]	glucose-ferment	no	88.922	no

Availability in culture collections External links

[Ref.: #17839]

Culture collection no.

DSM 25080, JCM 15738, NRIC 0753, KMM 3891, KCTC 42352

[Ref.: #86902]

SI-ID 401425

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Umboniibacter marinipuniceus gen. nov., sp. nov., a marine gammaproteobacterium isolated from the mollusc Umbonium costatum from the Sea of Japan.	Romanenko LA, Tanaka N, Frolova GM	Int J Syst Evol Microbiol	10.1099/ijs.0.010728-0	2009	*

References

#17839

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25080

#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 )

#29313

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 #25726 (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 )

#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 .

#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 )

#86902

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-ID401425.1 )

#25726

IJSEM 603 2010 ( DOI 10.1099/ijs.0.010728-0 , PubMed 19654350 )

* These data were automatically processed and therefore are not curated

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Umboniibacter marinipuniceus DSM 25080

Umboniibacter marinipuniceus strain DSM 25080

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