Name: Salegentibacter mishustinae DSM 23404
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5642

Type strain:

Species: Salegentibacter mishustinae

Culture col. no.: DSM 23404, KCTC 12263, KMM 6049, LMG 22584, NBRC 100592

Strain history: <- Y. Nakagawa, NBRC <- S. B. Kim, KCTC <- O. I. Nedashkovskaya, Pacific Inst. Bioorg. Chem., RAS, Vladivostok

NCBI tax ID(s): 270918 (species)

SI-ID 131131

LMG 22584, KCTC 12263, NBRC 100592, DSM 23404

Section

Salegentibacter mishustinae DSM 23404 is a mesophilic bacterium that was isolated from sea urchin, Strongylocentrotus intermedius.

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	*Bacteroidota*
	Class	*Flavobacteriia*
	Order	*Flavobacteriales*
	Family	*Flavobacteriaceae*
	Genus	*Salegentibacter*
	Species	**Salegentibacter mishustinae**
	Full Scientific Name (LPSN)	Salegentibacter mishustinae Nedashkovskaya et al. 2005

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16846]

Culture medium

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

[Ref.: #16846]

Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #16846]			growth	28 °C

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Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	phenylmercury acetate degradation	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	purine metabolism	74.47	70 of 94
[Ref.: #66794]	tryptophan metabolism	73.68	28 of 38
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	pyrimidine metabolism	68.89	31 of 45
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	alanine metabolism	65.52	19 of 29
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	lysine metabolism	61.9	26 of 42
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	57.14	4 of 7
[Ref.: #66794]	d-xylose degradation	54.55	6 of 11
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	53.85	7 of 13
[Ref.: #66794]	Entner Doudoroff pathway	50	5 of 10
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	carotenoid biosynthesis	50	11 of 22
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	4-hydroxyphenylacetate degradation	50	5 of 10
[Ref.: #66794]	isoprenoid biosynthesis	50	13 of 26
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	oxidative phosphorylation	43.96	40 of 91
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	elloramycin biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	vitamin B1 metabolism	38.46	5 of 13
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
[Ref.: #66794]	degradation of pentoses	35.71	10 of 28
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	polyamine pathway	26.09	6 of 23
[Ref.: #66794]	phenol degradation	25	5 of 20
[Ref.: #66794]	degradation of sugar alcohols	25	4 of 16
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[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.: #16846]	Sample type/isolated from	sea urchin, Strongylocentrotus intermedius
[Ref.: #16846]	Host species	Strongylocentrotus intermedius
[Ref.: #16846]	Geographic location (country and/or sea, region)	Sea of Japan, Gulf of Peter the Great, Troitsa Bay
[Ref.: #16846]	Country	Russia
[Ref.: #16846]	Country ISO 3 Code	RUS
[Ref.: #16846]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host

#Invertebrates (Other)

#Echinodermata

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY576653 (>99% sequence identity) for Salegentibacter mishustinae from Microbeatlas

Aquatic Samples	79
Soil Samples	1
Animal Samples	4
Plant Samples	8
Total Samples	92

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

[Ref.: #16846]

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.: #16846]	Salegentibacter mishustinae strain KMM 6049 16S ribosomal RNA gene, partial sequence	AY576653	1438	ENA	270918 tax ID
[Ref.: #20218]	Salegentibacter mishustinae gene for 16S rRNA, partial sequence, strain: NBRC 100592	AB681203	1455	ENA	270918 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]	Salegentibacter mishustinae DSM 23404	2839527574	draft	JGI IMG/M	270918 tax ID	*
[Ref.: #66792]	Salegentibacter mishustinae KCTC 12263	GCA_014651335	contig	GenBank	270918 tax ID	*
[Ref.: #66792]	Salegentibacter mishustinae DSM 23404	GCA_003254095	scaffold	GenBank	270918 tax ID	*
[Ref.: #66792]	Salegentibacter mishustinae KCTC 12263	GCA_001431365	contig	GenBank	270918 tax ID	*
[Ref.: #66792]	Salegentibacter mishustinae strain DSM 23404	270918.14	wgs	PATRIC	270918 tax ID	*
[Ref.: #66792]	Salegentibacter mishustinae strain DSM 23404	270918.15	wgs	PATRIC	270918 tax ID	*

[Ref.: #16846]

GC-content

37.5 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Salegentibacter mishustinae DSM 23404 NCBI: GCA_003254095.1
[Ref.: #69480]	flagellated	no	93.685	no
[Ref.: #69480]	gram-positive	no	97.973	no
[Ref.: #69480]	anaerobic	no	98.643	no
[Ref.: #69480]	halophile	yes	67.204	no
[Ref.: #69480]	spore-forming	no	92.569	no
[Ref.: #69480]	aerobic	yes	87.152	no
[Ref.: #69480]	glucose-util	yes	88.811	no
[Ref.: #69480]	thermophile	no	99.562	no
[Ref.: #69480]	motile	no	88.864	no
[Ref.: #69480]	glucose-ferment	no	89.433	no

Availability in culture collections External links

[Ref.: #16846]

Culture collection no.

DSM 23404, KCTC 12263, KMM 6049, LMG 22584, NBRC 100592

[Ref.: #75125]

SI-ID 131131

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genome Sequence of Salegentibacter mishustinae KCTC 12263, Containing a Complete Subtype I-B CRISPR-Cas System.	Zhang F, Lin W, Zhang R, Zheng Q, Jiao N	Genome Announc	10.1128/genomeA.00267-16	2016	*
Phylogeny	Salegentibacter chungangensis sp. nov., isolated from a sea sand and emended description of the genus Salegentibacter.	Siamphan C, Kim W	Int J Syst Evol Microbiol	10.1099/ijs.0.059170-0	2014	*
Phylogeny	Salegentibacter mishustinae sp. nov., isolated from the sea urchin Strongylocentrotus intermedius.	Nedashkovskaya OI, Kim SB, Lysenko AM, Mikhailov VV, Bae KS, Kim IS	Int J Syst Evol Microbiol	10.1099/ijs.0.63297-0	2005	*

References

#16846

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23404

#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 )

#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) .

#75125

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-ID131131.1 )

* These data were automatically processed and therefore are not curated

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