Name: Phycisphaera mikurensis FYK2301M01
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 132890

Type strain:

Species: Phycisphaera mikurensis

Strain Designation: FYK2301M01

Culture col. no.: DSM 103959, NBRC 102666, KCTC 22515

Strain history: <- Y. Fukunaga, NITE (Natl. Inst. of Technol. and Evaluation), Kisarazu, Japan; FYK2301M01

NCBI tax ID(s): 1142394 (strain), 547188 (species)

SI-ID 402438

DSM 103959

Special Collections

DSMZ
KCTC

Section

Phycisphaera mikurensis FYK2301M01 is a Gram-negative bacterium that was isolated from Marine alga, Porphyra sp..

Gram-negative
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	*Planctomycetota*
	Class	*Phycisphaerae*
	Order	*Phycisphaerales*
	Family	*Phycisphaeraceae*
	Genus	*Phycisphaera*
	Species	**Phycisphaera mikurensis**
	Full Scientific Name (LPSN)	Phycisphaera mikurensis Fukunaga et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %95.957

Multimedia content

[Ref.: #24678]

Caption:

DSM 103959 grown on medium 514.

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Intellectual property rights:

Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH

Information on culture and growth conditions Culture and growth conditions

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Culture medium

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

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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.: #24678]			growth	25 °C

Information on physiology and metabolism Physiology and metabolism

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	isoleucine metabolism	100	8 of 8
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	allantoin degradation	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[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]	purine metabolism	81.91	77 of 94
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	peptidoglycan biosynthesis	73.33	11 of 15
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	d-xylose degradation	72.73	8 of 11
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	arginine metabolism	70.83	17 of 24
[Ref.: #66794]	isoprenoid biosynthesis	69.23	18 of 26
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	degradation of hexoses	66.67	12 of 18
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	66.67	4 of 6
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	lysine metabolism	64.29	27 of 42
[Ref.: #66794]	degradation of pentoses	64.29	18 of 28
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	oxidative phosphorylation	62.64	57 of 91
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	vitamin B1 metabolism	61.54	8 of 13
[Ref.: #66794]	threonine metabolism	60	6 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	ascorbate metabolism	59.09	13 of 22
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	lipid metabolism	48.39	15 of 31
[Ref.: #66794]	histidine metabolism	48.28	14 of 29
[Ref.: #66794]	degradation of sugar acids	48	12 of 25
[Ref.: #66794]	tryptophan metabolism	47.37	18 of 38
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	cysteine metabolism	44.44	8 of 18
[Ref.: #66794]	CO2 fixation in Crenarchaeota	44.44	4 of 9
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	methionine metabolism	42.31	11 of 26
[Ref.: #66794]	carotenoid biosynthesis	40.91	9 of 22
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	propionate fermentation	40	4 of 10
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	polyamine pathway	30.43	7 of 23
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	butanoate fermentation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	phenol degradation	25	5 of 20
[Ref.: #66794]	ppGpp biosynthesis	25	1 of 4
[Ref.: #66794]	arachidonic acid metabolism	22.22	4 of 18
[Ref.: #66794]	chlorophyll metabolism	22.22	4 of 18
		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.: #24678]	Sample type/isolated from	Marine alga, Porphyra sp.
[Ref.: #24678]	Host species	Porphyra sp.
[Ref.: #24678]	Geographic location (country and/or sea, region)	Mikurajima, Tokyo
[Ref.: #24678]	Country	Japan
[Ref.: #24678]	Country ISO 3 Code	JPN
[Ref.: #24678]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Host	#Algae	#Red algae

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB447464 (>99% sequence identity) for Phycisphaera mikurensis subclade from Microbeatlas

Aquatic Samples	1213
Soil Samples	198
Animal Samples	35
Plant Samples	5
Total Samples	1451

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

[Ref.: #24678]

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.: #24678]	Phycisphaera mikurensis gene for 16S ribosomal RNA, partial sequence, strain: NBRC 102666	AB447464	1461	GenBank ENA	1142394 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]	Phycisphaera mikurensis NBRC 102666 strain AE-24oct19-296	1142394.42	wgs	PATRIC	1142394 tax ID	*
[Ref.: #66792]	Phycisphaera mikurensis DSM 103959	GCA_014207395	scaffold	GenBank ENA	547188 tax ID	*
[Ref.: #66792]	Phycisphaera mikurensis NBRC 102666	1142394.8	complete	PATRIC	1142394 tax ID	*
[Ref.: #66792]	Phycisphaera mikurensis NBRC 102666	1142394.11	plasmid	PATRIC	1142394 tax ID	*
[Ref.: #66792]	Phycisphaera mikurensis strain DSM 103959	547188.13	wgs	PATRIC	547188 tax ID	*
[Ref.: #66792]	Phycisphaera mikurensis NBRC 102666	2561511149	complete	JGI IMG/M	1142394 tax ID	*

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Phycisphaera mikurensis NBRC 102666 NBRC 102666 NCBI: GCA_000284115.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	62	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Phycisphaera mikurensis NBRC 102666 NBRC 102666 NCBI: GCA_000284115.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	95.957	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	83.99	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	64.5	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	79.798	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	88.227	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	59.528	no

Availability in culture collections External links

[Ref.: #24678]

Culture collection no.

DSM 103959, NBRC 102666, KCTC 22515

[Ref.: #91170]

SI-ID 402438

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Phycisphaera mikurensis gen. nov., sp. nov., isolated from a marine alga, and proposal of Phycisphaeraceae fam. nov., Phycisphaerales ord. nov. and Phycisphaerae classis nov. in the phylum Planctomycetes.	Fukunaga Y, Kurahashi M, Sakiyama Y, Ohuchi M, Yokota A, Harayama S	J Gen Appl Microbiol	10.2323/jgam.55.267	2009	*
Phylogeny	Tepidisphaera mucosa gen. nov., sp. nov., a moderately thermophilic member of the class Phycisphaerae in the phylum Planctomycetes, and proposal of a new family, Tepidisphaeraceae fam. nov., and a new order, Tepidisphaerales ord. nov.	Kovaleva OL, Merkel AY, Novikov AA, Baslerov RV, Toshchakov SV, Bonch-Osmolovskaya EA	Int J Syst Evol Microbiol	10.1099/ijs.0.070151-0	2014	*
Phylogeny	Algisphaera agarilytica gen. nov., sp. nov., a novel representative of the class Phycisphaerae within the phylum Planctomycetes isolated from a marine alga.	Yoon J, Jang JH, Kasai H	Antonie Van Leeuwenhoek	10.1007/s10482-013-0076-1	2013	*

References

#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 )

#24678

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103959

#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 )

#91170

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-ID402438.1 )

* These data were automatically processed and therefore are not curated

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Phycisphaera mikurensis NBRC 102666 NBRC 102666

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