Name: Myroides profundi D25
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5622

Type strain:

Species: Myroides profundi

Strain Designation: D25

Culture col. no.: DSM 19823, CCTCC M 208030, CIP 110414, KCTC 23066

Strain history: CIP <- 2012, DSMZ <- Y.Z. Zhang, State Key Lab. Microbial Technol., Marine Biotechnol. Res. Center, Shandong Univ., Jinan, China: strain D25 <- H.Y. Dang

NCBI tax ID(s): 480520 (species)

SI-ID 361157

DSM 19823, CIP 110414, KCTC 23066

Other strains from Myroides profundi

M. profundi 28[81667], 100892, DSM 100892

Section

Myroides profundi D25 is a psychrophilic, Gram-negative bacterium that was isolated from deep sea sediments at a water depth of 1245m.

Gram-negative
psychrophilic
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	*Myroides*
	Species	**Myroides profundi**
	Full Scientific Name (LPSN)	Myroides profundi Zhang et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #121957]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #121957]	Cell shape	rod-shaped

[Ref.: #121957]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8335]

Culture medium

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

[Ref.: #8335]

Culture medium growth

[Ref.: #8335]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8335]

Culture medium composition

expand / minimize

[Ref.: #34210]

Culture medium

Marine agar (MA)

[Ref.: #34210]

Culture medium growth

[Ref.: #34210]

Culture medium composition

expand / minimize

[Ref.: #121957]

Culture medium

CIP Medium 13

[Ref.: #121957]

Culture medium growth

[Ref.: #121957]

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #8335]			growth	15-20 °C
[Ref.: #34210]			growth	15 °C

[Ref.: #8335]	Temperature range	psychrophilic
[Ref.: #34210]	Temperature range	psychrophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69480]

Ability of spore formation

no Confidence in %99.994

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[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]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	cysteine metabolism	72.22	13 of 18
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	tryptophan metabolism	71.05	27 of 38
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	pyrimidine metabolism	68.89	31 of 45
[Ref.: #66794]	glutamate and glutamine metabolism	67.86	19 of 28
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	purine metabolism	67.02	63 of 94
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	lysine metabolism	66.67	28 of 42
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	histidine metabolism	62.07	18 of 29
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	61.54	8 of 13
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	glycolysis	58.82	10 of 17
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	methionine metabolism	57.69	15 of 26
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	arginine metabolism	45.83	11 of 24
[Ref.: #66794]	oxidative phosphorylation	45.05	41 of 91
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	isoprenoid biosynthesis	42.31	11 of 26
[Ref.: #66794]	4-hydroxyphenylacetate degradation	40	4 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	Entner Doudoroff pathway	40	4 of 10
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA 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]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	reductive acetyl coenzyme A pathway	28.57	2 of 7
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	vitamin B12 metabolism	26.47	9 of 34
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	degradation of pentoses	25	7 of 28
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	23.53	4 of 17
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
[Ref.: #66794]	polyamine pathway	21.74	5 of 23
		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.: #8335]	Sample type/isolated from	deep sea sediments at a water depth of 1245m
[Ref.: #8335]	Geographic location (country and/or sea, region)	East China Sea (24°47.19'N,122°29.30'E) near the southern Okinawa Trough
[Ref.: #8335]	Country	China
[Ref.: #8335]	Country ISO 3 Code	CHN
[Ref.: #8335]	Continent	Asia
[Ref.: #8335]	Geographic location	24.7865°/122.4880°

[Ref.: #121957]	Sample type/isolated from	Environment, Deep sea sediments at a water depth of 1245m
[Ref.: #121957]	Geographic location (country and/or sea, region)	Near the Southern Okinawa Trough
[Ref.: #121957]	Country	China
[Ref.: #121957]	Country ISO 3 Code	CHN
[Ref.: #121957]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EU204978 (>99% sequence identity) for Myroides from Microbeatlas

Aquatic Samples	1514
Soil Samples	1153
Animal Samples	4454
Plant Samples	372
Total Samples	7493

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

[Ref.: #8335]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #121957]	Biosafety level	1	Risk group (French classification)

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.: #8335]	Myroides sp. D25 16S ribosomal RNA gene, partial sequence	EU204978	1479	ENA	480520 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]	Myroides profundi D25	GCA_000833025	complete	GenBank	480520 tax ID	*
[Ref.: #66792]	Myroides profundi DSM 19823	GCA_900111065	scaffold	GenBank	480520 tax ID	*
[Ref.: #66792]	Myroides profundi D25	480520.3	complete	PATRIC	480520 tax ID	*
[Ref.: #66792]	Myroides profundi strain DSM 19823	480520.4	wgs	PATRIC	480520 tax ID	*
[Ref.: #66792]	Myroides profundi D25	2648501242	complete	JGI IMG/M	480520 tax ID	*
[Ref.: #66792]	Myroides profundi DSM 19823	2622736514	draft	JGI IMG/M	480520 tax ID	*

[Ref.: #8335]

GC-content

33 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: Myroides profundi D25 NCBI: GCA_000833025.1
[Ref.: #69481]	spore-forming	no	80	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Myroides profundi D25 NCBI: GCA_000833025.1
[Ref.: #69480]	motile	no	89.833	no
[Ref.: #69480]	flagellated	no	93.895	no
[Ref.: #69480]	gram-positive	no	98.084	no
[Ref.: #69480]	anaerobic	no	99.369	no
[Ref.: #69480]	aerobic	yes	85.535	no
[Ref.: #69480]	halophile	no	83.951	no
[Ref.: #69480]	spore-forming	no	94.302	no
[Ref.: #69480]	glucose-util	yes	67.645	no
[Ref.: #69480]	thermophile	no	99.863	yes
[Ref.: #69480]	glucose-ferment	no	90.248	no

Availability in culture collections External links

[Ref.: #8335]

Culture collection no.

DSM 19823, CCTCC M 208030, CIP 110414, KCTC 23066

[Ref.: #75105]

SI-ID 361157

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Myroides injenensis sp. nov., a new member isolated from human urine.	Paek J, Shin JH, Shin Y, Park IS, Jin TE, Kook JK, Wie SH, Cho HG, Park SJ, Chang YH	Antonie Van Leeuwenhoek	10.1007/s10482-014-0317-y	2014	*
Phylogeny	Myroides profundi sp. nov., isolated from deep-sea sediment of the southern Okinawa Trough.	Zhang XY, Zhang YJ, Chen XL, Qin QL, Zhao DL, Li TG, Dang HY, Zhang YZ	FEMS Microbiol Lett	10.1111/j.1574-6968.2008.01299.x	2008	*

References

#8335

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19823

#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 )

#34210 ; Curators of the CIP;

#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 )

#75105

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-ID361157.1 )

#121957 Collection of Institut Pasteur ; Curators of the CIP; CIP 110414
* These data were automatically processed and therefore are not curated

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