Name: Marivirga tractuosa H-43
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5473

Type strain:

Species: Marivirga tractuosa

Strain Designation: H-43

Culture col. no.: DSM 4126, ATCC 23168, CIP 106410, IFO 15989, KCTC 2958, NBRC 15989, NCIMB 1408, VKM B-1430

Strain history: <- NCMB <- R.A. Lewin, H-43 (Microscilla tractuosa)

NCBI tax ID(s): 643867 (strain), 1006 (species)

Other strains from Marivirga tractuosa

M. tractuosa CIP 106411, NCIMB 1440, ATCC 23151, ...

Section

Marivirga tractuosa H-43 is a mesophilic bacterium that was isolated from beach sand.

mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	07-12-2022 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacteroidota*
	Class	*Cytophagia*
	Order	*Cytophagales*
	Family	*Marivirgaceae*
	Genus	*Marivirga*
	Species	**Marivirga tractuosa**
	Full Scientific Name (PNU)	Marivirga tractuosa (Lewin 1969) Nedashkovskaya et al. 2010

	Synonym	"Microscilla* tractuosa"*
	Synonym	Flexibacter tractuosus

Information on morphological and physiological properties Morphology

Multimedia content

[Ref.: #66793]

Caption:

electron microscopic image

[Ref.: #66793]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #1594]

Culture medium

CYTOPHAGA (marine) MEDIUM (DSMZ Medium 172)

[Ref.: #1594]

Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

[Ref.: #1594]

Culture medium composition

expand / minimize

[Ref.: #40308]

Culture medium

Marine agar (MA)

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Culture medium growth

[Ref.: #40308]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #1594]			growth	25 °C
[Ref.: #40308]			growth	25 °C

[Ref.: #1594]	Temperature range	mesophilic
[Ref.: #40308]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[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]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	lipid A biosynthesis	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]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	tryptophan metabolism	81.58	31 of 38
[Ref.: #66794]	lipid metabolism	80.65	25 of 31
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	purine metabolism	75.53	71 of 94
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	pyrimidine metabolism	73.33	33 of 45
[Ref.: #66794]	isoprenoid biosynthesis	73.08	19 of 26
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	carotenoid biosynthesis	68.18	15 of 22
[Ref.: #66794]	arginine metabolism	66.67	16 of 24
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	lysine metabolism	66.67	28 of 42
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[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]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	alanine metabolism	62.07	18 of 29
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	O-antigen biosynthesis	60	3 of 5
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	Entner Doudoroff pathway	60	6 of 10
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	oxidative phosphorylation	52.75	48 of 91
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	coenzyme A metabolism	50	2 of 4
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	catecholamine biosynthesis	50	2 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	vitamin B1 metabolism	46.15	6 of 13
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	degradation of sugar alcohols	43.75	7 of 16
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	degradation of pentoses	32.14	9 of 28
[Ref.: #66794]	phenol degradation	30	6 of 20
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	polyamine pathway	26.09	6 of 23
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	chlorophyll metabolism	22.22	4 of 18
[Ref.: #66794]	allantoin degradation	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.: #1594]	Sample type/isolated from	beach sand
[Ref.: #1594]	Geographic location (country and/or sea, region)	Nhatrang, South China Sea
[Ref.: #1594]	Country	Vietnam
[Ref.: #1594]	Country ISO 3 Code	VNM
[Ref.: #1594]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Coast
#Environmental	#Terrestrial	#Sandy

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB078072 (>99% sequence identity) for Marivirga tractuosa from Microbeatlas

Aquatic Samples	106
Soil Samples	19
Animal Samples	25
Plant Samples	3
Total Samples	153

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

[Ref.: #1594]

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.: #20218]	Flexibacter tractuosus 16S ribosomal RNA	M58789	1475	ENA	1006 tax ID	*
[Ref.: #1594]	Flexibacter tractuosus gene for 16S rRNA, strain:IFO 15989	AB078072	1476	ENA	643867 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Marivirga tractuosa DSM 4126 DSM 4126	GCA_000183425	complete	GenBank	643867 tax ID	*
[Ref.: #66792]	Marivirga tractuosa DSM 4126	643867.13	plasmid	PATRIC	643867 tax ID	*
[Ref.: #66792]	Marivirga tractuosa DSM 4126	643867.3	complete	PATRIC	643867 tax ID	*
[Ref.: #66792]	Marivirga tractuosa H-43, DSM 4126	649633065	complete	JGI IMG/M	643867 tax ID	*
[Ref.: #66792]	Gammaproteobacteria bacterium CSSed10_121	GCA_003560295	contig	PATRIC	1913989 tax ID	*
[Ref.: #66792]	Bacteroidales bacterium SC1158_S11_bin.15	GCA_009774765	scaffold	PATRIC	2030927 tax ID	*

[Ref.: #1594]

GC-content

36.1 mol%

thermal denaturation, midpoint method (Tm)

Availability in culture collections External links

[Ref.: #1594]

Culture collection no.

DSM 4126, ATCC 23168, CIP 106410, IFO 15989, KCTC 2958, NBRC 15989, NCIMB 1408, VKM B-1430

[Ref.: #20218]

Associated Passport(s) in StrainInfo

40360, 40359, 151186, 158650, 314542, 487129, 40362, 226961

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Reclassification of Flexibacter tractuosus (Lewin 1969) Leadbetter 1974 and 'Microscilla sericea' Lewin 1969 in the genus Marivirga gen. nov. as Marivirga tractuosa comb. nov. and Marivirga sericea nom. rev., comb. nov.	Nedashkovskaya OI, Vancanneyt M, Kim SB, Bae KS	Int J Syst Evol Microbiol	10.1099/ijs.0.016121-0	2009	*
Genetics	Complete genome sequence of Marivirga tractuosa type strain (H-43).	Pagani I, Chertkov O, Lapidus A, Lucas S, Del Rio TG, Tice H, Copeland A, Cheng JF, Nolan M, Saunders E, Pitluck S, Held B, Goodwin L, Liolios K, Ovchinikova G, Ivanova N, Mavromatis K, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Detter JC, Han C, Tapia R, Ngatchou-Djao OD, Rohde M, Goker M, Spring S, Sikorski J, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC	Stand Genomic Sci	10.4056/sigs.1623941	2011	*
Phylogeny	Nafulsella turpanensis gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from soil.	Zhang L, Shen X, Liu Y, Li S	Int J Syst Evol Microbiol	10.1099/ijs.0.044651-0	2012	*
Phylogeny	Marivirga lumbricoides sp. nov., a marine bacterium isolated from the South China Sea.	Xu Y, Zhang R, Li Q, Liu K, Jiao N	Int J Syst Evol Microbiol	10.1099/ijs.0.066027-0	2014	*
Phylogeny	Reclassification of Flexibacter tractuosus NBRC 15981T as Marivirga harenae sp. nov. in the family Flammeovirgaceae.	Muramatsu Y, Kamakura Y, Takahashi M, Nakagawa Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.001890	2017	*

References

#1594

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 4126

#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 )

#40308 ; 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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#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) .

* These data were automatically processed and therefore are not curated

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