Name: Nitratifractor salsuginis E9I37-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 10423

Type strain:

Species: Nitratifractor salsuginis

Strain Designation: E9I37-1

Culture col. no.: DSM 16511, JCM 12458

Strain history: S. Nakagawa E9I37-1.

NCBI tax ID(s): 749222 (strain), 269261 (species)

SI-ID 138023

DSM 16511, JCM 12458

Section

Nitratifractor salsuginis E9I37-1 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from deep-sea hydrothermal vent chimney.

Gram-negative
rod-shaped
facultative anaerobe
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	*Epsilonproteobacteria*
	Order	*Nautiliales*
	Family	*Nautiliaceae*
	Genus	*Nitratifractor*
	Species	**Nitratifractor salsuginis**
	Full Scientific Name (LPSN)	Nitratifractor salsuginis Nakagawa et al. 2005

Information on morphological and physiological properties Morphology

[Ref.: #31405]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %100

[Ref.: #31405]	Cell length	2.5 µm

[Ref.: #31405]	Cell width	0.6 µm

[Ref.: #31405]	Cell shape	rod-shaped

[Ref.: #31405]	Motility	no

Multimedia content

[Ref.: #66793]

Caption:

electron microscopic image

[Ref.: #66793]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6384]

Culture medium

NITRATIRUPTOR AND NITRATIFACTOR MEDIUM (DSMZ Medium 1024)

[Ref.: #6384]

Culture medium growth

[Ref.: #6384]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6384]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #6384]	growth	37 °C
[Ref.: #31405]	growth	28-40 °C
[Ref.: #31405]	optimum	37 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #6384]	Temperature range	mesophilic
[Ref.: #31405]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31405]			optimum	7
[Ref.: #31405]			growth	5.6-7.6

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31405]

Oxygen tolerance

facultative anaerobe

[Ref.: #31405]	Ability of spore formation	no
[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.: #31405]		NaCl		growth	1.5-3.5	%
[Ref.: #31405]		NaCl		optimum	3	%

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31405]		nitrate ChEBI	+	reduction

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	tetrahydrofolate metabolism	100	14 of 14
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	83.33	5 of 6
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	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]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	purine metabolism	62.77	59 of 94
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	starch degradation	60	6 of 10
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	alanine metabolism	55.17	16 of 29
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	non-pathway related	52.63	20 of 38
[Ref.: #66794]	oxidative phosphorylation	51.65	47 of 91
[Ref.: #66794]	pyrimidine metabolism	51.11	23 of 45
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	tryptophan metabolism	50	19 of 38
[Ref.: #66794]	propionate fermentation	50	5 of 10
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	histidine metabolism	48.28	14 of 29
[Ref.: #66794]	polyamine pathway	47.83	11 of 23
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	CO2 fixation in Crenarchaeota	44.44	4 of 9
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	lipid metabolism	41.94	13 of 31
[Ref.: #66794]	arginine metabolism	41.67	10 of 24
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	glycogen metabolism	40	2 of 5
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	methanogenesis from CO2	33.33	4 of 12
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	degradation of sugar alcohols	25	4 of 16
[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]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
		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.: #6384]	Sample type/isolated from	deep-sea hydrothermal vent chimney
[Ref.: #6384]	Geographic location (country and/or sea, region)	Iheya North hydrothermal field in the Mid-Okinawa Trough
[Ref.: #6384]	Country	Japan
[Ref.: #6384]	Country ISO 3 Code	JPN
[Ref.: #6384]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Deep-sea hydrothermal vent chimney structures at the Iheya North hydrothermal field in the Mid-Okinawa Trough
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Hydrothermal vent
#Environmental	#Aquatic	#Marine
#Condition	#Thermophilic (>45°C)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB175500 (>99% sequence identity) for Nitratifractor salsuginis subclade from Microbeatlas

Aquatic Samples	188
Soil Samples	6
Animal Samples	4
Plant Samples	1
Total Samples	199

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

[Ref.: #6384]

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.: #6384]	Nitratifractor salsuginis gene for 16S rRNA, partial sequence	AB175500	1439	ENA	749222 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Nitratifractor salsuginis DSM 16511	GCA_000186245	complete	GenBank	749222 tax ID	*
[Ref.: #66792]	Nitratifractor salsuginis DSM 16511	749222.3	complete	PATRIC	749222 tax ID	*
[Ref.: #66792]	Nitratifractor salsuginis E9I37-1, DSM 16511	649633076	complete	JGI IMG/M	749222 tax ID	*

[Ref.: #6384]	GC-content	35.5 mol%
[Ref.: #67770]	GC-content	35.5 mol%	high performance liquid chromatography (HPLC)

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: Nitratifractor salsuginis DSM 16511 DSM 16511 NCBI: GCA_000186245.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Nitratifractor salsuginis DSM 16511 DSM 16511 NCBI: GCA_000186245.1
[Ref.: #69480]	motile	no	88.479	yes
[Ref.: #69480]	flagellated	no	93.829	no
[Ref.: #69480]	gram-positive	no	99.009	yes
[Ref.: #69480]	anaerobic	yes	66.722	yes
[Ref.: #69480]	aerobic	no	97.188	yes
[Ref.: #69480]	halophile	no	85.664	no
[Ref.: #69480]	spore-forming	no	95.911	yes
[Ref.: #69480]	glucose-util	no	68.368	no
[Ref.: #69480]	thermophile	no	51.805	yes
[Ref.: #69480]	glucose-ferment	no	88.765	no

Availability in culture collections External links

[Ref.: #6384]

Culture collection no.

DSM 16511, JCM 12458

[Ref.: #79705]

SI-ID 138023

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Complete genome sequence of Nitratifractor salsuginis type strain (E9I37-1).	Anderson I, Sikorski J, Zeytun A, Nolan M, Lapidus A, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Huntemann M, Mavromatis K, Ovchinikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Ngatchou-Djao OD, Rohde M, Tindall BJ, Goker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC	Stand Genomic Sci	10.4056/sigs.1844518	2011	*
Phylogeny	Nitratiruptor tergarcus gen. nov., sp. nov. and Nitratifractor salsuginis gen. nov., sp. nov., nitrate-reducing chemolithoautotrophs of the epsilon-Proteobacteria isolated from a deep-sea hydrothermal system in the Mid-Okinawa Trough.	Nakagawa S, Takai K, Inagaki F, Horikoshi K, Sako Y	Int J Syst Evol Microbiol	10.1099/ijs.0.63480-0	2005	*

References

#6384

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16511

#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 )

#31405

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 #27714 (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) .

#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 )

#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 )

#79705

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-ID138023.1 )

#27714

IJSEM 925 2005 ( DOI 10.1099/ijs.0.63480-0 , PubMed 15774687 )

* These data were automatically processed and therefore are not curated

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Nitratifractor salsuginis DSM 16511 DSM 16511

Nitratifractor salsuginis DSM 16511 DSM 16511

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