Name: Natrinema pellirubrum 157
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 5891

Type strain:

Species: Natrinema pellirubrum

Strain Designation: 157

Culture col. no.: DSM 15624, CIP 106293, JCM 10476, NCIMB 786, CGMCC 1.3708, CGMCC 1.6174, IAM 13169

Strain history: CIP <- 1999, NCIMB, Halobacterium salinarium <- M. Formisano: strain 157

NCBI tax ID(s): 797303 (strain), 69525 (species)

SI-ID 58839

CIP 106293, IAM 13169, JCM 10476, NCIMB 786, NCMB 786, DSM 15624

Special Collections

Section

Natrinema pellirubrum 157 is an obligate aerobe, Gram-negative archaeon that was isolated from "Red heat" in salted hides.

Gram-negative
obligate aerobe
16S sequence
Archaea
genome sequence

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Archaea"
	Phylum	*Methanobacteriota*
	Class	*Halobacteria*
	Order	*Natrialbales*
	Family	*Natrialbaceae*
	Genus	*Natrinema*
	Species	**Natrinema pellirubrum**
	Full Scientific Name (LPSN)	Natrinema pellirubrum McGenity et al. 1998

Information on morphological and physiological properties Morphology

[Ref.: #121656]	Gram stain	negative

[Ref.: #121656]	Cell shape	oval-shaped

[Ref.: #121656]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %92

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5915]

Culture medium

HALOBACTERIA MEDIUM (DSMZ Medium 372)

[Ref.: #5915]

Culture medium growth

[Ref.: #5915]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5915]

Culture medium composition

expand / minimize

[Ref.: #5915]

Culture medium

PAYNE, SEGHAL & GIBBONS MEDIUM (DSMZ Medium 1160)

[Ref.: #5915]

Culture medium growth

[Ref.: #5915]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5915]

Culture medium composition

expand / minimize

[Ref.: #39832]

Culture medium

MEDIUM 330 - for Natrinema pallidum

[Ref.: #39832]

Culture medium growth

[Ref.: #39832]

Culture medium composition

expand / minimize

[Ref.: #121656]

Culture medium

CIP Medium 330

[Ref.: #121656]

Culture medium growth

[Ref.: #121656]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #5915]		growth	37 °C
[Ref.: #39832]		growth	37 °C
[Ref.: #67770]		growth	37 °C
[Ref.: #121656]		growth	25-45 °C
[Ref.: #121656]	no	growth	5 °C
[Ref.: #121656]	no	growth	15 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #121656]

Oxygen tolerance

obligate aerobe

[Ref.: #69481]

Ability of spore formation

no Confidence in %97

[Ref.: #67770]

Observation

quinones: MK-8, MK-8(H₂)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #121656]	hippurate ChEBI	-	hydrolysis
[Ref.: #121656]	nitrate ChEBI	-	builds gas from
[Ref.: #121656]	nitrate ChEBI	+	reduction
[Ref.: #121656]	nitrate ChEBI	-	respiration
[Ref.: #121656]	nitrite ChEBI	-	builds gas from
[Ref.: #121656]	nitrite ChEBI	-	reduction

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #121656]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	yes	no

	Metabolite production	Metabolite	Production
[Ref.: #121656]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #121656]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #121656]	beta-galactosidase	-	3.2.1.23
[Ref.: #121656]	catalase	+	1.11.1.6
[Ref.: #121656]	gamma-glutamyltransferase	+	2.3.2.2
[Ref.: #121656]	gelatinase	-
[Ref.: #121656]	lysine decarboxylase	-	4.1.1.18
[Ref.: #121656]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #121656]	oxidase	+
[Ref.: #121656]	tryptophan deaminase	-
[Ref.: #121656]	urease	-	3.5.1.5

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	isoleucine metabolism	100	8 of 8
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	factor 420 biosynthesis	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	flavin biosynthesis	93.33	14 of 15
[Ref.: #66794]	glutamate and glutamine metabolism	92.86	26 of 28
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	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]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	citric acid cycle	85.71	12 of 14
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	pantothenate biosynthesis	83.33	5 of 6
[Ref.: #66794]	glycolysis	82.35	14 of 17
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	nitrate assimilation	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	vitamin B12 metabolism	76.47	26 of 34
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	lipid metabolism	74.19	23 of 31
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	purine metabolism	67.02	63 of 94
[Ref.: #66794]	arginine metabolism	66.67	16 of 24
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	pyrimidine metabolism	66.67	30 of 45
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	tryptophan metabolism	65.79	25 of 38
[Ref.: #66794]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	carotenoid biosynthesis	63.64	14 of 22
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	4-hydroxyphenylacetate degradation	60	6 of 10
[Ref.: #66794]	3-chlorocatechol degradation	60	3 of 5
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	histidine 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]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	oxidative phosphorylation	50.55	46 of 91
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	androgen and estrogen metabolism	50	8 of 16
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	degradation of sugar acids	48	12 of 25
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	phenol degradation	45	9 of 20
[Ref.: #66794]	4-hydroxymandelate degradation	44.44	4 of 9
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	methanogenesis from CO2	41.67	5 of 12
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	degradation of pentoses	39.29	11 of 28
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	isoprenoid biosynthesis	38.46	10 of 26
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	35.29	6 of 17
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	peptidoglycan biosynthesis	33.33	5 of 15
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[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]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	ppGpp biosynthesis	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	phenylpropanoid biosynthesis	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.: #5915]	Sample type/isolated from	"Red heat" in salted hides

[Ref.: #121656]	Isolation date	1962
* marker position based on {}

Isolation sources categories

#Condition

#Saline

What are isolation sources categories?

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

[Ref.: #5915]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #121656]	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.: #5915]	Halobacterium salinarium NCIMB 786 16S rRNA gene	AJ002947	1458	GenBank ENA	797303 tax ID
[Ref.: #20218]	Natrinema pellirubrum gene for 16S rRNA, complete sequence, strain: JCM 10476	AB663464	1473	GenBank ENA	797303 tax ID	*
[Ref.: #124043]	Natrinema pellirubrum DSM 15624 strain JCM 10476 16S ribosomal RNA gene, partial sequence.	JF421974	1473	GenBank ENA	797303 tax ID	*
[Ref.: #20218]	Natrinema pellirubrum gene for 16S ribosomal RNA, partial sequence, strain: JCM 10476	AB477231	1433	GenBank ENA	797303 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.: #67770]	Natrinema pellirubrum DSM 15624	GCA_000337635	contig	GenBank ENA	797303 tax ID
[Ref.: #66792]	Natrinema pellirubrum DSM 15624	797303.4	complete	PATRIC	797303 tax ID	*
[Ref.: #66792]	Natrinema pellirubrum 157	2537562080	draft	JGI IMG/M	797303 tax ID	*
[Ref.: #66792]	Natrinema pellirubrum 157	2509601048	complete	JGI IMG/M	797303 tax ID	*
[Ref.: #66792]	Natrinema pellirubrum DSM 15624	797303.10	plasmid	PATRIC	797303 tax ID	*
[Ref.: #66792]	Natrinema pellirubrum DSM 15624	797303.11	plasmid	PATRIC	797303 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: Natrinema pellirubrum DSM 15624 DSM 15624 NCBI: GCA_000230735.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	97	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Natrinema pellirubrum DSM 15624 DSM 15624 NCBI: GCA_000230735.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	78.211	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	83.443	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	78.029	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	82.382	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	82.285	no
[Ref.: #69480]	flagellated	motile2+ⓘ	no	92	no

Availability in culture collections External links

[Ref.: #5915]

Culture collection no.

DSM 15624, CIP 106293, JCM 10476, NCIMB 786, CGMCC 1.3708, CGMCC 1.6174, IAM 13169

[Ref.: #75371]	SI-ID 58839	*
[Ref.: #75372]	SI-ID 312365	*

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Saliphagus infecundisoli gen. nov., sp. nov., an extremely halophilic archaeon isolated from a saline soil.	Yin XQ, Liu BB, Chu X, Salam N, Li X, Yang ZW, Zhang Y, Xiao M, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.002270	2017	*
Phylogeny	Natrinema ejinorense sp. nov., isolated from a saline lake in Inner Mongolia, China.	Castillo AM, Gutierrez MC, Kamekura M, Xue Y, Ma Y, Cowan DA, Jones BE, Grant WD, Ventosa A	Int J Syst Evol Microbiol	10.1099/ijs.0.64421-0	2006	*
Phylogeny	Proposal of a new halobacterial genus Natrinema gen. nov., with two species Natrinema pellirubrum nom. nov. and Natrinema pallidum nom. nov.	McGenity TJ, Gemmell RT, Grant WD	Int J Syst Bacteriol	10.1099/00207713-48-4-1187	1998	*

References

#5915

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15624

#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 )

#39832 ; 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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 )

#75371

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-ID58839.1 )

#75372

#121656 Collection of Institut Pasteur ; Curators of the CIP; CIP 106293

#124043

Dr. Isabel Schober, Dr. Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .

* These data were automatically processed and therefore are not curated

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Natrinema pellirubrum DSM 15624 DSM 15624

Natrinema pellirubrum DSM 15624 DSM 15624

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