Natrinema salifodinae (DSM 26231, CGMCC 1.12284, JCM 18547)

Name: Natrinema salifodinae (DSM 26231, CGMCC 1.12284, JCM 18547)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24085

Type strain

Strain Designation KCY07-B2

Culture col. no. DSM 26231 CGMCC 1.12284 JCM 18547 KCY07-B2

NCBI tax ID(s) 1202768

Special Collections DSMZ JCM Literature strains

History <- Z. Weiyan, Zhejiang Univ., Hangzhou, China; KCY07-B2 W. Zhang KCY07-B2.

Links

Natrinema salifodinae KCY07-B2 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from salt mine.

Gram-negative rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 397477

JCM 18547,DSM 26231

@ref 20215

Last LPSN update 2026-02-09 11:23:53

Domain Archaea

Phylum Methanobacteriota

Class Halobacteria

Order Halobacteriales

Family Natrialbaceae

Genus Natrinema

Species Natrinema salifodinae

Full scientific name Natrinema salifodinae (Zhang et al. 2013) de la Haba et al. 2022

Synonyms (2)

Halopiger salifodinae
"Natrinema salifodinae"

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
31060	negative	rod-shaped
125438			91
125439	negative		94.7

Pigmentation

31060

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
21174	HALOLAMINA MEDIUM (NOM-3) (DSMZ Medium 1528)		Medium recipe at MediaDive	Name: HALOLAMINA MEDIUM (NOM-3) (DSMZ Medium 1528) Composition: NaCl 184.0 g/l MgSO4 x 7 H2O 26.8 g/l MgCl2 x 6 H2O 23.0 g/l Agar 20.0 g/l KCl 5.4 g/l Yeast extract 1.0 g/l Bacto peptone 0.5 g/l K2HPO4 0.3 g/l NH4Cl 0.25 g/l CaCl2 x 2 H2O 0.25 g/l Sodium formate 0.25 g/l Sodium lactate 0.25 g/l Sodium acetate 0.25 g/l Sodium pyruvate 0.25 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
21174	positive	growth	37	mesophilic
31060	positive	growth	25-50
31060	positive	optimum	41	thermophilic
67770	positive	growth	37	mesophilic

Culture pH

@ref	Ability	Type	PH
31060	positive	optimum	7
31060	positive	growth	6.0-8.0

Physiology and metabolism

Oxygen tolerance

31060

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125439		95.8

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31060	NaCl	positive	growth	11.02-31.32 %
31060	NaCl	positive	optimum	18.27 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31060	30089 ChEBI	acetate	+	carbon source
31060	22653 ChEBI	asparagine	+	carbon source
31060	16947 ChEBI	citrate	+	carbon source
31060	4853 ChEBI	esculin	+	hydrolysis
31060	17234 ChEBI	glucose	+	carbon source
31060	29987 ChEBI	glutamate	+	carbon source
31060	15428 ChEBI	glycine	+	carbon source
31060	25115 ChEBI	malate	+	carbon source
31060	37684 ChEBI	mannose	+	carbon source
31060	17822 ChEBI	serine	+	carbon source
31060	30911 ChEBI	sorbitol	+	carbon source
31060	30031 ChEBI	succinate	+	carbon source
31060	26986 ChEBI	threonine	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
31060	16136 ChEBI	hydrogen sulfide

Enzymes

@ref	Value	Activity	Ec
31060	acid phosphatase	+	3.1.3.2
31060	catalase	+	1.11.1.6
31060	cytochrome oxidase	+	1.9.3.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	glycine betaine biosynthesis	100	5 of 5
66794	palmitate biosynthesis	100	22 of 22
66794	ethanol fermentation	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	vitamin K metabolism	100	5 of 5
66794	L-lactaldehyde degradation	100	3 of 3
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	aerobactin biosynthesis	100	1 of 1
66794	denitrification	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	flavin biosynthesis	93.33	14 of 15
66794	vitamin B1 metabolism	92.31	12 of 13
66794	threonine metabolism	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	citric acid cycle	85.71	12 of 14
66794	propanol degradation	85.71	6 of 7
66794	phenylalanine metabolism	84.62	11 of 13
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	factor 420 biosynthesis	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	hydrogen production	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	Entner Doudoroff pathway	80	8 of 10
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	valine metabolism	77.78	7 of 9
66794	lipid metabolism	77.42	24 of 31
66794	leucine metabolism	76.92	10 of 13
66794	ketogluconate metabolism	75	6 of 8
66794	gluconeogenesis	75	6 of 8
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	biotin biosynthesis	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	proline metabolism	72.73	8 of 11
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	photosynthesis	71.43	10 of 14
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	pyrimidine metabolism	71.11	32 of 45
66794	myo-inositol biosynthesis	70	7 of 10
66794	propionate fermentation	70	7 of 10
66794	purine metabolism	69.15	65 of 94
66794	alanine metabolism	68.97	20 of 29
66794	vitamin B12 metabolism	67.65	23 of 34
66794	pantothenate biosynthesis	66.67	4 of 6
66794	d-mannose degradation	66.67	6 of 9
66794	serine metabolism	66.67	6 of 9
66794	cyanate degradation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	enterobactin biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	glycolysis	64.71	11 of 17
66794	glutathione metabolism	64.29	9 of 14
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	heme metabolism	64.29	9 of 14
66794	degradation of sugar acids	64	16 of 25
66794	pentose phosphate pathway	63.64	7 of 11
66794	tryptophan metabolism	63.16	24 of 38
66794	non-pathway related	63.16	24 of 38
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	arginine metabolism	62.5	15 of 24
66794	histidine metabolism	62.07	18 of 29
66794	oxidative phosphorylation	61.54	56 of 91
66794	4-hydroxyphenylacetate degradation	60	6 of 10
66794	starch degradation	60	6 of 10
66794	lipoate biosynthesis	60	3 of 5
66794	3-chlorocatechol degradation	60	3 of 5
66794	nitrate assimilation	55.56	5 of 9
66794	cysteine metabolism	55.56	10 of 18
66794	lysine metabolism	54.76	23 of 42
66794	d-xylose degradation	54.55	6 of 11
66794	urea cycle	53.85	7 of 13
66794	3-phenylpropionate degradation	53.33	8 of 15
66794	carotenoid biosynthesis	50	11 of 22
66794	coenzyme M biosynthesis	50	5 of 10
66794	androgen and estrogen metabolism	50	8 of 16
66794	kanosamine biosynthesis II	50	1 of 2
66794	degradation of hexoses	50	9 of 18
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	CDP-diacylglycerol biosynthesis	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	lactate fermentation	50	2 of 4
66794	phenol degradation	50	10 of 20
66794	resorcinol degradation	50	1 of 2
66794	acetate fermentation	50	2 of 4
66794	methanogenesis from CO2	50	6 of 12
66794	phenylmercury acetate degradation	50	1 of 2
66794	tyrosine metabolism	50	7 of 14
66794	vitamin E metabolism	50	2 of 4
66794	degradation of pentoses	46.43	13 of 28
66794	sulfate reduction	46.15	6 of 13
66794	methionine metabolism	46.15	12 of 26
66794	metabolism of disaccharids	45.45	5 of 11
66794	lipid A biosynthesis	44.44	4 of 9
66794	arachidonic acid metabolism	44.44	8 of 18
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	degradation of sugar alcohols	43.75	7 of 16
66794	aclacinomycin biosynthesis	42.86	3 of 7
66794	mevalonate metabolism	42.86	3 of 7
66794	isoprenoid biosynthesis	42.31	11 of 26
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	arachidonate biosynthesis	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	gallate degradation	40	2 of 5
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	cholesterol biosynthesis	36.36	4 of 11
66794	polyamine pathway	34.78	8 of 23
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	allantoin degradation	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	ascorbate metabolism	31.82	7 of 22
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	chlorophyll metabolism	27.78	5 of 18
66794	vitamin B6 metabolism	27.27	3 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	peptidoglycan biosynthesis	26.67	4 of 15
66794	butanoate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	CMP-KDO biosynthesis	25	1 of 4
66794	sulfopterin metabolism	25	1 of 4

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Other	#Mine
#Condition	#Saline	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
21174	salt mine	Xinjiang Province, Akesu area, Kuche county	China	CHN	Asia
67770	Salt mine in Kuche county	Xinjiang	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence JX014296 (>99% sequence identity) for Halopiger salifodinae subclade from Microbeatlas

Aquatic Samples	1
Soil Samples	4
Animal Samples
Plant Samples	3
Total Samples	8

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21174	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	IMG-taxon 2671180170 annotated assembly for Natrinema salifodinae CGMCC 1.12284	scaffold	GCA_900110455	1202768.6	2671180170	1202768	69.23
67770	ASM78433v1 assembly for Natrinema salifodinae KCY07-B2	scaffold	GCA_000784335	1202768.4	2645727804	1202768	53.82

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
21174	Natrinema salifodinae strain KCY07-B2 16S ribosomal RNA gene, partial sequence	JX014296	1472		1202768
124043	Halopiger salifodinae gene for 16S ribosomal RNA, partial sequence, strain: JCM 18547.	AB935410	1472		1202768

GC content

@ref	GC-content (mol%)	Method
21174	62.5	high performance liquid chromatography (HPLC)
31060	62.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Natrinema salifodinae CGMCC 1.12284
NCBI: GCA_900110455

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.80	no
125439	motility	BacteriaNetⓘ	yes	64.90	no
125439	gram_stain	BacteriaNetⓘ	negative	94.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	78.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Halopiger salifodinae CGMCC 1.12284
NCBI: GCA_900110455.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	79.15	yes
125438	anaerobic	anaerobicⓘ	no	86.23	yes
125438	aerobic	aerobicⓘ	yes	77.63	yes
125438	spore-forming	spore-formingⓘ	no	86.64	no
125438	thermophilic	thermophileⓘ	no	78.44	no
125438	flagellated	motile2+ⓘ	no	91.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Draft genome sequence of Halopiger salifodinae KCY07-B2(T), an extremly halophilic archaeon isolated from a salt mine.	Zhang WY, Hu J, Pan J, Sun C, Wu M, Xu XW	Stand Genomic Sci	10.1186/s40793-015-0113-y	2015
Phylogeny	Halopiger salifodinae sp. nov., an extremely halophilic archaeon isolated from a salt mine.	Zhang WY, Meng Y, Zhu XF, Wu M	Int J Syst Evol Microbiol	10.1099/ijs.0.050971-0	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 )
#21174	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26231
#27389	IJSEM 3563 2013 ( DOI 10.1099/ijs.0.050971-0 , PubMed 23563233 )
#31060	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 #27389
#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;
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Natrinema salifodinae (DSM 26231, CGMCC 1.12284, JCM 18547)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900110455

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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