Natrinema limicola (CGMCC 1.5333, JCM 13563, AX-7)

Name: Natrinema limicola (CGMCC 1.5333, JCM 13563, AX-7)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 134201

Type strain

Strain Designation AX-7

Culture col. no. CGMCC 1.5333 JCM 13563 AX-7

NCBI tax ID(s) 1230457 370323

Special Collections JCM Literature strains

Links

Natrinema limicola AX-7 is an aerobe, Gram-negative, rod-shaped prokaryote that was isolated from salt lake.

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

Name and taxonomic classification

SI-ID 297211

CGMCC 1.5333,JCM 13563

@ref 20215

Last LPSN update 2025-12-16 10:01:59

Domain Methanobacteriati

Phylum Methanobacteriota

Class Halobacteria

Order Halobacteriales

Family Natrialbaceae

Genus Natrinema

Species Natrinema limicola

Full scientific name Natrinema limicola (Cui et al. 2006) de la Haba et al. 2022

Synonyms (2)

"Natrinema limicola"
Haloterrigena limicola

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
31816	negative	1.8-3.6 µm	0.6-0.8 µm	rod-shaped

Pigmentation

31816

Productionyes

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
31816	positive	growth	30-61
31816	positive	optimum	45-50	thermophilic
67770	positive	growth	37	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
31816	positive	optimum	7-7.5
31816	positive	growth	6.5-9	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31816	aerobe
125439	aerobe	93.7

Spore formation

31816

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31816	NaCl	positive	growth	0-4.06 %
31816	NaCl	positive	optimum	0.29 %

Observation

31816

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31816	30089 ChEBI	acetate	+	carbon source
31816	17632 ChEBI	nitrate	+	reduction
31816	15361 ChEBI	pyruvate	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
31816	16136 ChEBI	hydrogen sulfide

Enzymes

@ref	Value	Activity	Ec
31816	catalase	+	1.11.1.6
31816	cytochrome oxidase	+	1.9.3.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	ethanol fermentation	100	2 of 2
66794	flavin biosynthesis	100	15 of 15
66794	adipate degradation	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	lipoate biosynthesis	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	citric acid cycle	92.86	13 of 14
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	phenylalanine metabolism	84.62	11 of 13
66794	vitamin B1 metabolism	84.62	11 of 13
66794	pantothenate biosynthesis	83.33	5 of 6
66794	glycolysis	82.35	14 of 17
66794	vitamin K metabolism	80	4 of 5
66794	factor 420 biosynthesis	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	glycogen metabolism	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	photosynthesis	78.57	11 of 14
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	leucine metabolism	76.92	10 of 13
66794	glycogen biosynthesis	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	biotin 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	propanol degradation	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	propionate fermentation	70	7 of 10
66794	purine metabolism	68.09	64 of 94
66794	vitamin B12 metabolism	67.65	23 of 34
66794	pyrimidine metabolism	66.67	30 of 45
66794	serine metabolism	66.67	6 of 9
66794	cyanate degradation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	IAA biosynthesis	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	valine metabolism	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	methane metabolism	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	lipid metabolism	64.52	20 of 31
66794	carotenoid biosynthesis	63.64	14 of 22
66794	non-pathway related	63.16	24 of 38
66794	arginine metabolism	62.5	15 of 24
66794	3-chlorocatechol degradation	60	3 of 5
66794	Entner Doudoroff pathway	60	6 of 10
66794	alanine metabolism	58.62	17 of 29
66794	histidine metabolism	58.62	17 of 29
66794	tryptophan metabolism	57.89	22 of 38
66794	heme metabolism	57.14	8 of 14
66794	nitrate assimilation	55.56	5 of 9
66794	cholesterol biosynthesis	54.55	6 of 11
66794	pentose phosphate pathway	54.55	6 of 11
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	4-hydroxyphenylacetate degradation	50	5 of 10
66794	acetate fermentation	50	2 of 4
66794	kanosamine biosynthesis II	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	CDP-diacylglycerol biosynthesis	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	methionine metabolism	50	13 of 26
66794	tyrosine metabolism	50	7 of 14
66794	lysine metabolism	50	21 of 42
66794	degradation of sugar alcohols	50	8 of 16
66794	vitamin E metabolism	50	2 of 4
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	metabolism of disaccharids	45.45	5 of 11
66794	oxidative phosphorylation	45.05	41 of 91
66794	cysteine metabolism	44.44	8 of 18
66794	lipid A biosynthesis	44.44	4 of 9
66794	glutathione metabolism	42.86	6 of 14
66794	mevalonate metabolism	42.86	3 of 7
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	creatinine degradation	40	2 of 5
66794	gallate degradation	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	urea cycle	38.46	5 of 13
66794	sulfate reduction	38.46	5 of 13
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	degradation of sugar acids	36	9 of 25
66794	phenol degradation	35	7 of 20
66794	polyamine pathway	34.78	8 of 23
66794	isoprenoid biosynthesis	34.62	9 of 26
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	arachidonic acid metabolism	33.33	6 of 18
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	methanogenesis from CO2	33.33	4 of 12
66794	degradation of pentoses	32.14	9 of 28
66794	myo-inositol biosynthesis	30	3 of 10
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	d-xylose degradation	27.27	3 of 11
66794	vitamin B6 metabolism	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	ppGpp biosynthesis	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	CMP-KDO biosynthesis	25	1 of 4
66794	dTDPLrhamnose biosynthesis	25	2 of 8
66794	degradation of hexoses	22.22	4 of 18

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Lake (large)
#Condition	#Saline	-

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
31816	salt lake
67770	Aibi salt lake in Xin-Jiang	China	CHN	Asia

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM2010591v1 assembly for Natrinema longum JCM 13563	scaffold	GCA_020105915	370324.7		370324	69.36
67770	ASM33747v1 assembly for Natrinema limicola JCM 13563	contig	GCA_000337475	1230457.4	2554235498	1230457	54.31

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
31816	Haloterrigena limicola strain AX-7 16S ribosomal RNA gene, partial sequence	DQ367241	1474	1230457
67770	Haloterrigena limicola gene for 16S ribosomal RNA, partial sequence, strain: JCM 13563	AB477224	1434	1230457
124043	Haloterrigena limicola gene for 16S rRNA, complete sequence, strain: JCM 13563.	AB663445	1474	1230457

GC content

@ref	GC-content (mol%)	Method
31816	61.9
67770	61.9	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Natrinema longum JCM 13563
NCBI: GCA_020105915

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	89.10	no
125439	motility	BacteriaNetⓘ	yes	54.80	no
125439	gram_stain	BacteriaNetⓘ	negative	88.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	93.70	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Phylogenomics of Haloarchaea: The Controversy of the Genera Natrinema-Haloterrigena.	de la Haba RR, Minegishi H, Kamekura M, Shimane Y, Ventosa A.	Front Microbiol	10.3389/fmicb.2021.740909	2021
Phylogeny	Haloterrigena salina sp. nov., an extremely halophilic archaeon isolated from a salt lake.	Gutierrez MC, Castillo AM, Kamekura M, Ventosa A	Int J Syst Evol Microbiol	10.1099/ijs.0.2008/001602-0	2008
Phylogeny	Haloterrigena longa sp. nov. and Haloterrigena limicola sp. nov., extremely halophilic archaea isolated from a salt lake.	Cui HL, Tohty D, Zhou PJ, Liu SJ	Int J Syst Evol Microbiol	10.1099/ijs.0.64372-0	2006

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 )
#31816	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 #28084 (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) .
#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;
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 )

Rate our new design

Content

About us

Natrinema limicola (CGMCC 1.5333, JCM 13563, AX-7)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_020105915

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media