Name: Halopiger xanaduensis SH-6
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5973

Type strain:

Species: Halopiger xanaduensis

Strain Designation: SH-6

Culture col. no.: DSM 18323, CECT 7173, CGMCC 1.6379, JCM 14033

Strain history: A. Ventosa SH-6.

NCBI tax ID(s): 797210 (strain), 387343 (species)

SI-ID 309455

DSM 18323, CECT 7173, CGMCC 1.6379, JCM 14033

Section

Halopiger xanaduensis SH-6 is a mesophilic archaeon that was isolated from sediment of Shangmatala salt lake .

mesophilic
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	*Halopiger*
	Species	**Halopiger xanaduensis**
	Full Scientific Name (LPSN)	Halopiger xanaduensis Gutiérrez et al. 2007

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7505]

Culture medium

HALOPIGER MEDIUM (DSMZ Medium 1138)

[Ref.: #7505]

Culture medium growth

[Ref.: #7505]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7505]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #7505]			growth	37 °C
[Ref.: #67770]			growth	37 °C

[Ref.: #7505]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	factor 420 biosynthesis	100	5 of 5
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	isoleucine metabolism	100	8 of 8
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	glutamate and glutamine metabolism	89.29	25 of 28
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	flavin biosynthesis	86.67	13 of 15
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	pantothenate biosynthesis	83.33	5 of 6
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	pyrimidine metabolism	77.78	35 of 45
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	palmitate biosynthesis	77.27	17 of 22
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	purine metabolism	74.47	70 of 94
[Ref.: #66794]	vitamin B12 metabolism	73.53	25 of 34
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	lipid metabolism	70.97	22 of 31
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	degradation of sugar acids	68	17 of 25
[Ref.: #66794]	nitrate assimilation	66.67	6 of 9
[Ref.: #66794]	arginine metabolism	66.67	16 of 24
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	serine metabolism	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]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	alanine metabolism	65.52	19 of 29
[Ref.: #66794]	oxidative phosphorylation	64.84	59 of 91
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[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]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	3-chlorocatechol degradation	60	3 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	60	6 of 10
[Ref.: #66794]	histidine metabolism	58.62	17 of 29
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	tryptophan metabolism	55.26	21 of 38
[Ref.: #66794]	lysine metabolism	54.76	23 of 42
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	carotenoid biosynthesis	54.55	12 of 22
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	degradation of sugar alcohols	50	8 of 16
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	50	1 of 2
[Ref.: #66794]	degradation of hexoses	50	9 of 18
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	degradation of pentoses	46.43	13 of 28
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	isoprenoid biosynthesis	46.15	12 of 26
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	phenol degradation	45	9 of 20
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	methanogenesis from CO2	41.67	5 of 12
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	phenylpropanoid biosynthesis	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]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	chlorophyll metabolism	33.33	6 of 18
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	peptidoglycan biosynthesis	26.67	4 of 15
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	ppGpp biosynthesis	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	butanoate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lipid A biosynthesis	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.: #7505]	Sample type/isolated from	sediment of Shangmatala salt lake (43° 12' N 114° 01' E)
[Ref.: #7505]	Geographic location (country and/or sea, region)	Inner Mongolia
[Ref.: #7505]	Country	China
[Ref.: #7505]	Country ISO 3 Code	CHN
[Ref.: #7505]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Sediment of saline Lake Shangmatala in Inner Mongolia
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Lake (large)
#Environmental	#Aquatic	#Sediment
#Condition	#Saline	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AM268114 (>99% sequence identity) for Halopiger from Microbeatlas

Aquatic Samples
Soil Samples	4
Animal Samples
Plant Samples
Total Samples	4

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

[Ref.: #7505]

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.: #7505]	Halopiger xanaduensis 16S rRNA gene, type strain SH-6T	AM268114	1365	ENA	797210 tax ID
[Ref.: #20218]	Halopiger xanaduensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 14033	AB477974	1431	ENA	797210 tax ID	*
[Ref.: #20218]	Halopiger xanaduensis gene for 16S rRNA, complete sequence, strain: JCM 14033	AB663438	1471	ENA	797210 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.: #66792]	Halopiger xanaduensis SH-6	GCA_000217715	complete	GenBank	797210 tax ID	*
[Ref.: #66792]	Halopiger xanaduensis SH-6	2506520034	complete	JGI IMG/M	797210 tax ID	*
[Ref.: #66792]	Halopiger xanaduensis SH-6	797210.15	plasmid	PATRIC	797210 tax ID	*
[Ref.: #66792]	Halopiger xanaduensis SH-6	797210.16	plasmid	PATRIC	797210 tax ID	*
[Ref.: #66792]	Halopiger xanaduensis SH-6	797210.10	complete	PATRIC	797210 tax ID	*
[Ref.: #66792]	Halopiger xanaduensis SH-6	797210.14	plasmid	PATRIC	797210 tax ID	*

[Ref.: #7505]

GC-content

63.1 mol%

thermal denaturation, midpoint method (Tm)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Halopiger xanaduensis SH-6 SH-6 NCBI: GCA_000217715.1
[Ref.: #69480]	motile	no	82.099	no
[Ref.: #69480]	flagellated	no	95.08	no
[Ref.: #69480]	gram-positive	no	97.47	no
[Ref.: #69480]	anaerobic	no	97.16	no
[Ref.: #69480]	aerobic	yes	87.02	no
[Ref.: #69480]	halophile	yes	87.66	no
[Ref.: #69480]	spore-forming	no	92.59	no
[Ref.: #69480]	thermophile	no	87.315	no
[Ref.: #69480]	glucose-util	yes	87.826	no
[Ref.: #69480]	glucose-ferment	no	81.443	no

Availability in culture collections External links

[Ref.: #7505]

Culture collection no.

DSM 18323, CECT 7173, CGMCC 1.6379, JCM 14033

[Ref.: #75462]

SI-ID 309455

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Halopiger thermotolerans sp. nov., a thermo-tolerant haloarchaeon isolated from commercial salt.	Minegishi H, Shimogaki R, Enomoto S, Echigo A, Kondo Y, Nagaoka S, Shimane Y, Kamekura M, Itoh T, Ohkuma M, Nunoura T, Takai K, Usami R	Int J Syst Evol Microbiol	10.1099/ijsem.0.001455	2016	*
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	*
Genetics	Complete genome sequence of Halopiger xanaduensis type strain (SH-6(T)).	Anderson I, Tindall BJ, Rohde M, Lucas S, Han J, Lapidus A, Cheng JF, Goodwin L, Pitluck S, Peters L, Pati A, Mikhailova N, Pagani I, Teshima H, Han C, Tapia R, Land M, Woyke T, Klenk HP, Kyrpides N, Ivanova N	Stand Genomic Sci	10.4056/sigs.2505605	2012	*
Phylogeny	Halopiger aswanensis sp. nov., a polymer-producing and extremely halophilic archaeon isolated from hypersaline soil.	Hezayen FF, Gutierrez MC, Steinbuchel A, Tindall BJ, Rehm BHA	Int J Syst Evol Microbiol	10.1099/ijs.0.013078-0	2009	*
Phylogeny	Halopiger xanaduensis gen. nov., sp. nov., an extremely halophilic archaeon isolated from saline Lake Shangmatala in Inner Mongolia, China.	Gutierrez MC, Castillo AM, Kamekura M, Xue Y, Ma Y, Cowan DA, Jones BE, Grant WD, Ventosa A	Int J Syst Evol Microbiol	10.1099/ijs.0.65001-0	2007	*

References

#7505

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18323

#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 )

#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 .

#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) .

#75462

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-ID309455.1 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Halopiger xanaduensis in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Halopiger xanaduensis SH-6 SH-6

Change proposal

Change proposal