Halopiger xanaduensis (DSM 18323, CECT 7173, CGMCC 1.6379)

Name: Halopiger xanaduensis (DSM 18323, CECT 7173, CGMCC 1.6379)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5973

Type strain

Strain Designation SH-6

Culture col. no. DSM 18323 CECT 7173 CGMCC 1.6379 JCM 14033 SH-6

NCBI tax ID(s) 797210 387343

Special Collections DSMZ JCM

Links

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

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 309455

DSM 18323,CECT 7173,CGMCC 1.6379,JCM 14033

@ref 20215

Last LPSN update 2025-12-16 09:48:12

Domain Methanobacteriati

Phylum Methanobacteriota

Class Halobacteria

Order Halobacteriales

Family Natrialbaceae

Genus Halopiger

Species Halopiger xanaduensis

Full scientific name Halopiger xanaduensis Gutiérrez et al. 2007

Morphology

Cell morphology

@ref	Motility	Confidence	Gram stain
125438		91.5
125439		92.6	negative

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7505	HALOPIGER MEDIUM (DSMZ Medium 1138)		Medium recipe at MediaDive	Name: HALOPIGER MEDIUM (DSMZ Medium 1138) Composition: NaCl 195.0 g/l MgSO4 x 7 H2O 50.8 g/l MgCl2 x 6 H2O 32.5 g/l Yeast extract 5.0 g/l KCl 5.0 g/l CaCl2 x 2 H2O 0.8 g/l NaBr 0.6 g/l NaHCO3 0.16 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7505	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	aerobe	91.8

Spore formation

@ref	Spore formation	Confidence
125439		94.4

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	vitamin K metabolism	100	5 of 5
66794	gluconeogenesis	100	8 of 8
66794	denitrification	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	factor 420 biosynthesis	100	5 of 5
66794	suberin monomers biosynthesis	100	2 of 2
66794	isoleucine metabolism	100	8 of 8
66794	methylglyoxal degradation	100	5 of 5
66794	L-lactaldehyde degradation	100	3 of 3
66794	ethanol fermentation	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	adipate degradation	100	2 of 2
66794	vitamin B1 metabolism	92.31	12 of 13
66794	threonine metabolism	90	9 of 10
66794	Entner Doudoroff pathway	90	9 of 10
66794	glutamate and glutamine metabolism	89.29	25 of 28
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	flavin biosynthesis	86.67	13 of 15
66794	phenylalanine metabolism	84.62	11 of 13
66794	pantothenate biosynthesis	83.33	5 of 6
66794	cellulose degradation	80	4 of 5
66794	starch degradation	80	8 of 10
66794	propionate fermentation	80	8 of 10
66794	glycogen metabolism	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	heme metabolism	78.57	11 of 14
66794	pyrimidine metabolism	77.78	35 of 45
66794	valine metabolism	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	palmitate biosynthesis	77.27	17 of 22
66794	leucine metabolism	76.92	10 of 13
66794	glycogen biosynthesis	75	3 of 4
66794	biotin biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	purine metabolism	74.47	70 of 94
66794	vitamin B12 metabolism	73.53	25 of 34
66794	NAD metabolism	72.22	13 of 18
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	photosynthesis	71.43	10 of 14
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	glutathione metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	lipid metabolism	70.97	22 of 31
66794	glycolysis	70.59	12 of 17
66794	methionine metabolism	69.23	18 of 26
66794	degradation of sugar acids	68	17 of 25
66794	nitrate assimilation	66.67	6 of 9
66794	arginine metabolism	66.67	16 of 24
66794	acetoin degradation	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	octane oxidation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	alanine metabolism	65.52	19 of 29
66794	oxidative phosphorylation	64.84	59 of 91
66794	citric acid cycle	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	ketogluconate metabolism	62.5	5 of 8
66794	cysteine metabolism	61.11	11 of 18
66794	non-pathway related	60.53	23 of 38
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	3-chlorocatechol degradation	60	3 of 5
66794	4-hydroxyphenylacetate degradation	60	6 of 10
66794	histidine metabolism	58.62	17 of 29
66794	propanol degradation	57.14	4 of 7
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	tryptophan metabolism	55.26	21 of 38
66794	lysine metabolism	54.76	23 of 42
66794	pentose phosphate pathway	54.55	6 of 11
66794	proline metabolism	54.55	6 of 11
66794	carotenoid biosynthesis	54.55	12 of 22
66794	sulfate reduction	53.85	7 of 13
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	degradation of sugar alcohols	50	8 of 16
66794	CMP-KDO biosynthesis	50	2 of 4
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	CDP-diacylglycerol biosynthesis	50	1 of 2
66794	degradation of hexoses	50	9 of 18
66794	kanosamine biosynthesis II	50	1 of 2
66794	sulfopterin metabolism	50	2 of 4
66794	coenzyme M biosynthesis	50	5 of 10
66794	glycine metabolism	50	5 of 10
66794	phenylmercury acetate degradation	50	1 of 2
66794	resorcinol degradation	50	1 of 2
66794	tyrosine metabolism	50	7 of 14
66794	degradation of pentoses	46.43	13 of 28
66794	urea cycle	46.15	6 of 13
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	isoprenoid biosynthesis	46.15	12 of 26
66794	metabolism of disaccharids	45.45	5 of 11
66794	ascorbate metabolism	45.45	10 of 22
66794	phenol degradation	45	9 of 20
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	mevalonate metabolism	42.86	3 of 7
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	methanogenesis from CO2	41.67	5 of 12
66794	myo-inositol biosynthesis	40	4 of 10
66794	glycine betaine biosynthesis	40	2 of 5
66794	O-antigen biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	creatinine degradation	40	2 of 5
66794	gallate degradation	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	cholesterol biosynthesis	36.36	4 of 11
66794	vitamin B6 metabolism	36.36	4 of 11
66794	polyamine pathway	34.78	8 of 23
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	enterobactin biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	sphingosine metabolism	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	chlorophyll metabolism	33.33	6 of 18
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	peptidoglycan biosynthesis	26.67	4 of 15
66794	vitamin E metabolism	25	1 of 4
66794	ppGpp biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	butanoate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	lipid A biosynthesis	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7505	sediment of Shangmatala salt lake (43° 12' N 114° 01' E)	Inner Mongolia	China	CHN	Asia
67770	Sediment of saline Lake Shangmatala in Inner Mongolia		China	CHN	Asia

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7505	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM21771v1 assembly for Halopiger xanaduensis SH-6	complete	GCA_000217715	797210.10	2506520034	797210	98.29

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Halopiger xanaduensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 14033	AB477974	1431	797210
20218	Halopiger xanaduensis gene for 16S rRNA, complete sequence, strain: JCM 14033	AB663438	1471	797210
7505	Halopiger xanaduensis 16S rRNA gene, type strain SH-6T	AM268114	1365	797210

GC content

@ref	GC-content (mol%)	Method
7505	63.1	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: Halopiger xanaduensis SH-6
IMG: 2506520034

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	94.40	no
125439	motility	BacteriaNetⓘ	yes	61.40	no
125439	gram_stain	BacteriaNetⓘ	negative	92.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	91.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Halopiger xanaduensis SH-6 SH-6
NCBI: GCA_000217715.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	76.08	no
125438	anaerobic	anaerobicⓘ	no	80.63	no
125438	aerobic	aerobicⓘ	yes	76.05	no
125438	spore-forming	spore-formingⓘ	no	85.82	no
125438	thermophilic	thermophileⓘ	no	78.28	no
125438	flagellated	motile2+ⓘ	no	91.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Virome and metagenomic analysis reveal the distinct distribution of microbiota in human fetal gut during gestation.	Liu X, He G, Lan Y, Guo W, Liu X, Li J, Liu A, He M, Liu X, Fan Z, Zhang Y.	Front Immunol	10.3389/fimmu.2022.1079294	2022
Metabolism	d-Ribose Catabolism in Archaea: Discovery of a Novel Oxidative Pathway in Haloarcula Species.	Johnsen U, Sutter JM, Reinhardt A, Pickl A, Wang R, Xiang H, Schonheit P.	J Bacteriol	10.1128/jb.00608-19	2020
Genetics	Distribution and Implications of Haloarchaeal Plasmids Disseminated in Self-Encoded Plasmid Vesicles.	Lucking D, Alarcon-Schumacher T, Erdmann S.	Microorganisms	10.3390/microorganisms12010005	2023
Phylogeny	Further refinement of the phylogeny of the Halobacteriaceae based on the full-length RNA polymerase subunit B' (rpoB') gene.	Minegishi H, Kamekura M, Itoh T, Echigo A, Usami R, Hashimoto T.	Int J Syst Evol Microbiol	10.1099/ijs.0.017160-0	2010
	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
Enzymology	Double mutations far from the active site affect cold activity in an Antarctic halophilic beta-galactosidase.	Laye VJ, DasSarma S.	Protein Sci	10.1002/pro.4264	2022
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
Metabolism	The core and unique proteins of haloarchaea.	Capes MD, DasSarma P, DasSarma S.	BMC Genomics	10.1186/1471-2164-13-39	2012
Transcriptome	Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux.	Lynch EA, Langille MG, Darling A, Wilbanks EG, Haltiner C, Shao KS, Starr MO, Teiling C, Harkins TT, Edwards RA, Eisen JA, Facciotti MT.	PLoS One	10.1371/journal.pone.0041389	2012
Enzymology	Key amino acid residues conferring enhanced enzyme activity at cold temperatures in an Antarctic polyextremophilic beta-galactosidase.	Laye VJ, Karan R, Kim JM, Pecher WT, DasSarma P, DasSarma S.	Proc Natl Acad Sci U S A	10.1073/pnas.1711542114	2017
Enzymology	Bacterial CS2 hydrolases from Acidithiobacillus thiooxidans strains are homologous to the archaeal catenane CS2 hydrolase.	Smeulders MJ, Pol A, Venselaar H, Barends TR, Hermans J, Jetten MS, Op den Camp HJ.	J Bacteriol	10.1128/jb.00627-13	2013
Metabolism	Enoyl-CoA hydratase mediates polyhydroxyalkanoate mobilization in Haloferax mediterranei.	Liu G, Cai S, Hou J, Zhao D, Han J, Zhou J, Xiang H.	Sci Rep	10.1038/srep24015	2016
	Nucleotides Flanking the Start Codon in hsp70 mRNAs with Very Short 5'-UTRs Greatly Affect Gene Expression in Haloarchaea.	Chen W, Yang G, He Y, Zhang S, Chen H, Shen P, Chen X, Huang YP.	PLoS One	10.1371/journal.pone.0138473	2015
	Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: investigating acetamidase gene function.	Liao Y, Williams TJ, Walsh JC, Ji M, Poljak A, Curmi PM, Duggin IG, Cavicchioli R.	Sci Rep	10.1038/srep34639	2016
Metabolism	Identification of the haloarchaeal phasin (PhaP) that functions in polyhydroxyalkanoate accumulation and granule formation in Haloferax mediterranei.	Cai S, Cai L, Liu H, Liu X, Han J, Zhou J, Xiang H.	Appl Environ Microbiol	10.1128/aem.07114-11	2012
Metabolism	Sulfolobus acidocaldarius Transports Pentoses via a Carbohydrate Uptake Transporter 2 (CUT2)-Type ABC Transporter and Metabolizes Them through the Aldolase-Independent Weimberg Pathway.	Wagner M, Shen L, Albersmeier A, van der Kolk N, Kim S, Cha J, Brasen C, Kalinowski J, Siebers B, Albers SV.	Appl Environ Microbiol	10.1128/aem.01273-17	2018
Genetics	A comparative genomics perspective on the genetic content of the alkaliphilic haloarchaeon Natrialba magadii ATCC 43099T.	Siddaramappa S, Challacombe JF, Decastro RE, Pfeiffer F, Sastre DE, Gimenez MI, Paggi RA, Detter JC, Davenport KW, Goodwin LA, Kyrpides N, Tapia R, Pitluck S, Lucas S, Woyke T, Maupin-Furlow JA.	BMC Genomics	10.1186/1471-2164-13-165	2012
Enzymology	Glycerol dehydrogenase plays a dual role in glycerol metabolism and 2,3-butanediol formation in Klebsiella pneumoniae.	Wang Y, Tao F, Xu P.	J Biol Chem	10.1074/jbc.m113.525535	2014
	The complete genome sequence of Natrinema sp. J7-2, a haloarchaeon capable of growth on synthetic media without amino acid supplements.	Feng J, Liu B, Zhang Z, Ren Y, Li Y, Gan F, Huang Y, Chen X, Shen P, Wang L, Tang B, Tang XF.	PLoS One	10.1371/journal.pone.0041621	2012
	Haloarchaea and the formation of gas vesicles.	Pfeifer F.	Life (Basel)	10.3390/life5010385	2015
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	Natrarchaeobius chitinivorans gen. nov., sp. nov., and Natrarchaeobius halalkaliphilus sp. nov., alkaliphilic, chitin-utilizing haloarchaea from hypersaline alkaline lakes.	Sorokin DY, Elcheninov AG, Toshchakov SV, Bale NJ, Sinninghe Damste JS, Khijniak TV, Kublanov IV.	Syst Appl Microbiol	10.1016/j.syapm.2019.01.001	2019
Genetics	Non-contiguous finished genome sequence and description of Halopiger goleamassiliensis sp. nov.	Ikram HI, Catherine R, Caroline M, Didier R, Hocine H, Christelle D.	Stand Genomic Sci	10.4056/sigs.4618288	2014
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
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 .
#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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Halopiger xanaduensis (DSM 18323, CECT 7173, CGMCC 1.6379)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000217715

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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