Halomicrobium zhouii (CGMCC 1.10457, JCM 17095, TBN51)

Name: Halomicrobium zhouii (CGMCC 1.10457, JCM 17095, TBN51)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133717

Type strain

Strain Designation TBN51

Culture col. no. CGMCC 1.10457 JCM 17095 TBN51

NCBI tax ID(s) 767519

Special Collections JCM Literature strains

History JCM <-- H.-L. Cui; Jiangsu Univ., China; TBN51.

Links

Halomicrobium zhouii TBN51 is an aerobe, Gram-negative, motile archaeon that was isolated from marine sediment.

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

Name and taxonomic classification

SI-ID 133008

JCM 17095

@ref 20215

Last LPSN update 2026-05-29 08:38:09

Domain Archaea

Phylum Methanobacteriota

Class Halobacteria

Order Halobacteriales

Family Haloarculaceae

Genus Halomicrobium

Species Halomicrobium zhouii

Full scientific name Halomicrobium zhouii Yang and Cui 2012

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
30262	negative	rod-shaped

Pigmentation

30262

Productionyes

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
30262	positive	growth	20-55
30262	positive	optimum	42
67770	positive	growth	37

Culture pH

@ref	Ability	Type	PH	PH range
30262	positive	optimum	7
30262	positive	growth	5.5-9.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30262	aerobe
125439	facultative anaerobe	92.259

Spore formation

@ref	Spore formation	Confidence
125439		98.371

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30262	NaCl	positive	growth	8.12-29.58 %
30262	NaCl	positive	optimum	15.08 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30262	30089 ChEBI	acetate	+	carbon source
30262	28260 ChEBI	galactose	+	carbon source
30262	17234 ChEBI	glucose	+	carbon source
30262	29987 ChEBI	glutamate	+	carbon source
30262	17754 ChEBI	glycerol	+	carbon source
30262	24996 ChEBI	lactate	+	carbon source
30262	17716 ChEBI	lactose	+	carbon source
30262	37684 ChEBI	mannose	+	carbon source
30262	17632 ChEBI	nitrate	+	reduction
30262	15361 ChEBI	pyruvate	+	carbon source
30262	17992 ChEBI	sucrose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
30262	16136 ChEBI	hydrogen sulfide

Enzymes

@ref	Value	Activity	Ec
30262	catalase	+	1.11.1.6
30262	cytochrome oxidase	+	1.9.3.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	gluconeogenesis	100	8 of 8
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	phenylmercury acetate degradation	100	2 of 2
66794	L-lactaldehyde degradation	100	3 of 3
66794	denitrification	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	methylglyoxal degradation	100	5 of 5
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	threonine metabolism	90	9 of 10
66794	Entner Doudoroff pathway	90	9 of 10
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	palmitate biosynthesis	86.36	19 of 22
66794	phenylalanine metabolism	84.62	11 of 13
66794	pantothenate biosynthesis	83.33	5 of 6
66794	vitamin K metabolism	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	cellulose degradation	80	4 of 5
66794	factor 420 biosynthesis	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	sulfopterin metabolism	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	ppGpp biosynthesis	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	NAD metabolism	72.22	13 of 18
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	purine metabolism	71.28	67 of 94
66794	non-pathway related	71.05	27 of 38
66794	starch degradation	70	7 of 10
66794	degradation of sugar acids	68	17 of 25
66794	lipid metabolism	67.74	21 of 31
66794	acetoin degradation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	serine metabolism	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	pyrimidine metabolism	66.67	30 of 45
66794	glycolysis	64.71	11 of 17
66794	vitamin B12 metabolism	64.71	22 of 34
66794	citric acid cycle	64.29	9 of 14
66794	photosynthesis	64.29	9 of 14
66794	heme metabolism	64.29	9 of 14
66794	pentose phosphate pathway	63.64	7 of 11
66794	d-xylose degradation	63.64	7 of 11
66794	metabolism of disaccharids	63.64	7 of 11
66794	ketogluconate metabolism	62.5	5 of 8
66794	histidine metabolism	62.07	18 of 29
66794	leucine metabolism	61.54	8 of 13
66794	gallate degradation	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	4-hydroxyphenylacetate degradation	60	6 of 10
66794	3-chlorocatechol degradation	60	3 of 5
66794	propionate fermentation	60	6 of 10
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	oxidative phosphorylation	59.34	54 of 91
66794	alanine metabolism	58.62	17 of 29
66794	arginine metabolism	58.33	14 of 24
66794	reductive acetyl coenzyme A pathway	57.14	4 of 7
66794	propanol degradation	57.14	4 of 7
66794	lysine metabolism	57.14	24 of 42
66794	nitrate assimilation	55.56	5 of 9
66794	tryptophan metabolism	55.26	21 of 38
66794	vitamin B6 metabolism	54.55	6 of 11
66794	lactate fermentation	50	2 of 4
66794	acetate fermentation	50	2 of 4
66794	CDP-diacylglycerol biosynthesis	50	1 of 2
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	degradation of pentoses	50	14 of 28
66794	resorcinol degradation	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	degradation of sugar alcohols	50	8 of 16
66794	biotin biosynthesis	50	2 of 4
66794	selenocysteine biosynthesis	50	3 of 6
66794	urea cycle	46.15	6 of 13
66794	proline metabolism	45.45	5 of 11
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	mevalonate metabolism	42.86	3 of 7
66794	tyrosine metabolism	42.86	6 of 14
66794	methanogenesis from CO2	41.67	5 of 12
66794	ascorbate metabolism	40.91	9 of 22
66794	3-phenylpropionate degradation	40	6 of 15
66794	lipoate biosynthesis	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	bacilysin biosynthesis	40	2 of 5
66794	phenol degradation	40	8 of 20
66794	coenzyme M biosynthesis	40	4 of 10
66794	creatinine degradation	40	2 of 5
66794	degradation of hexoses	38.89	7 of 18
66794	arachidonic acid metabolism	38.89	7 of 18
66794	cysteine metabolism	38.89	7 of 18
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	methionine metabolism	38.46	10 of 26
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	carotenoid biosynthesis	36.36	8 of 22
66794	cholesterol biosynthesis	36.36	4 of 11
66794	glutathione metabolism	35.71	5 of 14
66794	polyamine pathway	34.78	8 of 23
66794	isoprenoid biosynthesis	34.62	9 of 26
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	lipid A biosynthesis	33.33	3 of 9
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	sulfate reduction	30.77	4 of 13
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	peptidoglycan biosynthesis	26.67	4 of 15
66794	carnitine metabolism	25	2 of 8
66794	catecholamine biosynthesis	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	butanoate fermentation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	chlorophyll metabolism	22.22	4 of 18

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
30262	marine sediment
67770	Marine solar saltern in Jiangsu	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
67770	IMG-taxon 2667527389 annotated assembly for Halomicrobium zhouii CGMCC 1.10457	scaffold	GCA_900114435	767519.3	2667527389	767519	68.41

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
30262	Halomicrobium zhouii 16S ribosomal RNA gene, partial sequence	HQ215547	1474	767519
67770	Halomicrobium zhouii strain TBN51 16S ribosomal RNA gene, complete sequence	HM063952	1472	767519
67770	Halomicrobium zhouii 16S ribosomal RNA gene, partial sequence	HQ215546	1474	767519
124043	Halomicrobium zhouii gene for 16S ribosomal RNA, partial sequence.	AB771432	1473	767519

GC content

@ref	GC-content (mol%)	Method
30262	69.1
67770	69.1	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: IMG-taxon 2667527389 annotated assembly for Halomicrobium zhouii CGMCC 1.10457
BV-BRC: 767519.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	negative	79.46	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	92.26	no
125439	motility	BacteriaNetⓘ	yes	51.24	no
125439	spore_formation	BacteriaNetⓘ	no	98.37	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Cellulose metabolism in halo(natrono)archaea: a comparative genomics study.	Elcheninov AG, Ugolkov YA, Elizarov IM, Klyukina AA, Kublanov IV, Sorokin DY.	Front Microbiol	10.3389/fmicb.2023.1112247	2023
	Exploring tRNA gene cluster in archaea.	Morgado SM, Vicente ACP.	Mem Inst Oswaldo Cruz	10.1590/0074-02760180348	2019
	Selective enrichment on a wide polysaccharide spectrum allowed isolation of novel metabolic and taxonomic groups of haloarchaea from hypersaline lakes.	Sorokin DY, Elcheninov AG, Khijniak TV, Kolganova TV, Kublanov IV.	Front Microbiol	10.3389/fmicb.2022.1059347	2022
Phylogeny	Halomicrobium zhouii sp. nov., a halophilic archaeon from a marine solar saltern.	Yang X, Cui HL	Int J Syst Evol Microbiol	10.1099/ijs.0.031989-0	2011

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 )
#26603	IJSEM 1235 2012 ( DOI 10.1099/ijs.0.031989-0 , PubMed 21764983 )
#30262	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 #26603
#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 )

Content

About us

Halomicrobium zhouii (CGMCC 1.10457, JCM 17095, TBN51)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

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

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_900114435

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media