Pseudohalioglobus lutimaris (KCTC 42395, MCCC 1H00127, HF004)

Name: Pseudohalioglobus lutimaris (KCTC 42395, MCCC 1H00127, HF004)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158634

Type strain

Strain Designation HF004

Culture col. no. KCTC 42395 MCCC 1H00127 HF004

NCBI tax ID(s) 1737061

Special Collections KCTC Literature strains

Links

Pseudohalioglobus lutimaris HF004 is an aerobe, Gram-negative, rod-shaped prokaryote that forms circular colonies and was isolated from marine sediment sample.

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

Name and taxonomic classification

SI-ID 27999

KCTC 42395

@ref 20215

Last LPSN update 2025-12-16 10:08:04

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Cellvibrionales

Family Halieaceae

Genus Pseudohalioglobus

Species Pseudohalioglobus lutimaris

Full scientific name Pseudohalioglobus lutimaris (Shi et al. 2018) Kang et al. 2020

Synonyms (1)

Halioglobus lutimaris

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
65359	negative	0.7-1.5 µm	0.4-0.5 µm	rod-shaped
125439	negative
125438	negative

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
65359	0.5-0.8 mm	beige	circular	3 days	marine agar 2216

Culture and growth conditions

Culture medium

@ref	Name	Growth
65359	Marine agar (MA)

Culture temp

@ref	Growth	Type	Temperature (°C)
65359	positive	growth	15-37
65359	positive	optimum	28
67771	positive	growth	25-30

Culture pH

@ref	Ability	Type	PH
65359	positive	optimum	7.5-8
65359	positive	growth	6-8.5

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
65359	aerobe
67771	aerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.8
125438		92.109

Halophily

@ref	Salt	Growth	Tested relation	Concentration
65359	NaCl	positive	growth	0.5-6 %(w/v)
65359	NaCl	positive	optimum	2-3 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
65359	30916 ChEBI	2-oxoglutarate	+	oxidation
65359	30089 ChEBI	acetate	+	oxidation
65359	13705 ChEBI	acetoacetate	+	oxidation
65359	2509 ChEBI	agar	-	hydrolysis
65359	58187 ChEBI	alginate	-	hydrolysis
65359	62968 ChEBI	cellulose	-	hydrolysis
65359	16947 ChEBI	citrate	+	assimilation
65359	16988 ChEBI	D-ribose	+	builds acid from
65359	16443 ChEBI	D-tagatose	+	builds acid from
65359	28066 ChEBI	gentiobiose	+	oxidation
65359	32323 ChEBI	glucuronamide	+	oxidation
65359	15589 ChEBI	L-malate	+	oxidation
65359	17632 ChEBI	nitrate	+	reduction
65359		potassium 5-dehydro-D-gluconate	+	builds acid from
65359	28017 ChEBI	starch	-	hydrolysis
65359	17992 ChEBI	sucrose	+	oxidation
65359	32528 ChEBI	turanose	+	oxidation
65359	53424 ChEBI	tween 20	+	hydrolysis
65359	53423 ChEBI	tween 40	+	hydrolysis
65359	53425 ChEBI	tween 60	+	hydrolysis
65359	53426 ChEBI	tween 80	+	hydrolysis

Antibiotic resistance

@ref	ChEBI	Metabolite	Sensitivity conc.
65359	31168	acetylspiramycin	30 µg (disc)
65359	204928	cefotaxime	30 µg (disc)
65359	29007	ceftriaxone	30 µg (disc)
65359	3745	clindamycin
65359	48923	erythromycin	15 µg (disc)
65359	17833	gentamicin	10 µg (disc)
65359	6472	lincomycin
65359	100246	norfloxacin	10 µg (disc)
65359	7731	ofloxacin	5 µg (disc)
65359	18208	penicillin g	10 µg (disc)
65359	17076	streptomycin	10 µg (disc)
65359	53727	sulfamethoxydiazine	5 µg (disc)
65359	27902	tetracycline
65359	28001	vancomycin

Metabolite production

@ref	Chebi-ID	Metabolite	Production
65359	15688 ChEBI	acetoin
65359	16136 ChEBI	hydrogen sulfide

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
65359	15688 ChEBI	acetoin	-

Enzymes

@ref	Value	Activity	Ec
65359	acid phosphatase	+	3.1.3.2
65359	alkaline phosphatase	+	3.1.3.1
65359	alpha-chymotrypsin	-	3.4.21.1
65359	alpha-galactosidase	-	3.2.1.22
65359	alpha-glucosidase	-	3.2.1.20
65359	alpha-mannosidase	-	3.2.1.24
65359	beta-D-fucosidase	-	3.2.1.38
65359	beta-galactosidase	-	3.2.1.23
65359	beta-glucosidase	-	3.2.1.21
65359	beta-glucuronidase	-	3.2.1.31
65359	catalase	+	1.11.1.6
65359	cystine arylamidase	+	3.4.11.3
65359	cytochrome oxidase	-	1.9.3.1
65359	esterase (C 4)	+
65359	esterase Lipase (C 8)	+
65359	leucine arylamidase	+	3.4.11.1
65359	lipase (C 14)	-
65359	N-acetyl-beta-glucosaminidase	-	3.2.1.52
65359	naphthol-AS-BI-phosphohydrolase	+
65359	trypsin	-	3.4.21.4
65359	valine arylamidase	+

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	quinate degradation	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	denitrification	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	cardiolipin biosynthesis	100	7 of 7
66794	L-lactaldehyde degradation	100	3 of 3
66794	biotin biosynthesis	100	4 of 4
66794	ethanol fermentation	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	taurine degradation	100	1 of 1
66794	aspartate and asparagine metabolism	100	9 of 9
66794	palmitate biosynthesis	100	22 of 22
66794	folate polyglutamylation	100	1 of 1
66794	ceramide biosynthesis	100	1 of 1
66794	ubiquinone biosynthesis	100	7 of 7
66794	toluene degradation	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	citric acid cycle	92.86	13 of 14
66794	leucine metabolism	92.31	12 of 13
66794	phenylalanine metabolism	92.31	12 of 13
66794	Entner Doudoroff pathway	90	9 of 10
66794	glutamate and glutamine metabolism	89.29	25 of 28
66794	serine metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	alanine metabolism	79.31	23 of 29
66794	heme metabolism	78.57	11 of 14
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	chorismate metabolism	77.78	7 of 9
66794	lipid metabolism	77.42	24 of 31
66794	purine metabolism	76.6	72 of 94
66794	acetate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	NAD metabolism	72.22	13 of 18
66794	propanol degradation	71.43	5 of 7
66794	histidine metabolism	68.97	20 of 29
66794	androgen and estrogen metabolism	68.75	11 of 16
66794	octane oxidation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	pyrimidine metabolism	66.67	30 of 45
66794	acetoin degradation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	peptidoglycan biosynthesis	66.67	10 of 15
66794	tryptophan metabolism	65.79	25 of 38
66794	glutathione metabolism	64.29	9 of 14
66794	photosynthesis	64.29	9 of 14
66794	degradation of sugar acids	64	16 of 25
66794	vitamin B6 metabolism	63.64	7 of 11
66794	proline metabolism	63.64	7 of 11
66794	arginine metabolism	62.5	15 of 24
66794	urea cycle	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	non-pathway related	60.53	23 of 38
66794	phenol degradation	60	12 of 20
66794	starch degradation	60	6 of 10
66794	factor 420 biosynthesis	60	3 of 5
66794	gallate degradation	60	3 of 5
66794	threonine metabolism	60	6 of 10
66794	glycogen metabolism	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	4-hydroxyphenylacetate degradation	60	6 of 10
66794	bile acid biosynthesis, neutral pathway	58.82	10 of 17
66794	glycolysis	58.82	10 of 17
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	tyrosine metabolism	57.14	8 of 14
66794	polyamine pathway	56.52	13 of 23
66794	d-mannose degradation	55.56	5 of 9
66794	nitrate assimilation	55.56	5 of 9
66794	lysine metabolism	54.76	23 of 42
66794	pentose phosphate pathway	54.55	6 of 11
66794	sulfate reduction	53.85	7 of 13
66794	methionine metabolism	53.85	14 of 26
66794	3-phenylpropionate degradation	53.33	8 of 15
66794	glycine metabolism	50	5 of 10
66794	phenylmercury acetate degradation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	coenzyme A metabolism	50	2 of 4
66794	alginate biosynthesis	50	2 of 4
66794	degradation of sugar alcohols	50	8 of 16
66794	cyclohexanol degradation	50	2 of 4
66794	pantothenate biosynthesis	50	3 of 6
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	degradation of pentoses	46.43	13 of 28
66794	ascorbate metabolism	45.45	10 of 22
66794	arachidonic acid metabolism	44.44	8 of 18
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	vitamin K metabolism	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	degradation of hexoses	38.89	7 of 18
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	cholesterol biosynthesis	36.36	4 of 11
66794	metabolism of disaccharids	36.36	4 of 11
66794	oxidative phosphorylation	36.26	33 of 91
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	cyanate degradation	33.33	1 of 3
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	vitamin B1 metabolism	30.77	4 of 13
66794	coenzyme M biosynthesis	30	3 of 10
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	catecholamine biosynthesis	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	phenylpropanoid biosynthesis	23.08	3 of 13
66794	carotenoid biosynthesis	22.73	5 of 22

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture	Isolation procedure
65359	marine sediment sample	2013-09	coast of Weihai	China	CHN	Asia	37.533	122.063 37.533/122.063	marine agar 2216	The marine sediment sample was serially diluted to 10-5 with sterilized seawater, and 0.1 ml aliquots of each dilution were spread onto marine agar 2216
67771	From the coastal area of Weihai marine sediment			China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence KR528479 (>99% sequence identity) for Halioglobus from Microbeatlas

Aquatic Samples	1491
Soil Samples	37
Animal Samples	51
Plant Samples	9
Total Samples	1588

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM286682v1 assembly for Pseudohalioglobus lutimaris HF004	contig	GCA_002866825	1737061.5	2791354912	1737061	63.43

Genome browser: GCA_002866825

16S sequences

@ref	Description	Accession	Database
65359	Pseudohalioglobus lutimaris strain HF004 16S ribosomal RNA gene, partial sequence	KR528479

GC content

@ref	GC-content (mol%)	Method
65359	57.2	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pseudohalioglobus lutimaris HF004
NCBI: GCA_002866825

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.80	no
125439	motility	BacteriaNetⓘ	yes	87.60	no
125439	gram_stain	BacteriaNetⓘ	negative	99.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative aerobe	66.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudohalioglobus lutimaris HF004
NCBI: GCA_002866825.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.89	no
125438	anaerobic	anaerobicⓘ	no	96.28	yes
125438	aerobic	aerobicⓘ	yes	75.96	yes
125438	spore-forming	spore-formingⓘ	no	92.11	no
125438	thermophilic	thermophileⓘ	no	97.41	yes
125438	flagellated	motile2+ⓘ	yes	64.60	no

Literature

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 )
#65359	Ming-Jing Shi, Chong Wang, Xu-Ting Wang, Zong-Jun Du: Halioglobus lutimaris sp. nov., isolated from coastal sediment. IJSEM 68: 876 - 880 2018 ( DOI 10.1099/ijsem.0.002601 , PubMed 29458490 )
#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 )
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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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