Name: Pseudohalioglobus lutimaris HF004
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158634

Type strain:

Species: Pseudohalioglobus lutimaris

Strain Designation: HF004

Culture col. no.: KCTC 42395, MCCC 1H00127

Strain history: <- Zongjun Du, Shandong Univ.

NCBI tax ID(s): 1737061 (species)

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Cellvibrionales*
	Family	*Halieaceae*
	Genus	*Pseudohalioglobus*
	Species	**Pseudohalioglobus lutimaris**
	Full Scientific Name (LPSN)	Pseudohalioglobus lutimaris (Shi et al. 2018) Kang et al. 2020

Synonym

Halioglobus lutimaris

Information on morphological and physiological properties Morphology

[Ref.: #65359]	Gram stain	negative

[Ref.: #65359]	Cell length	0.7-1.5 µm

[Ref.: #65359]	Cell width	0.4-0.5 µm

[Ref.: #65359]	Cell shape	rod-shaped

[Ref.: #65359]	Motility	no

[Ref.: #65359]	Colony size	0.5-0.8 mm
[Ref.: #65359]	Colony color	beige
[Ref.: #65359]	Colony shape	circular
[Ref.: #65359]	Incubation period	3 days
[Ref.: #65359]	Cultivation medium used	marine agar 2216

Information on culture and growth conditions Culture and growth conditions

[Ref.: #65359]

Culture medium

Marine agar (MA)

[Ref.: #65359]

Culture medium growth

		Temperature
[Ref.: #65359]	growth	15-37 °C
[Ref.: #65359]	optimum	28 °C
[Ref.: #67771]	growth	25-30 °C

[Ref.: #65359]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #65359]			optimum	7.5-8
[Ref.: #65359]			growth	6-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #65359]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #65359]		NaCl		growth	0.5-6	%(w/v)
[Ref.: #65359]		NaCl		optimum	2-3	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65359]	2-oxoglutarate ChEBI	+	oxidation
[Ref.: #65359]	acetate ChEBI	+	oxidation
[Ref.: #65359]	acetoacetate ChEBI	+	oxidation
[Ref.: #65359]	agar ChEBI	-	hydrolysis
[Ref.: #65359]	alginate ChEBI	-	hydrolysis
[Ref.: #65359]	cellulose ChEBI	-	hydrolysis
[Ref.: #65359]	citrate ChEBI	+	assimilation
[Ref.: #65359]	D-ribose ChEBI	+	builds acid from
[Ref.: #65359]	D-tagatose ChEBI	+	builds acid from
[Ref.: #65359]	gentiobiose ChEBI	+	oxidation
[Ref.: #65359]	glucuronamide ChEBI	+	oxidation
[Ref.: #65359]	L-malate ChEBI	+	oxidation
[Ref.: #65359]	nitrate ChEBI	+	reduction
[Ref.: #65359]	potassium 5-dehydro-D-gluconate	+	builds acid from
[Ref.: #65359]	starch ChEBI	-	hydrolysis
[Ref.: #65359]	sucrose ChEBI	+	oxidation
[Ref.: #65359]	turanose ChEBI	+	oxidation
[Ref.: #65359]	tween 20 ChEBI	+	hydrolysis
[Ref.: #65359]	tween 40 ChEBI	+	hydrolysis
[Ref.: #65359]	tween 60 ChEBI	+	hydrolysis
[Ref.: #65359]	tween 80 ChEBI	+	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #65359]	acetylspiramycin ChEBI	yes	30	µg (disc)
[Ref.: #65359]	cefotaxime ChEBI	yes	30	µg (disc)
[Ref.: #65359]	ceftriaxone ChEBI	yes	30	µg (disc)
[Ref.: #65359]	clindamycin ChEBI				yes	30	µg (disc)
[Ref.: #65359]	erythromycin ChEBI	yes	15	µg (disc)
[Ref.: #65359]	gentamicin ChEBI	yes	10	µg (disc)
[Ref.: #65359]	lincomycin ChEBI				yes	2	µg (disc)
[Ref.: #65359]	norfloxacin ChEBI	yes	10	µg (disc)
[Ref.: #65359]	ofloxacin ChEBI	yes	5	µg (disc)
[Ref.: #65359]	penicillin g ChEBI	yes	10	µg (disc)
[Ref.: #65359]	streptomycin ChEBI	yes	10	µg (disc)
[Ref.: #65359]	sulfamethoxydiazine ChEBI	yes	5	µg (disc)
[Ref.: #65359]	tetracycline ChEBI				yes	30	µg (disc)
[Ref.: #65359]	vancomycin ChEBI				yes	30	µg (disc)
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #65359]		acetoin ChEBI	no
[Ref.: #65359]		hydrogen sulfide ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #65359]		acetoin ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #65359]	acid phosphatase	+	3.1.3.2
[Ref.: #65359]	alkaline phosphatase	+	3.1.3.1
[Ref.: #65359]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #65359]	alpha-galactosidase	-	3.2.1.22
[Ref.: #65359]	alpha-glucosidase	-	3.2.1.20
[Ref.: #65359]	alpha-mannosidase	-	3.2.1.24
[Ref.: #65359]	beta-D-fucosidase	-	3.2.1.38
[Ref.: #65359]	beta-galactosidase	-	3.2.1.23
[Ref.: #65359]	beta-glucosidase	-	3.2.1.21
[Ref.: #65359]	beta-glucuronidase	-	3.2.1.31
[Ref.: #65359]	catalase	+	1.11.1.6
[Ref.: #65359]	cystine arylamidase	+	3.4.11.3
[Ref.: #65359]	cytochrome oxidase	-	1.9.3.1
[Ref.: #65359]	esterase (C 4)	+
[Ref.: #65359]	esterase Lipase (C 8)	+
[Ref.: #65359]	leucine arylamidase	+	3.4.11.1
[Ref.: #65359]	lipase (C 14)	-
[Ref.: #65359]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #65359]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #65359]	trypsin	-	3.4.21.4
[Ref.: #65359]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	quinate degradation	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	toluene degradation	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	citric acid cycle	92.86	13 of 14
[Ref.: #66794]	leucine metabolism	92.31	12 of 13
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	glutamate and glutamine metabolism	89.29	25 of 28
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	chorismate metabolism	77.78	7 of 9
[Ref.: #66794]	lipid metabolism	77.42	24 of 31
[Ref.: #66794]	purine metabolism	76.6	72 of 94
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	75	6 of 8
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	androgen and estrogen metabolism	68.75	11 of 16
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	pyrimidine metabolism	66.67	30 of 45
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	peptidoglycan biosynthesis	66.67	10 of 15
[Ref.: #66794]	tryptophan metabolism	65.79	25 of 38
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	photosynthesis	64.29	9 of 14
[Ref.: #66794]	degradation of sugar acids	64	16 of 25
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	phenol degradation	60	12 of 20
[Ref.: #66794]	starch degradation	60	6 of 10
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	threonine metabolism	60	6 of 10
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	60	6 of 10
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	58.82	10 of 17
[Ref.: #66794]	glycolysis	58.82	10 of 17
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	tyrosine metabolism	57.14	8 of 14
[Ref.: #66794]	polyamine pathway	56.52	13 of 23
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	lysine metabolism	54.76	23 of 42
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	3-phenylpropionate degradation	53.33	8 of 15
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	coenzyme A metabolism	50	2 of 4
[Ref.: #66794]	alginate biosynthesis	50	2 of 4
[Ref.: #66794]	degradation of sugar alcohols	50	8 of 16
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	degradation of pentoses	46.43	13 of 28
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	arachidonic acid metabolism	44.44	8 of 18
[Ref.: #66794]	4-hydroxymandelate degradation	44.44	4 of 9
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	oxidative phosphorylation	36.26	33 of 91
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	vitamin B1 metabolism	30.77	4 of 13
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	carotenoid biosynthesis	22.73	5 of 22
		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.: #65359]	Sample type/isolated from	marine sediment sample
[Ref.: #65359]	Sampling date	2013-09
[Ref.: #65359]	Geographic location (country and/or sea, region)	coast of Weihai
[Ref.: #65359]	Country	China
[Ref.: #65359]	Country ISO 3 Code	CHN
[Ref.: #65359]	Continent	Asia
[Ref.: #65359]	Geographic location	37.5330°/122.0630°
[Ref.: #65359]	Enrichment culture	marine agar 2216
[Ref.: #65359]	Isolation/enrichment procedure	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

[Ref.: #67771]	Sample type/isolated from	From the coastal area of Weihai marine sediment
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #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

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.: #65359]	16S rRNA gene sequence	KR528479		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pseudohalioglobus lutimaris HF004	GCA_002866825	contig	GenBank	1737061 tax ID	*

[Ref.: #65359]

GC-content

57.2 mol%

genome sequence analysis

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pseudohalioglobus lutimaris HF004 NCBI: GCA_002866825.1
[Ref.: #69480]	flagellated	no	72.987	yes
[Ref.: #69480]	gram-positive	no	98.859	no
[Ref.: #69480]	anaerobic	no	97.7	no
[Ref.: #69480]	aerobic	yes	85.388	yes
[Ref.: #69480]	halophile	yes	55.526	no
[Ref.: #69480]	spore-forming	no	97.121	no
[Ref.: #69480]	glucose-util	yes	63.733	no
[Ref.: #69480]	thermophile	no	99.629	no
[Ref.: #69480]	motile	yes	68.268	yes
[Ref.: #69480]	glucose-ferment	no	87.166	no

Availability in culture collections External links

[Ref.: #65359]

Culture collection no.

KCTC 42395, MCCC 1H00127

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 .

#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) .

* 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 Halioglobus lutimaris in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF