Name: Oleiagrimonas citrea JCM 30904
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 140604

Type strain:

Species: Oleiagrimonas citrea

Culture col. no.: JCM 30904, KCCM 43131, MEBiC 09124

Strain history: K. K. Kwon; Korea Inst. of Ocean Sci. & Technol., South Korea; MEBiC09124.

NCBI tax ID(s): 1665687 (species)

Special Collections

Section

When using BacDive for research please cite our paper

Oleiagrimonas citrea JCM 30904 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from tidal flat sediment.

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

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Lysobacterales*
	Family	*Rhodanobacteraceae*
	Genus	*Oleiagrimonas*
	Species	**Oleiagrimonas citrea**
	Full Scientific Name (LPSN)	Oleiagrimonas citrea Yang et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #43265]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %98

[Ref.: #43265]	Cell length	1.4-3.6 µm

[Ref.: #43265]	Cell width	0.4-0.6 µm

[Ref.: #43265]	Cell shape	rod-shaped

[Ref.: #43265]	Motility	yes

[Ref.: #43265]	Colony size	0.5-1.0 mm
[Ref.: #43265]	Colony color	yellow
[Ref.: #43265]	Colony shape	circular
[Ref.: #43265]	Incubation period	2-3 days
[Ref.: #43265]	Cultivation medium used	MA

Information on culture and growth conditions Culture and growth conditions

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Culture medium

Marine agar (MA)

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Culture medium growth

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Culture medium

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Culture medium growth

		Temperature
[Ref.: #43265]	optimum	30 °C
[Ref.: #43265]	growth	18-38 °C
[Ref.: #67770]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #43265]			optimum	7.5
[Ref.: #43265]			growth	4.0-8.5

Information on physiology and metabolism Physiology and metabolism

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Oxygen tolerance

aerobe

[Ref.: #125438]

Ability of spore formation

no Confidence in %90.824

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43265]		NaCl		growth	0-6	%(w/v)
[Ref.: #43265]		NaCl		optimum	2.5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43265]	2-oxobutanoate ChEBI	+	oxidation
[Ref.: #43265]	2-oxoglutarate ChEBI	+	oxidation
[Ref.: #43265]	2-oxopentanoate ChEBI	+	oxidation
[Ref.: #43265]	3-hydroxybutyrate ChEBI	+	oxidation
[Ref.: #43265]	acetate ChEBI	-	oxidation
[Ref.: #43265]	alpha-D-glucose ChEBI	+	oxidation
[Ref.: #43265]	bromosuccinate ChEBI	+	oxidation
[Ref.: #43265]	D-fructose ChEBI	+	oxidation
[Ref.: #43265]	D-galactose ChEBI	-	oxidation
[Ref.: #43265]	dextrin ChEBI	+	oxidation
[Ref.: #43265]	gentiobiose ChEBI	-	oxidation
[Ref.: #43265]	glycogen ChEBI	+	oxidation
[Ref.: #43265]	glycyl-l-glutamate ChEBI	-	oxidation
[Ref.: #43265]	L-alaninamide ChEBI	+	oxidation
[Ref.: #43265]	L-alanine ChEBI	-	oxidation
[Ref.: #43265]	L-alanylglycine ChEBI	-	oxidation
[Ref.: #43265]	L-asparagine ChEBI	-	oxidation
[Ref.: #43265]	L-aspartate ChEBI	-	oxidation
[Ref.: #43265]	L-glutamate ChEBI	+	oxidation
[Ref.: #43265]	L-leucine ChEBI	-	oxidation
[Ref.: #43265]	L-ornithine ChEBI	-	oxidation
[Ref.: #43265]	L-phenylalanine ChEBI	-	oxidation
[Ref.: #43265]	L-proline ChEBI	-	oxidation
[Ref.: #43265]	L-serine ChEBI	+	oxidation
[Ref.: #43265]	maltose ChEBI	+	oxidation
[Ref.: #43265]	methyl pyruvate ChEBI	+	oxidation
[Ref.: #43265]	nitrate ChEBI	+	reduction
[Ref.: #43265]	starch ChEBI	-	hydrolysis
[Ref.: #43265]	succinamate ChEBI	+	oxidation
[Ref.: #43265]	trehalose ChEBI	+	oxidation
[Ref.: #43265]	turanose ChEBI	-	oxidation
[Ref.: #43265]	tween 40 ChEBI	+	oxidation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #43265]	amikacin ChEBI				yes	30	µg
[Ref.: #43265]	ampicillin ChEBI				yes	10	µg
[Ref.: #43265]	cefoxitin ChEBI				yes	30	µg
[Ref.: #43265]	cefuroxime sodium ChEBI				yes	30	µg
[Ref.: #43265]	cephalothin ChEBI				yes	30	µg
[Ref.: #43265]	chloramphenicol ChEBI				yes	30	µg
[Ref.: #43265]	ciprofloxacin ChEBI	yes	5	µg
[Ref.: #43265]	meropenem ChEBI				yes	10	µg
[Ref.: #43265]	ofloxacin ChEBI				yes	5	µg
[Ref.: #43265]	piperacillin ChEBI	yes	100	µg
[Ref.: #43265]	tetracycline ChEBI				yes	30	µg
	Only first 10 entries are displayed. Click here to see all.

	Group ID of combined antibiotics	Metabolite	Antibiotic resistance	Concentration
[Ref.: #43265]	10	amoxicillin ChEBI	yes	20	µg
[Ref.: #43265]	20	ampicillin ChEBI	yes	10	µg
[Ref.: #43265]	10	clavulanic acid ChEBI	yes	10	µg
[Ref.: #43265]	20	sulbactam ChEBI	yes	10	µg
[Ref.: #43265]	26	sulfamethoxazole ChEBI	yes	23.75	µg
[Ref.: #43265]	26	trimethoprim ChEBI	yes	1.25	µg

	Metabolite	Production
[Ref.: #43265]	acetoin ChEBI	yes
[Ref.: #43265]	hydrogen sulfide ChEBI	no
[Ref.: #43265]	indole ChEBI	no
[Ref.: #43265]	urea ChEBI	yes

	Enzyme	Enzyme activity	EC number
[Ref.: #43265]	acid phosphatase	+	3.1.3.2
[Ref.: #43265]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43265]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #43265]	alpha-fucosidase	-	3.2.1.51
[Ref.: #43265]	alpha-galactosidase	-	3.2.1.22
[Ref.: #43265]	alpha-glucosidase	+	3.2.1.20
[Ref.: #43265]	alpha-mannosidase	-	3.2.1.24
[Ref.: #43265]	arginine dihydrolase	-	3.5.3.6
[Ref.: #43265]	beta-galactosidase	-	3.2.1.23
[Ref.: #43265]	beta-glucosidase	+	3.2.1.21
[Ref.: #43265]	beta-glucuronidase	-	3.2.1.31
[Ref.: #43265]	catalase	+	1.11.1.6
[Ref.: #43265]	cystine arylamidase	+	3.4.11.3
[Ref.: #43265]	cytochrome oxidase	+	1.9.3.1
[Ref.: #43265]	esterase (C 4)	+
[Ref.: #43265]	esterase Lipase (C 8)	+
[Ref.: #43265]	gelatinase	+
[Ref.: #43265]	leucine arylamidase	+	3.4.11.1
[Ref.: #43265]	lipase (C 14)	+
[Ref.: #43265]	lysine decarboxylase	-	4.1.1.18
[Ref.: #43265]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #43265]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #43265]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #43265]	trypsin	+	3.4.21.4
[Ref.: #43265]	trypsin	-	3.4.21.4
[Ref.: #43265]	urease	+	3.5.1.5
[Ref.: #43265]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43265]

Fatty acid	Percentage
C15:0 iso	22.6
10-methyl C16:0 / iso-C17:1ω9c	22.5
C16:0 iso	16
C17:0 iso	10
C15:0 anteiso	3.5
C16:1 iso H	3
C13:0 iso 3OH	2.4
C14:0 iso	1.9
C16:1ω6c / C16:1ω7c	1.9
C16:0	1.3
C12:0 iso 3OH	1.1
C17:0 iso 3OH	1.1

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #43265]	Sample type/isolated from	tidal flat sediment
[Ref.: #43265]	Geographic location (country and/or sea, region)	Suncheon Bay, South Korea
[Ref.: #43265]	Country	Republic of Korea
[Ref.: #43265]	Country ISO 3 Code	KOR
[Ref.: #43265]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Tidal flat sediment of Suncheon Bay
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Tidal flat
#Environmental	#Terrestrial	#Sediment

What are isolation sources categories?

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.: #43265]	Oleiagrimonas citrea strain MEBic09124 16S ribosomal RNA gene, partial sequence	KP691065	1439	GenBank ENA	1665687 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Oleiagrimonas citrea MEBiC09124	GCA_012395255	contig	GenBank ENA	1665687 tax ID

[Ref.: #43265]

GC-content

66.1 mol%

high performance liquid chromatography (HPLC)

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Oleiagrimonas citrea MEBiC09124 NCBI: GCA_012395255.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	98	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	95.113	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	82.711	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	90.824	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	94.698	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	53.037	no

Availability in culture collections External links

[Ref.: #43265]

Culture collection no.

JCM 30904, KCCM 43131, MEBiC 09124

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Oleiagrimonas citrea sp. nov., a marine bacterium isolated from tidal flat sediment and emended description of the genus Oleiagrimonas Fang et al. 2015 and Oleiagrimonas soli.	Yang SH, Seo HS, Seong CN, Kwon KK	Int J Syst Evol Microbiol	10.1099/ijsem.0.001846	2017	*

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 )

#43265

Sung-Hyun Yang, Hyun-Seok Seo, Chi Nam Seong and Kae Kyoung Kwon: Oleiagrimonas citrea sp. nov., a marine bacterium isolated from tidal flat sediment and emended description of the genus Oleiagrimonas Fang et al. 2015 and Oleiagrimonas soli. IJSEM 67: 1672 - 1675 2017 ( DOI 10.1099/ijsem.0.001846 , PubMed 28211311 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 )

* These data were automatically processed and therefore are not curated

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Oleiagrimonas citrea MEBiC09124

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