Name: Sediminivirga luteola F23
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140907

Type strain:

Species: Sediminivirga luteola

Strain Designation: F23

Culture col. no.: JCM 19771, CGMCC 1.12785, MCCC 1A09945

Strain history: G. Zhang F23.

NCBI tax ID(s): 1774748 (species)

Section

Sediminivirga luteola F23 is an aerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from Marine Sediments collected from the western Pacific.

colony-forming
Gram-positive
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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Brevibacteriaceae*
	Genus	*Sediminivirga*
	Species	**Sediminivirga luteola**
	Full Scientific Name (LPSN)	Sediminivirga luteola Zhang et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43752]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #43752]	Cell length	1.3-1.8 µm

[Ref.: #43752]	Cell width	0.3-0.4 µm

[Ref.: #43752]	Cell shape	rod-shaped

[Ref.: #43752]	Motility	no

[Ref.: #43752]	Colony size	1-2 mm
[Ref.: #43752]	Colony color	Pale yellow, opaque
[Ref.: #43752]	Colony shape	circular
[Ref.: #43752]	Incubation period	3 days
[Ref.: #43752]	Cultivation medium used	MZ2

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43752]

Culture medium

MZ2

[Ref.: #43752]

Culture medium growth

		Temperature
[Ref.: #43752]	growth	4-55 °C
[Ref.: #43752]	optimum	35-37 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #43752]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43752]			optimum	8-9
[Ref.: #43752]			growth	6-12

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43752]

Oxygen tolerance

aerobe

[Ref.: #69480]

Ability of spore formation

no Confidence in %99.99

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43752]		NaCl		growth	0-10	%(w/v)
[Ref.: #43752]		NaCl		optimum	1	%(w/v)

[Ref.: #67770]

Observation

quinones: MK-8(H₂), MK-7(H₂)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43752]	(S)-lactate ChEBI	+	oxidation
[Ref.: #43752]	2-hydroxybutyrate ChEBI	+	oxidation
[Ref.: #43752]	2-oxopentanoate ChEBI	+	oxidation
[Ref.: #43752]	4-hydroxybutyrate ChEBI	+	oxidation
[Ref.: #43752]	acetate ChEBI	+	oxidation
[Ref.: #43752]	adenosine ChEBI	+	oxidation
[Ref.: #43752]	alpha-D-glucose ChEBI	+	oxidation
[Ref.: #43752]	amygdalin ChEBI	-	fermentation
[Ref.: #43752]	arabinose ChEBI	-	fermentation
[Ref.: #43752]	beta-hydroxybutyrate ChEBI	+	oxidation
[Ref.: #43752]	casein	+	hydrolysis
[Ref.: #43752]	cellulose ChEBI	-	hydrolysis
[Ref.: #43752]	D-fructose ChEBI	+	oxidation
[Ref.: #43752]	D-glucose 6-phosphate ChEBI	+/-	oxidation
[Ref.: #43752]	D-mannitol ChEBI	+	oxidation
[Ref.: #43752]	D-mannose ChEBI	+	oxidation
[Ref.: #43752]	dextrin ChEBI	+	oxidation
[Ref.: #43752]	glucose ChEBI	-	fermentation
[Ref.: #43752]	glycerol ChEBI	+	oxidation
[Ref.: #43752]	glycerol 1-phosphate ChEBI	+/-	oxidation
[Ref.: #43752]	glycyl-l-glutamate ChEBI	+/-	oxidation
[Ref.: #43752]	L-asparagine ChEBI	+	oxidation
[Ref.: #43752]	L-glutamate ChEBI	+/-	oxidation
[Ref.: #43752]	lactamide ChEBI	+/-	oxidation
[Ref.: #43752]	maltose ChEBI	+	oxidation
[Ref.: #43752]	maltotriose ChEBI	+	oxidation
[Ref.: #43752]	mannitol ChEBI	+	fermentation
[Ref.: #43752]	melibiose ChEBI	-	fermentation
[Ref.: #43752]	methyl (R)-lactate ChEBI	+	oxidation
[Ref.: #43752]	monomethyl succinate ChEBI	+	oxidation
[Ref.: #43752]	myo-inositol ChEBI	+	fermentation
[Ref.: #43752]	nitrate ChEBI	-	reduction
[Ref.: #43752]	propionate ChEBI	+/-	oxidation
[Ref.: #43752]	pyruvate ChEBI	+	oxidation
[Ref.: #43752]	rhamnose ChEBI	-	fermentation
[Ref.: #43752]	sorbitol ChEBI	-	fermentation
[Ref.: #43752]	sorbitol ChEBI	+/-	oxidation
[Ref.: #43752]	starch ChEBI	-	hydrolysis
[Ref.: #43752]	sucrose ChEBI	+	fermentation
[Ref.: #43752]	sucrose ChEBI	+	oxidation
[Ref.: #43752]	thymidine ChEBI	+	oxidation
[Ref.: #43752]	trehalose ChEBI	+	oxidation
[Ref.: #43752]	turanose ChEBI	+	oxidation
[Ref.: #43752]	tween 40 ChEBI	+	oxidation
[Ref.: #43752]	tween 80 ChEBI	+	oxidation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #43752]	acetoin ChEBI	yes
[Ref.: #43752]	hydrogen sulfide ChEBI	no
[Ref.: #43752]	indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #43752]		acetoin ChEBI	+
[Ref.: #43752]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #43752]	acid phosphatase	-	3.1.3.2
[Ref.: #43752]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43752]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #43752]	alpha-galactosidase	-	3.2.1.22
[Ref.: #43752]	alpha-glucosidase	+	3.2.1.20
[Ref.: #43752]	alpha-mannosidase	-	3.2.1.24
[Ref.: #43752]	arginine dihydrolase	+	3.5.3.6
[Ref.: #43752]	beta-D-fucosidase	-	3.2.1.38
[Ref.: #43752]	beta-galactosidase	-	3.2.1.23
[Ref.: #43752]	beta-glucosidase	-	3.2.1.21
[Ref.: #43752]	catalase	+	1.11.1.6
[Ref.: #43752]	cystine arylamidase	+	3.4.11.3
[Ref.: #43752]	cytochrome oxidase	-	1.9.3.1
[Ref.: #43752]	esterase (C 4)	+
[Ref.: #43752]	esterase Lipase (C 8)	+
[Ref.: #43752]	gelatinase	+
[Ref.: #43752]	leucine arylamidase	+	3.4.11.1
[Ref.: #43752]	lipase (C 14)	-
[Ref.: #43752]	lysine decarboxylase	-	4.1.1.18
[Ref.: #43752]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #43752]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #43752]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #43752]	trypsin	-	3.4.21.4
[Ref.: #43752]	tryptophan decarboxylase	+	4.1.1.27
[Ref.: #43752]	urease	-	3.5.1.5
[Ref.: #43752]	valine arylamidase	+
	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.: #43752]	Sample type/isolated from	Marine Sediments collected from the western Pacific
[Ref.: #43752]	Geographic location (country and/or sea, region)	Western Pacific Ocean
[Ref.: #43752]	Country	Pacific Ocean
[Ref.: #43752]	Geographic location	10.7000°/142.3250°

[Ref.: #67770]	Sample type/isolated from	Marine sediment from the western Pacific
* 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 KT728196 (>99% sequence identity) for Sediminivirga luteola subclade from Microbeatlas

Aquatic Samples	481
Soil Samples	570
Animal Samples	3737
Plant Samples	497
Total Samples	5285

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.: #43752]	16S rRNA gene sequence	KT728196		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sediminivirga luteola CGMCC 1.12785	GCA_014639315	contig	GenBank	1774748 tax ID	*
[Ref.: #66792]	Sediminivirga luteola strain CGMCC 1.12785	1774748.3	wgs	PATRIC	1774748 tax ID	*
[Ref.: #66792]	Sediminivirga luteola CGMCC 1.12785	GCA_021729215	contig	GenBank	1774748 tax ID	*

[Ref.: #43752]

GC-content

69 mol%

high performance liquid chromatography (HPLC)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Sediminivirga luteola strain CGMCC 1.12785 PATRIC: 1774748.3
[Ref.: #69481]	spore-forming	no	79	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sediminivirga luteola strain CGMCC 1.12785 PATRIC: 1774748.3
[Ref.: #69480]	motile	no	88.31	no
[Ref.: #69480]	gram-positive	yes	92.416	yes
[Ref.: #69480]	anaerobic	no	99.379	yes
[Ref.: #69480]	aerobic	yes	95.454	no
[Ref.: #69480]	halophile	yes	58.764	no
[Ref.: #69480]	spore-forming	no	92.21	no
[Ref.: #69480]	thermophile	no	98.899	no
[Ref.: #69480]	glucose-util	yes	84.982	no
[Ref.: #69480]	flagellated	no	97.272	yes
[Ref.: #69480]	glucose-ferment	no	91.113	no

Availability in culture collections External links

[Ref.: #43752]

Culture collection no.

JCM 19771, CGMCC 1.12785, MCCC 1A09945

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sediminivirga luteola gen. nov., sp. nov., a member of the family Brevibacteriaceae, isolated from marine sediment.	Zhang G, Wang S, Wang L	Int J Syst Evol Microbiol	10.1099/ijsem.0.000909	2016	*

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 )

#43752

Gaiyun Zhang, Shuang Wang, Lina Wang: Sediminivirga luteola gen. nov., sp. nov., a member of the family Brevibacteriaceae, isolated from marine sediment. IJSEM 66: 1494 - 1498 2016 ( DOI 10.1099/ijsem.0.000909 , PubMed 26791052 )

#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) .

#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 .

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

* These data were automatically processed and therefore are not curated

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Sediminivirga luteola strain CGMCC 1.12785

Sediminivirga luteola strain CGMCC 1.12785

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