Name: Flexivirga endophytica KCTC 39536
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140492

Type strain:

Species: Flexivirga endophytica

Culture col. no.: KCTC 39536, CGMCC 1.15085, YIM 7505, JCM 30628

Strain history: <- Wenjun Li

NCBI tax ID(s): 1849103 (species)

Section

Flexivirga endophytica KCTC 39536 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from leaf sample of Sweet Basil.

coccus-shaped
Gram-positive
aerobe
mesophilic
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	*Dermacoccaceae*
	Genus	*Flexivirga*
	Species	**Flexivirga endophytica**
	Full Scientific Name (LPSN)	Flexivirga endophytica Gao et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43104]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #43104]	Cell length	0.6-0.8 µm

[Ref.: #43104]	Cell width	0.6-0.8 µm

[Ref.: #43104]	Cell shape	coccus-shaped

[Ref.: #43104]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %93.653

[Ref.: #43104]	Colony color	orange-yellow
[Ref.: #43104]	Cultivation medium used	plant agar 8

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43104]

Culture medium

plant agar 8

[Ref.: #43104]

Culture medium growth

[Ref.: #43104]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #43104]	optimum	28-35 °C
[Ref.: #43104]	growth	20-45 °C
[Ref.: #67770]	growth	28 °C
[Ref.: #67771]	growth	28 °C

[Ref.: #43104]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43104]			optimum	7
[Ref.: #43104]			growth	5.0-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43104]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %92
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.925

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43104]		NaCl		growth	0-7	%
[Ref.: #43104]		NaCl		optimum	0-3	%

[Ref.: #67770]

Observation

quinones: MK-8(H₄)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43104]	2-dehydro-D-gluconate ChEBI	-	builds acid from
[Ref.: #43104]	5-dehydro-D-gluconate ChEBI	+	builds acid from
[Ref.: #43104]	adipate ChEBI	+	assimilation
[Ref.: #43104]	amygdalin ChEBI	-	builds acid from
[Ref.: #43104]	arabinitol ChEBI	-	builds acid from
[Ref.: #43104]	arabinose ChEBI	+	builds acid from
[Ref.: #43104]	arbutin ChEBI	-	builds acid from
[Ref.: #43104]	arginine ChEBI	+	carbon source
[Ref.: #43104]	casein	-	hydrolysis
[Ref.: #43104]	cellobiose ChEBI	+	carbon source
[Ref.: #43104]	cellobiose ChEBI	+	builds acid from
[Ref.: #43104]	D-arabinose ChEBI	+	carbon source
[Ref.: #43104]	D-arabitol ChEBI	-	carbon source
[Ref.: #43104]	D-arabitol ChEBI	+	builds acid from
[Ref.: #43104]	D-fructose ChEBI	+	carbon source
[Ref.: #43104]	D-fructose ChEBI	+	builds acid from
[Ref.: #43104]	D-fucose ChEBI	-	carbon source
[Ref.: #43104]	D-galactose ChEBI	-	builds acid from
[Ref.: #43104]	D-glucose ChEBI	+	carbon source
[Ref.: #43104]	D-glucose ChEBI	+	assimilation
[Ref.: #43104]	D-glucose ChEBI	+	builds acid from
[Ref.: #43104]	D-lyxose ChEBI	+	builds acid from
[Ref.: #43104]	D-mannitol ChEBI	+	carbon source
[Ref.: #43104]	D-mannitol ChEBI	+	assimilation
[Ref.: #43104]	D-mannitol ChEBI	+	builds acid from
[Ref.: #43104]	D-mannose ChEBI	+	carbon source
[Ref.: #43104]	D-mannose ChEBI	+	assimilation
[Ref.: #43104]	D-mannose ChEBI	-	builds acid from
[Ref.: #43104]	D-ribose ChEBI	-	carbon source
[Ref.: #43104]	D-ribose ChEBI	-	builds acid from
[Ref.: #43104]	D-tagatose ChEBI	-	builds acid from
[Ref.: #43104]	D-xylose ChEBI	-	carbon source
[Ref.: #43104]	decanoate ChEBI	-	assimilation
[Ref.: #43104]	erythritol ChEBI	-	builds acid from
[Ref.: #43104]	esculin ChEBI	+	hydrolysis
[Ref.: #43104]	esculin ChEBI	+	builds acid from
[Ref.: #43104]	fucose ChEBI	-	builds acid from
[Ref.: #43104]	galactitol ChEBI	-	builds acid from
[Ref.: #43104]	gelatin ChEBI	+	hydrolysis
[Ref.: #43104]	gentiobiose ChEBI	-	builds acid from
[Ref.: #43104]	gluconate ChEBI	-	builds acid from
[Ref.: #43104]	glucose ChEBI	-	fermentation
[Ref.: #43104]	glycerol ChEBI	+	carbon source
[Ref.: #43104]	glycerol ChEBI	+	builds acid from
[Ref.: #43104]	glycogen ChEBI	-	builds acid from
[Ref.: #43104]	inulin ChEBI	-	builds acid from
[Ref.: #43104]	L-arabinose ChEBI	+	assimilation
[Ref.: #43104]	L-glutamate ChEBI	+	carbon source
[Ref.: #43104]	L-rhamnose ChEBI	+	carbon source
[Ref.: #43104]	L-rhamnose ChEBI	+	builds acid from
[Ref.: #43104]	L-serine ChEBI	+	carbon source
[Ref.: #43104]	L-sorbose ChEBI	-	builds acid from
[Ref.: #43104]	lactose ChEBI	-	carbon source
[Ref.: #43104]	lactose ChEBI	-	builds acid from
[Ref.: #43104]	malate ChEBI	+	assimilation
[Ref.: #43104]	maltose ChEBI	+	carbon source
[Ref.: #43104]	maltose ChEBI	+	assimilation
[Ref.: #43104]	maltose ChEBI	-	builds acid from
[Ref.: #43104]	melezitose ChEBI	-	builds acid from
[Ref.: #43104]	melibiose ChEBI	-	builds acid from
[Ref.: #43104]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from
[Ref.: #43104]	methyl alpha-D-mannoside ChEBI	-	builds acid from
[Ref.: #43104]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from
[Ref.: #43104]	myo-inositol ChEBI	-	builds acid from
[Ref.: #43104]	N-acetylglucosamine ChEBI	+	assimilation
[Ref.: #43104]	N-acetylglucosamine ChEBI	+	builds acid from
[Ref.: #43104]	nitrate ChEBI	+	reduction
[Ref.: #43104]	phenylacetate ChEBI	+	assimilation
[Ref.: #43104]	potassium gluconate ChEBI	+	assimilation
[Ref.: #43104]	raffinose ChEBI	-	builds acid from
[Ref.: #43104]	ribitol ChEBI	-	builds acid from
[Ref.: #43104]	salicin ChEBI	-	builds acid from
[Ref.: #43104]	sodium citrate ChEBI	+	assimilation
[Ref.: #43104]	sorbitol ChEBI	-	builds acid from
[Ref.: #43104]	starch ChEBI	-	hydrolysis
[Ref.: #43104]	starch ChEBI	-	builds acid from
[Ref.: #43104]	sucrose ChEBI	+	carbon source
[Ref.: #43104]	sucrose ChEBI	+	builds acid from
[Ref.: #43104]	trehalose ChEBI	+	carbon source
[Ref.: #43104]	trehalose ChEBI	+	builds acid from
[Ref.: #43104]	turanose ChEBI	+	builds acid from
[Ref.: #43104]	tween 20 ChEBI	+	hydrolysis
[Ref.: #43104]	tween 40 ChEBI	+	hydrolysis
[Ref.: #43104]	tween 60 ChEBI	+	hydrolysis
[Ref.: #43104]	tween 80 ChEBI	+	hydrolysis
[Ref.: #43104]	xylitol ChEBI	-	builds acid from
[Ref.: #43104]	xylose ChEBI	-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #43104]	amikacin ChEBI	yes	30	µg (disc)
[Ref.: #43104]	cefuroxime sodium ChEBI	yes	30	µg (disc)
[Ref.: #43104]	chloramphenicol ChEBI	yes	30	µg (disc)
[Ref.: #43104]	ciprofloxacin ChEBI	yes	5	µg (disc)
[Ref.: #43104]	erythromycin ChEBI	yes	15	µg (disc)
[Ref.: #43104]	gentamicin ChEBI	yes	10	µg (disc)
[Ref.: #43104]	norfloxacin ChEBI				yes	10	µg (disc)
[Ref.: #43104]	novobiocin ChEBI				yes	30	µg (disc)
[Ref.: #43104]	optochin ChEBI				yes	5	µg (disc)
[Ref.: #43104]	oxacillin ChEBI				yes	1	µg (disc)
[Ref.: #43104]	penicillin ChEBI				yes	10	Unit (disc)
[Ref.: #43104]	piperacillin ChEBI				yes	100	µg (disc)
[Ref.: #43104]	polymyxin ChEBI	yes	300	Unit (disc)
[Ref.: #43104]	tetracycline ChEBI	yes	30	µg (disc)
[Ref.: #43104]	vancomycin ChEBI	yes	30	µg (disc)
	Only first 10 entries are displayed. Click here to see all.

	Antibiotica	Group ID of combined antibiotics	Metabolite	Antibiotic resistance	Concentration
[Ref.: #43104]		26	sulfamethoxazole ChEBI	yes	23.75	µg (disc)
[Ref.: #43104]		26	trimethoprim ChEBI	yes	1.25	µg (disc)

	Metabolite production	Metabolite	Production
[Ref.: #43104]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #43104]	acid phosphatase	+	3.1.3.2
[Ref.: #43104]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43104]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #43104]	alpha-galactosidase	-	3.2.1.22
[Ref.: #43104]	alpha-glucosidase	+	3.2.1.20
[Ref.: #43104]	alpha-mannosidase	+	3.2.1.24
[Ref.: #43104]	arginine dihydrolase	+	3.5.3.6
[Ref.: #43104]	beta-D-fucosidase	-	3.2.1.38
[Ref.: #43104]	beta-galactosidase	+	3.2.1.23
[Ref.: #43104]	beta-glucosidase	+	3.2.1.21
[Ref.: #43104]	beta-glucuronidase	-	3.2.1.31
[Ref.: #43104]	catalase	+	1.11.1.6
[Ref.: #43104]	cystine arylamidase	+	3.4.11.3
[Ref.: #43104]	cytochrome oxidase	-	1.9.3.1
[Ref.: #43104]	esterase (C 4)	+
[Ref.: #43104]	esterase Lipase (C 8)	+
[Ref.: #43104]	leucine arylamidase	+	3.4.11.1
[Ref.: #43104]	lipase (C 14)	-
[Ref.: #43104]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #43104]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #43104]	trypsin	+	3.4.21.4
[Ref.: #43104]	urease	+	3.5.1.5
[Ref.: #43104]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43104]

Fatty acid	Percentage
C16:0 iso	34
C15:0 iso	8.9
C17:0 anteiso	7.9
C16:0 10-methyl/iso-C17:1ω9c	6.8
C16:1 iso H	6.1
C17:1 anteiso ω9c	5.1

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

[Ref.: #43104]	Sample type/isolated from	leaf sample of Sweet Basil
[Ref.: #43104]	Geographic location (country and/or sea, region)	Impression Tobacco farm, Shilin County, Yunnan Province
[Ref.: #43104]	Country	China
[Ref.: #43104]	Country ISO 3 Code	CHN
[Ref.: #43104]	Continent	Asia
[Ref.: #43104]	Geographic location	24.0000°/103.0000°
[Ref.: #43104]	Enrichment culture	plant agar 8
[Ref.: #43104]	Enrichment culture duration	4 weeks
[Ref.: #43104]	Enrichment culture temperature	30 ̊C

[Ref.: #67771]	Sample type/isolated from	from the leaf of Sweet Basil
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Leaf of Sweet Basil from Impression Tobacco farm in Shilin County
[Ref.: #67770]	Geographic location (country and/or sea, region)	Yunnan Province, south-west China
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Leaf (Phyllosphere)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KX151661 (>99% sequence identity) for Flexivirga endophytica subclade from Microbeatlas

Aquatic Samples	57
Soil Samples	63
Animal Samples	181
Plant Samples	4
Total Samples	305

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.: #43104]	Flexivirga sp. YIM 7505 16S ribosomal RNA gene, partial sequence	KX151661	1516	GenBank	1849103 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Flexivirga endophytica CGMCC 1.15085	GCA_014640635	contig	GenBank	1849103 tax ID	*
[Ref.: #66792]	Flexivirga endophytica KCTC 39536	GCA_014652735	scaffold	GenBank	1849103 tax ID	*
[Ref.: #66792]	Flexivirga endophytica strain CGMCC 1.15085	1849103.3	wgs	PATRIC	1849103 tax ID	*
[Ref.: #66792]	Flexivirga endophytica strain KCTC 39536	1849103.4	wgs	PATRIC	1849103 tax ID	*

[Ref.: #67770]

GC-content

66.7 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: Flexivirga endophytica strain KCTC 39536 PATRIC: 1849103.4
[Ref.: #69481]	spore-forming	no	92	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Flexivirga endophytica KCTC 39536 NCBI: GCA_014652735.1
[Ref.: #69480]	motile	no	95.21	yes
[Ref.: #69480]	flagellated	no	98.446	no
[Ref.: #69480]	gram-positive	yes	88.964	yes
[Ref.: #69480]	anaerobic	no	99.107	yes
[Ref.: #69480]	aerobic	yes	92.349	yes
[Ref.: #69480]	halophile	no	91.726	no
[Ref.: #69480]	spore-forming	no	63.487	no
[Ref.: #69480]	glucose-util	yes	89.186	no
[Ref.: #69480]	thermophile	no	97.772	no
[Ref.: #69480]	glucose-ferment	no	87.557	yes

Availability in culture collections External links

[Ref.: #43104]

Culture collection no.

KCTC 39536, CGMCC 1.15085, YIM 7505, JCM 30628

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Flexivirga aerilata sp. nov., Isolated from an Automobile Air Conditioning System.	Chaudhary DK, Lee H, Dahal RH, Kim DH, Cha IT, Lee KE, Kim DU	Curr Microbiol	10.1007/s00284-020-02300-z	2020	*
Phylogeny	Flexivirga caeni sp. nov., isolated from activated sludge.	Keum DH, Lee YJ, Lee SY, Im WT	Int J Syst Evol Microbiol	10.1099/ijsem.0.003910	2020	*
Phylogeny	Flexivirga oryzae sp. nov., isolated from soil of a rice paddy, and emended description of the genus Flexivirga Anzai et al. 2012.	Hyeon JW, Kim HR, Lee HJ, Jeong SE, Choi SH, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijsem.0.001657	2017	*
Phylogeny	Flexivirga endophytica sp. nov., an endophytic actinobacterium isolated from a leaf of Sweet Basil.	Gao R, Liu BB, Yang W, Song PF, Chen W, Salam N, Duan YQ, Li QQ, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.001211	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 )

#43104

Rui Gao, Bing-Bing Liu, Wei Yang, Peng-Fei Song, Wei Chen, Nimaichand Salam, Yan-Qing Duan, Qing-Qing Li, Wen-Jun Li: Flexivirga endophytica sp. nov., an endophytic actinobacterium isolated from a leaf of Sweet Basil. IJSEM 66: 3388 - 3392 2016 ( DOI 10.1099/ijsem.0.001211 , PubMed 27264701 )

#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;
#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) .

#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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Flexivirga endophytica strain KCTC 39536

Flexivirga endophytica KCTC 39536

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