Virgibacillus kekensis (DSM 17056, CGMCC 1.6298, JCM 16510)

Name: Virgibacillus kekensis (DSM 17056, CGMCC 1.6298, JCM 16510)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1488

Type strain

Strain Designation YIM-kkny16

Culture col. no. DSM 17056 CGMCC 1.6298 JCM 16510 YIM-kkny16

NCBI tax ID(s) 202261

Special Collections DSMZ JCM Literature strains

History DSMZ <- X.L. Cui; YIM-kkny16 JCM <-- DSM 17056 <-- X. L. Cui YIM kkny16.

Links

Virgibacillus kekensis YIM-kkny16 is an obligate aerobe, moderately halophilic, spore-forming bacterium that forms circular colonies and was isolated from salt lake, mud samples.

colony-forming rod-shaped motile Gram-positive spore-forming moderately halophilic obligate aerobe Bacteria 16S sequence genome sequence

Name and taxonomic classification

SI-ID 343439

CGMCC 1.6298,DSM 17056,JCM 16510

@ref 20215

Last LPSN update 2026-05-29 08:25:16

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Bacillaceae

Genus Virgibacillus

Species Virgibacillus kekensis

Full scientific name Virgibacillus kekensis Chen et al. 2008

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
23058	positive	2.0-3.0 µm	0.3-0.5 µm	rod-shaped

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
23058	2.0-3.0 mm	creamy grey	circular	3 days	MA supplemented with 10 % (w/v) NaCl

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6725	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)	Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
23058	ISP medium 2 agar
23058	MA supplemented with 10 % (w/v) NaCl
23058	Nutrient agar (NA)
23058	trypticase soy agar (BBL)

Culture temp

@ref	Growth	Type	Temperature (°C)
6725	positive	growth	30
23058	positive	growth	10.0-50.0
23058	positive	optimum	37.0
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
23058	positive	optimum	7.0
23058	positive	growth	6.0-10.0	alkaliphile
23058	positive	growth	10.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
23058	obligate aerobe
125439	facultative anaerobe	92.123

Spore formation

@ref	Spore description	Type of spore	Spore formation	Confidence
23058	ellipsoidal,terminal,in swollen sporangia	endospore
125439				98.278

Halophily

@ref	Halophily level	Salt	Growth	Tested relation	Concentration
23058	moderately halophilic	NaCl	positive	growth	0.0-25.0 %(w/v)
23058		NaCl		optimum	10.0 %(w/v)
23058		NaCl	positive	growth	0.0 %(w/v)
23058		NaCl	positive	growth	20.0 %(w/v)

Murein

@ref	Murein short key	Type
23058	A31	A1gamma m-Dpm-direct

Observation

67770

Observationquinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
23058	16808 ChEBI	2-dehydro-D-gluconate	-	builds acid from
23058	17426 ChEBI	5-dehydro-D-gluconate	-	builds acid from
23058	27613 ChEBI	amygdalin	-	builds acid from
23058	18305 ChEBI	arbutin	-	builds acid from
23058		casein	-	hydrolysis
23058	17057 ChEBI	cellobiose	-	builds acid from
23058	62968 ChEBI	cellulose	-	hydrolysis
23058	17029 ChEBI	chitin	-	hydrolysis
23058	17108 ChEBI	D-arabinose	-	builds acid from
23058	18333 ChEBI	D-arabitol	-	builds acid from
23058	15824 ChEBI	D-fructose	-	builds acid from
23058	28847 ChEBI	D-fucose	-	builds acid from
23058	12936 ChEBI	D-galactose	-	builds acid from
23058	17634 ChEBI	D-glucose	+	builds acid from
23058	62318 ChEBI	D-lyxose	-	builds acid from
23058	16899 ChEBI	D-mannitol	+	builds acid from
23058	16024 ChEBI	D-mannose	+	builds acid from
23058	16988 ChEBI	D-ribose	-	builds acid from
23058	17924 ChEBI	D-sorbitol	-	builds acid from
23058	16443 ChEBI	D-tagatose	-	builds acid from
23058	65327 ChEBI	D-xylose	-	builds acid from
23058	17113 ChEBI	erythritol	-	builds acid from
23058	4853 ChEBI	esculin	-	builds acid from
23058	4853 ChEBI	esculin	-	hydrolysis
23058	16813 ChEBI	galactitol	-	builds acid from
23058	5291 ChEBI	gelatin	-	hydrolysis
23058	28066 ChEBI	gentiobiose	-	builds acid from
23058	24265 ChEBI	gluconate	-	builds acid from
23058	17234 ChEBI	glucose	-	fermentation
23058	17754 ChEBI	glycerol	-	builds acid from
23058	28087 ChEBI	glycogen	+	builds acid from
23058	15443 ChEBI	inulin	-	builds acid from
23058	30849 ChEBI	L-arabinose	-	builds acid from
23058	18403 ChEBI	L-arabitol	-	builds acid from
23058	18287 ChEBI	L-fucose	-	builds acid from
23058	62345 ChEBI	L-rhamnose	-	builds acid from
23058	17266 ChEBI	L-sorbose	-	builds acid from
23058	65328 ChEBI	L-xylose	-	builds acid from
23058	17716 ChEBI	lactose	-	builds acid from
23058	17306 ChEBI	maltose	+	builds acid from
23058	6731 ChEBI	melezitose	-	builds acid from
23058	28053 ChEBI	melibiose	-	builds acid from
23058	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from
23058	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from
23058	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from
23058	17268 ChEBI	myo-inositol	-	builds acid from
23058	506227 ChEBI	N-acetylglucosamine	-	builds acid from
23058	17632 ChEBI	nitrate	+	reduction
23058	16634 ChEBI	raffinose	-	builds acid from
23058	15963 ChEBI	ribitol	-	builds acid from
23058	17814 ChEBI	salicin	+	builds acid from
23058	28017 ChEBI	starch	+	builds acid from
23058	28017 ChEBI	starch	+	hydrolysis
23058	17992 ChEBI	sucrose	-	builds acid from
23058	27082 ChEBI	trehalose	-	builds acid from
23058	27082 ChEBI	trehalose	+	builds acid from
23058	27897 ChEBI	tryptophan	-	energy source
23058	32528 ChEBI	turanose	-	builds acid from
23058	53424 ChEBI	tween 20	-	hydrolysis
23058	53426 ChEBI	tween 80	-	hydrolysis
23058	17151 ChEBI	xylitol	-	builds acid from

Antibiotic resistance

@ref	ChEBI	Metabolite	Sensitivity conc.	Resistance conc.
23058	28971	ampicillin	30 µg
23058	17698	chloramphenicol	30 µg
23058	17833	gentamicin		10 µg
23058	6104	kanamycin		30 µg
23058	6472	lincomycin	2 µg
23058	100147	nalidixic acid		20 µg
23058	28368	novobiocin	30 µg
23058	8309	polymyxin b	30 µg
23058	28077	rifampicin	5 µg
23058	17076	streptomycin		10 µg
23058	27902	tetracycline	30 µg

Metabolite production

@ref	Chebi-ID	Metabolite
23058	15688 ChEBI	acetoin
23058	16136 ChEBI	hydrogen sulfide
23058	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test	Indole test
23058	15688 ChEBI	acetoin	-
23058	17234 ChEBI	glucose		-
23058	35581 ChEBI	indole			-

Enzymes

@ref	Value	Activity	Ec
23058	acid phosphatase	+	3.1.3.2
23058	alkaline phosphatase	+	3.1.3.1
23058	alpha-chymotrypsin	+	3.4.21.1
23058	alpha-fucosidase	-	3.2.1.51
23058	alpha-galactosidase	-	3.2.1.22
23058	alpha-glucosidase	+	3.2.1.20
23058	alpha-mannosidase	-	3.2.1.24
23058	beta-galactosidase	-	3.2.1.23
23058	beta-glucosidase	+	3.2.1.21
23058	beta-glucuronidase	+	3.2.1.31
23058	catalase	+	1.11.1.6
23058	cystine arylamidase	-	3.4.11.3
23058	cytochrome oxidase	+	1.9.3.1
23058	esterase (C 4)	+
23058	esterase lipase (C 8)	+
23058	leucine arylamidase	+	3.4.11.1
23058	lipase (C 14)	-
23058	N-acetyl-beta-glucosaminidase	-	3.2.1.52
23058	naphthol-AS-BI-phosphohydrolase	+
23058	trypsin	+	3.4.21.4
23058	tryptophan deaminase	-	4.1.99.1
23058	urease	-	3.5.1.5
23058	valine arylamidase	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Lake (large)
#Environmental	#Terrestrial	#Mud (Sludge)
#Condition	#Saline	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture duration	Enrichment culture temperature
6725	salt lake, mud samples		China	CHN	Asia
23058		Keke salt lake in the Qaidam Basin				Difco marine agar 2216 (MA; pH 7.2)	14 days	28.0
67770	Saline mud from the Keke salt lake in the Qaidam basin	Qinghai Province, north-west China	China	CHN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6725	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM4265412v1 assembly for Virgibacillus kekensis CGMCC 1.6298	scaffold	GCA_042654125	202261	74.11

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6725	Virgibacillus kekensis strain YIM kkny16 16S ribosomal RNA gene, partial sequence	AY121439	1562		202261

GC content

@ref	GC-content (mol%)	Method
6725	41.8
67770	41.8	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM4265412v1 assembly for Virgibacillus kekensis CGMCC 1.6298
NCBI: GCA_042654125

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	92.12	no
125439	gram_stain	BacteriaNetⓘ	variable	73.60	no
125439	motility	BacteriaNetⓘ	yes	87.93	no
125439	spore_formation	BacteriaNetⓘ	yes	98.28	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Melghiribacillus thermohalophilus gen. nov., sp. nov., a novel filamentous, endospore-forming, thermophilic and halophilic bacterium.	Addou NA, Schumann P, Sproer C, Ben Hania W, Hacene H, Fauque G, Cayol JL, Fardeau ML	Int J Syst Evol Microbiol	10.1099/ijs.0.000075	2015
Phylogeny	Virgibacillus kekensis sp. nov., a moderately halophilic bacterium isolated from a salt lake in China.	Chen YG, Cui XL, Fritze D, Chai LH, Schumann P, Wen ML, Wang YX, Xu LH, Jiang CL	Int J Syst Evol Microbiol	10.1099/ijs.0.65365-0	2008

References

#6725	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17056
#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 )
#23058	Yi-Guang Chen,Xiao-Long Cui,Dagmar Fritze,Li-Hong Chai,Peter Schumann,Meng-Liang Wen,Yong-Xia Wang,Li-Hua Xu,Cheng-Lin Jiang: Virgibacillus kekensis sp. nov., a moderately halophilic bacterium isolated from a salt lake in China. IJSEM 58: 647 - 653 2008 ( DOI 10.1099/ijs.0.65365-0 , PubMed 18319472 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Virgibacillus kekensis (DSM 17056, CGMCC 1.6298, JCM 16510)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Murein

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_042654125

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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