Name: Virgibacillus sediminis DSM 19797
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 1489

Type strain:

Species: Virgibacillus sediminis

Culture col. no.: DSM 19797, CCTCC AA 207023, KCTC 13193, YIM kkny3

Strain history: <- X. L. Cui, YIM; YIM kkny3

NCBI tax ID(s): 202260 (species)

SI-ID 399680

DSM 19797

Section

Virgibacillus sediminis DSM 19797 is an obligate aerobe, moderately halophilic, spore-forming bacterium that forms circular colonies and was isolated from saline sediment.

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

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Bacillaceae*
	Genus	*Virgibacillus*
	Species	**Virgibacillus sediminis**
	Full Scientific Name (LPSN)	Virgibacillus sediminis Chen et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #23059]	Gram stain	positive

[Ref.: #23059]	Cell length	2.5-4.0 µm

[Ref.: #23059]	Cell width	0.4-0.7 µm

[Ref.: #23059]	Cell shape	rod-shaped

[Ref.: #23059]	Motility	yes

[Ref.: #23059]	Flagellum arrangement	peritrichous

[Ref.: #23059]	Colony size	2.0-3.0 mm
[Ref.: #23059]	Colony color	creamy white to pale yellow
[Ref.: #23059]	Colony shape	circular
[Ref.: #23059]	Incubation period	3 days
[Ref.: #23059]	Cultivation medium used	MA supplemented with 5 % (w/v) NaCl

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8325]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #8325]

Culture medium growth

[Ref.: #8325]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8325]

Culture medium composition

expand / minimize

[Ref.: #23059]

Culture medium

MA supplemented with 5 % (w/v) NaCl

[Ref.: #23059]

Culture medium growth

		Temperature
[Ref.: #8325]	growth	30 °C
[Ref.: #23059]	growth	10.0-55.0 °C
[Ref.: #23059]	optimum	35.0-40.0 °C

[Ref.: #8325]

Temperature range

mesophilic

		pH
[Ref.: #23059]	optimum	7.5-8.0
[Ref.: #23059]	growth	6.0-10.5
[Ref.: #23059]	growth	10.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #23059]

Oxygen tolerance

obligate aerobe

[Ref.: #23059]	Spore description	ellipsoidal,subterminal,in swollen sporangia
[Ref.: #23059]	Type of spore	endospore
[Ref.: #23059]	Ability of spore formation	yes

[Ref.: #23059]

Halophily / tolerance level

moderately halophilic

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #23059]		NaCl	no	growth	0.0	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #23059]	2-dehydro-D-gluconate ChEBI	-	builds acid from
[Ref.: #23059]	5-dehydro-D-gluconate ChEBI	-	builds acid from
[Ref.: #23059]	amygdalin ChEBI	-	builds acid from
[Ref.: #23059]	arbutin ChEBI	-	builds acid from
[Ref.: #23059]	casein	-	hydrolysis
[Ref.: #23059]	cellobiose ChEBI	+	builds acid from
[Ref.: #23059]	D-arabinose ChEBI	-	builds acid from
[Ref.: #23059]	D-arabitol ChEBI	-	builds acid from
[Ref.: #23059]	D-fructose ChEBI	+	builds acid from
[Ref.: #23059]	D-fucose ChEBI	-	builds acid from
[Ref.: #23059]	D-galactose ChEBI	-	builds acid from
[Ref.: #23059]	D-glucose ChEBI	+	builds acid from
[Ref.: #23059]	D-lyxose ChEBI	-	builds acid from
[Ref.: #23059]	D-mannitol ChEBI	-	builds acid from
[Ref.: #23059]	D-mannose ChEBI	+	builds acid from
[Ref.: #23059]	D-ribose ChEBI	-	builds acid from
[Ref.: #23059]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #23059]	D-tagatose ChEBI	-	builds acid from
[Ref.: #23059]	D-trehalose ChEBI	-	builds acid from
[Ref.: #23059]	D-xylose ChEBI	-	builds acid from
[Ref.: #23059]	erythritol ChEBI	-	builds acid from
[Ref.: #23059]	esculin ChEBI	-	builds acid from
[Ref.: #23059]	esculin ChEBI	+	hydrolysis
[Ref.: #23059]	galactitol ChEBI	-	builds acid from
[Ref.: #23059]	gelatin ChEBI	+	hydrolysis
[Ref.: #23059]	gentiobiose ChEBI	-	builds acid from
[Ref.: #23059]	gluconate ChEBI	-	builds acid from
[Ref.: #23059]	glucose ChEBI	-	fermentation
[Ref.: #23059]	glucose ChEBI	+	oxidation
[Ref.: #23059]	glycerol ChEBI	-	builds acid from
[Ref.: #23059]	glycogen ChEBI	-	builds acid from
[Ref.: #23059]	inulin ChEBI	-	builds acid from
[Ref.: #23059]	L-arabinose ChEBI	-	builds acid from
[Ref.: #23059]	L-arabitol ChEBI	-	builds acid from
[Ref.: #23059]	L-fucose ChEBI	-	builds acid from
[Ref.: #23059]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #23059]	L-sorbose ChEBI	-	builds acid from
[Ref.: #23059]	L-xylose ChEBI	-	builds acid from
[Ref.: #23059]	lactose ChEBI	-	builds acid from
[Ref.: #23059]	maltose ChEBI	-	builds acid from
[Ref.: #23059]	melezitose ChEBI	-	builds acid from
[Ref.: #23059]	melibiose ChEBI	-	builds acid from
[Ref.: #23059]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from
[Ref.: #23059]	methyl alpha-D-mannoside ChEBI	-	builds acid from
[Ref.: #23059]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from
[Ref.: #23059]	myo-inositol ChEBI	-	builds acid from
[Ref.: #23059]	N-acetylglucosamine ChEBI	-	builds acid from
[Ref.: #23059]	nitrate ChEBI	+	reduction
[Ref.: #23059]	nitrite ChEBI	-	reduction
[Ref.: #23059]	raffinose ChEBI	-	builds acid from
[Ref.: #23059]	ribitol ChEBI	-	builds acid from
[Ref.: #23059]	salicin ChEBI	-	builds acid from
[Ref.: #23059]	starch ChEBI	-	builds acid from
[Ref.: #23059]	starch ChEBI	-	hydrolysis
[Ref.: #23059]	sucrose ChEBI	-	builds acid from
[Ref.: #23059]	turanose ChEBI	+	builds acid from
[Ref.: #23059]	tween 20 ChEBI	-	hydrolysis
[Ref.: #23059]	tween 40 ChEBI	-	hydrolysis
[Ref.: #23059]	tween 60 ChEBI	-	hydrolysis
[Ref.: #23059]	tween 80 ChEBI	-	hydrolysis
[Ref.: #23059]	urea ChEBI	-	hydrolysis
[Ref.: #23059]	xylitol ChEBI	-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #23059]	ampicillin ChEBI				yes	30	µg
[Ref.: #23059]	chloramphenicol ChEBI	yes	30	µg
[Ref.: #23059]	gentamicin ChEBI				yes	10	µg
[Ref.: #23059]	kanamycin ChEBI	yes	30	µg
[Ref.: #23059]	lincomycin ChEBI	yes	2	µg
[Ref.: #23059]	nalidixic acid ChEBI				yes	20	µg
[Ref.: #23059]	novobiocin ChEBI	yes	30	µg
[Ref.: #23059]	polymyxin b ChEBI	yes	30	µg
[Ref.: #23059]	rifampicin ChEBI	yes	5	µg
[Ref.: #23059]	streptomycin ChEBI	yes	10	µg
[Ref.: #23059]	tetracycline ChEBI	yes	30	µg
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #23059]	acetoin ChEBI	no
[Ref.: #23059]	hydrogen sulfide ChEBI	no
[Ref.: #23059]	indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #23059]		acetoin ChEBI	-
[Ref.: #23059]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #23059]	acid phosphatase	+	3.1.3.2
[Ref.: #23059]	alkaline phosphatase	-	3.1.3.1
[Ref.: #23059]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #23059]	alpha-fucosidase	-	3.2.1.51
[Ref.: #23059]	alpha-galactosidase	-	3.2.1.22
[Ref.: #23059]	alpha-glucosidase	+	3.2.1.20
[Ref.: #23059]	alpha-mannosidase	-	3.2.1.24
[Ref.: #23059]	arginine dihydrolase	-	3.5.3.6
[Ref.: #23059]	beta-galactosidase	-	3.2.1.23
[Ref.: #23059]	beta-glucosidase	-	3.2.1.21
[Ref.: #23059]	beta-glucuronidase	+	3.2.1.31
[Ref.: #23059]	catalase	+	1.11.1.6
[Ref.: #23059]	cystine arylamidase	-	3.4.11.3
[Ref.: #23059]	cytochrome oxidase	+	1.9.3.1
[Ref.: #23059]	esterase (C 4)	+
[Ref.: #23059]	esterase lipase (C 8)	-
[Ref.: #23059]	gelatinase	+
[Ref.: #23059]	leucine arylamidase	+	3.4.11.1
[Ref.: #23059]	lipase (C 14)	-
[Ref.: #23059]	lysine decarboxylase	-	4.1.1.18
[Ref.: #23059]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #23059]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #23059]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #23059]	trypsin	-	3.4.21.4
[Ref.: #23059]	tryptophan deaminase	-	4.1.99.1
[Ref.: #23059]	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.: #8325]	Sample type/isolated from	saline sediment
[Ref.: #8325]	Geographic location (country and/or sea, region)	Qinghai Province, Qaidam Basin, Keke salt lake
[Ref.: #8325]	Country	China
[Ref.: #8325]	Country ISO 3 Code	CHN
[Ref.: #8325]	Continent	Asia

[Ref.: #23059]	Enrichment culture	Difco marine agar 2216 (MA) supplemented with 5 % (w/v) NaCl
[Ref.: #23059]	Enrichment culture composition	containing approximately 7 % NaCl and 8.4 % total salts (hereafter referred to as MA5)
[Ref.: #23059]	Enrichment culture duration	14 days
[Ref.: #23059]	Enrichment culture temperature	37.0 ̊C
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Sediment
#Condition	#Saline	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY121430 (>99% sequence identity) for Virgibacillus sediminis subclade from Microbeatlas

Aquatic Samples	1
Soil Samples	3
Animal Samples	3
Plant Samples	1
Total Samples	8

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #8325]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #8325]	Virgibacillus sediminis strain YIM kkny3 16S ribosomal RNA gene, partial sequence	AY121430	1562	ENA	202260 tax ID

[Ref.: #8325]

GC-content

40.9 mol%

high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #8325]

Culture collection no.

DSM 19797, CCTCC AA 207023, KCTC 13193, YIM kkny3

[Ref.: #71135]

SI-ID 399680

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Virgibacillus sediminis sp. nov., a moderately halophilic bacterium isolated from a salt lake in China.	Chen YG, Cui XL, Wang YX, Zhang YQ, Tang SK, Li WJ, Liu ZX, Wen ML, Peng Q	Int J Syst Evol Microbiol	10.1099/ijs.0.003624-0	2009	*

References

#8325

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19797

#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 )

#23059

Yi-Guang Chen,Xiao-Long Cui,Yong-Xia Wang,Yu-Qin Zhang,Shu-Kun Tang,Wen-Jun Li,Zhu-Xiang Liu,Meng-Liang Wen,Qian Peng: Virgibacillus sediminis sp. nov., a moderately halophilic bacterium isolated from a salt lake in China. IJSEM 59: 2058 - 2063 2009 ( DOI 10.1099/ijs.0.003624-0 , PubMed 19605714 )

#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 .

#71135

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID399680.1 )

* 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 Virgibacillus sediminis in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF