Virgibacillus sediminis (DSM 19797, CCTCC AA 207023, KCTC 13193)

Name: Virgibacillus sediminis (DSM 19797, CCTCC AA 207023, KCTC 13193)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1489

Type strain

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

NCBI tax ID(s) 202260

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

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

Name and taxonomic classification

SI-ID 399680

DSM 19797

@ref 20215

Last LPSN update 2025-12-16 09:47:07

Domain Bacillati

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Bacillaceae

Genus Virgibacillus

Species Virgibacillus sediminis

Full scientific name Virgibacillus sediminis Chen et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Flagellum arrangement
23059	positive	2.5-4.0 µm	0.4-0.7 µm	rod-shaped		peritrichous

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
23059	2.0-3.0 mm	creamy white to pale yellow	circular	3 days	MA supplemented with 5 % (w/v) NaCl

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
8325	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514; with strain-specific modifications) Composition: NaCl 50.0 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
23059	MA supplemented with 5 % (w/v) NaCl

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
8325	positive	growth	30	mesophilic
23059	positive	growth	10.0-55.0
23059	positive	optimum	35.0-40.0

Culture pH

@ref	Ability	Type	PH	PH range
23059	positive	optimum	7.5-8.0
23059	positive	growth	6.0-10.5	alkaliphile
23059	positive	growth	10.0

Physiology and metabolism

Oxygen tolerance

23059

Oxygen toleranceobligate aerobe

Spore formation

@ref	Spore description	Type of spore	Spore formation
23059	ellipsoidal,subterminal,in swollen sporangia	endospore

Halophily

@ref	Halophily level	Salt	Growth	Tested relation	Concentration
23059	moderately halophilic	NaCl		growth	0.0 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
23059	16808 ChEBI	2-dehydro-D-gluconate	-	builds acid from
23059	17426 ChEBI	5-dehydro-D-gluconate	-	builds acid from
23059	27613 ChEBI	amygdalin	-	builds acid from
23059	18305 ChEBI	arbutin	-	builds acid from
23059		casein	-	hydrolysis
23059	17057 ChEBI	cellobiose	+	builds acid from
23059	17108 ChEBI	D-arabinose	-	builds acid from
23059	18333 ChEBI	D-arabitol	-	builds acid from
23059	15824 ChEBI	D-fructose	+	builds acid from
23059	28847 ChEBI	D-fucose	-	builds acid from
23059	12936 ChEBI	D-galactose	-	builds acid from
23059	17634 ChEBI	D-glucose	+	builds acid from
23059	62318 ChEBI	D-lyxose	-	builds acid from
23059	16899 ChEBI	D-mannitol	-	builds acid from
23059	16024 ChEBI	D-mannose	+	builds acid from
23059	16988 ChEBI	D-ribose	-	builds acid from
23059	17924 ChEBI	D-sorbitol	-	builds acid from
23059	16443 ChEBI	D-tagatose	-	builds acid from
23059	16551 ChEBI	D-trehalose	-	builds acid from
23059	65327 ChEBI	D-xylose	-	builds acid from
23059	17113 ChEBI	erythritol	-	builds acid from
23059	4853 ChEBI	esculin	-	builds acid from
23059	4853 ChEBI	esculin	+	hydrolysis
23059	16813 ChEBI	galactitol	-	builds acid from
23059	5291 ChEBI	gelatin	+	hydrolysis
23059	28066 ChEBI	gentiobiose	-	builds acid from
23059	24265 ChEBI	gluconate	-	builds acid from
23059	17234 ChEBI	glucose	-	fermentation
23059	17234 ChEBI	glucose	+	oxidation
23059	17754 ChEBI	glycerol	-	builds acid from
23059	28087 ChEBI	glycogen	-	builds acid from
23059	15443 ChEBI	inulin	-	builds acid from
23059	30849 ChEBI	L-arabinose	-	builds acid from
23059	18403 ChEBI	L-arabitol	-	builds acid from
23059	18287 ChEBI	L-fucose	-	builds acid from
23059	62345 ChEBI	L-rhamnose	-	builds acid from
23059	17266 ChEBI	L-sorbose	-	builds acid from
23059	65328 ChEBI	L-xylose	-	builds acid from
23059	17716 ChEBI	lactose	-	builds acid from
23059	17306 ChEBI	maltose	-	builds acid from
23059	6731 ChEBI	melezitose	-	builds acid from
23059	28053 ChEBI	melibiose	-	builds acid from
23059	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from
23059	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from
23059	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from
23059	17268 ChEBI	myo-inositol	-	builds acid from
23059	506227 ChEBI	N-acetylglucosamine	-	builds acid from
23059	17632 ChEBI	nitrate	+	reduction
23059	16301 ChEBI	nitrite	-	reduction
23059	16634 ChEBI	raffinose	-	builds acid from
23059	15963 ChEBI	ribitol	-	builds acid from
23059	17814 ChEBI	salicin	-	builds acid from
23059	28017 ChEBI	starch	-	builds acid from
23059	28017 ChEBI	starch	-	hydrolysis
23059	17992 ChEBI	sucrose	-	builds acid from
23059	32528 ChEBI	turanose	+	builds acid from
23059	53424 ChEBI	tween 20	-	hydrolysis
23059	53423 ChEBI	tween 40	-	hydrolysis
23059	53425 ChEBI	tween 60	-	hydrolysis
23059	53426 ChEBI	tween 80	-	hydrolysis
23059	16199 ChEBI	urea	-	hydrolysis
23059	17151 ChEBI	xylitol	-	builds acid from

Antibiotic resistance

@ref	ChEBI	Metabolite	Resistance conc.	Sensitivity conc.
23059	28971	ampicillin	30 µg
23059	17698	chloramphenicol		30 µg
23059	17833	gentamicin	10 µg
23059	6104	kanamycin		30 µg
23059	6472	lincomycin		2 µg
23059	100147	nalidixic acid	20 µg
23059	28368	novobiocin		30 µg
23059	8309	polymyxin b		30 µg
23059	28077	rifampicin		5 µg
23059	17076	streptomycin		10 µg
23059	27902	tetracycline		30 µg

Metabolite production

@ref	Chebi-ID	Metabolite
23059	15688 ChEBI	acetoin
23059	16136 ChEBI	hydrogen sulfide
23059	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
23059	15688 ChEBI	acetoin	-
23059	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
23059	acid phosphatase	+	3.1.3.2
23059	alkaline phosphatase	-	3.1.3.1
23059	alpha-chymotrypsin	-	3.4.21.1
23059	alpha-fucosidase	-	3.2.1.51
23059	alpha-galactosidase	-	3.2.1.22
23059	alpha-glucosidase	+	3.2.1.20
23059	alpha-mannosidase	-	3.2.1.24
23059	arginine dihydrolase	-	3.5.3.6
23059	beta-galactosidase	-	3.2.1.23
23059	beta-glucosidase	-	3.2.1.21
23059	beta-glucuronidase	+	3.2.1.31
23059	catalase	+	1.11.1.6
23059	cystine arylamidase	-	3.4.11.3
23059	cytochrome oxidase	+	1.9.3.1
23059	esterase (C 4)	+
23059	esterase lipase (C 8)	-
23059	gelatinase	+
23059	leucine arylamidase	+	3.4.11.1
23059	lipase (C 14)	-
23059	lysine decarboxylase	-	4.1.1.18
23059	N-acetyl-beta-glucosaminidase	-	3.2.1.52
23059	naphthol-AS-BI-phosphohydrolase	+
23059	ornithine decarboxylase	-	4.1.1.17
23059	trypsin	-	3.4.21.4
23059	tryptophan deaminase	-	4.1.99.1
23059	valine arylamidase	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Sediment
#Condition	#Saline	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture composition	Enrichment culture duration	Enrichment culture temperature
8325	saline sediment	Qinghai Province, Qaidam Basin, Keke salt lake	China	CHN	Asia
23059						Difco marine agar 2216 (MA) supplemented with 5 % (w/v) NaCl	containing approximately 7 % NaCl and 8.4 % total salts (hereafter referred to as MA5)	14 days	37.0

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8325	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM4264326v1 assembly for Virgibacillus sediminis KCTC 13193	contig	GCA_042643265	202260	71.3

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
8325	Virgibacillus sediminis strain YIM kkny3 16S ribosomal RNA gene, partial sequence	AY121430	1562		202260

GC content

@ref	GC-content (mol%)	Method
8325	40.9	high performance liquid chromatography (HPLC)

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
	Analysis of the association between microbiota and flavor formation during Zizhong Dongjian fermentation process.	Li Z, Wang M, Yang Z.	Food Sci Nutr	10.1002/fsn3.4460	2024
Pathogenicity	Two-stage phyto-microremediation of tannery effluent by Spirodela polyrrhiza (L.) Schleid. and chromium resistant bacteria.	Singh A, Vyas D, Malaviya P.	Bioresour Technol	10.1016/j.biortech.2016.06.025	2016
Enzymology	Isolation and diversity of sediment bacteria in the hypersaline aiding lake, China.	Guan TW, Lin YJ, Ou MY, Chen KB.	PLoS One	10.1371/journal.pone.0236006	2020
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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 sediminis (DSM 19797, CCTCC AA 207023, KCTC 13193)

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

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_042643265

16S sequences

GC content

Genome-based predictions

Literature

Literature

References

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