Bacillus benzoevorans (DSM 5391, ATCC 49005, CCM 3364)

Name: Bacillus benzoevorans (DSM 5391, ATCC 49005, CCM 3364)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1069

Type strain

Strain Designation B1

Culture col. no. DSM 5391 ATCC 49005 CCM 3364 LMD 79.7 NCIB 12555 4 more

NCBI tax ID(s) 1456

Special Collections DSMZ CIP

Links

Bacillus benzoevorans B1 is a facultative anaerobe, spore-forming, mesophilic prokaryote that was isolated from soil.

spore-forming Gram-positive motile rod-shaped facultative anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 1098

LMG 9582,ATCC 49005,CCM 3364,DSM 5391,NCIMB 12555,LMG 20225,CCUG 28522,NRRL B-14535,CIP 103477,NCIB 12555,LMD 79.7,KCTC 3392,CCUG 47198,BCRC 15917,CCRC 15917,KACC 10911,CFBP 4252,NCAIM B.01955,CGMCC 1.3665,VTT E-011770

@ref 20215

Last LPSN update 2025-12-16 09:47:01

Domain Bacillati

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Bacillaceae

Genus Bacillus

Species Bacillus benzoevorans

Full scientific name Bacillus benzoevorans Pichinoty et al. 1987

BacDive ID	Other strains from **Bacillus benzoevorans** (13)	Type strain
1068	B. benzoevorans DSM 3078
1070	B. benzoevorans B4, DSM 5392, LMD 79.10, NCIB 12556, CIP ...
1071	B. benzoevorans B7, DSM 6385, CIP 104567
1072	B. benzoevorans B8, DSM 6410, CIP 103484
134965	B. benzoevorans B4, CIP 103480
135253	B. benzoevorans B2, CIP 103478
135254	B. benzoevorans B6, CIP 103483
135257	B. benzoevorans Pobh 7, CIP 103492
136211	B. benzoevorans B5, CIP 103482
136493	B. benzoevorans B3, CIP 103479
138794	B. benzoevorans CC 4, CIP 103494
151754	B. benzoevorans CCUG 44796 A
152441	B. benzoevorans CCUG 46794

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
116785	positive	rod-shaped

Colony morphology

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
2134	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: Agar 15.0 g/l Peptone 5.0 g/l Yeast extract 4.0 g/l Meat extract 3.0 g/l Na-benzoate 2.0 g/l Distilled water
35555	MEDIUM 3 - Columbia agar		Columbia agar (39.000 g);distilled water (1000.000 ml)
116785	CIP Medium 3	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
2134	positive	growth	30	mesophilic
35555	positive	growth	30	mesophilic
116785	positive	growth	22-37
116785	negative	growth	10
116785	negative	growth	45
116785	negative	growth	55

Culture pH

@ref	Ability	Type	PH
116785		growth	6

Physiology and metabolism

Oxygen tolerance

116785

Oxygen tolerancefacultative anaerobe

Spore formation

@ref	Spore formation
116785
125439

Halophily

@ref	Salt	Growth	Tested relation	Concentration
116785	NaCl	positive	growth	0 %
116785	NaCl		growth	2 %
116785	NaCl		growth	4 %
116785	NaCl		growth	6 %
116785	NaCl		growth	8 %
116785	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	-	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	-	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	-	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	-	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
116785	4853 ChEBI	esculin	-	hydrolysis
68371	4853 ChEBI	esculin	-	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
116785	606565 ChEBI	hippurate	-	hydrolysis
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68371	17306 ChEBI	maltose	-	builds acid from	from API 50CH acid
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
116785	17632 ChEBI	nitrate	+	reduction
116785	17632 ChEBI	nitrate	+	respiration
116785	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Metabolite production

@ref	Chebi-ID	Metabolite	Production
116785	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
116785	15688 ChEBI	acetoin	+
116785	17234 ChEBI	glucose

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
116785	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	-	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
116785	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
116785	beta-galactosidase	-	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
116785	caseinase	-	3.4.21.50
116785	catalase	-	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
116785	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
116785	gamma-glutamyltransferase	-	2.3.2.2
116785	gelatinase	-
68382	leucine arylamidase	-	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
116785	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
116785	ornithine decarboxylase	-	4.1.1.17
116785	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
116785	tween esterase	-
116785	urease	+	3.5.1.5
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
116785	-	-	+	+	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
116785	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
116785	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	+	-	-	-	-	+	-	+	-	+	-	-	+	+	+	+	-	-	-	-	-	+	-	-	-	+	+	-	+	-	-	-	-	-	+	-	-	-	-	-	+	-	+	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
2134	soil	Marseille	France	FRA	Europe
116785	Environment, Soil	Marseille	France	FRA	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
2134	1	Risk group (German classification) According to TRBA 466
116785	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1420753v1 assembly for Bacillus benzoevorans DSM 5391	scaffold	GCA_014207535	1456.3	2861430565	1456	59.24
124043	ASM4243142v1 assembly for Bacillus benzoevorans CCM 3364	contig	GCA_042431425			1456	57.57

Genome browser: GCA_014207535

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Bacillus benzoevorans strain DSM5391 DNA for 16S ribosomal RNA, partial sequence	D78311	1433	1456
20218	B.benzeovorans 16S ribosomal RNA	X60611	1430	1456
124043	Bacillus benzoevorans strain CCM 3364 16S ribosomal RNA gene, partial sequence.	MT760051	1354	1456
124043	Bacillus benzoevorans strain CCM 3364 16S ribosomal RNA gene, partial sequence.	MT757997	1354	1456

GC content

2134

GC-content (mol%)42.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Bacillus benzoevorans DSM 5391
NCBI: GCA_014207535

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	92.40	no
125439	motility	BacteriaNetⓘ	yes	85.70	no
125439	gram_stain	BacteriaNetⓘ	variable	87.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	88.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bacillus benzoevorans DSM 5391
NCBI: GCA_014207535.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	65.86	no
125438	anaerobic	anaerobicⓘ	no	91.35	yes
125438	aerobic	aerobicⓘ	yes	60.60	no
125438	spore-forming	spore-formingⓘ	yes	88.42	no
125438	thermophilic	thermophileⓘ	no	90.55	yes
125438	flagellated	motile2+ⓘ	yes	76.61	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Noncontiguous finished genome sequences and description of Bacillus massiliglaciei, Bacillus mediterraneensis, Bacillus massilinigeriensis, Bacillus phocaeensis and Bacillus tuaregi, five new species identified by culturomics.	Cadoret F, Alou MT, Afouda P, Traore IS, Brechard L, Michelle C, Di Pinto F, Andrieu C, Delerce J, Levasseur A, Fournier PE, Raoult D.	New Microbes New Infect	10.1016/j.nmni.2017.04.005	2017
Genetics	Genomics Analysis of Bacillus megaterium 1259 as a Probiotic and Its Effects on Performance in Lactating Dairy Cows.	Deng B, Wang L, Ma Q, Yu T, Liu D, Dai Y, Zhao G.	Animals (Basel)	10.3390/ani11020397	2021
	Suppressive potential of Paenibacillus strains isolated from the tomato phyllosphere against fusarium crown and root rot of tomato.	Sato I, Yoshida S, Iwamoto Y, Aino M, Hyakumachi M, Shimizu M, Takahashi H, Ando S, Tsushima S.	Microbes Environ	10.1264/jsme2.me13172	2014
Phylogeny	Bacillus oryzisoli sp. nov., isolated from rice rhizosphere.	Zhang XX, Gao JS, Zhang L, Zhang CW, Ma XT, Zhang J	Int J Syst Evol Microbiol	10.1099/ijsem.0.001215	2016
Phylogeny	Bacillus nealsonii sp. nov., isolated from a spacecraft-assembly facility, whose spores are gamma-radiation resistant.	Venkateswaran K, Kempf M, Chen F, Satomi M, Nicholson W, Kern R	Int J Syst Evol Microbiol	10.1099/ijs.0.02311-0	2003
Metabolism	[Biochemical characterization of Bacillus benzoevorans sp. nov., a new filamentous, sheathed mesophilic species, degrading various aromatic acids and phenols].	Pichinoty F, Asselineau J, Mandel M	Ann Microbiol (Paris)		1984

References

#2134	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5391
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#35555	; Curators of the CIP;
#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) .
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#116785	Collection of Institut Pasteur ; Curators of the CIP; CIP 103477
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#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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Bacillus benzoevorans (DSM 5391, ATCC 49005, CCM 3364)

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

Metabolite production

Metabolite tests

Enzymes

API zym

API 50CHac

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014207535

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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