Helcobacillus massiliensis (DSM 23040, CCUG 53859, CIP 109418)

Name: Helcobacillus massiliensis (DSM 23040, CCUG 53859, CIP 109418)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 3920

Type strain

Strain Designation 6401990

Culture col. no. DSM 23040 CCUG 53859 CIP 109418 CSUR P17 6401990 1 more

NCBI tax ID(s) 521392

Special Collections DSMZ CCUG JCM CIP Wink compendium Literature strains

History CIP <- 2006, V. Roux, Timone Hosp., Marseille, France: strain 6401990 DSMZ <- CCUG JCM <-- CIP 109418 <-- V. Roux; La Timone Hosp., France; 6401990. CIP <- 2006, V. Roux, Timone Hosp., Marseille, France: strain 6401990

Links

Helcobacillus massiliensis 6401990 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from human cutaneous discharge sample.

Gram-positive rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 364148

DSM 23040,JCM 30721,CCUG 53859,CIP 109418

@ref 20215

Last LPSN update 2026-05-29 08:25:49

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Dermabacteraceae

Genus Helcobacillus

Species Helcobacillus massiliensis

Full scientific name Helcobacillus massiliensis Renvoise et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
28991	positive	1.1 µm	0.85 µm	rod-shaped
120851	positive			rod-shaped
125438					95
125438	positive				92.873
125439					92.365
125439	positive				97.618

Colony morphology

@ref	Colony color	Incubation period	Medium used	Hemolysis ability
19802	Beige	10-14 days	ISP 2
19802	Ivory	10-14 days	ISP 3
19802	Light ivory	10-14 days	ISP 4
19802	Light ivory	10-14 days	ISP 5
19802	Ivory	10-14 days	ISP 6
19802	Oyster white	10-14 days	ISP 7
60039		1 day
120851				1

Multicellular morphology

@ref	Forms multicellular complex	Medium name
19802		ISP 2
19802		ISP 3
19802		ISP 4
19802		ISP 5
19802		ISP 6
19802		ISP 7

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
16666	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)	Medium recipe at MediaDive	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
19802	ISP 2		Name: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19802	ISP 3		Name: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19802	ISP 4		Name: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19802	ISP 5		Name: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19802	ISP 6		Name: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19802	ISP 7		Name: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
37556	MEDIUM 45 - for Columbia agar with sheep blood		Distilled water make up to (1000.000 ml);Columbia agar (39.000 g);Sheepblood (100.000 ml)
120851	CIP Medium 45	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
16666	positive	growth	28
19802	positive	optimum	28
28991	positive	growth	25-44
28991	positive	optimum	37
37556	positive	growth	37
60039	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
28991	aerobe
60039	aerobe
120851	obligate aerobe
125439	obligate aerobe	91.695

Spore formation

28991

Spore formationno

Observation

67770

Observationquinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
28991	16449 ChEBI	alanine	+	carbon source
19802	22599 ChEBI	arabinose	+
28991	22599 ChEBI	arabinose	+	carbon source
28991	22653 ChEBI	asparagine	+	carbon source
19802	62968 ChEBI	cellulose	-
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
68379	4853 ChEBI	esculin	+	hydrolysis	from API Coryne
19802	28757 ChEBI	fructose	+/-
28991	28757 ChEBI	fructose	+	carbon source
28991	28260 ChEBI	galactose	+	carbon source
68379	5291 ChEBI	gelatin	+	hydrolysis	from API Coryne
19802	17234 ChEBI	glucose	+
28991	17234 ChEBI	glucose	+	carbon source
28991	29987 ChEBI	glutamate	+	carbon source
28991	17754 ChEBI	glycerol	+	carbon source
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
28991	24996 ChEBI	lactate	+	carbon source
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
19802	29864 ChEBI	mannitol	-
28991	29864 ChEBI	mannitol	+	carbon source
28991	37684 ChEBI	mannose	+	carbon source
28991	51850 ChEBI	methyl pyruvate	+	carbon source
19802	17268 ChEBI	myo-inositol	+/-
28991	506227 ChEBI	N-acetylglucosamine	+	carbon source
28991	17632 ChEBI	nitrate	+	reduction
120851	17632 ChEBI	nitrate	+	reduction
120851	16301 ChEBI	nitrite	-	reduction
19802	16634 ChEBI	raffinose	-
19802	26546 ChEBI	rhamnose	-
28991	33942 ChEBI	ribose	+	carbon source
28991	17822 ChEBI	serine	+	carbon source
28991	30911 ChEBI	sorbitol	+	carbon source
19802	17992 ChEBI	sucrose	+
28991	17992 ChEBI	sucrose	+	carbon source
68379	17992 ChEBI	sucrose	+	fermentation	from API Coryne
28991	27082 ChEBI	trehalose	+	carbon source
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne
19802	18222 ChEBI	xylose	-
28991	18222 ChEBI	xylose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
120851	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
28991	alkaline phosphatase	+	3.1.3.1
68382	alkaline phosphatase	-	3.1.3.1	from API zym
68379	alkaline phosphatase	-	3.1.3.1	from API Coryne
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
68379	alpha-glucosidase	+	3.2.1.20	from API Coryne
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68379	beta-galactosidase	+	3.2.1.23	from API Coryne
68379	beta-glucosidase	+	3.2.1.21	from API Coryne
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
28991	catalase	+	1.11.1.6
120851	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	-		from API zym
68379	gelatinase	+		from API Coryne
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68379	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API Coryne
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
120851	oxidase	-
28991	pyrazinamidase	+	3.5.1.B15
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	-	3.4.19.3	from API Coryne
68382	trypsin	+	3.4.21.4	from API zym
28991	urease	+	3.5.1.5
120851	urease	-	3.5.1.5
68379	urease	-	3.5.1.5	from API Coryne
68382	valine arylamidase	-		from API zym

API coryne

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
19802	+/-	-	-	-	-	+	+	-	+	-	+	not determinedn.d.	+/-	-	-	-	+/-	-	+	-	not determinedn.d.

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
19802	not determinedn.d.	-	-	-	-	+	-	+	+	+	+	+	-	-	-	+	+	-	-	-
120851	-	-	-	-	-	+	-	+	+	-	+	+	-	+	-	+	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	-
#Host Body-Site	#Organ	#Skin, Nail, Hair
#Host Body Product	#Fluids	-

Isolation

@ref	Sample type	Host species	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
16666	human cutaneous discharge sample	Homo sapiens		Hospital de la Timone	France	FRA	Europe
60039	Human gall bladder,58-yr-old man	Homo sapiens	2006-09-01	Marseille,Timone hospital	France	FRA	Europe
67770	Human cutaneous discharge	Homo sapiens
120851	Human, Liver	Homo sapiens		Marseille	France	FRA	Europe	2006

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Biosafety level	Biosafety level comment
16666	yes, in single cases	1	Risk group (German classification) According to TRBA 466
120851		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	ASM1419142v1 assembly for Helcobacillus massiliensis DSM 23040	contig	GCA_014191425	521392.5	2824228552	521392	66.26

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16666	Helcobacillus massiliensis strain 6401990 16S ribosomal RNA gene, partial sequence	EU477050	1448		1204722

GC content

@ref	GC-content (mol%)	Method
16666	68.6
67770	68.6	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1419142v1 assembly for Helcobacillus massiliensis DSM 23040
BV-BRC: 521392.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	91.70	no
125439	gram_stain	BacteriaNetⓘ	positive	97.62	no
125439	motility	BacteriaNetⓘ	no	92.37	no
125439	spore_formation	BacteriaNetⓘ	no	73.57	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Helcobacillus massiliensis strain DSM 23040
PATRIC: 521392.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	92.87	yes
125438	anaerobic	anaerobicⓘ	no	94.31	no
125438	spore-forming	spore-formingⓘ	no	81.96	yes
125438	aerobic	aerobicⓘ	yes	72.54	yes
125438	thermophilic	thermophileⓘ	no	93.17	yes
125438	flagellated	motile2+ⓘ	no	95.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Dermabacter vaginalis sp. nov., isolated from human vaginal fluid.	Chang DH, Rhee MS, Kim BC	Int J Syst Evol Microbiol	10.1099/ijsem.0.000960	2016
Phylogeny	Helcobacillus massiliensis gen. nov., sp. nov., a novel representative of the family Dermabacteraceae isolated from a patient with a cutaneous discharge.	Renvoise A, Aldrovandi N, Raoult D, Roux V	Int J Syst Evol Microbiol	10.1099/ijs.0.003319-0	2009

References

#16666	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23040
#19802	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#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 )
#25424	IJSEM 2346 2004 ( DOI 10.1099/ijs.0.003319-0 , PubMed 19620359 )
#28991	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #25424
#37556	; Curators of the CIP;
#60039	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 53859
#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;
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#120851	Collection of Institut Pasteur ; Curators of the CIP; CIP 109418
#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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Helcobacillus massiliensis (DSM 23040, CCUG 53859, CIP 109418)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Metabolite production

Enzymes

API coryne

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014191425

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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