Bacillus carboniphilus (DSM 17613, ATCC 700100, CIP 109750)

Name: Bacillus carboniphilus (DSM 17613, ATCC 700100, CIP 109750)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1239

Type strain

Culture col. no. DSM 17613 ATCC 700100 CIP 109750 JCM 9731 kASUMI 6t 5 more

NCBI tax ID(s) 86663

Special Collections DSMZ JCM KCTC CIP Literature strains

History DSMZ <- JCM <- T. Fujita <- M. Matsuhashi, Kasumi-6 KCTC <- JCM <- T. Fujita <- M. Matsuhashi strain Kasumi-6 JCM <-- T. Fujita <-- M. Matsuhashi strain Kasumi-6. CIP <- 2007, DSMZ <- JCM <- T. Fujita <- M. Matsuhashi, Tokai Univ., Shizuoka, Japan: strain Kasumi 6

Links

Bacillus carboniphilus DSM 17613 is an obligate aerobe, spore-forming, Gram-positive bacterium that forms circular colonies and has a brown red pigmentation.

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

Name and taxonomic classification

SI-ID 10705

LMG 18001,ATCC 700100,JCM 9731,NCIMB 13460,KCTC 3837,KACC 10916,DSM 17613,CGMCC 1.3652,CIP 109750

@ref 20215

Last LPSN update 2026-05-29 08:25:12

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Bacillaceae

Genus Bacillus

Species Bacillus carboniphilus

Full scientific name Bacillus carboniphilus Fujita et al. 1996

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement
23316	positive	3.0-5.0 µm	0.5-0.9 µm	rod-shaped	peritrichous
67771				rod-shaped	peritrichous
67771	positive
117178	positive			rod-shaped

Colony morphology

@ref	Colony color	Colony shape	Medium used
23316	grayish yellow	circular	Nutrient agar

Pigmentation

@ref	Production	Color
23316		brown red

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7086	CASO AGAR (MERCK 105458) (DSMZ Medium 220)	Medium recipe at MediaDive	Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
23316	Nutrient agar (NA)
36103	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
117178	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
7086	positive	growth	30
23316	positive	maximum	47
23316	positive	minimum	17
36103	positive	growth	30
67770	positive	growth	30
67771	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
23316	obligate aerobe
67771	aerobe
117178	obligate aerobe
125439	facultative anaerobe	92.637

Spore formation

@ref	Spore description	Type of spore	Spore formation
23316	ellipsoidal, central or terminal, unswollen sporangia	endospore

Halophily

@ref	Salt	Growth	Tested relation	Concentration
23316	NaCl	positive	growth	7 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
23316	30916 ChEBI	2-oxoglutarate	-	carbon source
23316	30089 ChEBI	acetate	-	carbon source
23316	58187 ChEBI	alginate	-	carbon source
23316	29016 ChEBI	arginine	-	degradation
23316		casein	+	hydrolysis
23316	17057 ChEBI	cellobiose	-	builds acid from
23316	16947 ChEBI	citrate	-	carbon source
23316	15824 ChEBI	D-fructose	-	builds acid from
23316	12936 ChEBI	D-galactose	-	builds acid from
23316	8391 ChEBI	D-gluconate	-	carbon source
23316	17634 ChEBI	D-glucose	-	builds acid from
23316	17634 ChEBI	D-glucose	-	builds gas from
23316	16899 ChEBI	D-mannitol	-	builds acid from
23316	16899 ChEBI	D-mannitol	-	builds gas from
23316	16024 ChEBI	D-mannose	-	builds acid from
23316	16988 ChEBI	D-ribose	-	builds acid from
23316	17317 ChEBI	D-sorbose	-	builds acid from
23316	65327 ChEBI	D-xylose	-	builds acid from
23316	65327 ChEBI	D-xylose	-	builds gas from
23316	17113 ChEBI	erythritol	-	builds acid from
23316	4853 ChEBI	esculin	-	hydrolysis
23316	29806 ChEBI	fumarate	-	carbon source
23316	5291 ChEBI	gelatin	+	hydrolysis
23316	17754 ChEBI	glycerol	-	builds acid from
23316	606565 ChEBI	hippurate	+	hydrolysis
23316	30849 ChEBI	L-arabinose	-	builds acid from
23316	30849 ChEBI	L-arabinose	-	builds gas from
23316	29991 ChEBI	L-aspartate	-	carbon source
23316	29985 ChEBI	L-glutamate	-	carbon source
23316	15589 ChEBI	L-malate	-	carbon source
23316	62345 ChEBI	L-rhamnose	-	builds acid from
23316	24996 ChEBI	lactate	-	carbon source
23316	17716 ChEBI	lactose	-	builds acid from
23316	25094 ChEBI	lysine	-	degradation
23316	15792 ChEBI	malonate	-	carbon source
23316	17306 ChEBI	maltose	-	builds acid from
23316	28053 ChEBI	melibiose	-	builds acid from
23316	17268 ChEBI	myo-inositol	-	builds acid from
23316	17632 ChEBI	nitrate	-	reduction
117178	17632 ChEBI	nitrate	+	reduction
117178	16301 ChEBI	nitrite	-	reduction
23316	18257 ChEBI	ornithine	-	degradation
23316	17272 ChEBI	propionate	-	carbon source
23316	15361 ChEBI	pyruvate	-	carbon source
23316	16634 ChEBI	raffinose	-	builds acid from
23316	15963 ChEBI	ribitol	-	builds acid from
23316	17814 ChEBI	salicin	-	builds acid from
23316	28017 ChEBI	starch	-	builds acid from
23316	28017 ChEBI	starch	+	hydrolysis
23316	30031 ChEBI	succinate	-	carbon source
23316	17992 ChEBI	sucrose	-	builds acid from
23316	132950 ChEBI	tartrate	-	carbon source
23316	27082 ChEBI	trehalose	-	builds acid from
23316	53426 ChEBI	tween 80	+	hydrolysis
23316	16199 ChEBI	urea	-	hydrolysis

Metabolite production

@ref	Chebi-ID	Metabolite	Production
23316	15688 ChEBI	acetoin
117178	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
23316	15688 ChEBI	acetoin	-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
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
23316	beta-galactosidase	-	3.2.1.23
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
23316	catalase	+	1.11.1.6
117178	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
23316	cytochrome oxidase	+	1.9.3.1
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
117178	oxidase	-
68382	trypsin	+	3.4.21.4	from API zym
117178	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
117178	-	+	+	+	-	+	+	+	+	+	+	+	-	-	-	+	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Environmental	#Air

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7086	Air	Tokai University, Numazu	Japan	JPN	Asia
67770	Air	Tokai University, Numazu, Shizuoka Pref.	Japan	JPN	Asia
67771	From air	Tokai University, Numazu, Shizuoka Pref.	Japan	JPN	Asia
117178	Environment, Air		Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB021182 (>99% sequence identity) for Bacillus carboniphilus from Microbeatlas

Aquatic Samples	9
Soil Samples	23
Animal Samples	13
Plant Samples	2
Total Samples	47

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7086	1	Risk group (German classification) According to TRBA 466
117178	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM3952236v1 assembly for Bacillus carboniphilus JCM 9731	contig	GCA_039522365	86663	64.52

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7086	Bacillus carboniphilus gene for 16S ribosomal RNA	AB021182	1504		86663

GC content

@ref	GC-content (mol%)	Method
7086	37.9
23316	37.9	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: ASM3952236v1 assembly for Bacillus carboniphilus JCM 9731
NCBI: GCA_039522365

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	92.64	no
125439	gram_stain	BacteriaNetⓘ	variable	68.18	no
125439	motility	BacteriaNetⓘ	yes	78.35	no
125439	spore_formation	BacteriaNetⓘ	yes	77.67	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Physical communication pathways in bacteria: an extra layer to quorum sensing.	de la Viuda V, Buceta J, Grobas I.	Biophys Rev	10.1007/s12551-025-01290-1	2025
	Calcium (II) - and dipicolinic acid mediated-biostimulation of oil-bioremediation under multiple stresses by heat, oil and heavy metals.	Radwan SS, Al-Mailem DM, Kansour MK.	Sci Rep	10.1038/s41598-017-10121-7	2017
Metabolism	Sound Stimulation Can Affect Saccharomyces cerevisiae Growth and Production of Volatile Metabolites in Liquid Medium.	Harris A, Lindsay MA, Ganley ARD, Jeffs A, Villas-Boas SG.	Metabolites	10.3390/metabo11090605	2021
	Bio-Tailored Sensing at the Nanoscale: Biochemical Aspects and Applications.	Fata F, Gabriele F, Angelucci F, Ippoliti R, Di Leandro L, Giansanti F, Ardini M.	Sensors (Basel)	10.3390/s23020949	2023
Enzymology	Purification and biochemical properties of a thermostable, haloalkaline cellulase from Bacillus licheniformis AMF-07 and its application for hydrolysis of different cellulosic substrates to bioethanol production.	Azadian F, Badoei-Dalfard A, Namaki-Shoushtari A, Hassanshahian M.	Mol Biol Res Commun		2016
	Production of sound waves by bacterial cells and the response of bacterial cells to sound.	Matsuhashi M, Pankrushina AN, Takeuchi S, Ohshima H, Miyoi H, Endoh K, Murayama K, Watanabe H, Endo S, Tobi M, Mano Y, Hyodo M, Kobayashi T, Kaneko T, Otani S, Yoshimura S, Harata A, Sawada T.	J Gen Appl Microbiol	10.2323/jgam.44.49	1998
Pathogenicity	Cellular signals regulating antibiotic sensitivities of bacteria.	Matsuhashi M, Shindo A, Ohshima H, Tobi M, Endo S, Watanabe H, Endoh K, Pankrushina AN.	Microb Drug Resist	10.1089/mdr.1996.2.91	1996
	Growth-promoting effect of carbon material upon bacterial cells propagating through a distance.	Matsuhashi M, Endoh K, Pankrushina AN, Watanabe H, Yamamura H, Komiyama M, Endo S, Tobi M, Ohshima H, Mano Y, Hyodo M, Kaneko T, Otani S.	J Gen Appl Microbiol	10.2323/jgam.43.225	1997
	Airborne Bacteria in Earth's Lower Stratosphere Resemble Taxa Detected in the Troposphere: Results From a New NASA Aircraft Bioaerosol Collector (ABC).	Smith DJ, Ravichandar JD, Jain S, Griffin DW, Yu H, Tan Q, Thissen J, Lusby T, Nicoll P, Shedler S, Martinez P, Osorio A, Lechniak J, Choi S, Sabino K, Iverson K, Chan L, Jaing C, McGrath J.	Front Microbiol	10.3389/fmicb.2018.01752	2018
Enzymology	Biodiversity and phylogenetic analysis of culturable bacteria indigenous to Khewra salt mine of pakistan and their industrial importance.	Akhtar N, Ghauri MA, Iqbal A, Anwar MA, Akhtar K.	Braz J Microbiol	10.1590/s1517-838220080001000029	2008
Phylogeny	Bacillus arenosi sp. nov., Bacillus arvi sp. nov. and Bacillus humi sp. nov., isolated from soil.	Heyrman J, Rodriguez-Diaz M, Devos J, Felske A, Logan NA, De Vos P.	Int J Syst Evol Microbiol	10.1099/ijs.0.63240-0	2005
Phylogeny	Bacillus fonticola sp. nov., isolated from deep sea cold seep sediment.	Sun YY, Zhou HZ, Sun QL	Arch Microbiol	10.1007/s00203-021-02401-8	2021
Phylogeny	Bacillus oleivorans sp. nov., a diesel oil-degrading and solvent-tolerant bacterium.	Azmatunnisa M, Rahul K, Subhash Y, Sasikala C, Ramana CV	Int J Syst Evol Microbiol	10.1099/ijs.0.000103	2015
Phylogeny	Bacillus oceani sp. nov., a new slightly halophilic bacterium, isolated from a deep sea sediment environment.	Liu YJ, Long LJ, Huang XF, You ZQ, Wang FZ, Li J, Kim CJ, Tian XP, Zhang S	Antonie Van Leeuwenhoek	10.1007/s10482-013-9995-0	2013

References

#7086	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17613
#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 )
#23316	TAKASHI FUJITA, OSAMU SHIDA, HIROAKI TAKAGI, KIYOHIKO KUNUGITA, A. N. PANKRUSHINA, MICHIO MATSUHASHI: Description of Bacillus carboniphilus sp. nov.. IJSEM 46: 116 - 118 1996 ( DOI 10.1099/00207713-46-1-116 )
#36103	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68382	Automatically annotated from API zym .
#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 .
#117178	Collection of Institut Pasteur ; Curators of the CIP; CIP 109750
#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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Bacillus carboniphilus (DSM 17613, ATCC 700100, CIP 109750)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_039522365

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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