Cytobacillus kochii (DSM 23667, CCUG 59877, LMG 25855)

Name: Cytobacillus kochii (DSM 23667, CCUG 59877, LMG 25855)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1318

Type strain

Strain Designation do080905 5-1, G 5819

Culture col. no. DSM 23667 CCUG 59877 LMG 25855 WCC 4582 do080905 5-1 1 more

NCBI tax ID(s) 859143

Special Collections DSMZ CCUG Literature strains

History <- H. Seiler, Research Center for Nutrition and Food Sci. (ZIEL), TU Munich, GERMANY; WCC 4582

Links

Cytobacillus kochii do080905 5-1 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from dairy product.

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

Name and taxonomic classification

SI-ID 402969

DSM 23667,CCUG 59877

@ref 20215

Last LPSN update 2026-02-09 11:18:04

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Cytobacillaceae

Genus Cytobacillus

Species Cytobacillus kochii

Full scientific name Cytobacillus kochii (Seiler et al. 2012) Patel and Gupta 2020

Synonyms (1)

Bacillus kochii

BacDive ID	Other strains from **Cytobacillus kochii** (2)	Type strain
1319	C. kochii G 5690, DSM 24673, WCC 4581
140042	C. kochii C2_3, DSM 103982

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
29978	positive	3-13 µm	0.5-0.8 µm	rod-shaped

Pigmentation

29978

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17333	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

Culture temp

@ref	Growth	Type	Temperature (°C)
17333	positive	growth	30
29978	positive	growth	10-40
29978	positive	optimum	30
62149	positive	growth	37

Culture pH

@ref	Ability	Type	PH	PH range
29978	positive	optimum	7
29978	positive	growth	6-10.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
29978	aerobe
62149	aerobe

Spore formation

29978

Spore formationyes

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29978	NaCl	positive	growth	0-10 %
29978	NaCl	positive	optimum	0.50 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29978	16193 ChEBI	3-hydroxybenzoate	+	carbon source
29978	37054 ChEBI	3-hydroxybutyrate	+	carbon source
29978	30089 ChEBI	acetate	+	carbon source
29978	16449 ChEBI	alanine	+	carbon source
29978	16947 ChEBI	citrate	+	carbon source
29978	24265 ChEBI	gluconate	+	carbon source
29978	17240 ChEBI	itaconate	+	carbon source
29978	25115 ChEBI	malate	+	carbon source
29978	18401 ChEBI	phenylacetate	+	carbon source
29978	26271 ChEBI	proline	+	carbon source
29978	17272 ChEBI	propionate	+	carbon source
29978	33942 ChEBI	ribose	+	carbon source
29978	17822 ChEBI	serine	+	carbon source
29978	53424 ChEBI	tween 20	+	carbon source
29978	53423 ChEBI	tween 40	+	carbon source
29978	53425 ChEBI	tween 60	+	carbon source
29978	53426 ChEBI	tween 80	+	carbon source
29978	31011 ChEBI	valerate	+	carbon source

Enzymes

@ref	Value	Activity	Ec
29978	acid phosphatase	+	3.1.3.2
29978	alkaline phosphatase	+	3.1.3.1
29978	catalase	+	1.11.1.6
29978	gelatinase	+

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	valine metabolism	100	9 of 9
66794	vitamin K metabolism	100	5 of 5
66794	glycolate and glyoxylate degradation	100	6 of 6
66794	aminopropanol phosphate biosynthesis	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	threonine metabolism	100	10 of 10
66794	aspartate and asparagine metabolism	100	9 of 9
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	enterobactin biosynthesis	100	3 of 3
66794	lipoate biosynthesis	100	5 of 5
66794	propanol degradation	100	7 of 7
66794	palmitate biosynthesis	100	22 of 22
66794	L-lactaldehyde degradation	100	3 of 3
66794	methylglyoxal degradation	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	aerobactin biosynthesis	100	1 of 1
66794	ceramide biosynthesis	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	propionate fermentation	100	10 of 10
66794	teichoic acid biosynthesis	100	1 of 1
66794	NAD metabolism	94.44	17 of 18
66794	vitamin B1 metabolism	92.31	12 of 13
66794	4-hydroxyphenylacetate degradation	90	9 of 10
66794	alanine metabolism	89.66	26 of 29
66794	glutamate and glutamine metabolism	89.29	25 of 28
66794	serine metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	ketogluconate metabolism	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	photosynthesis	85.71	12 of 14
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	citric acid cycle	85.71	12 of 14
66794	heme metabolism	85.71	12 of 14
66794	phenylalanine metabolism	84.62	11 of 13
66794	leucine metabolism	84.62	11 of 13
66794	proline metabolism	81.82	9 of 11
66794	pentose phosphate pathway	81.82	9 of 11
66794	purine metabolism	80.85	76 of 94
66794	methionine metabolism	80.77	21 of 26
66794	flavin biosynthesis	80	12 of 15
66794	glycine betaine biosynthesis	80	4 of 5
66794	3-phenylpropionate degradation	80	12 of 15
66794	gallate degradation	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	starch degradation	80	8 of 10
66794	pyrimidine metabolism	80	36 of 45
66794	tryptophan metabolism	78.95	30 of 38
66794	allantoin degradation	77.78	7 of 9
66794	glycolysis	76.47	13 of 17
66794	glycogen biosynthesis	75	3 of 4
66794	biotin biosynthesis	75	3 of 4
66794	ppGpp biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	phenol degradation	75	15 of 20
66794	butanoate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	glutathione metabolism	71.43	10 of 14
66794	arginine metabolism	70.83	17 of 24
66794	urea cycle	69.23	9 of 13
66794	histidine metabolism	68.97	20 of 29
66794	oxidative phosphorylation	68.13	62 of 91
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	cysteine metabolism	66.67	12 of 18
66794	non-pathway related	65.79	25 of 38
66794	degradation of sugar alcohols	62.5	10 of 16
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	lipid metabolism	61.29	19 of 31
66794	cellulose degradation	60	3 of 5
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	3-chlorocatechol degradation	60	3 of 5
66794	lysine metabolism	57.14	24 of 42
66794	d-mannose degradation	55.56	5 of 9
66794	sulfate reduction	53.85	7 of 13
66794	phenylpropanoid biosynthesis	53.85	7 of 13
66794	androgen and estrogen metabolism	50	8 of 16
66794	acetate fermentation	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	pantothenate biosynthesis	50	3 of 6
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	coenzyme M biosynthesis	50	5 of 10
66794	toluene degradation	50	2 of 4
66794	Entner Doudoroff pathway	50	5 of 10
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	ethanol fermentation	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	vitamin B6 metabolism	45.45	5 of 11
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	tyrosine metabolism	42.86	6 of 14
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	vitamin B12 metabolism	41.18	14 of 34
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	creatinine degradation	40	2 of 5
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	cholesterol biosynthesis	36.36	4 of 11
66794	ascorbate metabolism	36.36	8 of 22
66794	degradation of pentoses	35.71	10 of 28
66794	polyamine pathway	34.78	8 of 23
66794	IAA biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	arachidonic acid metabolism	33.33	6 of 18
66794	octane oxidation	33.33	1 of 3
66794	nitrate assimilation	33.33	3 of 9
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	degradation of hexoses	33.33	6 of 18
66794	degradation of sugar acids	32	8 of 25
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	metabolism of disaccharids	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	vitamin E metabolism	25	1 of 4

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Dairy product

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
17333	dairy product		Ochsenfurt, Bavaria	Germany	DEU	Europe
62149	Dairy product	2008	Bavaria,Ochsenfurt	Germany	DEU	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17333	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM4264954v1 assembly for Cytobacillus kochii CCUG 59877	scaffold	GCA_042649545			859143	71.88
124043	ASM3081297v1 assembly for Cytobacillus kochii DSM 23667	contig	GCA_030812975	859143.27	2926483779	859143	70.39

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
17333	Bacillus kochii partial 16S rRNA gene, type strain WCC 4582T	FN995265	1511	859143
124043	Bacillus kochii strain WCC 4582 16S ribosomal RNA gene, partial sequence.	MN075515	1525	859143
124043	Cytobacillus kochii strain WCC 4582 16S ribosomal RNA gene, partial sequence.	PQ248453	601	859143
124043	Cytobacillus kochii strain WCC 4582 16S ribosomal RNA gene, partial sequence.	MW111207	599	859143
124043	Cytobacillus kochii strain WCC 4582 16S ribosomal RNA gene, partial sequence.	MW198081	601	859143

GC content

@ref	GC-content (mol%)	Method
17333	36.4	high performance liquid chromatography (HPLC)
29978	36.4

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
	Isolation and characterization of biosurfactant-producing bacteria from the Thar Desert.	Thakur SS, Lone AR, Ratnasari A, Gonzalez SS, Jain SK.	Antonie Van Leeuwenhoek	10.1007/s10482-025-02189-3	2025
	Intraspecific and interspecific comparison among bacterial communities in salivary glands and gut of five Culicoides spp. (Diptera: Ceratopogonidae), vectors of bluetongue virus.	Sarkar A, Banerjee P, Mazumdar A.	Acta Trop	10.1016/j.actatropica.2025.107778	2025
Biotechnology	Microbial decontamination of African nutmeg (Monodora myristica) powder using high-energy electron beam and gamma rays.	Ocloo FCK, Fiadey SE, Agyei-Amponsah J, Gryczka U.	Food Addit Contam Part A Chem Anal Control Expo Risk Assess	10.1080/19440049.2025.2506103	2025
	Efficiency of microbial fermentation on microbial shifts, enzymatic activity, and transcriptions in black soldier fly larvae during the sugarcane waste conversion.	Memon FU, Li C, Ahmad S, Cui Y, Feng X, Zeng P, Nabi F, Huang Z, Tettamanti G, Chen T, Tian L.	Environ Pollut	10.1016/j.envpol.2025.126588	2025
	The native Iranian soil bacteria with high potential to produce extracellular methionine gamma-lyase.	Nasirian M, Mobini-Dehkordi M, Khosravian P.	Front Microbiol	10.3389/fmicb.2024.1504742	2024
	Isotropic Silver Nanoparticles from Cytobacillus kochii Strain SW6 Isolated from Bay of Bengal Sea Sediment Water and Their Antimicrobial, Antioxidant, and Catalytic Potential.	Vadivel M, Mondal M, Gurusamy R, Sakthivel N.	Curr Microbiol	10.1007/s00284-023-03178-3	2023
Phylogeny	Dataset of 16S ribosomal DNA sequence-based identification of endophytic bacteria isolated from healthy and diseased Sabah red algae, Kappaphycus alvarezii.	Mangun VV, Sugumaran R, Lym Yong WT, Yusof NA.	Data Brief	10.1016/j.dib.2023.109785	2023
	Assessing Normandy Soil Microbial Diversity for Antibacterial Activities Using Traditional Culture and iChip Methods.	Perrier F, Morice J, Gueulle S, Gery A, Riboulet-Bisson E, Garon D, Muller C, Desriac F.	Microorganisms	10.3390/microorganisms12122422	2024
	Single Molecule Real-Time Sequencing and Traditional Cultivation Techniques Reveal Complex Community Structures and Regional Variations of Psychrotrophic Bacteria in Raw Milk.	Du B, Meng L, Liu H, Zheng N, Zhang Y, Zhao S, Wang J.	Front Microbiol	10.3389/fmicb.2022.853263	2022
Phylogeny	Bacillus ciccensis sp. nov., isolated from maize (Zea mays L.) seeds.	Liu Y, Li N, Eom MK, Schumann P, Zhang X, Cao Y, Ge Y, Xiao M, Zhao J, Cheng C, Kim SG	Int J Syst Evol Microbiol	10.1099/ijsem.0.002341	2017
Phylogeny	Bacillus praedii sp. nov., isolated from purplish paddy soil.	Liu B, Liu GH, Sengonca C, Schumann P, Wang JP, Zhu YJ, Liu QY, Wang MK	Int J Syst Evol Microbiol	10.1099/ijsem.0.002030	2017
Phylogeny	Bacillus solimangrovi sp. nov., isolated from mangrove soil.	Lee GH, Rhee MS, Chang DH, Kwon KK, Bae KS, Yang SH, Kim BC	Int J Syst Evol Microbiol	10.1099/ijs.0.058230-0	2014
Phylogeny	Bacillus kochii sp. nov., isolated from foods and a pharmaceuticals manufacturing site.	Seiler H, Schmidt V, Wenning M, Scherer S	Int J Syst Evol Microbiol	10.1099/ijs.0.027771-0	2011

References

#17333	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23667
#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 )
#26346	IJSEM 1092 2012 ( DOI 10.1099/ijs.0.027771-0 , PubMed 21705449 )
#29978	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 #26346
#62149	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 59877
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#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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Cytobacillus kochii (DSM 23667, CCUG 59877, LMG 25855)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_042649545

16S sequences

GC content

Genome-based predictions

Literature

Literature

References

BacDive

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