Name: Cytobacillus kochii do080905 5-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 1318

Type strain:

Species: Cytobacillus kochii

Strain Designation: do080905 5-1, G 5819

Culture col. no.: DSM 23667, CCUG 59877, LMG 25855, WCC 4582

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

NCBI tax ID(s): 859143 (species)

SI-ID 402969

DSM 23667, CCUG 59877

Other strains from Cytobacillus kochii

C. kochii G 5690, DSM 24673, WCC 4581
C. kochii C2_3, DSM 103982

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Bacillaceae*
	Genus	*Cytobacillus*
	Species	**Cytobacillus kochii**
	Full Scientific Name (LPSN)	Cytobacillus kochii (Seiler et al. 2012) Patel and Gupta 2020

Synonym

Bacillus kochii

Information on morphological and physiological properties Morphology

[Ref.: #29978]	Gram stain	positive

[Ref.: #29978]	Cell length	3-13 µm

[Ref.: #29978]	Cell width	0.5-0.8 µm

[Ref.: #29978]	Cell shape	rod-shaped

[Ref.: #29978]	Motility	yes

[Ref.: #29978]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17333]

Culture medium

CASO AGAR (MERCK 105458) (DSMZ Medium 220)

[Ref.: #17333]

Culture medium growth

[Ref.: #17333]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17333]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #17333]	growth	30 °C
[Ref.: #29978]	growth	10-40 °C
[Ref.: #29978]	optimum	30 °C
[Ref.: #62149]	growth	37 °C

[Ref.: #17333]	Temperature range	mesophilic
[Ref.: #29978]	Temperature range	mesophilic
[Ref.: #62149]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29978]			optimum	7
[Ref.: #29978]			growth	6-10.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29978]	Oxygen tolerance	aerobe
[Ref.: #62149]	Oxygen tolerance	aerobe

[Ref.: #29978]

Ability of spore formation

yes

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29978]		NaCl		growth	0-10	%
[Ref.: #29978]		NaCl		optimum	0.50	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29978]	3-hydroxybenzoate ChEBI	+	carbon source
[Ref.: #29978]	3-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #29978]	acetate ChEBI	+	carbon source
[Ref.: #29978]	alanine ChEBI	+	carbon source
[Ref.: #29978]	citrate ChEBI	+	carbon source
[Ref.: #29978]	gluconate ChEBI	+	carbon source
[Ref.: #29978]	itaconate ChEBI	+	carbon source
[Ref.: #29978]	malate ChEBI	+	carbon source
[Ref.: #29978]	phenylacetate ChEBI	+	carbon source
[Ref.: #29978]	proline ChEBI	+	carbon source
[Ref.: #29978]	propionate ChEBI	+	carbon source
[Ref.: #29978]	ribose ChEBI	+	carbon source
[Ref.: #29978]	serine ChEBI	+	carbon source
[Ref.: #29978]	tween 20 ChEBI	+	carbon source
[Ref.: #29978]	tween 40 ChEBI	+	carbon source
[Ref.: #29978]	tween 60 ChEBI	+	carbon source
[Ref.: #29978]	tween 80 ChEBI	+	carbon source
[Ref.: #29978]	valerate ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #29978]	acid phosphatase	+	3.1.3.2
[Ref.: #29978]	alkaline phosphatase	+	3.1.3.1
[Ref.: #29978]	catalase	+	1.11.1.6
[Ref.: #29978]	gelatinase	+

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

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #17333]	Sample type/isolated from	dairy product
[Ref.: #17333]	Geographic location (country and/or sea, region)	Ochsenfurt, Bavaria
[Ref.: #17333]	Country	Germany
[Ref.: #17333]	Country ISO 3 Code	DEU
[Ref.: #17333]	Continent	Europe

[Ref.: #62149]	Sample type/isolated from	Dairy product
[Ref.: #62149]	Sampling date	2008
[Ref.: #62149]	Geographic location (country and/or sea, region)	Bavaria,Ochsenfurt
[Ref.: #62149]	Country	Germany
[Ref.: #62149]	Country ISO 3 Code	DEU
[Ref.: #62149]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered

#Food production

#Dairy product

What are isolation sources categories?

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #17333]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #17333]	Bacillus kochii partial 16S rRNA gene, type strain WCC 4582T	FN995265	1511	ENA	859143 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Cytobacillus kochii DSM 23667	2926483779	draft	JGI IMG/M	859143 tax ID	*

[Ref.: #17333]	GC-content	36.4 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29978]	GC-content	36.4 mol%

Availability in culture collections External links

[Ref.: #17333]

Culture collection no.

DSM 23667, CCUG 59877, LMG 25855, WCC 4582

[Ref.: #70968]

SI-ID 402969

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 )

#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 (see below)

#62149 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 59877

#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) .

#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 )

#70968

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID402969.1 )

#26346

IJSEM 1092 2012 ( DOI 10.1099/ijs.0.027771-0 , PubMed 21705449 )

* These data were automatically processed and therefore are not curated

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