Intrasporangium calvum (DSM 43043, ATCC 23552, CUB 430)

Cell morphology

Colony morphology

Multicellular morphology

Multimedia

• @ref:	66793
  multimedia content:	EM_DSM_43043_1.jpg
  multimedia.multimedia content:	EM_DSM_43043_1.jpg
  caption:	electron microscopic image
  intellectual property rights:	© HZI/Manfred Rohde
  manual_annotation:	1

Culture medium

@ref	Name	Growth	Medium link	Composition
10713	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)		Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
19932	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
19932	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:
19932	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
19932	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
19932	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
19932	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
10713	BHI MEDIUM (DSMZ Medium 215)		Medium recipe at MediaDive	Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water

Culture temp

Oxygen tolerance

Murein

Observation

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
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
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
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
68382	trypsin	-	3.4.21.4	from API zym
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions	external links
66794	biotin biosynthesis	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	glycine betaine biosynthesis	100	5 of 5
66794	vitamin K metabolism	100	5 of 5
66794	glycogen metabolism	100	5 of 5
66794	aspartate and asparagine metabolism	100	9 of 9
66794	ethanol fermentation	100	2 of 2
66794	metabolism of amino sugars and derivatives	100	5 of 5
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	adipate degradation	100	2 of 2
66794	starch degradation	100	10 of 10
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	cardiolipin biosynthesis	100	7 of 7
66794	threonine metabolism	100	10 of 10
66794	lipoate biosynthesis	100	5 of 5
66794	valine metabolism	100	9 of 9
66794	suberin monomers biosynthesis	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	ppGpp biosynthesis	100	4 of 4
66794	lactate fermentation	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	denitrification	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	phenylalanine metabolism	92.31	12 of 13
66794	leucine metabolism	92.31	12 of 13
66794	proline metabolism	90.91	10 of 11
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	pyrimidine metabolism	86.67	39 of 45
66794	vitamin B12 metabolism	85.29	29 of 34
66794	purine metabolism	84.04	79 of 94
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	NAD metabolism	83.33	15 of 18
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	metabolism of disaccharids	81.82	9 of 11
66794	pentose phosphate pathway	81.82	9 of 11
66794	phenol degradation	80	16 of 20
66794	flavin biosynthesis	80	12 of 15
66794	methylglyoxal degradation	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	3-phenylpropionate degradation	80	12 of 15
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	factor 420 biosynthesis	80	4 of 5
66794	tyrosine metabolism	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	photosynthesis	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	glycolysis	76.47	13 of 17
66794	alanine metabolism	75.86	22 of 29
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	d-xylose degradation	72.73	8 of 11
66794	histidine metabolism	72.41	21 of 29
66794	glutathione metabolism	71.43	10 of 14
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	citric acid cycle	71.43	10 of 14
66794	non-pathway related	71.05	27 of 38
66794	lipid metabolism	70.97	22 of 31
66794	Entner Doudoroff pathway	70	7 of 10
66794	vitamin B1 metabolism	69.23	9 of 13
66794	lysine metabolism	69.05	29 of 42
66794	oxidative phosphorylation	67.03	61 of 91
66794	cyanate degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	nitrate assimilation	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	tryptophan metabolism	65.79	25 of 38
66794	methionine metabolism	65.38	17 of 26
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	androgen and estrogen metabolism	62.5	10 of 16
66794	degradation of sugar alcohols	62.5	10 of 16
66794	arginine metabolism	62.5	15 of 24
66794	ketogluconate metabolism	62.5	5 of 8
66794	gluconeogenesis	62.5	5 of 8
66794	urea cycle	61.54	8 of 13
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	myo-inositol biosynthesis	60	6 of 10
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	propanol degradation	57.14	4 of 7
66794	cysteine metabolism	55.56	10 of 18
66794	phosphatidylethanolamine bioynthesis	53.85	7 of 13
66794	sulfate reduction	53.85	7 of 13
66794	coenzyme M biosynthesis	50	5 of 10
66794	4-hydroxyphenylacetate degradation	50	5 of 10
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	toluene degradation	50	2 of 4
66794	cyclohexanol degradation	50	2 of 4
66794	pantothenate biosynthesis	50	3 of 6
66794	phenylmercury acetate degradation	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	glycine metabolism	50	5 of 10
66794	vitamin B6 metabolism	45.45	5 of 11
66794	lipid A biosynthesis	44.44	4 of 9
66794	polyamine pathway	43.48	10 of 23
66794	arachidonate biosynthesis	40	2 of 5
66794	cellulose degradation	40	2 of 5
66794	gallate degradation	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	creatinine degradation	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	ascorbate metabolism	36.36	8 of 22
66794	degradation of sugar acids	36	9 of 25
66794	degradation of pentoses	35.71	10 of 28
66794	methane metabolism	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	degradation of hexoses	33.33	6 of 18
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	chlorophyll metabolism	27.78	5 of 18
66794	cholesterol biosynthesis	27.27	3 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	carnitine metabolism	25	2 of 8
66794	catecholamine biosynthesis	25	1 of 4
66794	phenylpropanoid biosynthesis	23.08	3 of 13
66794	allantoin degradation	22.22	2 of 9

API zym

Isolation source categories

Isolation

Taxonmaps

69479

Global distribution of 16S sequence AJ566282 (>99% sequence identity) for Intrasporangium calvum from Microbeatlas

Aquatic Samples	443
Soil Samples	2412
Animal Samples	694
Plant Samples	222
Total Samples	3771

Risk assessment

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM18468v1 assembly for Intrasporangium calvum DSM 43043	complete	GCA_000184685	710696.3	649633057	710696	99.08

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Intrasporangium calvum 16S rRNA gene, type strain DSM 43043T	AJ566282	1469		710696
20218	Intrasporangium calvum gene for 16S ribosomal RNA, partial sequence	D85486	1475		710696

GC content

Predictions

Literature

Title	Authors	Journal	DOI	Year
Complete genome sequence of Intrasporangium calvum type strain (7 KIP).	Del Rio TG, Chertkov O, Yasawong M, Lucas S, Deshpande S, Cheng JF, Detter C, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Pukall R, Sikorski J, Goker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A.	Stand Genomic Sci	10.4056/sigs.1263355	2010
Unravelling the antibiotic and heavy metal resistome of a chronically polluted soil.	Salam LB.	3 Biotech	10.1007/s13205-020-02219-z	2020
Cyanuric acid hydrolase: evolutionary innovation by structural concatenation.	Peat TS, Balotra S, Wilding M, French NG, Briggs LJ, Panjikar S, Cowieson N, Newman J, Scott C.	Mol Microbiol	10.1111/mmi.12249	2013
Lengths of Orthologous Prokaryotic Proteins Are Affected by Evolutionary Factors.	Tatarinova T, Salih B, Dien Bard J, Cohen I, Bolshoy A.	Biomed Res Int	10.1155/2015/786861	2015
Defining sequence space and reaction products within the cyanuric acid hydrolase (AtzD)/barbiturase protein family.	Seffernick JL, Erickson JS, Cameron SM, Cho S, Dodge AG, Richman JE, Sadowsky MJ, Wackett LP.	J Bacteriol	10.1128/jb.00791-12	2012
Methods of combinatorial optimization to reveal factors affecting gene length.	Bolshoy A, Tatarinova T.	Bioinform Biol Insights	10.4137/bbi.s10525	2012
Developmental biology of Streptomyces from the perspective of 100 actinobacterial genome sequences.	Chandra G, Chater KF.	FEMS Microbiol Rev	10.1111/1574-6976.12047	2014
Phylogenetic framework and molecular signatures for the main clades of the phylum Actinobacteria.	Gao B, Gupta RS.	Microbiol Mol Biol Rev	10.1128/mmbr.05011-11	2012
Characterization of a Novel cis-3-Hydroxy-l-Proline Dehydratase and a trans-3-Hydroxy-l-Proline Dehydratase from Bacteria.	Watanabe S, Fukumori F, Miyazaki M, Tagami S, Watanabe Y.	J Bacteriol	10.1128/jb.00255-17	2017
A Real-Time Multiplexed Microbial Growth Intervalometer for Capturing High-Resolution Growth Curves.	Vuono DC, Lipp B, Staub C, Loney E, Harrold ZR, Grzymski JJ.	Front Microbiol	10.3389/fmicb.2019.01135	2019
Resource Concentration Modulates the Fate of Dissimilated Nitrogen in a Dual-Pathway Actinobacterium.	Vuono DC, Read RW, Hemp J, Sullivan BW, Arnone JA, Neveux I, Blank RR, Loney E, Miceli D, Winkler MH, Chakraborty R, Stahl DA, Grzymski JJ.	Front Microbiol	10.3389/fmicb.2019.00003	2019
Crystal structures of aconitase X enzymes from bacteria and archaea provide insights into the molecular evolution of the aconitase superfamily.	Watanabe S, Murase Y, Watanabe Y, Sakurai Y, Tajima K.	Commun Biol	10.1038/s42003-021-02147-5	2021
Polyamine profiles within genera of the class Actinobacteria with LL-diaminopimelic acid in the peptidoglycan.	Busse HJ, Schumann P.	Int J Syst Bacteriol	10.1099/00207713-49-1-179	1999
Involvement of NO3- in Ecophysiological Regulation of Dissimilatory Nitrate/Nitrite Reduction to Ammonium (DNRA) Is Implied by Physiological Characterization of Soil DNRA Bacteria Isolated via a Colorimetric Screening Method.	Heo H, Kwon M, Song B, Yoon S.	Appl Environ Microbiol	10.1128/aem.01054-20	2020
Genomic Analyses of the Quinol Oxidases and/or Quinone Reductases Involved in Bacterial Extracellular Electron Transfer.	Zhong Y, Shi L.	Front Microbiol	10.3389/fmicb.2018.03029	2018
Experimental and computational investigation of enzyme functional annotations uncovers misannotation in the EC 1.1.3.15 enzyme class.	Rembeza E, Engqvist MKM.	PLoS Comput Biol	10.1371/journal.pcbi.1009446	2021
Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics.	Martinez Arbas S, Narayanasamy S, Herold M, Lebrun LA, Hoopmann MR, Li S, Lam TJ, Kunath BJ, Hicks ND, Liu CM, Price LB, Laczny CC, Gillece JD, Schupp JM, Keim PS, Moritz RL, Faust K, Tang H, Ye Y, Skupin A, May P, Muller EEL, Wilmes P.	Nat Microbiol	10.1038/s41564-020-00794-8	2021
Uracil DNA glycosylase (UDG) activities in Bradyrhizobium diazoefficiens: characterization of a new class of UDG with broad substrate specificity.	Chembazhi UV, Patil VV, Sah S, Reeve W, Tiwari RP, Woo E, Varshney U.	Nucleic Acids Res	10.1093/nar/gkx209	2017
Ultramicroscopic structure of Intrasporangium calvum (Actinomycetales).	Lechevalier H, Lechevalier MP.	J Bacteriol	10.1128/jb.100.1.522-525.1969	1969
Denitrifying bacteria isolated from terrestrial subsurface sediments exposed to mixed-waste contamination.	Green SJ, Prakash O, Gihring TM, Akob DM, Jasrotia P, Jardine PM, Watson DB, Brown SD, Palumbo AV, Kostka JE.	Appl Environ Microbiol	10.1128/aem.03069-09	2010
Genome-Based Taxonomic Classification of the Phylum Actinobacteria.	Nouioui I, Carro L, Garcia-Lopez M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Goker M.	Front Microbiol	10.3389/fmicb.2018.02007	2018
Terracoccus luteus gen. nov., sp. nov., an LL-diaminopimelic acid-containing coccoid actinomycete from soil.	Prauser H, Schumann P, Rainey FA, Kroppenstedt RM, Stackebrandt E.	Int J Syst Bacteriol	10.1099/00207713-47-4-1218	1997
Proposal of Intrasporangium mesophilum sp. nov., and reclassification of Humihabitans oryzae Kageyama et al. 2007 as Intrasporangium oryzae comb. nov.	Yang LL, Ao T, Wang XH, He J, Klenk HP, Tang SK, Li WJ	Int J Syst Evol Microbiol	10.1099/ijs.0.029934-0	2011
Intrasporangium chromatireducens sp. nov., a chromate-reducing actinobacterium isolated from manganese mining soil, and emended description of the genus Intrasporangium.	Liu H, Wang H, Wang G	Int J Syst Evol Microbiol	10.1099/ijs.0.030528-0	2011
Humihabitans oryzae gen. nov., sp. nov.	Kageyama A, Takahashi Y, Omura S	Int J Syst Evol Microbiol	10.1099/ijs.0.65069-0	2007