Streptomyces griseocarneus (DSM 40004, AS 4.1368, ATCC 12628)

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

Multimedia

• @ref:	69336
  multimedia content:	DSM_40004_image5.jpeg
  multimedia.multimedia content:	DSM_40004_image5.jpeg
  caption:	(ISP6, ISP7)
  intellectual property rights:	Helmholtz-Zentrum für Infektionsforschung GmbH
  manual_annotation:	1

• @ref:	69336
  multimedia content:	DSM_40004_image6.jpeg
  multimedia.multimedia content:	DSM_40004_image6.jpeg
  caption:	(ISP6, ISP7)
  intellectual property rights:	Helmholtz-Zentrum für Infektionsforschung GmbH
  manual_annotation:	1

Culture medium

@ref	Name	Growth	Medium link	Composition
9209	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
32896	MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulum			Distilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
9209	ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)		Medium recipe at MediaDive	Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water
119745	CIP Medium 57		Medium recipe at CIP

Culture temp

Oxygen tolerance

Spore formation

Compound production

Halophily

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
69336	22599 ChEBI	arabinose	-	growth
68368	29016 ChEBI	arginine	+	hydrolysis	from API 20E
69336	62968 ChEBI	cellulose	-	growth
119745	16947 ChEBI	citrate	-	carbon source
68368	16947 ChEBI	citrate	+	assimilation	from API 20E
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
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
119745	4853 ChEBI	esculin	-	hydrolysis
68379	4853 ChEBI	esculin	-	hydrolysis	from API Coryne
69336	28757 ChEBI	fructose	-	growth
68379	5291 ChEBI	gelatin	+	hydrolysis	from API Coryne
68368	5291 ChEBI	gelatin	+	hydrolysis	from API 20E
69336	17234 ChEBI	glucose	+	growth
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
119745	606565 ChEBI	hippurate	+	hydrolysis
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68368	25094 ChEBI	lysine	+	degradation	from API 20E
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
69336	37684 ChEBI	mannose	-	growth
69336	17268 ChEBI	myo-inositol	+/-	growth
119745	17632 ChEBI	nitrate	-	reduction
119745	17632 ChEBI	nitrate	-	respiration
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
119745	16301 ChEBI	nitrite	-	reduction
68368	18257 ChEBI	ornithine	+	degradation	from API 20E
69336	16634 ChEBI	raffinose	-	growth
69336	26546 ChEBI	rhamnose	-	growth
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
69336	17992 ChEBI	sucrose	-	growth
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E
69336	18222 ChEBI	xylose	-	growth

Antibiotic resistance

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68368	15688 ChEBI	acetoin		from API 20E
68368	16136 ChEBI	hydrogen sulfide		from API 20E
67770	24750 ChEBI	hydroxystreptomycin
119745	35581 ChEBI	indole
68368	35581 ChEBI	indole		from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test	Indole test
119745	15688 ChEBI	acetoin	-
68368	15688 ChEBI	acetoin	-			from API 20E
119745	17234 ChEBI	glucose		-
68368	35581 ChEBI	indole			-	from API 20E

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
119745	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68379	alkaline phosphatase	+	3.1.3.1	from API Coryne
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
68379	alpha-glucosidase	-	3.2.1.20	from API Coryne
68382	alpha-mannosidase	+	3.2.1.24	from API zym
119745	amylase	+
68368	arginine dihydrolase	+	3.5.3.6	from API 20E
68382	beta-galactosidase	-	3.2.1.23	from API zym
119745	beta-galactosidase	+	3.2.1.23
68379	beta-galactosidase	-	3.2.1.23	from API Coryne
68368	beta-galactosidase	+	3.2.1.23	from API 20E
68382	beta-glucosidase	-	3.2.1.21	from API zym
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
119745	caseinase	+	3.4.21.50
119745	catalase	+	1.11.1.6
119745	DNase	+
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
119745	gamma-glutamyltransferase	+	2.3.2.2
119745	gelatinase	+
68379	gelatinase	+		from API Coryne
68368	gelatinase	+		from API 20E
119745	lecithinase	+
68382	leucine arylamidase	+	3.4.11.1	from API zym
119745	lipase	-
68382	lipase (C 14)	-		from API zym
119745	lysine decarboxylase	-	4.1.1.18
68368	lysine decarboxylase	+	4.1.1.18	from API 20E
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68379	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API Coryne
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
119745	ornithine decarboxylase	-	4.1.1.17
68368	ornithine decarboxylase	+	4.1.1.17	from API 20E
119745	oxidase	-
119745	phenylalanine ammonia-lyase	-	4.3.1.24
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	-	3.4.19.3	from API Coryne
119745	tryptophan deaminase	-
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
119745	tween esterase	+
119745	urease	-	3.5.1.5
68379	urease	-	3.5.1.5	from API Coryne
68368	urease	-	3.5.1.5	from API 20E
68382	valine arylamidase	+		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions	external links
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	pentose phosphate pathway	100	11 of 11
66794	ribulose monophosphate pathway	100	2 of 2
66794	cyanate degradation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	glycine betaine biosynthesis	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	glycogen metabolism	100	5 of 5
66794	grixazone biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
66794	enterobactin biosynthesis	100	3 of 3
66794	glycolate and glyoxylate degradation	100	6 of 6
66794	metabolism of amino sugars and derivatives	100	5 of 5
66794	chorismate metabolism	100	9 of 9
66794	starch degradation	100	10 of 10
66794	valine metabolism	100	9 of 9
66794	biotin biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	IAA biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	cardiolipin biosynthesis	100	7 of 7
66794	cellulose degradation	100	5 of 5
66794	taurine degradation	100	1 of 1
66794	aerobactin biosynthesis	100	1 of 1
66794	aspartate and asparagine metabolism	100	9 of 9
66794	threonine metabolism	100	10 of 10
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	acetate fermentation	100	4 of 4
66794	NAD metabolism	94.44	17 of 18
66794	phenylalanine metabolism	92.31	12 of 13
66794	degradation of aromatic, nitrogen containing compounds	91.67	11 of 12
66794	proline metabolism	90.91	10 of 11
66794	myo-inositol biosynthesis	90	9 of 10
66794	propionate fermentation	90	9 of 10
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	flavin biosynthesis	86.67	13 of 15
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	heme metabolism	85.71	12 of 14
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	photosynthesis	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	leucine metabolism	84.62	11 of 13
66794	alanine metabolism	82.76	24 of 29
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	purine metabolism	81.91	77 of 94
66794	metabolism of disaccharids	81.82	9 of 11
66794	tryptophan metabolism	81.58	31 of 38
66794	methionine metabolism	80.77	21 of 26
66794	Entner Doudoroff pathway	80	8 of 10
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	hydrogen production	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	vitamin B12 metabolism	79.41	27 of 34
66794	citric acid cycle	78.57	11 of 14
66794	allantoin degradation	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	urea cycle	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	glycogen biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	cyclohexanol degradation	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	lipid metabolism	74.19	23 of 31
66794	pyrimidine metabolism	73.33	33 of 45
66794	cholesterol biosynthesis	72.73	8 of 11
66794	histidine metabolism	72.41	21 of 29
66794	propanol degradation	71.43	5 of 7
66794	oxidative phosphorylation	70.33	64 of 91
66794	phenol degradation	70	14 of 20
66794	glycine metabolism	70	7 of 10
66794	phosphatidylethanolamine bioynthesis	69.23	9 of 13
66794	vitamin B1 metabolism	69.23	9 of 13
66794	isoprenoid biosynthesis	69.23	18 of 26
66794	androgen and estrogen metabolism	68.75	11 of 16
66794	non-pathway related	68.42	26 of 38
66794	octane oxidation	66.67	2 of 3
66794	4-hydroxymandelate degradation	66.67	6 of 9
66794	cysteine metabolism	66.67	12 of 18
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	lysine metabolism	66.67	28 of 42
66794	arginine metabolism	66.67	16 of 24
66794	glutathione metabolism	64.29	9 of 14
66794	tyrosine metabolism	64.29	9 of 14
66794	carnitine metabolism	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	sulfate reduction	61.54	8 of 13
66794	factor 420 biosynthesis	60	3 of 5
66794	arachidonate biosynthesis	60	3 of 5
66794	vitamin K metabolism	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	coenzyme M biosynthesis	60	6 of 10
66794	4-hydroxyphenylacetate degradation	60	6 of 10
66794	ascorbate metabolism	59.09	13 of 22
66794	phenylpropanoid biosynthesis	53.85	7 of 13
66794	degradation of pentoses	53.57	15 of 28
66794	3-phenylpropionate degradation	53.33	8 of 15
66794	toluene degradation	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	catecholamine biosynthesis	50	2 of 4
66794	CMP-KDO biosynthesis	50	2 of 4
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	vitamin E metabolism	50	2 of 4
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	d-xylose degradation	45.45	5 of 11
66794	arachidonic acid metabolism	44.44	8 of 18
66794	degradation of hexoses	44.44	8 of 18
66794	lipid A biosynthesis	44.44	4 of 9
66794	nitrate assimilation	44.44	4 of 9
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	carotenoid biosynthesis	40.91	9 of 22
66794	bacilysin biosynthesis	40	2 of 5
66794	gallate degradation	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	vitamin B6 metabolism	36.36	4 of 11
66794	degradation of sugar acids	36	9 of 25
66794	sphingosine metabolism	33.33	2 of 6
66794	pantothenate biosynthesis	33.33	2 of 6
66794	methane metabolism	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	chlorophyll metabolism	33.33	6 of 18
66794	mevalonate metabolism	28.57	2 of 7
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	daunorubicin biosynthesis	22.22	2 of 9

API 20E

API coryne

API zym

API biotype100

Isolation source categories

Isolation

Taxonmaps

69479

Global distribution of 16S sequence AB920588 (>99% sequence identity) for Streptomyces from Microbeatlas

Aquatic Samples	19
Soil Samples	79
Animal Samples	56
Plant Samples	24
Total Samples	178

Risk assessment

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1465559v1 assembly for Streptomyces griseocarneus JCM 4580	scaffold	GCA_014655595	51201.8	2997593292	51201	69.27
66792	ASM2009339v1 assembly for Streptomyces griseocarneus CGMCC4.1088	scaffold	GCA_020093395	51201.10		51201	57.25

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Streptomyces sp. NTRH3 gene for 16S ribosomal RNA, partial sequence	AB920588	1287		1571724
20218	Streptomyces griseocarneus 16S rRNA gene, strain DSM40004	X99943	1515		51201
20218	Streptomyces griseocarneus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4095	D44004	120		51201
20218	Streptomyces griseocarneus gene for 16S rRNA, partial sequence, strain: NBRC 12776	AB184135	1431		51201
124043	Streptomyces griseocarneus strain JCM 4580 16S ribosomal RNA gene, partial sequence.	MT760576	1369		51201

Predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Enzymatic synthesis of aminocyclitol moieties of aminoglycoside antibiotics from inositol by Streptomyces spp.: detection of glutamine-aminocyclitol aminotransferase and diaminocyclitol aminotransferase activities in a spectinomycin producer.	Walker JB.	J Bacteriol	10.1128/jb.177.3.818-822.1995	1995
Metabolism	Enzymatic synthesis of aminoglycoside antibiotics: novel adenosylmethionine:2-deoxystreptamine N-methyltransferase activities in hygromycin B- and spectinomycin-producing Streptomyces spp. and uses of the methylated products.	Walker JB.	Appl Environ Microbiol	10.1128/aem.68.5.2404-2410.2002	2002
	Studies on Streptomyces griseocarneus and the production of hydroxystreptomycin.	BENEDICT RG, LINDENFELSER LA, STODOLA FH, TRAUFLER DH.	J Bacteriol	10.1128/jb.62.4.487-497.1951	1951
	Griseocazines: Neuroprotective Multiprenylated Cyclodipeptides Identified through Targeted Genome Mining.	Malit JJL, Wu C, Tian X, Liu W, Huang D, Sung HH, Liu LL, Williams ID, Qian PY.	Org Lett	10.1021/acs.orglett.2c00745	2022
Enzymology	Structural basis for the high thermal stability and optimum pH of sphingomyelinase C from Streptomyces griseocarneus.	Fujisawa I, Hamana H, Tomita Y, Matsumoto Y, Murayama K, Sugimori D.	J Biosci Bioeng	10.1016/j.jbiosc.2020.09.005	2021
Pathogenicity	1-Methoxypyrrole-2-carboxamide-A new pyrrole compound isolated from Streptomyces griseocarneus SWW368.	Wattanasuepsin W, Intra B, Euanorasetr J, Watanabe Y, Mingma R, Fukasawa W, Mori M, Matsumoto A, Shiomi K, Panbangred W.	J Gen Appl Microbiol	10.2323/jgam.2016.10.006	2017
	Influence of medium modifications (optimization) on high nematicidal activity of the fermentation broth of Clostridium beijerinckii.	Liu S, Zhang K, Yu Y, Lian X, Jiang L, Meng F, Wang Y, Zhu X, Duan Y.	Front Bioeng Biotechnol	10.3389/fbioe.2023.1283112	2023
	Extracellular production of a sphingomyelinase from Streptomyces griseocarneus using Streptomyces lividans	Sugimori D, Tomita Y, Matsumoto Y, Ogino C.	Biotechnol Lett		2011
Metabolism	Extracellular production of a sphingomyelinase from Streptomyces griseocarneus using Streptomyces lividans.	Sugimori D, Tomita Y, Matsumoto Y, Ogino C.	Biotechnol Lett	10.1007/s10529-010-0480-9	2011
Metabolism	Kinetic characterization and Mg2+ enhancement of Streptomyces griseocarneus sphingomyelinase C produced by recombinant Streptomyces lividans.	Sugimori D, Matsumoto Y, Tomita Y, Murayama K, Ogino C.	Protein Expr Purif	10.1016/j.pep.2011.10.004	2012
Enzymology	Purification, characterization, and gene cloning of sphingomyelinase C from Streptomyces griseocarneus NBRC13471.	Sugimori D.	J Biosci Bioeng	10.1016/j.jbiosc.2009.04.013	2009
Genetics	Metagenomic characterization of sphingomyelinase C in the microbiome of humans and environments.	Jeon J, Kang S, Hur JK, Rho M.	Front Cell Infect Microbiol	10.3389/fcimb.2022.1015706	2022
Genetics	Whole genome analysis of Streptomyces sp. RerS4, a Rehmannia glutinosa rhizosphere microbe producing a new lipopeptide.	He H, Huang J, Zhao Z, Du P, Li J, Xin J, Xu H, Feng W, Zheng X.	Heliyon	10.1016/j.heliyon.2023.e19543	2023
Genetics	Genome-Wide Pathway Exploration of the Epidermidibacterium keratini EPI-7T.	Oh Y, Mun S, Choi YB, Jo H, Lee DG, Han K.	Microorganisms	10.3390/microorganisms11040870	2023
Metabolism	APHE-3, a spore-associated antibiotic of Streptomyces griseocarneus NCIMB 40447.	Cruz R, Arias ME, Soliveri J.	Appl Microbiol Biotechnol	10.1007/s002530051645	2000
Metabolism	Optimization of fermentation conditions through response surface methodology for enhanced antibacterial metabolite production by Streptomyces sp. 1-14 from cassava rhizosphere.	Yun TY, Feng RJ, Zhou DB, Pan YY, Chen YF, Wang F, Yin LY, Zhang YD, Xie JH.	PLoS One	10.1371/journal.pone.0206497	2018
Enzymology	Identification and biochemical characterization of an acid sphingomyelinase-like protein from the bacterial plant pathogen Ralstonia solanacearum that hydrolyzes ATP to AMP but not sphingomyelin to ceramide.	Airola MV, Tumolo JM, Snider J, Hannun YA.	PLoS One	10.1371/journal.pone.0105830	2014
Enzymology	Properties of delta5-3beta-hydroxysteroid oxidoreductase isolated from Streptomyces griseocarneus.	Kerenyi G, Szentirmai A, Natonek M.	Acta Microbiol Acad Sci Hung		1975
Phylogeny	Taxonomic re-evaluation of whorl-forming Streptomyces (formerly Streptoverticillium) species by using phenotypes, DNA-DNA hybridization and sequences of gyrB, and proposal of Streptomyces luteireticuli (ex Katoh and Arai 1957) corrig., sp. nov., nom. rev.	Hatano K, Nishii T, Kasai H.	Int J Syst Evol Microbiol	10.1099/ijs.0.02238-0	2003
Phylogeny	Streptomyces gobiensis sp. nov., an antimicrobial producing actinobacterium isolated from soil under black Gobi rocks.	Wen Y, Zhang G, Bahadur A, Liu Y, Zhang Z, Chen T, Liu G, Zhang W	Int J Syst Evol Microbiol	10.1099/ijsem.0.005318	2022