Streptomyces alni (DSM 42036, CGMCC 4.3510, NRRL B-24611)

Name: Streptomyces alni (DSM 42036, CGMCC 4.3510, NRRL B-24611)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 16453

Type strain

Strain Designation D65

Culture col. no. DSM 42036 CGMCC 4.3510 NRRL B-24611 D65 JCM 16122

NCBI tax ID(s) 380248

Special Collections DSMZ JCM Literature strains

History DSMZ <- D. P. Labeda, NRRL; NRRL B-24611 <- Y. Huang, CGMCC; CGMCC 4.3510 JCM <-- CGMCC 4.3510 <-- N. Liu et al. D65.

Links

Streptomyces alni D65 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from roots of a wild tree, Alnus nepalensis.

spore-forming Gram-positive aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 399855

JCM 16122,DSM 42036

@ref 20215

Last LPSN update 2026-05-29 08:28:47

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Kitasatosporales

Family Streptomycetaceae

Genus Streptomyces

Species Streptomyces alni

Full scientific name Streptomyces alni Liu et al. 2009

Synonyms (1)

Actinacidiphila alni

Morphology

Cell morphology

@ref	Confidence	Gram stain
32610		positive
125439	93.482
125439	99.027	positive

Pigmentation

32610

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17713	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

Culture temp

@ref	Growth	Type	Temperature (°C)
17713	positive	growth	28
32610	positive	growth	10-45
32610	positive	optimum	27.5
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
32610	positive	optimum	7
32610	positive	growth	4.5-9.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
32610	aerobe
125439	obligate aerobe	98.561

Spore formation

@ref	Spore formation	Confidence
32610
125438		92.894
125439		93.916

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32610	NaCl	positive	growth	<3 %

Observation

67770

Observationquinones: MK-9(H₆), MK-9(H₈)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32610	30089 ChEBI	acetate	+	carbon source
32610	22599 ChEBI	arabinose	+	carbon source
32610	16947 ChEBI	citrate	+	carbon source
32610	4853 ChEBI	esculin	+	hydrolysis
32610	28757 ChEBI	fructose	+	carbon source
32610	17716 ChEBI	lactose	+	carbon source
32610	15792 ChEBI	malonate	+	carbon source
32610	17306 ChEBI	maltose	+	carbon source
32610	28044 ChEBI	phenylalanine	+	carbon source
32610	16634 ChEBI	raffinose	+	carbon source
32610	17814 ChEBI	salicin	+	carbon source
32610	30911 ChEBI	sorbitol	+	carbon source
32610	17992 ChEBI	sucrose	+	carbon source
32610	27082 ChEBI	trehalose	+	carbon source
32610	18222 ChEBI	xylose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
67770	28197 ChEBI	daidzein
67770	125610 ChEBI	N-acetyltyramine

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	kanosamine biosynthesis II	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	cardiolipin biosynthesis	100	7 of 7
66794	formaldehyde oxidation	100	3 of 3
66794	glycogen metabolism	100	5 of 5
66794	coenzyme A metabolism	100	4 of 4
66794	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	ethylmalonyl-CoA pathway	100	5 of 5
66794	ribulose monophosphate pathway	100	2 of 2
66794	pentose phosphate pathway	100	11 of 11
66794	biotin biosynthesis	100	4 of 4
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	starch degradation	100	10 of 10
66794	metabolism of amino sugars and derivatives	100	5 of 5
66794	glycolate and glyoxylate degradation	100	6 of 6
66794	enterobactin biosynthesis	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	valine metabolism	100	9 of 9
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	aerobactin biosynthesis	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	acetate fermentation	100	4 of 4
66794	cellulose degradation	100	5 of 5
66794	threonine metabolism	100	10 of 10
66794	3-chlorocatechol degradation	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	photosynthesis	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	myo-inositol biosynthesis	90	9 of 10
66794	propionate fermentation	90	9 of 10
66794	Entner Doudoroff pathway	90	9 of 10
66794	d-mannose degradation	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	flavin biosynthesis	86.67	13 of 15
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	heme metabolism	85.71	12 of 14
66794	urea cycle	84.62	11 of 13
66794	leucine metabolism	84.62	11 of 13
66794	vitamin B12 metabolism	82.35	28 of 34
66794	glycolysis	82.35	14 of 17
66794	metabolism of disaccharids	81.82	9 of 11
66794	gallate degradation	80	4 of 5
66794	factor 420 biosynthesis	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	degradation of sugar acids	80	20 of 25
66794	peptidoglycan biosynthesis	80	12 of 15
66794	purine metabolism	79.79	75 of 94
66794	alanine metabolism	79.31	23 of 29
66794	citric acid cycle	78.57	11 of 14
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	allantoin degradation	77.78	7 of 9
66794	degradation of hexoses	77.78	14 of 18
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	isoleucine metabolism	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	cyclohexanol degradation	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	phenol degradation	75	15 of 20
66794	sulfopterin metabolism	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	pyrimidine metabolism	73.33	33 of 45
66794	methionine metabolism	73.08	19 of 26
66794	proline metabolism	72.73	8 of 11
66794	oxidative phosphorylation	71.43	65 of 91
66794	non-pathway related	71.05	27 of 38
66794	lipid metabolism	70.97	22 of 31
66794	isoprenoid biosynthesis	69.23	18 of 26
66794	histidine metabolism	68.97	20 of 29
66794	degradation of sugar alcohols	68.75	11 of 16
66794	tryptophan metabolism	68.42	26 of 38
66794	cyanate degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	4-hydroxymandelate degradation	66.67	6 of 9
66794	arginine metabolism	66.67	16 of 24
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
66794	acetoin degradation	66.67	2 of 3
66794	cysteine metabolism	66.67	12 of 18
66794	IAA biosynthesis	66.67	2 of 3
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	glutathione metabolism	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	androgen and estrogen metabolism	62.5	10 of 16
66794	arachidonate biosynthesis	60	3 of 5
66794	vitamin K metabolism	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	lysine metabolism	59.52	25 of 42
66794	bile acid biosynthesis, neutral pathway	58.82	10 of 17
66794	degradation of pentoses	57.14	16 of 28
66794	propanol degradation	57.14	4 of 7
66794	tyrosine metabolism	57.14	8 of 14
66794	daunorubicin biosynthesis	55.56	5 of 9
66794	nitrate assimilation	55.56	5 of 9
66794	ascorbate metabolism	54.55	12 of 22
66794	sulfate reduction	53.85	7 of 13
66794	3-phenylpropionate degradation	53.33	8 of 15
66794	polyamine pathway	52.17	12 of 23
66794	pantothenate biosynthesis	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	4-hydroxyphenylacetate degradation	50	5 of 10
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	toluene degradation	50	2 of 4
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	CMP-KDO biosynthesis	50	2 of 4
66794	quinate degradation	50	1 of 2
66794	grixazone biosynthesis	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	phenylmercury acetate degradation	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	lipid A biosynthesis	44.44	4 of 9
66794	chlorophyll metabolism	44.44	8 of 18
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	bacilysin biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	arachidonic acid metabolism	38.89	7 of 18
66794	carnitine metabolism	37.5	3 of 8
66794	cholesterol biosynthesis	36.36	4 of 11
66794	carotenoid biosynthesis	36.36	8 of 22
66794	vitamin B6 metabolism	36.36	4 of 11
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
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	catecholamine biosynthesis	25	1 of 4
66794	alginate biosynthesis	25	1 of 4

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Root (Rhizome)

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
17713	roots of a wild tree, Alnus nepalensis		Yunnan Province, Xishuangbanna, Nannuo Mountain	China	CHN	Asia
67770	Root of Alnus nepalensis in the rainforest of Nannuo Mountain	Alnus nepalensis	Xishuangbanna, Yunnan Province	China	CHN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17713	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
67770	IMG-taxon 2667527403 annotated assembly for Actinacidiphila alni CGMCC 4.3510	scaffold	GCA_900112845	380248.4	2667527403	380248	68.24

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17713	Streptomyces alni strain D65 16S ribosomal RNA gene, partial sequence	DQ460470	1426		380248

GC content

@ref	GC-content (mol%)	Method
17713	70.2
67770	72.1	genome sequence analysis
67770	70.2	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2667527403 annotated assembly for Actinacidiphila alni CGMCC 4.3510
NCBI: GCA_900112845

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	positive	99.03	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.56	no
125439	motility	BacteriaNetⓘ	no	93.48	no
125439	spore_formation	BacteriaNetⓘ	yes	93.92	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Streptomyces alni strain CGMCC 4.3510
PATRIC: 380248.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	89.97	yes
125438	anaerobic	anaerobicⓘ	no	95.73	yes
125438	spore-forming	spore-formingⓘ	yes	92.89	yes
125438	aerobic	aerobicⓘ	yes	86.25	yes
125438	thermophilic	thermophileⓘ	no	95.00	yes
125438	flagellated	motile2+ⓘ	no	87.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Cas12a-assisted precise targeted cloning using in vivo Cre-lox recombination.	Enghiad B, Huang C, Guo F, Jiang G, Wang B, Tabatabaei SK, Martin TA, Zhao H.	Nat Commun	10.1038/s41467-021-21275-4	2021
Phylogeny	Streptomyces alni sp. nov., a daidzein-producing endophyte isolated from a root of Alnus nepalensis D. Don.	Liu N, Wang H, Liu M, Gu Q, Zheng W, Huang Y	Int J Syst Evol Microbiol	10.1099/ijs.0.65769-0	2009

References

#17713	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 42036
#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 )
#28823	IJSEM 254 2009 ( DOI 10.1099/ijs.0.65769-0 , PubMed 19196762 )
#32610	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 #28823
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#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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Streptomyces alni (DSM 42036, CGMCC 4.3510, NRRL B-24611)

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

Observation

Metabolite utilization

Metabolite production

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900112845

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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