Name: Streptomyces cavernae DSM 104115
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 159626

Type strain:

Species: Streptomyces cavernae

Culture col. no.: DSM 104115, KCTC 39850, SYSU K10008

Strain history: <- W.-J. Li, Sun Yat-Sen University, Guangzhou, China; SYSU K10008 <- B. Fang, Sun Yat-Sen University, Guangzhou, China; SYSU K10008

NCBI tax ID(s): 2259034 (species)

SI-ID 408132

DSM 104115

Special Collections

Section

When using BacDive for research please cite our paper

Streptomyces cavernae DSM 104115 is an aerobe, mesophilic, Gram-positive bacterium that builds aerial hyphae and was isolated from karst cave soil.

Gram-positive
aerobe
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Kitasatosporales*
	Family	*Streptomycetaceae*
	Genus	*Streptomyces*
	Species	**Streptomyces cavernae**
	Full Scientific Name (LPSN)	Streptomyces cavernae Fang et al. 2020

Information on morphological and physiological properties Morphology

[Ref.: #69497]	Gram stain	positive
[Ref.: #125439]	Gram stain	positive Confidence in %99.7

[Ref.: #69497]	Motility	no
[Ref.: #125439]	Motility	no Confidence in %92.2

[Ref.: #69272]	Colony color	Beige (1001), light ivory (1015)
[Ref.: #69272]	Cultivation medium used	suter with tyrosine

[Ref.: #69272]	Colony color	Light ivory (1015)
[Ref.: #69272]	Cultivation medium used	ISP 3

[Ref.: #69272]	Colony color	Light ivory (1015)
[Ref.: #69272]	Cultivation medium used	suter without tyrosine

[Ref.: #69272]	Colony color	Light ivory (1015), sand yellow (1002)
[Ref.: #69272]	Cultivation medium used	ISP 7

[Ref.: #69272]	Colony color	Oyster white (1013), ochre yellow (1024)
[Ref.: #69272]	Cultivation medium used	ISP 5

[Ref.: #69272]	Colony color	Sand yellow (1002)
[Ref.: #69272]	Cultivation medium used	ISP 2

[Ref.: #69272]	Colony color	Sand yellow (1002)
[Ref.: #69272]	Cultivation medium used	ISP 6

[Ref.: #69497]	Cultivation medium used	ISP 2

[Ref.: #69272]	Pigment production	no
[Ref.: #69272]	Pigment name	Melanin
[Ref.: #69272]	Pigment production	no
[Ref.: #69272]	Pigment name	soluble pigment

[Ref.: #69272]	Multicellular complex forming ability	no
[Ref.: #69272]	Multicellular complex name	Aerial mycelium
[Ref.: #69272]	Medium Name (multicellularity)	ISP 2

[Ref.: #69272]	Multicellular complex forming ability	no
[Ref.: #69272]	Multicellular complex name	Aerial mycelium
[Ref.: #69272]	Medium Name (multicellularity)	ISP 3

[Ref.: #69272]	Multicellular complex forming ability	no
[Ref.: #69272]	Multicellular complex name	Aerial mycelium
[Ref.: #69272]	Medium Name (multicellularity)	ISP 5

[Ref.: #69272]	Multicellular complex forming ability	no
[Ref.: #69272]	Multicellular complex name	Aerial mycelium
[Ref.: #69272]	Medium Name (multicellularity)	ISP 6

[Ref.: #69272]	Multicellular complex forming ability	no
[Ref.: #69272]	Multicellular complex name	Aerial mycelium
[Ref.: #69272]	Medium Name (multicellularity)	ISP 7

[Ref.: #69272]	Multicellular complex forming ability	no
[Ref.: #69272]	Multicellular complex name	Aerial mycelium
[Ref.: #69272]	Medium Name (multicellularity)	suter with tyrosine

[Ref.: #69272]	Multicellular complex forming ability	no
[Ref.: #69272]	Multicellular complex name	Aerial mycelium
[Ref.: #69272]	Medium Name (multicellularity)	suter without tyrosine

[Ref.: #69497]	Multicellular complex forming ability	yes
[Ref.: #69497]	Multicellular complex name	aerial hyphae
[Ref.: #69497]	Multicellular complex color	black
[Ref.: #69497]	Medium Name (multicellularity)	ISP 3
[Ref.: #69497]	Multicellular complex further description	yellowish-brown extensively branched substrate mycelia

Multimedia content

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Caption:

Medium 65 28°C

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Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

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Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

[Ref.: #69497]

Culture medium

ISP 5

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Culture medium growth

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Culture medium

ISP 6

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Culture medium growth

[Ref.: #69497]

Culture medium

ISP 7

[Ref.: #69497]

Culture medium growth

[Ref.: #69497]

Culture medium

ISP 2

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Culture medium growth

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Culture medium

ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)

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Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #66461]	growth	28 °C
[Ref.: #69497]	growth	20.0-37.0 °C
[Ref.: #69497]	optimum	28 °C

	pH	Kind of pH		pH
[Ref.: #69497]			growth	6.0-10.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69497]	Oxygen tolerance	aerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %98.7

[Ref.: #125439]	Ability of spore formation	yes Confidence in %92.7
[Ref.: #125438]	Ability of spore formation	yes Confidence in %91.153

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #69272]		NaCl		growth	0-2.5	%
[Ref.: #69497]		NaCl		growth	0.0-6.0	%(w/v)

[Ref.: #69497]	Observation	The polar lipid profile consists of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside.
[Ref.: #69497]	Observation	ll-Diaminopimelic acid is the diagnostic diamino acid in cell-wall peptidoglycan.
[Ref.: #69497]	Observation	The predominant menaquinone is MK-9(H6).

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #69272]	arabinose ChEBI	+	growth
[Ref.: #69497]	cellobiose ChEBI	+	carbon source
[Ref.: #69272]	cellulose ChEBI	+	growth
[Ref.: #69497]	cellulose ChEBI	+	hydrolysis
[Ref.: #69497]	D-fructose ChEBI	+	carbon source
[Ref.: #69497]	D-galactose ChEBI	+	carbon source
[Ref.: #69497]	D-glucose ChEBI	+	carbon source
[Ref.: #68379]	D-glucose ChEBI	-	fermentation	* from API Coryne
[Ref.: #69497]	D-mannitol ChEBI	+	carbon source
[Ref.: #68379]	D-mannitol ChEBI	-	fermentation	* from API Coryne
[Ref.: #69497]	D-mannose ChEBI	+	carbon source
[Ref.: #69497]	D-ribose ChEBI	+	carbon source
[Ref.: #68379]	D-ribose ChEBI	-	fermentation	* from API Coryne
[Ref.: #69497]	D-sorbitol ChEBI	+	carbon source
[Ref.: #69497]	D-xylose ChEBI	+	carbon source
[Ref.: #68379]	D-xylose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	esculin ChEBI	+	hydrolysis	* from API Coryne
[Ref.: #69272]	fructose ChEBI	+	growth
[Ref.: #69497]	gelatin ChEBI	+	hydrolysis
[Ref.: #68379]	gelatin ChEBI	+	hydrolysis	* from API Coryne
[Ref.: #69272]	glucose ChEBI	+	growth
[Ref.: #69497]	glycerol ChEBI	+	carbon source
[Ref.: #69497]	glycine ChEBI	+	nitrogen source
[Ref.: #68379]	glycogen ChEBI	-	fermentation	* from API Coryne
[Ref.: #69272]	inositol ChEBI	+	growth
[Ref.: #69497]	L-alanine ChEBI	+	nitrogen source
[Ref.: #69497]	L-arabinose ChEBI	+	carbon source
[Ref.: #69497]	L-arginine ChEBI	-	nitrogen source
[Ref.: #69497]	L-aspartate ChEBI	+	nitrogen source
[Ref.: #69497]	L-cysteine ChEBI	-	nitrogen source
[Ref.: #69497]	L-glutamate ChEBI	+	nitrogen source
[Ref.: #69497]	L-glutamine ChEBI	+	nitrogen source
[Ref.: #69497]	L-histidine ChEBI	+	nitrogen source
[Ref.: #69497]	L-lysine ChEBI	-	nitrogen source
[Ref.: #69497]	L-methionine ChEBI	+	nitrogen source
[Ref.: #69497]	L-phenylalanine ChEBI	+	nitrogen source
[Ref.: #69497]	L-rhamnose ChEBI	+	carbon source
[Ref.: #69497]	L-serine ChEBI	+	nitrogen source
[Ref.: #69497]	L-threonine ChEBI	+	nitrogen source
[Ref.: #69497]	L-tryptophan ChEBI	-	nitrogen source
[Ref.: #69497]	L-tyrosine ChEBI	+	nitrogen source
[Ref.: #69497]	L-valine ChEBI	+	nitrogen source
[Ref.: #69497]	lactose ChEBI	+	carbon source
[Ref.: #68379]	lactose ChEBI	-	fermentation	* from API Coryne
[Ref.: #69497]	maltose ChEBI	+	carbon source
[Ref.: #68379]	maltose ChEBI	-	fermentation	* from API Coryne
[Ref.: #69272]	mannose ChEBI	+	growth
[Ref.: #69497]	myo-inositol ChEBI	+	carbon source
[Ref.: #69497]	nitrate ChEBI	-	reduction
[Ref.: #68379]	nitrate ChEBI	+	reduction	* from API Coryne
[Ref.: #69272]	raffinose ChEBI	+	growth
[Ref.: #69497]	raffinose ChEBI	+	carbon source
[Ref.: #69272]	rhamnose ChEBI	+	growth
[Ref.: #69497]	starch ChEBI	-	hydrolysis
[Ref.: #69272]	sucrose ChEBI	+	growth
[Ref.: #69497]	sucrose ChEBI	+	carbon source
[Ref.: #68379]	sucrose ChEBI	-	fermentation	* from API Coryne
[Ref.: #69497]	tween 20 ChEBI	-	hydrolysis
[Ref.: #69497]	tween 40 ChEBI	-	hydrolysis
[Ref.: #69497]	tween 60 ChEBI	-	hydrolysis
[Ref.: #69497]	tween 80 ChEBI	+	hydrolysis
[Ref.: #68379]	urea ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #69497]	xylitol ChEBI	+	carbon source
[Ref.: #69272]	xylose ChEBI	+	growth
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #69497]		hydrogen sulfide ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68379]	alkaline phosphatase	+	3.1.3.1	* from API Coryne, API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	+	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68379]	alpha-glucosidase	-	3.2.1.20	* from API Coryne
[Ref.: #68382]	alpha-mannosidase	+	3.2.1.24	* from API zym
[Ref.: #68379]	beta-galactosidase	+	3.2.1.23	* from API Coryne, API zym
[Ref.: #68379]	beta-glucosidase	+	3.2.1.21	* from API Coryne, API zym
[Ref.: #68379]	beta-glucuronidase	-	3.2.1.31	* from API Coryne, API zym
[Ref.: #69497]	catalase	+	1.11.1.6
[Ref.: #69497]	cytochrome oxidase	-	1.9.3.1
[Ref.: #68379]	gelatinase	+		* from API Coryne
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym
[Ref.: #68379]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API Coryne
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #68379]	pyrazinamidase	-	3.5.1.B15	* from API Coryne
[Ref.: #68379]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API Coryne
[Ref.: #69497]	urease	+	3.5.1.5
[Ref.: #68379]	urease	-	3.5.1.5	* from API Coryne
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #69497]

Fatty acid	Percentage
C16:0	20.4
iso-C16:0	19
anteiso-C15:0	15
C16:1 w7c / C16:1 w6c	10.2

API® Coryne:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitrateNIT	PyrazinamidasePYZ	Pyrrolidonyl arylamidasePYRA	Alkaline phosphatasePAL	beta-Glucuronidasebeta GUR	beta-Galactosidasebeta GAL	alpha-Glucosidasealpha GLU	N-Acetyl-beta-Glucosidasebeta NAG	Esculin hydrolysis/beta-GlucosidaseESC	Urease/urea hydrolysisURE	Gelatinase/gelatin hydrolysisGEL	Control fermentationControl	Fermentation of D-glucoseGLU	Fermentation of D-riboseRIB	Fermentation of D-xyloseXYL	Fermentation of D-mannitolMAN	Fermentation of maltoseMAL	Fermentation of lactoseLAC	Fermentation of sucroseSAC	Fermentation of glycogenGLYG	CatalaseCAT
[Ref.: #69272]	3766	+	-	-	+	-	+	-	-	+	-	+	not determinedn.d.	-	-	-	-	-	-	-	-	not determinedn.d.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #69272]	5950	not determinedn.d.	+	+/-	+/-	-	+	+	+/-	+/-	-	+	+	+	+	-	+	+	+	+	-

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

[Ref.: #66461]	Sample type/isolated from	karst cave soil
[Ref.: #66461]	Geographic location (country and/or sea, region)	Xingyi
[Ref.: #66461]	Country	China
[Ref.: #66461]	Country ISO 3 Code	CHN
[Ref.: #66461]	Continent	Asia
[Ref.: #66461]	Geographic location	25.1500°/104.7670°

[Ref.: #69497]	Sample type/isolated from	soil sample karst cave
[Ref.: #69497]	Geographic location (country and/or sea, region)	Xingyi County, Guizhou Province
[Ref.: #69497]	Country	China
[Ref.: #69497]	Country ISO 3 Code	CHN
[Ref.: #69497]	Continent	Asia
[Ref.: #69497]	Geographic location	25.1500°/104.7670°
[Ref.: #69497]	Enrichment culture	humic acid-vitamin agar
[Ref.: #69497]	Enrichment culture composition	supplemented with cycloheximide (50 mg/l) and nalidixic acid (20 mg/l)
[Ref.: #69497]	Enrichment culture duration	14 days
[Ref.: #69497]	Enrichment culture temperature	28 ̊C
[Ref.: #69497]	Isolation/enrichment procedure	dilution plate method
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Geologic
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

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.: #66461]	Streptomyces cavernae 16S ribosomal RNA gene, partial sequence	MH553382	1517	GenBank ENA	2259034 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #69272]	Streptomyces cavernae SYSU K10008	GCA_004023625	scaffold	GenBank ENA	2259034 tax ID
[Ref.: #69497]	genome sequence	RPDJ00000000		GenBank ENA	2259034 tax ID

[Ref.: #66461]	GC-content	70.5 mol%	sequence analysis
[Ref.: #69497]	GC-content	70.5 mol%	genome sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Streptomyces cavernae SYSU K10008 NCBI: GCA_004023625.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	88.195	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	95.963	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	87.531	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	yes	91.153	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	93.5	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	88.5	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Streptomyces cavernae SYSU K10008 NCBI: GCA_004023625
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	yes	92.7
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	92.2
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	positive	99.7
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	98.7

Availability in culture collections External links

[Ref.: #66461]

Culture collection no.

DSM 104115, KCTC 39850, SYSU K10008

[Ref.: #112100]

SI-ID 408132

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Streptomyces cavernae sp. nov., a novel actinobacterium isolated from a karst cave sediment sample.	Fang BZ, Han MX, Jiao JY, Xie YG, Zhang XT, Liu L, Zhang ZT, Xiao M, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.003724	2020	*

References

#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 )

#66461

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 104115

#68379

Automatically annotated from API Coryne .

#68382

Automatically annotated from API zym .

#69272

Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .

#69497

Bei Li, Yuying Li, Ronghua Liu, Chunxu Xue, Xiaoyu Zhu, Xiaorong Tian, Xiaolei Wang, Jinchang Liang, Yanfen Zheng, Xiao-Hua Zhang: Streptomyces cavernae sp. nov., a novel actinobacterium isolated from a karst cave sediment sample. IJSEM 70: 2020 ( DOI 10.1099/ijsem.0.003724 )

#112100

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-ID408132.1 )

#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 .

* These data were automatically processed and therefore are not curated

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Streptomyces cavernae SYSU K10008

Streptomyces cavernae SYSU K10008

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