Amycolatopsis rubida (DSM 44637, AS 4.1541, CIP 107102)

Name: Amycolatopsis rubida (DSM 44637, AS 4.1541, CIP 107102)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13243

Type strain

Strain Designation 13.4

Culture col. no. DSM 44637 AS 4.1541 CIP 107102 JCM 10871 NRRL B-24150 5 more

NCBI tax ID(s) 112413

Special Collections DSMZ JCM KCTC CIP Wink compendium

History <- T. Kudo, JCM <- Z. Liu; 13.4 Z. Liu 13.4. CIP <- 2001, JCM <- Z. Liu: strain 13.4

Links

Amycolatopsis rubida 13.4 is an obligate aerobe, Gram-positive, filament-shaped bacterium that was isolated from soil of a conifer forest.

Gram-positive filament-shaped obligate aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 100502

AS 4.1541,JCM 10871,DSM 44637,CIP 107102,NRRL B-24150,KCTC 19909,ATCC BAA-726,NBRC 100041,CGMCC 4.1541

@ref 20215

Last LPSN update 2026-02-09 11:21:05

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Pseudonocardiales

Family Pseudonocardiaceae

Genus Amycolatopsis

Species Amycolatopsis rubida

Full scientific name Amycolatopsis rubida Huang et al. 2001

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
122282	positive	filament-shaped
125439	positive			98.8

Colony morphology

@ref	Colony color	Incubation period	Medium used
20084	Beige (1001)	10-14 days	ISP 2
20084	Beige (1001)	10-14 days	ISP 3
20084	Beige (1001)	10-14 days	ISP 4
20084	Beige (1001)	10-14 days	ISP 5
20084	Beige (1001)	10-14 days	ISP 6
20084	Beige (1001)	10-14 days	ISP 7
122282

Multicellular morphology

@ref	Forms multicellular complex	Medium name
20084		ISP 2
20084		ISP 3
20084		ISP 4
20084		ISP 5
20084		ISP 6
20084		ISP 7

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
11946	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
20084	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
20084	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:
20084	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
20084	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
20084	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
20084	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
39659	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122282	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
11946	positive	growth	28
20084	positive	optimum	28
39659	positive	growth	30
67770	positive	growth	28
122282	positive	growth	25-37
122282	negative	growth	10
122282	negative	growth	41
122282	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
122282	obligate aerobe
125438	aerobe	90.602
125439	obligate aerobe	97.4

Halophily

@ref	Salt	Growth	Tested relation	Concentration
122282	NaCl	positive	growth	0-10 %

Observation

67770

Observationquinones: MK-9(H₆)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
122282	16947 ChEBI	citrate	-	carbon source
122282	4853 ChEBI	esculin	-	hydrolysis
122282	606565 ChEBI	hippurate	-	hydrolysis
122282	17632 ChEBI	nitrate	-	reduction
122282	17632 ChEBI	nitrate	-	respiration
122282	16301 ChEBI	nitrite	-	reduction

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
122282	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
122282	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
122282	15688 ChEBI	acetoin	-
122282	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
122282	alcohol dehydrogenase	-	1.1.1.1
68382	alpha-chymotrypsin	+	3.4.21.1	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
122282	amylase	-
122282	beta-galactosidase	-	3.2.1.23
68382	beta-glucuronidase	-	3.2.1.31	from API zym
122282	caseinase	+	3.4.21.50
122282	catalase	+	1.11.1.6
122282	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
122282	gamma-glutamyltransferase	+	2.3.2.2
122282	gelatinase	+
122282	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
122282	lipase	+
122282	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
122282	ornithine decarboxylase	-	4.1.1.17
122282	oxidase	-
122282	phenylalanine ammonia-lyase	-	4.3.1.24
122282	protease	+
122282	tryptophan deaminase	-
122282	tween esterase	-
122282	urease	+	3.5.1.5

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
20084	not determinedn.d.	+	+	+	+	+	+	+	+	+	+	+	-	+	-	+	+	+	+	+
122282	-	-	+	+	-	+	-	-	-	+	+	+	-	-	-	-	-	+	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
122282	not determinedn.d.	+	+	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-	+	+	+	-	+	-	-	+	-	+	-	-	-	-	+	+	+	-	-	-	+	-	+	+	-	-	-	-	-	-	-	+	+	+	-	-	+	+	-	+	-	-	+	+	+	+	-	-	+	-	-	-	-	-	+	+	+	+	+	-	-	-	+	+	-	-	-	-	-	+	-	+	+	+	+	+	+	+	-	+	+	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Forest
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
11946	soil of a conifer forest	Guangxi Province	China	CHN	Asia
67770	Soil of a conifer forest	Guangxi Province	China	CHN	Asia
122282	Environment, Soil, conifer forest	Guangxi	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AF222022 (>99% sequence identity) for Amycolatopsis from Microbeatlas

Aquatic Samples
Soil Samples	59
Animal Samples	14
Plant Samples	28
Total Samples	101

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
11946	1	Risk group (German classification) According to TRBA 466
20084	1	German classification According to TRBA 466
122282	1	Risk group (French 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 2675903692 annotated assembly for Amycolatopsis rubida DSM 44637	contig	GCA_900115345	112413.4	2675903692	112413	68.59

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Amycolatopsis rubidus 16S ribosomal RNA gene, partial sequence	AF222022	1402		112413

GC content

@ref	GC-content (mol%)	Method
67770	69.8	genome sequence analysis
67770	67.4	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: Amycolatopsis rubida DSM 44637
NCBI: GCA_900115345

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	78.10	no
125439	motility	BacteriaNetⓘ	no	89.90	no
125439	gram_stain	BacteriaNetⓘ	positive	98.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Amycolatopsis rubida strain DSM 44637
PATRIC: 112413.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	85.43	no
125438	anaerobic	anaerobicⓘ	no	97.42	yes
125438	spore-forming	spore-formingⓘ	yes	82.31	no
125438	aerobic	aerobicⓘ	yes	90.60	no
125438	thermophilic	thermophileⓘ	no	96.00	yes
125438	flagellated	motile2+ⓘ	no	89.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Amycolatopsis dendrobii sp. nov., an endophytic actinomycete isolated from Dendrobium heterocarpum Lindl.	Tedsree N, Tanasupawat S, Sritularak B, Kuncharoen N, Likhitwitayawuid K	Int J Syst Evol Microbiol	10.1099/ijsem.0.004902	2021
Phylogeny	Amycolatopsis rubida sp. nov., a new Amycolatopsis species from soil.	Huang Y, Qi W, Lu Z, Liu Z, Goodfellow M	Int J Syst Evol Microbiol	10.1099/00207713-51-3-1093	2001

References

#11946	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44637
#20084	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#39659	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68382	Automatically annotated from API zym .
#69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .
#122282	Collection of Institut Pasteur ; Curators of the CIP; CIP 107102
#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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Amycolatopsis rubida (DSM 44637, AS 4.1541, CIP 107102)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

API zym

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900115345

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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