Amycolatopsis acidiphila (KCTC 39523, JCM 30562, 2-5)

Name: Amycolatopsis acidiphila (KCTC 39523, JCM 30562, 2-5)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 141006

Type strain

Strain Designation 2-5

Culture col. no. KCTC 39523 JCM 30562 2-5

NCBI tax ID(s) 715473

Special Collections JCM KCTC Literature strains

History S. B. Kim; Chungnam Natl. Univ., South Korea; 2-5. <- SB Kim, CNU

Links

Amycolatopsis acidiphila 2-5 is an aerobe bacterium that has a light brown pigmentation and was isolated from coal mine soil from coal mine site, Nalaikh Province, Ulaanbataar, Mongolia.

pigmented aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 26833

KCTC 39523,JCM 30562

@ref 20215

Last LPSN update 2026-02-09 11:33:47

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Pseudonocardiales

Family Pseudonocardiaceae

Genus Amycolatopsis

Species Amycolatopsis acidiphila

Full scientific name Amycolatopsis acidiphila Oyuntsetseg et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	positive	99.4

Colony morphology

@ref	Colony color	Medium used
43897	light yellow	Starch casein agar
43897	light yellow	modified Benett's agar
43897	light yellow	ISP 2 agar
43897	light yellow	ISP 3 agar

Pigmentation

@ref	Production	Color	Name
43897		light brown	diffusible pigments

Culture and growth conditions

Culture medium

@ref	Name	Composition
43897	ISP 2 agar
43897	ISP 3 agar
43897	modified Bennett's agar	glucose 10 g/L, casitone 2 g/L, yeast extract 1 g/L, Lab-Lemco powder 0.8 g/L and agar 15 /L, pH 5.5
43897	Starch casein agar	soluble starch 10 g/L, casein 0.3 g/L, KNO3 2 g/L, NaCl2 g/L, K2HPO4 2 g/L, MgSO4.7H2O 0.05 g/L, CaCO3 0.02 g/L, FeSO4.7H2O 0.01 g/L, agar 15 g/L, pH 4.5, supplemented with cycloheximide and nystatin (50 µg/mL)

Culture temp

@ref	Growth	Type	Temperature (°C)
43897	positive	growth	15-40
43897	positive	optimum	30
67770	positive	growth	28
67771	positive	growth	30

Culture pH

@ref	Ability	Type	PH
43897	positive	optimum	5.5-6.0
43897	positive	growth	4.5-7.5

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
67771	aerobe
125439	obligate aerobe	97.9

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43897	NaCl	positive	optimum	0 %(w/v)
43897	NaCl	positive	growth	0-6 %(w/v)

Observation

@ref	Observation
43897	quinone MK-9
67770	quinones: MK-9(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43897	85146 ChEBI	carboxymethylcellulose	-	degradation
43897		casein	+	degradation
43897	15824 ChEBI	D-fructose	+	carbon source
43897	12936 ChEBI	D-galactose	+	carbon source
43897	17634 ChEBI	D-glucose	+	carbon source
43897	16899 ChEBI	D-mannitol	+	carbon source
43897	17924 ChEBI	D-sorbitol	+	carbon source
43897	65327 ChEBI	D-xylose	+	carbon source
43897	16991 ChEBI	dna	-	degradation
43897	5291 ChEBI	gelatin	+	degradation
43897		L-alanine 4-nitroanilide	-	carbon source
43897	30849 ChEBI	L-arabinose	+	carbon source
43897	16467 ChEBI	L-arginine	+	carbon source
43897	17196 ChEBI	L-asparagine	+	carbon source
43897	18050 ChEBI	L-glutamine	+	carbon source
43897	15971 ChEBI	L-histidine	+	carbon source
43897	17191 ChEBI	L-isoleucine	+	carbon source
43897	18019 ChEBI	L-lysine	-	carbon source
43897	62345 ChEBI	L-rhamnose	+	carbon source
43897	28053 ChEBI	melibiose	+	carbon source
43897	17268 ChEBI	myo-inositol	+	carbon source
43897	17632 ChEBI	nitrate	-	reduction
43897	16634 ChEBI	raffinose	+	carbon source
43897	17814 ChEBI	salicin	+	carbon source
43897	15611 ChEBI	sarcosine	+	carbon source
43897	28017 ChEBI	starch	-	degradation
43897	35020 ChEBI	tributyrin	-	degradation
43897	53424 ChEBI	tween 20	+	degradation
43897	53423 ChEBI	tween 40	+	degradation
43897	53425 ChEBI	tween 60	+	degradation
43897	53426 ChEBI	tween 80	+	degradation
43897	15318 ChEBI	xanthine	+	degradation

Enzymes

@ref	Value	Activity	Ec
43897	acid phosphatase	+	3.1.3.2
43897	alkaline phosphatase	-	3.1.3.1
43897	alpha-chymotrypsin	+	3.4.21.1
43897	alpha-fucosidase	-	3.2.1.51
43897	alpha-galactosidase	-	3.2.1.22
43897	alpha-glucosidase	+	3.2.1.20
43897	alpha-mannosidase	+/-	3.2.1.24
43897	beta-galactosidase	+/-	3.2.1.23
43897	beta-glucosidase	+	3.2.1.21
43897	beta-glucuronidase	-	3.2.1.31
43897	cystine arylamidase	+/-	3.4.11.3
43897	esterase (C 4)	+
43897	esterase Lipase (C 8)	+
43897	leucine arylamidase	+	3.4.11.1
43897	lipase (C 14)	+/-
43897	N-acetyl-beta-glucosaminidase	+	3.2.1.52
43897	naphthol-AS-BI-phosphohydrolase	+
43897	trypsin	-	3.4.21.4
43897	valine arylamidase	+/-

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	ethanol fermentation	100	2 of 2
66794	4-hydroxymandelate degradation	100	9 of 9
66794	enterobactin biosynthesis	100	3 of 3
66794	acetate fermentation	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	cyanate degradation	100	3 of 3
66794	methylglyoxal degradation	100	5 of 5
66794	resorcinol degradation	100	2 of 2
66794	valine metabolism	100	9 of 9
66794	phenol degradation	100	20 of 20
66794	starch degradation	100	10 of 10
66794	biotin biosynthesis	100	4 of 4
66794	propanol degradation	100	7 of 7
66794	cardiolipin biosynthesis	100	7 of 7
66794	Entner Doudoroff pathway	100	10 of 10
66794	aerobactin biosynthesis	100	1 of 1
66794	taurine degradation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	vitamin K metabolism	100	5 of 5
66794	ribulose monophosphate pathway	100	2 of 2
66794	glycolate and glyoxylate degradation	100	6 of 6
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	pentose phosphate pathway	100	11 of 11
66794	ethylmalonyl-CoA pathway	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	gallate degradation	100	5 of 5
66794	isoleucine metabolism	100	8 of 8
66794	glycogen metabolism	100	5 of 5
66794	cellulose degradation	100	5 of 5
66794	adipate degradation	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	flavin biosynthesis	93.33	14 of 15
66794	citric acid cycle	92.86	13 of 14
66794	leucine metabolism	92.31	12 of 13
66794	phenylalanine metabolism	92.31	12 of 13
66794	proline metabolism	90.91	10 of 11
66794	4-hydroxyphenylacetate degradation	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	tryptophan metabolism	89.47	34 of 38
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	allantoin degradation	88.89	8 of 9
66794	degradation of hexoses	88.89	16 of 18
66794	ketogluconate metabolism	87.5	7 of 8
66794	3-phenylpropionate degradation	86.67	13 of 15
66794	alanine metabolism	86.21	25 of 29
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	aclacinomycin biosynthesis	85.71	6 of 7
66794	pyrimidine metabolism	84.44	38 of 45
66794	degradation of sugar acids	84	21 of 25
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	propionate fermentation	80	8 of 10
66794	3-chlorocatechol degradation	80	4 of 5
66794	factor 420 biosynthesis	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	hydrogen production	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	purine metabolism	79.79	75 of 94
66794	vitamin B12 metabolism	79.41	27 of 34
66794	photosynthesis	78.57	11 of 14
66794	tyrosine metabolism	78.57	11 of 14
66794	glutathione metabolism	78.57	11 of 14
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	urea cycle	76.92	10 of 13
66794	vitamin B1 metabolism	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	non-pathway related	76.32	29 of 38
66794	gluconeogenesis	75	6 of 8
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	butanoate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	degradation of aromatic, nitrogen containing compounds	75	9 of 12
66794	cyclohexanol degradation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	arginine metabolism	75	18 of 24
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	toluene degradation	75	3 of 4
66794	lipid metabolism	74.19	23 of 31
66794	methionine metabolism	73.08	19 of 26
66794	vitamin B6 metabolism	72.73	8 of 11
66794	histidine metabolism	72.41	21 of 29
66794	degradation of pentoses	71.43	20 of 28
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	myo-inositol biosynthesis	70	7 of 10
66794	androgen and estrogen metabolism	68.75	11 of 16
66794	degradation of sugar alcohols	68.75	11 of 16
66794	oxidative phosphorylation	68.13	62 of 91
66794	octane oxidation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	IAA biosynthesis	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	cholesterol biosynthesis	63.64	7 of 11
66794	d-xylose degradation	63.64	7 of 11
66794	sulfate reduction	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	coenzyme M biosynthesis	60	6 of 10
66794	creatinine degradation	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	lysine metabolism	59.52	25 of 42
66794	carotenoid biosynthesis	59.09	13 of 22
66794	bile acid biosynthesis, neutral pathway	58.82	10 of 17
66794	benzoyl-CoA degradation	57.14	4 of 7
66794	nitrate assimilation	55.56	5 of 9
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	CMP-KDO biosynthesis	50	2 of 4
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	phenylmercury acetate degradation	50	1 of 2
66794	carnitine metabolism	50	4 of 8
66794	pantothenate biosynthesis	50	3 of 6
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	lipid A biosynthesis	44.44	4 of 9
66794	arachidonic acid metabolism	44.44	8 of 18
66794	polyamine pathway	43.48	10 of 23
66794	ascorbate metabolism	40.91	9 of 22
66794	elloramycin biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	sphingosine metabolism	33.33	2 of 6
66794	sulfoquinovose degradation	33.33	1 of 3
66794	chlorophyll metabolism	33.33	6 of 18
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	mevalonate metabolism	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	methanogenesis from CO2	25	3 of 12
66794	alginate biosynthesis	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	daunorubicin biosynthesis	22.22	2 of 9

Fatty acid profile

Metadata FA analysis

@ref

43897

Fatty acid	Percentage
C16:0 iso	35
C17:1ω6c	18.9
C15:0 iso	13.5
C15:0 anteiso	11.1
C16:0	9.3
C16:1 iso H	2.8
C17:0 iso	2.1
C17:0 anteiso	2
C14:0 iso	1.7

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Other	#Mine
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture composition	Enrichment culture duration	Enrichment culture temperature
43897	coal mine soil (pH 5.9) from coal mine site, Nalaikh Province, Ulaanbataar, Mongolia	Nalaikh Province, Ulaanbataar	Mongolia	MNG	Asia	acidified starch casein agar	soluble starch 10 g/L, casein 0.3 g/L, KNO3 2 g/L, NaCl2 g/L, K2HPO4 2 g/L, MgSO4.7H2O 0.05 g/L, CaCO3 0.02 g/L, FeSO4.7H2O 0.01 g/L, agar 15 g/L, pH 4.5, supplemented with cycloheximide and nystatin (50 µg/mL)	1 week	30
67770	Soil at Nalaikh coal mining site	Nalaikh Province	Mongolia	MNG	Asia
67771	Mongolian Coal mining soil		Mongolia	MNG	Asia

Taxonmaps

69479

Global distribution of 16S sequence GU132436 (>99% sequence identity) for Amycolatopsis from Microbeatlas

Aquatic Samples	7
Soil Samples	97
Animal Samples	14
Plant Samples	1
Total Samples	119

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM2139149v1 assembly for Amycolatopsis acidiphila KCTC 39523	complete	GCA_021391495	715473.5	8112554572	715473	96.12
66792	ASM771374v1 assembly for Amycolatopsis acidiphila JCM 30562	contig	GCA_007713745	715473.3	2899342247	715473	33.67

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
43897	Amycolatopsis acidiphila 16S ribosomal RNA gene, partial sequence	GU132436
124043	Amycolatopsis acidiphila strain JCM 30562 16S ribosomal RNA gene, partial sequence.	MN399888	1521		715473

GC content

@ref	GC-content (mol%)	Method
43897	72	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 acidiphila JCM 30562
NCBI: GCA_007713745

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	71.60	no
125439	motility	BacteriaNetⓘ	no	86.00	no
125439	gram_stain	BacteriaNetⓘ	positive	99.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Amycolatopsis acidiphila KCTC 39523
NCBI: GCA_021391495.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	89.96	no
125438	anaerobic	anaerobicⓘ	no	95.21	no
125438	aerobic	aerobicⓘ	yes	89.75	yes
125438	spore-forming	spore-formingⓘ	yes	76.31	no
125438	thermophilic	thermophileⓘ	no	94.39	yes
125438	flagellated	motile2+ⓘ	no	84.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	3-Hydroxypyridine Dehydrogenase HpdA Is Encoded by a Novel Four-Component Gene Cluster and Catalyzes the First Step of 3-Hydroxypyridine Catabolism in Ensifer adhaerens HP1.	Wang H, Wang X, Ren H, Wang X, Lu Z.	Appl Environ Microbiol	10.1128/aem.01313-20	2020
Phylogeny	Amycolatopsis acididurans sp. nov., isolated from peat swamp forest soil in Thailand.	Teo WFA, Lipun K, Srisuk N, Duangmal K	J Antibiot (Tokyo)	10.1038/s41429-020-00382-2	2020
Phylogeny	Amycolatopsis acidicola sp. nov., isolated from peat swamp forest soil.	Teo WFA, Srisuk N, Duangmal K	Int J Syst Evol Microbiol	10.1099/ijsem.0.003933	2020
Phylogeny	Amycolatopsis acidiphila sp. nov., a moderately acidophilic species isolated from coal mine soil.	Oyuntsetseg B, Cho SH, Jeon SJ, Lee HB, Shin KS, Kim IS, Kim SB	Int J Syst Evol Microbiol	10.1099/ijsem.0.002126	2017

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 )
#43897	Bilguun Oyuntsetseg, Sung-Heun Cho, Sun Jeong Jeon, Hyang Burm Lee, Kee-Sun Shin, In-Seop Kim, Seung Bum Kim: Amycolatopsis acidiphila sp. nov., a moderately acidophilic species isolated from coal mine soil. IJSEM 67: 3387 - 3392 2017 ( DOI 10.1099/ijsem.0.002126 , PubMed 28857027 )
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#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;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 acidiphila (KCTC 39523, JCM 30562, 2-5)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Halophily

Observation

Metabolite utilization

Enzymes

Pathway annotation

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_021391495

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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