Acidipila rosea (DSM 103428, KCTC 23427, NBRC 107607)

Name: Acidipila rosea (DSM 103428, KCTC 23427, NBRC 107607)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132249

Type strain

Strain Designation AP8

Culture col. no. DSM 103428 KCTC 23427 NBRC 107607 AP8

NCBI tax ID(s) 768535

Special Collections DSMZ KCTC

History <- KCTC; KCTC 23427

Links

Acidipila rosea AP8 is a bacterium that was isolated from acid mine drainage.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 397443

KCTC 23427,NBRC 107607,DSM 103428

@ref 20215

Last LPSN update 2026-02-09 11:31:39

Domain Bacteria

Phylum Acidobacteriota

Class Terriglobia

Order Terriglobales

Family Acidobacteriaceae

Genus Acidipila

Species Acidipila rosea

Full scientific name Acidipila rosea Okamura et al. 2015

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	92.414

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
24038	SSE/HD1:10 (DSMZ Medium 1426)		Medium recipe at MediaDive	Name: SSE/HD 1:10 MEDIUM (DSMZ Medium 1426) Composition: MES 1.95 g/l Peptone 0.5 g/l CaSO4 x 2 H2O 0.4303 g/l MgSO4 x 7 H2O 0.3695 g/l Yeast extract 0.25 g/l Na NO3 0.212 g/l CaCl2 x 2 H2O 0.1469 g/l Ca(NO3)2 x 4 H2O 0.118 g/l MgCl2 x 6 H2O 0.1018 g/l Glucose 0.1 g/l (NH4)2SO4 0.09915 g/l NH4Cl 0.05345 g/l K2SO4 0.0435 g/l FeSO4 x 7 H2O 0.00555 g/l KH2PO4 0.00340213 g/l HCl 0.0025 g/l FeCl2 x 4 H2O 0.0015 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 4 H2O 0.0001 g/l ZnCl2 7e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l Pyridoxine hydrochloride 1e-05 g/l H3BO3 6e-06 g/l Lipoic acid 5e-06 g/l D-Calcium pantothenate 5e-06 g/l Nicotinic acid 5e-06 g/l Riboflavin 5e-06 g/l Thiamine-HCl x 2 H2O 5e-06 g/l p-Aminobenzoic acid 5e-06 g/l Folic acid 2e-06 g/l Biotin 2e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Vitamin B12 1e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
24038	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	aerobe	95.8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	-	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68382	alkaline phosphatase	+	3.1.3.1	from API zym
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
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	+	3.2.1.23	from API zym
68382	beta-glucosidase	+	3.2.1.21	from API zym
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
68382	beta-glucuronidase	+	3.2.1.31	from API zym
68369	cytochrome oxidase	-	1.9.3.1	from API 20NE
68382	esterase (C 4)	+		from API zym
68369	gelatinase	-		from API 20NE
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
68382	trypsin	+	3.4.21.4	from API zym
68369	urease	-	3.5.1.5	from API 20NE
68382	valine arylamidase	+		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	quinate degradation	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	cardiolipin biosynthesis	100	7 of 7
66794	kanosamine biosynthesis II	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	valine metabolism	100	9 of 9
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	threonine metabolism	100	10 of 10
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	glycogen metabolism	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	acetate fermentation	100	4 of 4
66794	suberin monomers biosynthesis	100	2 of 2
66794	palmitate biosynthesis	95.45	21 of 22
66794	phenylalanine metabolism	92.31	12 of 13
66794	pentose phosphate pathway	90.91	10 of 11
66794	starch degradation	90	9 of 10
66794	Entner Doudoroff pathway	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	d-mannose degradation	88.89	8 of 9
66794	ketogluconate metabolism	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	heme metabolism	85.71	12 of 14
66794	photosynthesis	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	purine metabolism	81.91	77 of 94
66794	peptidoglycan biosynthesis	80	12 of 15
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	lipid A biosynthesis	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	histidine metabolism	75.86	22 of 29
66794	CMP-KDO biosynthesis	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	tryptophan metabolism	73.68	28 of 38
66794	pyrimidine metabolism	73.33	33 of 45
66794	proline metabolism	72.73	8 of 11
66794	d-xylose degradation	72.73	8 of 11
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	citric acid cycle	71.43	10 of 14
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	propionate fermentation	70	7 of 10
66794	leucine metabolism	69.23	9 of 13
66794	methionine metabolism	69.23	18 of 26
66794	urea cycle	69.23	9 of 13
66794	degradation of pentoses	67.86	19 of 28
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	acetoin degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	1,4-dihydroxy-6-naphthoate biosynthesis	66.67	4 of 6
66794	degradation of hexoses	66.67	12 of 18
66794	alanine metabolism	65.52	19 of 29
66794	tyrosine metabolism	64.29	9 of 14
66794	metabolism of disaccharids	63.64	7 of 11
66794	non-pathway related	63.16	24 of 38
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	lipid metabolism	61.29	19 of 31
66794	3-chlorocatechol degradation	60	3 of 5
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	factor 420 biosynthesis	60	3 of 5
66794	degradation of sugar acids	60	15 of 25
66794	vitamin K metabolism	60	3 of 5
66794	arginine metabolism	58.33	14 of 24
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	propanol degradation	57.14	4 of 7
66794	glutathione metabolism	57.14	8 of 14
66794	nitrate assimilation	55.56	5 of 9
66794	cysteine metabolism	55.56	10 of 18
66794	carotenoid biosynthesis	54.55	12 of 22
66794	phenylpropanoid biosynthesis	53.85	7 of 13
66794	lysine metabolism	52.38	22 of 42
66794	cyclohexanol degradation	50	2 of 4
66794	carnitine metabolism	50	4 of 8
66794	ribulose monophosphate pathway	50	1 of 2
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	myo-inositol biosynthesis	50	5 of 10
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	glycine metabolism	50	5 of 10
66794	phenylmercury acetate degradation	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	lactate fermentation	50	2 of 4
66794	catecholamine biosynthesis	50	2 of 4
66794	phenol degradation	50	10 of 20
66794	ethanol fermentation	50	1 of 2
66794	polyamine pathway	47.83	11 of 23
66794	3-phenylpropionate degradation	46.67	7 of 15
66794	oxidative phosphorylation	46.15	42 of 91
66794	ascorbate metabolism	45.45	10 of 22
66794	gallate degradation	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	sulfate reduction	38.46	5 of 13
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	octane oxidation	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	sphingosine metabolism	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	vitamin B6 metabolism	27.27	3 of 11
66794	cholesterol biosynthesis	27.27	3 of 11
66794	toluene degradation	25	1 of 4
66794	biotin biosynthesis	25	1 of 4
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13

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
24038	-	+	+	+/-	+/-	+	+	+/-	+	-	+	+	+	+	+	-	+	+	-	+

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
24038	-	-	-	-	-	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Other	#Mine
#Environmental	#Aquatic	-
#Condition	#Acidic	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
24038	acid mine drainage	Matsuo mine, Iwate Prefecture	Japan	JPN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24038	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM433972v1 assembly for Acidipila rosea DSM 103428	scaffold	GCA_004339725	768535.4	2757320406	768535	74.26

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24038	Acidopila rosea gene for 16S rRNA, partial sequence	AB561884	1461		768535

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Acidipila rosea DSM 103428
NCBI: GCA_004339725

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	70.00	no
125439	motility	BacteriaNetⓘ	yes	62.90	no
125439	gram_stain	BacteriaNetⓘ	negative	89.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	95.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Acidipila rosea DSM 103428
NCBI: GCA_004339725.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	92.41	no
125438	anaerobic	anaerobicⓘ	no	95.27	no
125438	aerobic	aerobicⓘ	yes	81.04	no
125438	spore-forming	spore-formingⓘ	no	81.23	no
125438	thermophilic	thermophileⓘ	no	90.93	yes
125438	flagellated	motile2+ⓘ	no	52.17	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	What Is in Umbilicaria pustulata? A Metagenomic Approach to Reconstruct the Holo-Genome of a Lichen.	Greshake Tzovaras B, Segers FHID, Bicker A, Dal Grande F, Otte J, Anvar SY, Hankeln T, Schmitt I, Ebersberger I.	Genome Biol Evol	10.1093/gbe/evaa049	2020
Phylogeny	Silvibacterium bohemicum gen. nov. sp. nov., an acidobacterium isolated from coniferous soil in the Bohemian Forest National Park.	Llado S, Benada O, Cajthaml T, Baldrian P, Garcia-Fraile P.	Syst Appl Microbiol	10.1016/j.syapm.2015.12.005	2016
Metabolism	Terracidiphilus gabretensis gen. nov., sp. nov., an Abundant and Active Forest Soil Acidobacterium Important in Organic Matter Transformation.	Garcia-Fraile P, Benada O, Cajthaml T, Baldrian P, Llado S.	Appl Environ Microbiol	10.1128/aem.03353-15	2016
Phylogeny	Acidipila rosea gen. nov., sp. nov., an acidophilic chemoorganotrophic bacterium belonging to the phylum Acidobacteria.	Okamura K, Kawai A, Yamada T, Hiraishi A	FEMS Microbiol Lett	10.1111/j.1574-6968.2011.02224.x	2011

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 )
#24038	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103428
#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 )
#68369	Automatically annotated from API 20NE .
#68382	Automatically annotated from API zym .
#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 )

Rate our new design

Content

About us

Acidipila rosea (DSM 103428, KCTC 23427, NBRC 107607)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API zym

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_004339725

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media