Acidocella aminolytica (DSM 11237, ATCC 51361, JCM 8796)

Name: Acidocella aminolytica (DSM 11237, ATCC 51361, JCM 8796)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 32

Type strain

Culture col. no. DSM 11237 ATCC 51361 JCM 8796

NCBI tax ID(s) 1120923 33998

Special Collections DSMZ JCM

Links

Acidocella aminolytica DSM 11237 is a mesophilic prokaryote that was isolated from acidic mine drainage.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 42948

ATCC 51361,JCM 8796,DSM 11237

@ref 20215

Last LPSN update 2025-12-16 09:46:45

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodospirillales

Family Acetobacteraceae

Genus Acidocella

Species Acidocella aminolytica

Full scientific name Acidocella aminolytica corrig. (Kishimoto et al. 1994) Kishimoto et al. 1996

Synonyms (2)

Acidiphilium aminilyticum
Acidiphilium aminolytica

BacDive ID	Other strains from **Acidocella aminolytica** (1)	Type strain
165988	A. aminolytica JCM 9059, ATCC 51362

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	94.5
125439	negative	90.2

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
4254	ACIDIPHILIUM MEDIUM (DSMZ Medium 269)		Medium recipe at MediaDive	Name: ACIDIPHILIUM MEDIUM (DSMZ Medium 269; with strain-specific modifications) Composition: (NH4)2SO4 2.0 g/l D-Glucose 1.0 g/l MgSO4 x 7 H2O 0.5 g/l K2HPO4 0.5 g/l Yeast extract 0.1 g/l KCl 0.1 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
4254	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		92.7

Observation

67770

Observationquinones: Q-10

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	quinate degradation	100	2 of 2
66794	acetate fermentation	100	4 of 4
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	gallate degradation	100	5 of 5
66794	adipate degradation	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	formaldehyde oxidation	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	butanoate fermentation	100	4 of 4
66794	resorcinol degradation	100	2 of 2
66794	propanol degradation	100	7 of 7
66794	valine metabolism	100	9 of 9
66794	L-lactaldehyde degradation	100	3 of 3
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	biotin biosynthesis	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	tetrahydrofolate metabolism	100	14 of 14
66794	gluconeogenesis	100	8 of 8
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	CMP-KDO biosynthesis	100	4 of 4
66794	palmitate biosynthesis	95.45	21 of 22
66794	Entner Doudoroff pathway	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	glutamate and glutamine metabolism	89.29	25 of 28
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	vitamin B12 metabolism	88.24	30 of 34
66794	photosynthesis	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	citric acid cycle	85.71	12 of 14
66794	vitamin B1 metabolism	84.62	11 of 13
66794	phenylalanine metabolism	84.62	11 of 13
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	NAD metabolism	83.33	15 of 18
66794	histidine metabolism	82.76	24 of 29
66794	methionine metabolism	80.77	21 of 26
66794	glycogen metabolism	80	4 of 5
66794	4-hydroxyphenylacetate degradation	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	myo-inositol biosynthesis	80	8 of 10
66794	3-chlorocatechol degradation	80	4 of 5
66794	alanine metabolism	79.31	23 of 29
66794	heme metabolism	78.57	11 of 14
66794	glutathione metabolism	78.57	11 of 14
66794	tyrosine metabolism	78.57	11 of 14
66794	4-hydroxymandelate degradation	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	urea cycle	76.92	10 of 13
66794	purine metabolism	75.53	71 of 94
66794	isoleucine metabolism	75	6 of 8
66794	ketogluconate metabolism	75	6 of 8
66794	flavin biosynthesis	73.33	11 of 15
66794	proline metabolism	72.73	8 of 11
66794	pentose phosphate pathway	72.73	8 of 11
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	arginine metabolism	70.83	17 of 24
66794	glycolysis	70.59	12 of 17
66794	propionate fermentation	70	7 of 10
66794	isoprenoid biosynthesis	69.23	18 of 26
66794	leucine metabolism	69.23	9 of 13
66794	tryptophan metabolism	68.42	26 of 38
66794	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	allantoin degradation	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	methane metabolism	66.67	2 of 3
66794	oxidative phosphorylation	63.74	58 of 91
66794	non-pathway related	63.16	24 of 38
66794	6-hydroxymethyl-dihydropterin diphosphate 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	cysteine metabolism	61.11	11 of 18
66794	degradation of pentoses	60.71	17 of 28
66794	3-phenylpropionate degradation	60	9 of 15
66794	creatinine degradation	60	3 of 5
66794	cellulose degradation	60	3 of 5
66794	phenol degradation	60	12 of 20
66794	lysine metabolism	59.52	25 of 42
66794	nitrate assimilation	55.56	5 of 9
66794	sulfate reduction	53.85	7 of 13
66794	pyrimidine metabolism	53.33	24 of 45
66794	polyamine pathway	52.17	12 of 23
66794	degradation of sugar acids	52	13 of 25
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	glycine metabolism	50	5 of 10
66794	phenylmercury acetate degradation	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	glycogen biosynthesis	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	cholesterol biosynthesis	45.45	5 of 11
66794	metabolism of disaccharids	45.45	5 of 11
66794	degradation of hexoses	44.44	8 of 18
66794	ascorbate metabolism	40.91	9 of 22
66794	vitamin K metabolism	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	phenylacetate degradation (aerobic)	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	hydrogen production	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	vitamin B6 metabolism	36.36	4 of 11
66794	d-xylose degradation	36.36	4 of 11
66794	sphingosine metabolism	33.33	2 of 6
66794	enterobactin biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	carotenoid biosynthesis	31.82	7 of 22
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	starch degradation	30	3 of 10
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	toluene degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17

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
4254	acidic mine drainage	Okayama, Yanahara mine	Japan	JPN	Asia
67770	Acidic mine drainage

Taxonmaps

69479

Global distribution of 16S sequence D30771 (>99% sequence identity) for Acidocella aminolytica subclade from Microbeatlas

Aquatic Samples	387
Soil Samples	754
Animal Samples	159
Plant Samples	251
Total Samples	1551

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
4254	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 2582581264 annotated assembly for Acidocella aminolytica 101 = DSM 11237	scaffold	GCA_900129125	1120923.5	2582581264	1120923	56.86
67770	ASM96438v1 assembly for Acidocella aminolytica 101 = DSM 11237	scaffold	GCA_000964385	1120923.7		1120923
124043	ASM2599529v1 assembly for Acidocella aminolytica 101 = DSM 11237	contig	GCA_025995295	1120923.10	8118685629	1120923

Genome browser: GCA_900129125

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
4254	Acidocella aminolytica gene for 16S ribosomal RNA	D30771	1406		33998

GC content

@ref	GC-content (mol%)
4254	58.7
67770	59.1

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Acidocella aminolytica 101 = DSM 11237
NCBI: GCA_000964385

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative aerobe	71.30	no
125439	gram_stain	BacteriaNetⓘ	negative	90.20	no
125439	motility	BacteriaNetⓘ	yes	50.50	no
125439	spore_formation	BacteriaNetⓘ	no	92.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Acidocella aminolytica 101 = DSM 11237
PATRIC: 1120923.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	94.50	no
125438	anaerobic	anaerobicⓘ	no	91.67	no
125438	spore-forming	spore-formingⓘ	no	83.99	no
125438	aerobic	aerobicⓘ	yes	83.57	no
125438	thermophilic	thermophileⓘ	no	95.45	no
125438	flagellated	motile2+ⓘ	yes	76.23	no

Literature

References

#4254	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 11237
#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 )
#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;
#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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