Thiobacillus denitrificans (DSM 12475, ATCC 23644, JCM 3870)

Name: Thiobacillus denitrificans (DSM 12475, ATCC 23644, JCM 3870)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6143

Type strain

Strain Designation AB7

Culture col. no. DSM 12475 ATCC 23644 JCM 3870 NCIMB 9548 AB7 2 more

NCBI tax ID(s) 1123392 36861

Special Collections DSMZ JCM CIP

Links

Thiobacillus denitrificans AB7 is an anaerobe, mesophilic, Gram-negative prokaryote that was isolated from domestic sewage lagoon.

Gram-negative rod-shaped anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 38146

ATCC 23644,NCIB 9548,CIP 104767,JCM 3870,NCIMB 9548,DSM 12475,NCIB 8327,BCRC 17603,CCRC 17603

@ref 20215

Last LPSN update 2025-12-16 09:48:15

Domain Pseudomonadati

Phylum Pseudomonadota

Class Betaproteobacteria

Order Spirillales

Family Thiobacillaceae

Genus Thiobacillus

Species Thiobacillus denitrificans

Full scientific name Thiobacillus denitrificans (ex Beijerinck 1904) Kelly and Harrison 1989

Synonyms (1)

"Thiobacillus denitrificans"

BacDive ID	Other strains from **Thiobacillus denitrificans** (3)	Type strain
6141	T. denitrificans GP3, DSM 739
6142	T. denitrificans RT, DSM 807, ATCC 29685
164863	T. denitrificans JCM 3869, ATCC 23642, BCRC 13020, NCIMB 9546

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
118907	negative	rod-shaped
125438	negative		98.5
125439	negative		98.1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
4732	THIOBACILLUS DENITRIFICANS MEDIUM (DSMZ Medium 113)	Medium recipe at MediaDive	Name: THIOBACILLUS DENITRIFICANS MEDIUM (DSMZ Medium 113) Composition: Agar 14.9551 g/l (optional) Na2S2O3 x 5 H2O 4.98504 g/l KH2PO4 1.99402 g/l KNO3 1.99402 g/l NaHCO3 0.997009 g/l NH4Cl 0.997008 g/l MgSO4 x 7 H2O 0.797607 g/l FeSO4 x 7 H2O 0.00199402 g/l Na2-EDTA 0.000997009 g/l H3BO3 0.000598205 g/l CoCl2 x 6 H2O 0.000398804 g/l ZnSO4 x 7 H2O 0.000199402 g/l MnCl2 x 4 H2O 5.98205e-05 g/l Na2MoO4 x 2 H2O 5.98205e-05 g/l NiCl2 x 6 H2O 3.98804e-05 g/l CuCl2 x 2 H2O 1.99402e-05 g/l H2SO4 Distilled water
39095	MEDIUM 177 - for Thiobacillus denitrificans		Sodium hydrogen carbonate (0.500 g);Distilled water make up to (1000.000 ml);Manganese II sulphate monohydrate (0.030 g);Magnesium sulphate heptahydrate (0.100 g);Calcium chloride dihydrate (0.040 g);Agar (15.000 g);Ammonium sulphate (0.100 g);Potassiumni
118907	CIP Medium 124	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
4732	positive	growth	30	mesophilic
39095	positive	growth	30	mesophilic
67770	positive	growth	30	mesophilic
118907	positive	growth	25-30	mesophilic
118907	negative	growth	5
118907	negative	growth	10
118907	negative	growth	37
118907	negative	growth	41

Physiology and metabolism

Oxygen tolerance

4732

Oxygen toleranceanaerobe

Spore formation

@ref	Spore formation	Confidence
125439		98.8

Observation

67770

Observationquinones: Q-8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	-	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	-	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	-	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	-	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68371	4853 ChEBI	esculin	-	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68371	17306 ChEBI	maltose	-	builds acid from	from API 50CH acid
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
118907	17632 ChEBI	nitrate	+	reduction
118907	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Metabolite production

@ref	Chebi-ID	Metabolite	Production
118907	35581 ChEBI	indole

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
68382	beta-galactosidase	-	3.2.1.23	from API zym
118907	beta-galactosidase	-	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
118907	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	-		from API zym
118907	gelatinase	-
68382	leucine arylamidase	-	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
118907	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
118907	tryptophan deaminase	-
118907	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	photosynthesis	100	14 of 14
66794	formaldehyde oxidation	100	3 of 3
66794	cardiolipin biosynthesis	100	7 of 7
66794	biotin biosynthesis	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	denitrification	100	2 of 2
66794	ubiquinone biosynthesis	100	7 of 7
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	lipid A biosynthesis	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	NAD metabolism	83.33	15 of 18
66794	pentose phosphate pathway	81.82	9 of 11
66794	hydrogen production	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	starch degradation	80	8 of 10
66794	threonine metabolism	80	8 of 10
66794	glycogen metabolism	80	4 of 5
66794	heme metabolism	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	d-mannose degradation	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	leucine metabolism	76.92	10 of 13
66794	vitamin B1 metabolism	76.92	10 of 13
66794	purine metabolism	75.53	71 of 94
66794	isoleucine metabolism	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	metabolism of disaccharids	72.73	8 of 11
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	propanol degradation	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	Entner Doudoroff pathway	70	7 of 10
66794	acetoin degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	pyrimidine metabolism	66.67	30 of 45
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	glutathione metabolism	64.29	9 of 14
66794	citric acid cycle	64.29	9 of 14
66794	vitamin B6 metabolism	63.64	7 of 11
66794	proline metabolism	63.64	7 of 11
66794	ketogluconate metabolism	62.5	5 of 8
66794	gluconeogenesis	62.5	5 of 8
66794	flavin biosynthesis	60	9 of 15
66794	lipoate biosynthesis	60	3 of 5
66794	cellulose degradation	60	3 of 5
66794	alanine metabolism	58.62	17 of 29
66794	non-pathway related	57.89	22 of 38
66794	urea cycle	53.85	7 of 13
66794	lysine metabolism	52.38	22 of 42
66794	histidine metabolism	51.72	15 of 29
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	ethanol fermentation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	butanoate fermentation	50	2 of 4
66794	propionate fermentation	50	5 of 10
66794	degradation of sugar alcohols	50	8 of 16
66794	suberin monomers biosynthesis	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	phenylmercury acetate degradation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	arginine metabolism	50	12 of 24
66794	cysteine metabolism	50	9 of 18
66794	methionine metabolism	50	13 of 26
66794	tyrosine metabolism	50	7 of 14
66794	lipid metabolism	48.39	15 of 31
66794	sulfate reduction	46.15	6 of 13
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	oxidative phosphorylation	46.15	42 of 91
66794	cholesterol biosynthesis	45.45	5 of 11
66794	tryptophan metabolism	44.74	17 of 38
66794	nitrate assimilation	44.44	4 of 9
66794	vitamin B12 metabolism	41.18	14 of 34
66794	arachidonate biosynthesis	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	degradation of sugar acids	36	9 of 25
66794	degradation of pentoses	35.71	10 of 28
66794	polyamine pathway	34.78	8 of 23
66794	IAA biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	pantothenate biosynthesis	33.33	2 of 6
66794	degradation of hexoses	33.33	6 of 18
66794	sulfoquinovose degradation	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	coenzyme M biosynthesis	30	3 of 10
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	d-xylose degradation	27.27	3 of 11
66794	ascorbate metabolism	27.27	6 of 22
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	vitamin E metabolism	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	androgen and estrogen metabolism	25	4 of 16
66794	carotenoid biosynthesis	22.73	5 of 22

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
118907	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
118907	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

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
118907	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Waste	#Wastewater

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
4732	domestic sewage lagoon	Sheffield Sewage Work	United Kingdom	GBR	Europe
67770	Domestic sewage
118907	Environment, Domestic sewage lagoon	Sheffield	United Kingdom	GBR	Europe

Taxonmaps

69479

Global distribution of 16S sequence AJ243144 (>99% sequence identity) for Thiobacillus denitrificans from Microbeatlas

Aquatic Samples	43
Soil Samples	7
Animal Samples	1
Plant Samples	1
Total Samples	52

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
4732	1	Risk group (German classification) According to TRBA 466
118907	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	ASM37642v1 assembly for Thiobacillus denitrificans DSM 12475	contig	GCA_000376425	1123392.3	2515154078	1123392	71.43

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
4732	Thiobacillus denitrificans partial 16S rRNA gene, strain NCIMB 9548	AJ243144	1510		36861

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Thiobacillus denitrificans DSM 12475
NCBI: GCA_000376425

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.80	no
125439	motility	BacteriaNetⓘ	yes	85.00	no
125439	gram_stain	BacteriaNetⓘ	negative	98.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	82.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Thiobacillus denitrificans DSM 12475
PATRIC: 1123392.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	no
125438	anaerobic	anaerobicⓘ	no	55.83	yes
125438	spore-forming	spore-formingⓘ	no	88.85	no
125438	aerobic	aerobicⓘ	no	54.39	yes
125438	thermophilic	thermophileⓘ	no	96.61	yes
125438	flagellated	motile2+ⓘ	yes	82.08	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Evaluation of Thiobacillus denitrificans' sustainability in nitrate-reducing Fe(II) oxidation and the potential significance of Fe(II) as a growth-supporting reductant.	Becker S, Dang TT, Wei R, Kappler A.	FEMS Microbiol Ecol	10.1093/femsec/fiaf024	2025
Enzymology	Biohybrid-based pyroelectric bio-denitrification driven by temperature fluctuations.	Ye J, Wang S, Yang C, Zuo Z, Gu W, Zhang B, Zhou S.	Nat Commun	10.1038/s41467-025-60908-w	2025
	Bioleaching and chemical leaching of magnesium from serpentinites (Zlatibor Mt. ophiolite massif, Serbia) with potential application in mineral carbonation process for CO₂ sequestration.	Stankovic S, Atanackovic N, Strbacki J, Kovac S, Saric K, Niksic D, Schippers A.	Front Microbiol	10.3389/fmicb.2025.1646341	2025
	An Organic Solvent-Tolerant alpha-L-Rhamnosidase from Dictyoglomus thermophilum and Its Application in Production of Icariside I from Icariin.	Hu J, Song L, Zhao L, Zheng X, Feng W, Jia H.	Molecules	10.3390/molecules30132847	2025
	Fungal Methane Production Under High Hydrostatic Pressure in Deep Subseafloor Sediments.	Zhao M, Li D, Liu J, Fang J, Liu C.	Microorganisms	10.3390/microorganisms12112160	2024
	Gorse (Ulex europeaus) wastes with 5,6-dimethyl benzimidazole supplementation can support growth of vitamin B12 producing commensal gut microbes.	Iyer A, Soto Martin EC, Cameron GA, Louis P, Duncan SH, Bestwick CS, Russell WR.	PLoS One	10.1371/journal.pone.0290052	2024
	Draft Genome Sequence of Desulfobacter hydrogenophilus DSM 3380, a Psychrotolerant Sulfate-Reducing Bacterium.	Bertran E, Ward LM, Johnston DT.	Microbiol Resour Announc	10.1128/mra.00203-20	2020
Metabolism	Improving 2-phenylethanol and 6-pentyl-alpha-pyrone production with fungi by microparticle-enhanced cultivation (MPEC).	Etschmann MM, Huth I, Walisko R, Schuster J, Krull R, Holtmann D, Wittmann C, Schrader J.	Yeast	10.1002/yea.3022	2015
Genetics	Comparative genomic analysis of an emerging Pseudomonadaceae member, Thiopseudomonas alkaliphila.	Burcham ZM.	Microbiol Spectr	10.1128/spectrum.04157-23	2024
Biotechnology	An artificial coculture fermentation system for industrial propanol production.	Hocq R, Sauer M.	FEMS Microbes	10.1093/femsmc/xtac013	2022
Metabolism	Impact of metabolism and growth phase on the hydrogen isotopic composition of microbial fatty acids.	Heinzelmann SM, Villanueva L, Sinke-Schoen D, Sinninghe Damste JS, Schouten S, van der Meer MT.	Front Microbiol	10.3389/fmicb.2015.00408	2015
	Myxinidin-Derived Peptide against Biofilms Caused by Cystic Fibrosis Emerging Pathogens.	Bellavita R, Maione A, Braccia S, Sinoca M, Galdiero S, Galdiero E, Falanga A.	Int J Mol Sci	10.3390/ijms24043092	2023
	Bioleaching of Transition Metals From Limonitic Laterite Deposits and Reassessment of the Multiple Roles of Sulfur-Oxidizing Acidophiles in the Process.	Johnson DB, Smith SL, Santos AL.	Front Microbiol	10.3389/fmicb.2021.703177	2021
Metabolism	Structural characterization of the bacterial proteasome homolog BPH reveals a tetradecameric double-ring complex with unique inner cavity properties.	Fuchs ACD, Maldoner L, Hipp K, Hartmann MD, Martin J.	J Biol Chem	10.1074/jbc.m117.815258	2018
	Novel Insights on Extracellular Electron Transfer Networks in the Desulfovibrionaceae Family: Unveiling the Potential Significance of Horizontal Gene Transfer.	Gonzalez V, Abarca-Hurtado J, Arancibia A, Claverias F, Guevara MR, Orellana R.	Microorganisms	10.3390/microorganisms12091796	2024
	Water Stress-Driven Changes in Bacterial Cell Surface Properties.	Karagulyan M, Goebel MO, Diehl D, Abu Quba AA, Kastner M, Bachmann J, Wick LY, Schaumann GE, Miltner A.	Appl Environ Microbiol	10.1128/aem.00732-22	2022
Metabolism	Fungal biotransformation of (+/-)-linalool.	Mirata MA, Wust M, Mosandl A, Schrader J.	J Agric Food Chem	10.1021/jf800099h	2008
Genetics	DciA is an ancestral replicative helicase operator essential for bacterial replication initiation.	Brezellec P, Vallet-Gely I, Possoz C, Quevillon-Cheruel S, Ferat JL.	Nat Commun	10.1038/ncomms13271	2016
	Influence of Extremophiles on the Generation of Acid Mine Drainage at the Abandoned Pan de Azúcar Mine (Argentina).	Plaza-Cazon J, Benitez L, Murray J, Kirschbaum P, Donati E.	Microorganisms	10.3390/microorganisms9020281	2021
	Diversity of cultivable protease-producing bacteria and their extracellular proteases associated to scleractinian corals.	Su H, Xiao Z, Yu K, Huang Q, Wang G, Wang Y, Liang J, Huang W, Huang X, Wei F, Chen B.	PeerJ	10.7717/peerj.9055	2020
	Sticky Bacteria: Understanding the Behavior of a D-Galactose Adapted Consortium of Acidophilic Chemolithotroph Bacteria and Their Attachment on a Concentrate of Polymetallic Mineral.	Aguirre P, Saavedra A, Moncayo E, Hedrich S, Guerrero K, Gentina JC.	Front Microbiol	10.3389/fmicb.2021.767639	2021
Enzymology	Biochemical Basis of Xylooligosaccharide Utilisation by Gut Bacteria.	Singh RP, Bhaiyya R, Thakur R, Niharika J, Singh C, Latousakis D, Saalbach G, Nepogodiev SA, Singh P, Sharma SC, Sengupta S, Juge N, Field RA.	Int J Mol Sci	10.3390/ijms23062992	2022
	Permanent draft genome of Thiobacillus thioparus DSM 505^T, an obligately chemolithoautotrophic member of the Betaproteobacteria.	Hutt LP, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy T, Daum C, Shapiro N, Ivanova N, Kyrpides N, Woyke T, Boden R.	Stand Genomic Sci	10.1186/s40793-017-0229-3	2017
Genetics	Metagenomic survey of methanesulfonic acid (MSA) catabolic genes in an Atlantic Ocean surface water sample and in a partial enrichment.	Henriques AC, Azevedo RM, De Marco P.	PeerJ	10.7717/peerj.2498	2016
	Sulfobacillus thermosulfidooxidans strain Cutipay enhances chalcopyrite bioleaching under moderate thermophilic conditions in the presence of chloride ion.	Bobadilla-Fazzini RA, Cortes MP, Maass A, Parada P.	AMB Express	10.1186/s13568-014-0084-1	2014
	Evolution of Type IV CRISPR-Cas Systems: Insights from CRISPR Loci in Integrative Conjugative Elements of Acidithiobacillia.	Moya-Beltran A, Makarova KS, Acuna LG, Wolf YI, Covarrubias PC, Shmakov SA, Silva C, Tolstoy I, Johnson DB, Koonin EV, Quatrini R.	CRISPR J	10.1089/crispr.2021.0051	2021
Metabolism	Flavonol 2,4-dioxygenase from Aspergillus niger DSM 821, a type 2 CuII-containing glycoprotein.	Hund HK, Breuer J, Lingens F, Huttermann J, Kappl R, Fetzner S.	Eur J Biochem	10.1046/j.1432-1327.1999.00574.x	1999
	Structural basis of colibactin activation by the ClbP peptidase.	Velilla JA, Volpe MR, Kenney GE, Walsh RM, Balskus EP, Gaudet R.	Nat Chem Biol	10.1038/s41589-022-01142-z	2023
Metabolism	Characterization of a novel thermostable and xylose-tolerant GH 39 beta-xylosidase from Dictyoglomus thermophilum.	Li Q, Wu T, Qi Z, Zhao L, Pei J, Tang F.	BMC Biotechnol	10.1186/s12896-018-0440-3	2018
Phylogeny	Application of denaturing high-performance liquid chromatography for monitoring sulfate-reducing bacteria in oil fields.	Priha O, Nyyssonen M, Bomberg M, Laitila A, Simell J, Kapanen A, Juvonen R.	Appl Environ Microbiol	10.1128/aem.01015-13	2013
	In situ production of branched glycerol dialkyl glycerol tetraethers in a great basin hot spring (USA).	Zhang CL, Wang J, Dodsworth JA, Williams AJ, Zhu C, Hinrichs KU, Zheng F, Hedlund BP.	Front Microbiol	10.3389/fmicb.2013.00181	2013
Metabolism	Preferential reduction of the thermodynamically less favorable electron acceptor, sulfate, by a nitrate-reducing strain of the sulfate-reducing bacterium Desulfovibrio desulfuricans 27774.	Marietou A, Griffiths L, Cole J.	J Bacteriol	10.1128/jb.01171-08	2009
	Application of antisera raised against sulfate-reducing bacteria for indirect immunofluorescent detection of immunoreactive bacteria in sediment from the German Baltic Sea.	Lillebaek R.	Appl Environ Microbiol	10.1128/aem.61.9.3436-3442.1995	1995
Phylogeny	Phylogenetic analyses of some extremely halophilic archaea isolated from Dead Sea water, determined on the basis of their 16S rRNA sequences.	Arahal DR, Dewhirst FE, Paster BJ, Volcani BE, Ventosa A.	Appl Environ Microbiol	10.1128/aem.62.10.3779-3786.1996	1996
Metabolism	Community structure, cellular rRNA content, and activity of sulfate-reducing bacteria in marine arctic sediments.	Ravenschlag K, Sahm K, Knoblauch C, Jorgensen BB, Amann R.	Appl Environ Microbiol	10.1128/aem.66.8.3592-3602.2000	2000
	Phylogenetic analysis of the genera Thiobacillus and Thiomicrospira by 5S rRNA sequences.	Lane DJ, Stahl DA, Olsen GJ, Heller DJ, Pace NR.	J Bacteriol	10.1128/jb.163.1.75-81.1985	1985
Phylogeny	Diversity of Betaproteobacteria revealed by novel primers suggests their role in arsenic cycling.	Chakraborty A, DasGupta CK, Bhadury P.	Heliyon	10.1016/j.heliyon.2019.e03089	2020
Genetics	The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitrificans.	Beller HR, Chain PS, Letain TE, Chakicherla A, Larimer FW, Richardson PM, Coleman MA, Wood AP, Kelly DP.	J Bacteriol	10.1128/jb.188.4.1473-1488.2006	2006
Phylogeny	Phylogenetic characterization of 16S rRNA gene clones from deep-groundwater microorganisms that pass through 0.2-micrometer-pore-size filters.	Miyoshi T, Iwatsuki T, Naganuma T.	Appl Environ Microbiol	10.1128/aem.71.2.1084-1088.2005	2005
	Large-scale metabolic interaction network of the mouse and human gut microbiota.	Lim R, Cabatbat JJT, Martin TLP, Kim H, Kim S, Sung J, Ghim CM, Kim PJ.	Sci Data	10.1038/s41597-020-0516-5	2020
Phylogeny	Phylogenetic assessment of culture collection strains of Thiobacillus thioparus, and definitive 16S rRNA gene sequences for T. thioparus, T. denitrificans, and Halothiobacillus neapolitanus.	Boden R, Cleland D, Green PN, Katayama Y, Uchino Y, Murrell JC, Kelly DP	Arch Microbiol	10.1007/s00203-011-0747-0	2011
Phylogeny	Bacteria involved in sulfur amendment oxidation and acidification processes of alkaline 'alperujo' compost.	Garcia-de-la-Fuente R, Cuesta G, Sanchis-Jimenez E, Botella S, Abad M, Fornes F	Bioresour Technol	10.1016/j.biortech.2010.09.103	2010
Phylogeny	Confirmation of Thiobacillus denitrificans as a species of the genus Thiobacillus, in the beta-subclass of the Proteobacteria, with strain NCIMB 9548 as the type strain.	Kelly DP, Wood AP	Int J Syst Evol Microbiol	10.1099/00207713-50-2-547	2000
Phylogeny	Limnobacter olei sp. nov., a Novel Diesel-Degrading Bacterium Isolated from Oil-Contaminated Soil.	Liu Y, Xu S, Li J, Ouyang Y, Gao S, Yang P, Chu C, He J, Yang T, Ma K, Li L, Wang C.	Curr Microbiol	10.1007/s00284-024-04053-5	2025
	Limnobacter parvus sp. nov., a Thiosulfate-Oxidizing Bacterium Isolated from Lake Water.	Xamxidin M, Huang X, Yang X, Wang T, Chen C, Wu M.	Curr Microbiol	10.1007/s00284-022-03128-5	2022
Phylogeny	Arthrobacter enclensis sp. nov., isolated from sediment sample.	Dastager SG, Liu Q, Tang SK, Krishnamurthi S, Lee JC, Li WJ.	Arch Microbiol	10.1007/s00203-014-1016-9	2014
Phylogeny	Achromobacter sediminum sp. nov., isolated from deep subseafloor sediment of South Pacific Gyre.	Zhang Z, Fan X, Gao X, Zhang XH.	Int J Syst Evol Microbiol	10.1099/ijs.0.062265-0	2014
Phylogeny	Castellaniella caeni sp. nov., a denitrifying bacterium isolated from sludge of a leachate treatment plant.	Liu QM, Ten LN, Im WT, Lee ST.	Int J Syst Evol Microbiol	10.1099/ijs.0.65314-0	2008
Metabolism	Metabolic and taxonomic insights into the Gram-negative natural rubber degrading bacterium Steroidobacter cummioxidans sp. nov., strain 35Y.	Sharma V, Siedenburg G, Birke J, Mobeen F, Jendrossek D, Prakash T.	PLoS One	10.1371/journal.pone.0197448	2018
Metabolism	Characterization of two tetrachloroethene-reducing, acetate-oxidizing anaerobic bacteria and their description as Desulfuromonas michiganensis sp. nov.	Sung Y, Ritalahti KM, Sanford RA, Urbance JW, Flynn SJ, Tiedje JM, Loffler FE.	Appl Environ Microbiol	10.1128/aem.69.5.2964-2974.2003	2003

References

#4732	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 12475
#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 )
#39095	; Curators of the CIP;
#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;
#68371	Automatically annotated from API 50CH acid .
#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 .
#118907	Collection of Institut Pasteur ; Curators of the CIP; CIP 104767
#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

Thiobacillus denitrificans (DSM 12475, ATCC 23644, JCM 3870)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Metabolite production

Enzymes

Pathway annotation

API zym

API 50CHac

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000376425

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media