Name: Tolumonas auensis TA4
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 294

Type strain:

Species: Tolumonas auensis

Strain Designation: TA4

Culture col. no.: DSM 9187

Strain history: <- C. Fischer, TA4

NCBI tax ID(s): 595494 (strain), 43948 (species)

SI-ID 48591

DSM 9187

Section

Tolumonas auensis TA4 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from freshwater mud.

Gram-negative
rod-shaped
anaerobe
mesophilic
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Aeromonadales*
	Family	*Aeromonadaceae*
	Genus	*Tolumonas*
	Species	**Tolumonas auensis**
	Full Scientific Name (LPSN)	Tolumonas auensis Fischer-Romero et al. 1996

Information on morphological and physiological properties Morphology

[Ref.: #23264]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.979

[Ref.: #23264]	Cell length	2.5-3.2 µm

[Ref.: #23264]	Cell width	0.9-1.2 µm

[Ref.: #23264]	Cell shape	rod-shaped

[Ref.: #23264]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #3506]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

CLOSTRIDIUM (GV) MEDIUM (DSMZ Medium 500)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #3506]			growth	28 °C
[Ref.: #23264]			optimum	22 °C

[Ref.: #3506]	Temperature range	mesophilic
[Ref.: #23264]	Temperature range	psychrophilic

	pH	Kind of pH		pH
[Ref.: #23264]			optimum	7.2

Information on physiology and metabolism Physiology and metabolism

[Ref.: #3506]	Oxygen tolerance	anaerobe
[Ref.: #23264]	Oxygen tolerance	aerobe
[Ref.: #23264]	Oxygen tolerance	anaerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.984

[Ref.: #3506]	Name of produced compound	toluene
[Ref.: #3506]	Name of produced compound	phenol

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #23264]	(-)-quinic acid ChEBI	+	aerobic catabolization
[Ref.: #23264]	2-oxoglutarate ChEBI	+	aerobic catabolization
[Ref.: #23264]	4-hydroxybutyrate ChEBI	+	aerobic catabolization
[Ref.: #23264]	acetate ChEBI	+	aerobic catabolization
[Ref.: #23264]	cellobiose ChEBI	+	anaerobic catabolization
[Ref.: #23264]	cis-aconitate ChEBI	+	aerobic catabolization
[Ref.: #23264]	D-arabinose ChEBI	+	anaerobic catabolization
[Ref.: #23264]	D-fructose ChEBI	+	aerobic catabolization
[Ref.: #23264]	D-fructose ChEBI	+	anaerobic catabolization
[Ref.: #23264]	D-galactose ChEBI	+	aerobic catabolization
[Ref.: #23264]	D-galacturonic acid ChEBI	+	aerobic catabolization
[Ref.: #23264]	D-gluconate ChEBI	+	aerobic catabolization
[Ref.: #23264]	D-glucose ChEBI	+	aerobic catabolization
[Ref.: #23264]	D-glucose ChEBI	+	anaerobic catabolization
[Ref.: #23264]	D-glucuronate ChEBI	+	aerobic catabolization
[Ref.: #23264]	D-mannitol ChEBI	+	anaerobic catabolization
[Ref.: #23264]	D-mannose ChEBI	+	anaerobic catabolization
[Ref.: #23264]	D-ribose ChEBI	+	anaerobic catabolization
[Ref.: #23264]	D-sorbitol ChEBI	+	anaerobic catabolization
[Ref.: #23264]	D-trehalose ChEBI	+	anaerobic catabolization
[Ref.: #23264]	glucuronamide ChEBI	+	aerobic catabolization
[Ref.: #23264]	glycogen ChEBI	+	anaerobic catabolization
[Ref.: #23264]	inosine ChEBI	+	aerobic catabolization
[Ref.: #23264]	inulin ChEBI	+	anaerobic catabolization
[Ref.: #23264]	L-alanine ChEBI	+	aerobic catabolization
[Ref.: #23264]	L-arabinose ChEBI	+	aerobic catabolization
[Ref.: #23264]	L-asparagine ChEBI	+	aerobic catabolization
[Ref.: #23264]	L-aspartate ChEBI	+	aerobic catabolization
[Ref.: #23264]	L-glutamate ChEBI	+	aerobic catabolization
[Ref.: #23264]	L-histidine ChEBI	+	aerobic catabolization
[Ref.: #23264]	L-rhamnose ChEBI	+	anaerobic catabolization
[Ref.: #23264]	L-threonine ChEBI	+	aerobic catabolization
[Ref.: #23264]	lactate ChEBI	+	aerobic catabolization
[Ref.: #23264]	malonate ChEBI	+	aerobic catabolization
[Ref.: #23264]	maltose ChEBI	+	anaerobic catabolization
[Ref.: #23264]	melezitose ChEBI	+	anaerobic catabolization
[Ref.: #23264]	melibiose ChEBI	+	anaerobic catabolization
[Ref.: #23264]	pyruvate ChEBI	+	aerobic catabolization
[Ref.: #23264]	raffinose ChEBI	+	anaerobic catabolization
[Ref.: #23264]	salicin ChEBI	+	anaerobic catabolization
[Ref.: #23264]	sebacic acid ChEBI	+	aerobic catabolization
[Ref.: #23264]	succinate ChEBI	+	aerobic catabolization
[Ref.: #23264]	sucrose ChEBI	+	anaerobic catabolization
[Ref.: #23264]	tween 40 ChEBI	+	aerobic catabolization
[Ref.: #23264]	tween 80 ChEBI	+	aerobic catabolization
[Ref.: #23264]	urocanic acid ChEBI	+	aerobic catabolization
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #23264]	acetate ChEBI	yes
[Ref.: #23264]	ethanol ChEBI	yes
[Ref.: #23264]	formate ChEBI	yes
[Ref.: #23264]	hydrogen sulfide ChEBI	no
[Ref.: #23264]	indole ChEBI	no
[Ref.: #23264]	toluene ChEBI	yes

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #23264]		catalase	+/-	1.11.1.6
[Ref.: #23264]		cytochrome oxidase	-	1.9.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	alginate biosynthesis	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	aminopropanol phosphate biosynthesis	100	2 of 2
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	tetrahydrofolate metabolism	100	14 of 14
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	heme metabolism	92.86	13 of 14
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	ketogluconate metabolism	87.5	7 of 8
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	vitamin B12 metabolism	85.29	29 of 34
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	vitamin B6 metabolism	81.82	9 of 11
[Ref.: #66794]	degradation of sugar alcohols	81.25	13 of 16
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	purine metabolism	75.53	71 of 94
[Ref.: #66794]	dTDPLrhamnose biosynthesis	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	pyrimidine metabolism	73.33	33 of 45
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	d-xylose degradation	72.73	8 of 11
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	degradation of sugar acids	72	18 of 25
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	non-pathway related	71.05	27 of 38
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	oxidative phosphorylation	69.23	63 of 91
[Ref.: #66794]	degradation of pentoses	67.86	19 of 28
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	degradation of hexoses	66.67	12 of 18
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	CO2 fixation in Crenarchaeota	55.56	5 of 9
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	tryptophan metabolism	55.26	21 of 38
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	53.85	7 of 13
[Ref.: #66794]	histidine metabolism	51.72	15 of 29
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	50	5 of 10
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	lipid metabolism	41.94	13 of 31
[Ref.: #66794]	3-phenylpropionate degradation	40	6 of 15
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	cellulose degradation	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	propionate fermentation	40	4 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	allantoin degradation	33.33	3 of 9
[Ref.: #66794]	phenol degradation	30	6 of 20
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	arachidonic acid metabolism	22.22	4 of 18
		Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #3506]	Sample type/isolated from	freshwater mud
[Ref.: #3506]	Geographic location (country and/or sea, region)	Lake Au
[Ref.: #3506]	Country	Switzerland
[Ref.: #3506]	Country ISO 3 Code	CHE
[Ref.: #3506]	Continent	Europe

[Ref.: #23264]	Sample type/isolated from	anoxic sediment of a freshwater lake
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Freshwater
#Environmental	#Terrestrial	#Mud (Sludge)

What are isolation sources categories?

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #3506]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Tolumonas auensis DSM 9187	GCA_000023065	complete	GenBank	595494 tax ID	*
[Ref.: #66792]	Tolumonas auensis DSM 9187	595494.3	complete	PATRIC	595494 tax ID	*
[Ref.: #66792]	Tolumonas auensis TA 4, DSM 9187	643692052	complete	JGI IMG/M	595494 tax ID	*

[Ref.: #3506]	GC-content	49.2 mol%	high performance liquid chromatography (HPLC)
[Ref.: #23264]	GC-content	49.00 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Tolumonas auensis DSM 9187 DSM 9187 NCBI: GCA_000023065.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Tolumonas auensis DSM 9187 DSM 9187 NCBI: GCA_000023065.1
[Ref.: #69480]	motile	no	85.855	no
[Ref.: #69480]	flagellated	no	92.526	no
[Ref.: #69480]	gram-positive	no	98.219	no
[Ref.: #69480]	anaerobic	no	91.551	no
[Ref.: #69480]	aerobic	no	84.477	no
[Ref.: #69480]	halophile	no	87.694	no
[Ref.: #69480]	spore-forming	no	94.88	no
[Ref.: #69480]	thermophile	no	98.588	yes
[Ref.: #69480]	glucose-util	yes	89.199	no
[Ref.: #69480]	glucose-ferment	yes	80.949	no

Availability in culture collections External links

[Ref.: #3506]

Culture collection no.

DSM 9187

[Ref.: #69976]

SI-ID 48591

References

#3506

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 9187

#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 )

#23264

C. FISCHER-ROMERO, B. J. TINDALL, F. JüTTNER: Tolumonas auensis gen. nov., sp. nov., a Toluene-Producing Bacterium from Anoxic Sediments of a Freshwater Lake. IJSEM 46: 183 - 188 1996 ( DOI 10.1099/00207713-46-1-183 , PubMed 8573493 )

#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 )

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#69976

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID48591.1 )

* These data were automatically processed and therefore are not curated

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Tolumonas auensis DSM 9187 DSM 9187

Tolumonas auensis DSM 9187 DSM 9187

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