Name: Syntrophaceticus schinkii Sp3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 18085

Type strain:

Species: Syntrophaceticus schinkii

Strain Designation: Sp3

Culture col. no.: DSM 21860, JCM 16669

Strain history: A. Schnürer Sp3.

NCBI tax ID(s): 499207 (species)

SI-ID 402782

DSM 21860

Section

Syntrophaceticus schinkii Sp3 is an anaerobe, mesophilic bacterium that was isolated from upflow anaerobic filter treating waste water from a fish meal factory.

anaerobe
mesophilic
16S sequence
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	*Bacillota*
	Class	*Clostridia*
	Order	*Thermoanaerobacterales*
	Family	*Thermoanaerobacteraceae*
	Genus	*Syntrophaceticus*
	Species	**Syntrophaceticus schinkii**
	Full Scientific Name (LPSN)	Syntrophaceticus schinkii Westerholm et al. 2011

Information on morphological and physiological properties Morphology

[Ref.: #15997]

Incubation period

>14 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15997]

Culture medium

TEPIDANAEROBACTER MEDIUM (DSMZ Medium 1051)

[Ref.: #15997]

Culture medium growth

[Ref.: #15997]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15997]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #15997]			growth	37 °C
[Ref.: #67770]			growth	37 °C

[Ref.: #15997]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #15997]

Oxygen tolerance

anaerobe

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	aminopropanol phosphate biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	90.91	20 of 22
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	selenocysteine biosynthesis	83.33	5 of 6
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	vitamin B12 metabolism	79.41	27 of 34
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	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]	coenzyme A metabolism	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	purine metabolism	72.34	68 of 94
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	starch degradation	70	7 of 10
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	pyrimidine metabolism	64.44	29 of 45
[Ref.: #66794]	glutamate and glutamine metabolism	64.29	18 of 28
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	oxidative phosphorylation	63.74	58 of 91
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	alanine metabolism	62.07	18 of 29
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	55.56	5 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	55.56	5 of 9
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	tryptophan metabolism	52.63	20 of 38
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	gluconeogenesis	50	4 of 8
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	degradation of hexoses	50	9 of 18
[Ref.: #66794]	non-pathway related	50	19 of 38
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	50	3 of 6
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	cysteine metabolism	44.44	8 of 18
[Ref.: #66794]	glutathione metabolism	42.86	6 of 14
[Ref.: #66794]	citric acid cycle	42.86	6 of 14
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	Entner Doudoroff pathway	40	4 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	lysine metabolism	35.71	15 of 42
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	lipid metabolism	32.26	10 of 31
[Ref.: #66794]	degradation of pentoses	32.14	9 of 28
[Ref.: #66794]	vitamin B1 metabolism	30.77	4 of 13
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	phenol degradation	30	6 of 20
[Ref.: #66794]	propionate fermentation	30	3 of 10
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	cardiolipin biosynthesis	28.57	2 of 7
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	ppGpp biosynthesis	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
		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.: #15997]	Sample type/isolated from	upflow anaerobic filter treating waste water from a fish meal factory
[Ref.: #15997]	Geographic location (country and/or sea, region)	Santiago de Compostella
[Ref.: #15997]	Country	Spain
[Ref.: #15997]	Country ISO 3 Code	ESP
[Ref.: #15997]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Sludge from an upflow anaerobic filtering wastewater from a fishmeal factory
* marker position based on {}

Isolation sources categories

#Engineered	#Industrial	#Engineered product
#Engineered	#Industrial	#Plant (Factory)
#Engineered	#Waste	#Wastewater
#Condition	#Anoxic (anaerobic)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EU386162 (>99% sequence identity) for Syntrophaceticus schinkii subclade from Microbeatlas

Aquatic Samples	830
Soil Samples	370
Animal Samples	2431
Plant Samples	128
Total Samples	3759

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

[Ref.: #15997]

Biosafety level

Risk group (German classification)
According to TRBA 466

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

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #15997]	Syntrophaceticus schinkii strain Sp3 16S ribosomal RNA gene, partial sequence	EU386162	1416	ENA	499207 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Syntrophaceticus schinkii Sp3	GCA_000946815	contig	GenBank	499207 tax ID
[Ref.: #66792]	Syntrophaceticus schinkii Sp3	2622736413	draft	JGI IMG/M	499207 tax ID	*

[Ref.: #15997]

GC-content

45.6 mol%

Availability in culture collections External links

[Ref.: #15997]

Culture collection no.

DSM 21860, JCM 16669

[Ref.: #87073]

SI-ID 402782

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Syntrophaceticus schinkii gen. nov., sp. nov., an anaerobic, syntrophic acetate-oxidizing bacterium isolated from a mesophilic anaerobic filter.	Westerholm M, Roos S, Schnurer A	FEMS Microbiol Lett	10.1111/j.1574-6968.2010.02023.x	2010	*

References

#15997

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21860

#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 )

#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;

#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 .

#87073

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-ID402782.1 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Syntrophaceticus schinkii in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF