Name: Syntrophomonas zehnderi OL-4
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 16690

Type strain:

Species: Syntrophomonas zehnderi

Strain Designation: OL-4

Culture col. no.: DSM 17840, JCM 13948

Strain history: <- D. Z. Sousa, IBB-Institute for Biotechnology and Bioengineering, University of Minho, Braga, Portugal; OL-4 <- D. Z. Sousa; {2005}

NCBI tax ID(s): 690567 (strain), 404335 (species)

SI-ID 397085

DSM 17840

Special Collections

Section

When using BacDive for research please cite our paper

Syntrophomonas zehnderi OL-4 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from anaerobic sludge sampled from an EGSB reactor to treat oleate-based effluent.

Gram-variable
motile
rod-shaped
spore-forming
anaerobe
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Syntrophomonadaceae*
	Genus	*Syntrophomonas*
	Species	**Syntrophomonas zehnderi**
	Full Scientific Name (LPSN)	Syntrophomonas zehnderi Sousa et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #31971]	Gram stain	variable

[Ref.: #31971]	Cell length	5.25 µm

[Ref.: #31971]	Cell width	0.4 µm

[Ref.: #31971]	Cell shape	rod-shaped

[Ref.: #31971]	Motility	yes

[Ref.: #7135]

Incubation period

>14 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7135]

Culture medium

SYNTROPHOMONAS ZEHNDERI MEDIUM (DSMZ Medium 347a)

[Ref.: #7135]

Culture medium growth

[Ref.: #7135]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7135]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7135]	growth	37 °C
[Ref.: #31971]	growth	25-40 °C
[Ref.: #31971]	optimum	31 °C

	pH	Kind of pH		pH
[Ref.: #31971]			optimum	7
[Ref.: #31971]			growth	6.5-7.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #7135]	Oxygen tolerance	anaerobe
[Ref.: #31971]	Oxygen tolerance	anaerobe
[Ref.: #125439]	Oxygen tolerance	anaerobe Confidence in %93.9

[Ref.: #31971]

Ability of spore formation

yes

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31971]		decanoate ChEBI	+	carbon source

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	chorismate metabolism	100	9 of 9
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	vitamin B12 metabolism	70.59	24 of 34
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	alanine metabolism	68.97	20 of 29
[Ref.: #66794]	purine metabolism	67.02	63 of 94
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	66.67	6 of 9
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	oxidative phosphorylation	64.84	59 of 91
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	62.5	5 of 8
[Ref.: #66794]	pyrimidine metabolism	62.22	28 of 45
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	Entner Doudoroff pathway	60	6 of 10
[Ref.: #66794]	starch degradation	60	6 of 10
[Ref.: #66794]	histidine metabolism	58.62	17 of 29
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	methionine metabolism	57.69	15 of 26
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	benzoyl-CoA degradation	57.14	4 of 7
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	tryptophan metabolism	55.26	21 of 38
[Ref.: #66794]	d-xylose degradation	54.55	6 of 11
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	polyamine pathway	52.17	12 of 23
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	gluconeogenesis	50	4 of 8
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	50	3 of 6
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	citric acid cycle	42.86	6 of 14
[Ref.: #66794]	non-pathway related	42.11	16 of 38
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	propionate fermentation	40	4 of 10
[Ref.: #66794]	glycogen metabolism	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	vitamin B1 metabolism	38.46	5 of 13
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	glutathione metabolism	35.71	5 of 14
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	phenol degradation	30	6 of 20
[Ref.: #66794]	degradation of pentoses	28.57	8 of 28
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
		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.: #7135]	Sample type/isolated from	anaerobic sludge sampled from an EGSB reactor to treat oleate-based effluent
[Ref.: #7135]	Geographic location (country and/or sea, region)	Braga
[Ref.: #7135]	Country	Portugal
[Ref.: #7135]	Country ISO 3 Code	PRT
[Ref.: #7135]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered	#Biodegradation	#Anaerobic digestor
#Engineered	#Waste	#Industrial wastewater
#Environmental	#Terrestrial	#Mud (Sludge)
#Condition	#Anoxic (anaerobic)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ898277 (>99% sequence identity) for Syntrophomonas zehnderi subclade from Microbeatlas

Aquatic Samples	729
Soil Samples	289
Animal Samples	1295
Plant Samples	119
Total Samples	2432

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

[Ref.: #7135]

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.: #7135]	Syntrophomonas zehnderi strain OL-4 16S ribosomal RNA gene, partial sequence	DQ898277	1467	GenBank ENA	690567 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Syntrophomonas zehnderi OL-4	GCA_000983115	scaffold	GenBank ENA	690567 tax ID	*
[Ref.: #66792]	Syntrophomonas zehnderi OL-4	690567.3	wgs	PATRIC	690567 tax ID	*
[Ref.: #66792]	Syntrophomonas zehnderi OL-4	2675903293	draft	JGI IMG/M	690567 tax ID	*

[Ref.: #31971]

GC-content

37.6 mol%

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Syntrophomonas zehnderi OL-4 OL-4 NCBI: GCA_000983115.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	56.714	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	yes	88.849	no
[Ref.: #125438]	aerobic	aerobicⓘ	no	92.513	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	yes	78.585	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	62.54	no
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	69.174	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Syntrophomonas zehnderi OL-4 NCBI: GCA_000983115
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	59.5
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	61.7
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	variable	85
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	anaerobe	93.9

Availability in culture collections External links

[Ref.: #7135]

Culture collection no.

DSM 17840, JCM 13948

[Ref.: #85709]

SI-ID 397085

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Syntrophomonas zehnderi sp. nov., an anaerobe that degrades long-chain fatty acids in co-culture with Methanobacterium formicicum.	Sousa DZ, Smidt H, Alves MM, Stams AJM	Int J Syst Evol Microbiol	10.1099/ijs.0.64734-0	2007	*

References

#7135

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17840

#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 )

#31971

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28226 (see below)

#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 )

#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 .

#85709

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-ID397085.1 )

#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 .

#28226

IJSEM 609 2007 ( DOI 10.1099/ijs.0.64734-0 , PubMed 17329794 )

* These data were automatically processed and therefore are not curated

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Syntrophomonas zehnderi OL-4 OL-4

Syntrophomonas zehnderi OL-4

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