Syntrophomonas zehnderi (DSM 17840, JCM 13948, OL-4)

Name: Syntrophomonas zehnderi (DSM 17840, JCM 13948, OL-4)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 16690

Type strain

Strain Designation OL-4

Culture col. no. DSM 17840 JCM 13948 OL-4

NCBI tax ID(s) 690567 404335

Special Collections DSMZ JCM Literature strains

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

Links

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

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

Name and taxonomic classification

SI-ID 397085

DSM 17840

@ref 20215

Last LPSN update 2026-02-09 11:22:01

Domain Bacteria

Phylum Bacillota

Class Syntrophomonadia

Order Syntrophomonadales

Family Syntrophomonadaceae

Genus Syntrophomonas

Species Syntrophomonas zehnderi

Full scientific name Syntrophomonas zehnderi Sousa et al. 2007

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
31971	variable	5.25 µm	0.4 µm	rod-shaped

Colony morphology

7135

Incubation period>14 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7135	SYNTROPHOMONAS ZEHNDERI MEDIUM (DSMZ Medium 347a)		Medium recipe at MediaDive	Name: SYNTROPHOMONAS ZEHNDERI MEDIUM (DSMZ Medium 347a) Composition: PIPES 14.8957 g/l Na2SO4 2.78053 g/l Na-laurate 2.76068 g/l CaCl2 x 2 H2O 1.82721 g/l Na2CO3 1.48957 g/l KH2PO4 0.496524 g/l NH4Cl 0.39722 g/l NaCl 0.39722 g/l MgCl2 x 6 H2O 0.327706 g/l Na2S x 9 H2O 0.297915 g/l L-Cysteine HCl x H2O 0.297915 g/l HCl 0.00248262 g/l FeCl2 x 4 H2O 0.00148957 g/l Sodium resazurin 0.000496524 g/l Pyridoxine hydrochloride 0.000297915 g/l Nicotinic acid 0.00019861 g/l Thiamine-HCl x 2 H2O 0.00019861 g/l CoCl2 x 6 H2O 0.000188679 g/l MnCl2 x 4 H2O 9.93049e-05 g/l Calcium pantothenate 9.93049e-05 g/l Vitamin B12 9.93049e-05 g/l p-Aminobenzoic acid 7.94439e-05 g/l ZnCl2 6.95134e-05 g/l Na2MoO4 x 2 H2O 3.57498e-05 g/l NiCl2 x 6 H2O 2.38332e-05 g/l D-(+)-biotin 1.9861e-05 g/l H3BO3 5.95829e-06 g/l CuCl2 x 2 H2O 1.9861e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
7135	positive	growth	37
31971	positive	growth	25-40
31971	positive	optimum	31

Culture pH

@ref	Ability	Type	PH
31971	positive	optimum	7
31971	positive	growth	6.5-7.5

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
7135	anaerobe
31971	anaerobe
125439	anaerobe	93.9

Spore formation

31971

Spore formationyes

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31971	27689 ChEBI	decanoate	+	carbon source

Pathway annotation

Computationally determined by

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

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Biodegradation	#Anaerobic digestor
#Engineered	#Waste	#Industrial wastewater
#Environmental	#Terrestrial	#Mud (Sludge)
#Condition	#Anoxic (anaerobic)	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7135	anaerobic sludge sampled from an EGSB reactor to treat oleate-based effluent	Braga	Portugal	PRT	Europe

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7135	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
66792	Syntrophomonas Zehnderi OL-4 assembly for Syntrophomonas zehnderi OL-4	scaffold	GCA_000983115	690567.9	2675903293	690567	51.56
66792	Syntrophomonas zehnderi OL-4	contig		690567.3		690567	51.2

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7135	Syntrophomonas zehnderi strain OL-4 16S ribosomal RNA gene, partial sequence	DQ898277	1467		690567

GC content

31971

GC-content (mol%)37.6

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Syntrophomonas zehnderi OL-4
NCBI: GCA_000983115

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	59.50	no
125439	motility	BacteriaNetⓘ	no	61.70	no
125439	gram_stain	BacteriaNetⓘ	variable	85.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	93.90	no

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	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	56.71	no
125438	anaerobic	anaerobicⓘ	yes	88.85	no
125438	aerobic	aerobicⓘ	no	92.51	yes
125438	spore-forming	spore-formingⓘ	yes	78.59	yes
125438	thermophilic	thermophileⓘ	no	62.54	no
125438	flagellated	motile2+ⓘ	yes	69.17	no

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 )
#28226	IJSEM 609 2007 ( DOI 10.1099/ijs.0.64734-0 , PubMed 17329794 )
#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
#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 .
#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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Syntrophomonas zehnderi (DSM 17840, JCM 13948, OL-4)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000983115

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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