Syntrophus aciditrophicus (DSM 26646, ATCC 700169, JCM 18717)

Name: Syntrophus aciditrophicus (DSM 26646, ATCC 700169, JCM 18717)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 23324

Type strain

Strain Designation SB

Culture col. no. DSM 26646 ATCC 700169 JCM 18717 SB

NCBI tax ID(s) 316277

Special Collections DSMZ JCM

History <- M. J. McInerney, Dept. Plant Biology and Microbiol., Univ. Oklahoma, USA; SB <- B. Hopkins {1994} M. J. McInerney strain SB.

Links

Syntrophus aciditrophicus SB is an anaerobe, mesophilic prokaryote that was isolated from secondary anaerobic digestor sludge.

anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 407116

JCM 18717,DSM 26646

@ref 20215

Last LPSN update 2026-02-09 11:23:43

Domain Bacteria

Phylum Thermodesulfobacteriota

Class Syntrophia

Order Syntrophales

Family Syntrophaceae

Genus Syntrophus

Species Syntrophus aciditrophicus

Full scientific name Syntrophus aciditrophicus Jackson et al. 2015

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	96.6
125438	negative	94.479

Colony morphology

19044

Incubation period3-7 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
19044	PELOTOMACULUM MEDIUM (DSMZ Medium 960)		Medium recipe at MediaDive	Name: PELOTOMACULUM MEDIUM (DSMZ Medium 960; with strain-specific modifications) Composition: Na2CO3 1.49701 g/l Na-crotonate 0.858283 g/l NH4Cl 0.538922 g/l Yeast extract 0.499002 g/l Na2S x 9 H2O 0.299401 g/l L-Cysteine HCl x H2O 0.299401 g/l MgCl2 x 6 H2O 0.199601 g/l KH2PO4 0.139721 g/l Nitrilotriacetic acid 0.0127745 g/l NaCl 0.000998004 g/l FeCl2 x 4 H2O 0.000998004 g/l Sodium resazurin 0.000499002 g/l CaCl2 x 2 H2O 9.98004e-05 g/l NiCl2 x 6 H2O 9.98004e-05 g/l MnCl2 x 4 H2O 9.98004e-05 g/l Pyridoxine hydrochloride 9.98004e-05 g/l ZnCl2 9.98004e-05 g/l p-Aminobenzoic acid 4.99002e-05 g/l Nicotinic acid 4.99002e-05 g/l Calcium D-(+)-pantothenate 4.99002e-05 g/l (DL)-alpha-Lipoic acid 4.99002e-05 g/l Thiamine HCl 4.99002e-05 g/l Riboflavin 4.99002e-05 g/l Na2WO4 x 2 H2O 3.99202e-05 g/l CoCl2 x 6 H2O 2.99401e-05 g/l Na2MoO4 x 2 H2O 2.99401e-05 g/l Na2SeO3 x 5 H2O 2.99401e-05 g/l CuCl2 1.99601e-05 g/l Biotin 1.99601e-05 g/l Folic acid 1.99601e-05 g/l H3BO3 9.98004e-06 g/l Vitamin B12 9.98004e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
19044	positive	growth	35	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
19044	anaerobe
125439	anaerobe	99.2

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
19044	secondary anaerobic digestor sludge	OK, Norman	USA	USA	North America
67770	Sewage sludge from the second anaerobic digestor at the municipal wastewater treatment plant in Norman	OK	USA	USA	North America

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
19044	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	ASM1340v1 assembly for Syntrophus aciditrophicus SB	complete	GCA_000013405	56780.15	637000317	56780	96.24

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
19044	Syntrophus acidotrophicus 16S ribosomal RNA gene, partial sequence	U86447	1290		316277
124043	Syntrophus aciditrophicus strain ATCC 700169 16S ribosomal RNA gene, partial sequence.	GU993263	1509		316277

GC content

@ref	GC-content (mol%)	Method
19044	51.5	sequence analysis
67770	43.1	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Syntrophus aciditrophicus SB
PATRIC: 56780.15

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	88.10	no
125439	motility	BacteriaNetⓘ	no	61.00	no
125439	gram_stain	BacteriaNetⓘ	negative	96.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Syntrophus aciditrophicus SB SB
NCBI: GCA_000013405.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	94.48	no
125438	anaerobic	anaerobicⓘ	yes	85.29	yes
125438	aerobic	aerobicⓘ	no	86.64	yes
125438	spore-forming	spore-formingⓘ	no	79.49	no
125438	thermophilic	thermophileⓘ	no	80.24	yes
125438	flagellated	motile2+ⓘ	yes	64.99	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Proteome	The Acyl-Proteome of Syntrophus aciditrophicus Reveals Metabolic Relationships in Benzoate Degradation.	Muroski JM, Fu JY, Nguyen HH, Wofford NQ, Mouttaki H, James KL, McInerney MJ, Gunsalus RP, Loo JA, Ogorzalek Loo RR.	Mol Cell Proteomics	10.1016/j.mcpro.2022.100215	2022
	Cryo-EM identifies F-ENA of Bacillus thuringiensis as a widespread family of endospore appendages across Firmicutes.	Sleutel M, Sogues A, Van Gerven N, Jonsmoen UL, Van Molle I, Fislage M, Theunissen LD, Bellis NF, Baquero DP, Egelman EH, Krupovic M, Wang F, Aspholm M, Remaut H.	Nat Commun	10.1038/s41467-025-62896-3	2025
Metabolism	Syntrophus aciditrophicus uses the same enzymes in a reversible manner to degrade and synthesize aromatic and alicyclic acids.	James KL, Kung JW, Crable BR, Mouttaki H, Sieber JR, Nguyen HH, Yang Y, Xie Y, Erde J, Wofford NQ, Karr EA, Loo JA, Ogorzalek Loo RR, Gunsalus RP, McInerney MJ.	Environ Microbiol	10.1111/1462-2920.14601	2019
Enzymology	Enoyl-Coenzyme A Respiration via Formate Cycling in Syntrophic Bacteria.	Agne M, Appel L, Seelmann C, Boll M.	mBio	10.1128/mbio.03740-21	2021
	Development of a Bioelectrochemical System as a Tool to Enrich H₂-Producing Syntrophic Bacteria.	Guzman JJL, Sousa DZ, Angenent LT.	Front Microbiol	10.3389/fmicb.2019.00110	2019
Metabolism	Pyrophosphate-Dependent ATP Formation from Acetyl Coenzyme A in Syntrophus aciditrophicus, a New Twist on ATP Formation.	James KL, Rios-Hernandez LA, Wofford NQ, Mouttaki H, Sieber JR, Sheik CS, Nguyen HH, Yang Y, Xie Y, Erde J, Rohlin L, Karr EA, Loo JA, Ogorzalek Loo RR, Hurst GB, Gunsalus RP, Szweda LI, McInerney MJ.	mBio	10.1128/mbio.01208-16	2016
Metabolism	Development and Validation of Broad-Range Qualitative and Clade-Specific Quantitative Molecular Probes for Assessing Mercury Methylation in the Environment.	Christensen GA, Wymore AM, King AJ, Podar M, Hurt RA, Santillan EU, Soren A, Brandt CC, Brown SD, Palumbo AV, Wall JD, Gilmour CC, Elias DA.	Appl Environ Microbiol	10.1128/aem.01271-16	2016
Metabolism	Two pathways for glutamate biosynthesis in the syntrophic bacterium Syntrophus aciditrophicus.	Kim M, Le HM, Xie X, Feng X, Tang YJ, Mouttaki H, McInerney MJ, Buckel W.	Appl Environ Microbiol	10.1128/aem.02323-15	2015
Metabolism	Identification and characterization of re-citrate synthase in Syntrophus aciditrophicus.	Kim M, Le H, McInerney MJ, Buckel W.	J Bacteriol	10.1128/jb.02185-12	2013
Metabolism	Metabolism of hydroxylated and fluorinated benzoates by Syntrophus aciditrophicus and detection of a fluorodiene metabolite.	Mouttaki H, Nanny MA, McInerney MJ.	Appl Environ Microbiol	10.1128/aem.01870-08	2009
Metabolism	Cyclohexane carboxylate and benzoate formation from crotonate in Syntrophus aciditrophicus.	Mouttaki H, Nanny MA, McInerney MJ.	Appl Environ Microbiol	10.1128/aem.02227-06	2007

References

#19044	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26646
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Syntrophus aciditrophicus (DSM 26646, ATCC 700169, JCM 18717)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000013405

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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