Clostridium ljungdahlii (DSM 13528, ATCC 55383, PETC)

Name: Clostridium ljungdahlii (DSM 13528, ATCC 55383, PETC)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2802

Type strain

Strain Designation PETC

Culture col. no. DSM 13528 ATCC 55383 PETC NBRC 117003

NCBI tax ID(s) 748727 1538

Special Collections DSMZ

History DSMZ <- ATCC; ATCC 55383 <- S. Barik, University of Arkansas Medical Sciences, Little Rock, USA; PETC

Links

Clostridium ljungdahlii PETC is an anaerobe bacterium that was isolated from chicken yard waste.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 43583

ATCC 55383,DSM 13528

@ref 20215

Last LPSN update 2026-05-29 08:25:33

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Clostridiaceae

Genus Clostridium

Species Clostridium ljungdahlii

Full scientific name Clostridium ljungdahlii Tanner et al. 1993

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
5077	CLOSTRIDIUM LJUNGDAHLII MEDIUM (DSMZ Medium 879)		Medium recipe at MediaDive	Name: CLOSTRIDIUM LJUNGDAHLII MEDIUM (DSMZ Medium 879) Composition: D-Fructose 4.9456 g/l NaHCO3 0.98912 g/l NH4Cl 0.98912 g/l Yeast extract 0.98912 g/l Na2S x 9 H2O 0.296736 g/l L-Cysteine HCl x H2O 0.296736 g/l KH2PO4 0.098912 g/l KCl 0.098912 g/l MgSO4 x 7 H2O 0.0296736 g/l Nitrilotriacetic acid 0.0148368 g/l NaCl 0.0098912 g/l MnSO4 x H2O 0.0049456 g/l CoSO4 x 7 H2O 0.00178042 g/l ZnSO4 x 7 H2O 0.00178042 g/l CaCl2 x 2 H2O 0.00098912 g/l FeSO4 x 7 H2O 0.00098912 g/l Sodium resazurin 0.00049456 g/l NiCl2 x 6 H2O 0.000296736 g/l AlK(SO4)2 x 12 H2O 0.000197824 g/l CuSO4 x 5 H2O 9.8912e-05 g/l H3BO3 9.8912e-05 g/l Pyridoxine hydrochloride 9.8912e-05 g/l Na2MoO4 x 2 H2O 9.8912e-05 g/l p-Aminobenzoic acid 4.9456e-05 g/l (DL)-alpha-Lipoic acid 4.9456e-05 g/l Calcium D-(+)-pantothenate 4.9456e-05 g/l Nicotinic acid 4.9456e-05 g/l Riboflavin 4.9456e-05 g/l Thiamine HCl 4.9456e-05 g/l Folic acid 1.97824e-05 g/l Biotin 1.97824e-05 g/l Na2WO4 x 2 H2O 3.95648e-06 g/l Na2SeO3 x 5 H2O 2.96736e-06 g/l Vitamin B12 9.8912e-07 g/l Distilled water
5077	CALDICELLULOSIRUPTOR MEDIUM (DSMZ Medium 640)		Medium recipe at MediaDive	Name: CALDICELLULOSIRUPTOR MEDIUM (DSMZ Medium 640; with strain-specific modifications) Composition: D-Fructose 5.0 g/l Trypticase peptone 2.0 g/l K2HPO4 1.5 g/l Yeast extract 1.0 g/l NH4Cl 0.9 g/l NaCl 0.9 g/l KH2PO4 0.75 g/l L-Cysteine HCl x H2O 0.75 g/l MgCl2 x 6 H2O 0.4 g/l HCl 0.0025 g/l FeCl3 x 6 H2O 0.0025 g/l FeCl2 x 4 H2O 0.0015 g/l Sodium resazurin 0.0005 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 4 H2O 0.0001 g/l ZnCl2 7e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l H3BO3 6e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
5077	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
5077	anaerobe
125439	facultative anaerobe	96.478

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Livestock (Husbandry)
#Engineered	#Waste	#Solid waste
#Host	#Birds	#Chicken

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
5077	chicken yard waste	Arkansas	USA	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence FR733688 (>99% sequence identity) for Clostridium from Microbeatlas

Aquatic Samples	1409
Soil Samples	2899
Animal Samples	13922
Plant Samples	372
Total Samples	18602

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5077	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	ASM14368v1 assembly for Clostridium ljungdahlii DSM 13528	complete	GCA_000143685	1538.8	648028017	748727	98.21
66792	ASM163685v1 assembly for Clostridium ljungdahlii DSM 13528 PETC	scaffold	GCA_001636855	748727.19	2740892543	748727	66.41

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Clostridium ljungdahlii strain DSM 13528 16S ribosomal RNA gene, partial sequence	DQ911275	320	748727
20218	Clostridium ljungdahlii strain ATCC 55383 16S ribosomal RNA gene, partial sequence	GU139552	1471	1538
5077	Clostridium ljungdahlii partial 16S rRNA gene, type strain DSM13528T	FR733688	1499	748727

GC content

@ref	GC-content (mol%)	Method
5077	31	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM14368v1 assembly for Clostridium ljungdahlii DSM 13528
BV-BRC: 1538.8

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	96.48	no
125439	gram_stain	BacteriaNetⓘ	positive	49.23	no
125439	motility	BacteriaNetⓘ	yes	77.28	no
125439	spore_formation	BacteriaNetⓘ	yes	85.26	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Clostridium ljungdahlii DSM 13528 DSM 13528
NCBI: GCA_000143685.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	62.27	no
125438	anaerobic	anaerobicⓘ	yes	87.21	yes
125438	aerobic	aerobicⓘ	no	93.96	yes
125438	spore-forming	spore-formingⓘ	yes	72.83	no
125438	thermophilic	thermophileⓘ	no	90.26	yes
125438	flagellated	motile2+ⓘ	yes	72.29	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Inducible promoters of bacterial microcompartments improve the CRISPR/Cas9 tools for efficient metabolic engineering of Clostridium ljungdahlii.	Zhang J-Z, Li Y-Z, Xi Z-N, Zhang Y, Liu Z-Y, Ma X-Q, Li F-L.	Appl Environ Microbiol	10.1128/aem.02183-24	2025
	Separate, separated, and together: the transcriptional program of the Clostridium acetobutylicum-Clostridium ljungdahlii syntrophy leading to interspecies cell fusion.	Willis NB, Papoutsakis ET.	mSystems	10.1128/msystems.00030-25	2025
	Evaluation of Yeast Alcohol Acetyltransferases for Ethyl Acetate Production in Clostridium ljungdahlii.	Boto ST, Gerges K, Bardl B, Rosenbaum MA.	Eng Life Sci	10.1002/elsc.202400076	2025
Metabolism	Protocol to obtain genetically engineered Acetobacterium woodii and Eubacterium callanderi strains.	Baur KS, Ruhle B, Reith T, Krieg A, Bengelsdorf FR.	STAR Protoc	10.1016/j.xpro.2025.104011	2025
Genetics	Enzyme-constrained metabolic model and in silico metabolic engineering of Clostridium ljungdahlii for the development of sustainable production processes.	Caivano A, van Winden W, Dragone G, Mussatto SI.	Comput Struct Biotechnol J	10.1016/j.csbj.2023.09.015	2023
Genetics	Implementation of a Clostridium luticellarii genome-scale model for upgrading syngas fermentations.	Scott WT, Rockx S, Marien Q, Regueira A, Candry P, Ganigue R, Koehorst JJ, Schaap PJ.	Comput Struct Biotechnol J	10.1016/j.csbj.2025.01.013	2025
	Microbial electrosynthesis with Clostridium ljungdahlii benefits from hydrogen electron mediation and permits a greater variety of products.	Boto ST, Bardl B, Harnisch F, Rosenbaum MA.	Green Chem	10.1039/d3gc00471f	2023
Metabolism	Effectively Converting Cane Molasses into 2,3-Butanediol Using Clostridiumljungdahlii by an Integrated Fermentation and Membrane Separation Process.	Yang Y, Deng T, Cao W, Shen F, Liu S, Zhang J, Liang X, Wan Y.	Molecules	10.3390/molecules27030954	2022
	Developing a genetic engineering method for Acetobacterium wieringae to expand one-carbon valorization pathways.	Moreira JPC, Heap JT, Alves JI, Domingues L.	Biotechnol Biofuels Bioprod	10.1186/s13068-023-02259-6	2023
	Online monitoring applying the anaerobic respiratory monitoring system reveals iron(II) limitation in YTF medium for Clostridium ljungdahlii.	Mann M, Wittke D, Buchs J.	Eng Life Sci	10.1002/elsc.202000054	2021
	Acetogenic production of 3-Hydroxybutyrate using a native 3-Hydroxybutyryl-CoA Dehydrogenase.	Lo J, Humphreys JR, Magnusson L, Wachter B, Urban C, Hebdon SD, Xiong W, Chou KJ, Ching Maness P.	Front Microbiol	10.3389/fmicb.2022.948369	2022
	Flavonoid-converting capabilities of Clostridium butyricum.	Braune A.	Appl Microbiol Biotechnol	10.1007/s00253-025-13434-0	2025
	Species-specific ribosomal RNA-FISH identifies interspecies cellular-material exchange, active-cell population dynamics and cellular localization of translation machinery in clostridial cultures and co-cultures.	Hill JD, Hill JD, Papoutsakis ET.	mSystems	10.1128/msystems.00572-24	2024
	Electrobiocorrosion by microbes without outer-surface cytochromes.	Holmes DE, Woodard TL, Smith JA, Musat F, Lovley DR.	mLife	10.1002/mlf2.12111	2024
Enzymology	H₂ Consumption by Various Acetogenic Bacteria Follows First-Order Kinetics up to H₂ Saturation.	Munoz-Duarte L, Chakraborty S, Gron LV, Bambace MF, Catalano J, Philips J.	Biotechnol Bioeng	10.1002/bit.28904	2025
	Pleiotropic Regulator GssR Positively Regulates Autotrophic Growth of Gas-Fermenting Clostridium ljungdahlii.	Zhang H, Zhang C, Nie X, Wu Y, Yang C, Jiang W, Gu Y.	Microorganisms	10.3390/microorganisms11081968	2023
	Deletion of atypical type II restriction genes in Clostridium cellulovorans using a Cas9-based gene editing system.	Schollkopf AI, Almeida L, Krammer K, Rivero CG, Liebl W, Ehrenreich A.	Appl Microbiol Biotechnol	10.1007/s00253-025-13404-6	2025
Metabolism	Ethanol Metabolism Dynamics in Clostridium ljungdahlii Grown on Carbon Monoxide.	Liu ZY, Jia DC, Zhang KD, Zhu HF, Zhang Q, Jiang WH, Gu Y, Li FL.	Appl Environ Microbiol	10.1128/aem.00730-20	2020
	Modeling of nitrogen fixation and polymer production in the heterotrophic diazotroph Azotobacter vinelandii DJ.	Campos DT, Zuniga C, Passi A, Del Toro J, Tibocha-Bonilla JD, Zepeda A, Betenbaugh MJ, Zengler K.	Metab Eng Commun	10.1016/j.mec.2020.e00132	2020
Enzymology	A rapid and sensitive enzymatic assay for 2,3-butanediol.	Lee GB, Kim YJ, Lim JK, Kim TW, Kang SG, Lee JH, Lee HS.	3 Biotech	10.1007/s13205-019-1705-9	2019
	Protein acetylation-mediated cross regulation of acetic acid and ethanol synthesis in the gas-fermenting Clostridium ljungdahlii.	Liu Y, Zhang Z, Jiang W, Gu Y.	J Biol Chem	10.1016/j.jbc.2021.101538	2022
Metabolism	Effect of ethanol and butanol on autotrophic growth of model homoacetogens.	Ramio-Pujol S, Ganigue R, Baneras L, Colprim J.	FEMS Microbiol Lett	10.1093/femsle/fny084	2018
	The Metabolism of Clostridium ljungdahlii in Phosphotransacetylase Negative Strains and Development of an Ethanologenic Strain.	Lo J, Humphreys JR, Jack J, Urban C, Magnusson L, Xiong W, Gu Y, Ren ZJ, Maness PC.	Front Bioeng Biotechnol	10.3389/fbioe.2020.560726	2020
	Energy Conservation and Carbon Flux Distribution During Fermentation of CO or H₂/CO₂ by Clostridium ljungdahlii.	Zhu HF, Liu ZY, Zhou X, Yi JH, Lun ZM, Wang SN, Tang WZ, Li FL.	Front Microbiol	10.3389/fmicb.2020.00416	2020
Metabolism	Robustness and Complexity of Directed and Weighted Metabolic Hypergraphs.	Traversa P, Ferraz de Arruda G, Vazquez A, Moreno Y.	Entropy (Basel)	10.3390/e25111537	2023
	Identifying and Engineering Bottlenecks of Autotrophic Isobutanol Formation in Recombinant C. ljungdahlii by Systemic Analysis.	Hermann M, Teleki A, Weitz S, Niess A, Freund A, Bengelsdorf FR, Durre P, Takors R.	Front Bioeng Biotechnol	10.3389/fbioe.2021.647853	2021
	DNA transfer between two different species mediated by heterologous cell fusion in Clostridium coculture.	Charubin K, Hill JD, Papoutsakis ET.	mBio	10.1128/mbio.03133-23	2024
	Thermodynamic and Kinetic Modeling Directs Pathway Optimization for Isopropanol Production in a Gas-Fermenting Bacterium.	Lo J, Wu C, Humphreys JR, Yang B, Jiang Z, Wang X, Maness P, Tsesmetzis N, Xiong W.	mSystems	10.1128/msystems.01274-22	2023
	Acetogenic Fermentation From Oxygen Containing Waste Gas.	Mohr T, Infantes A, Biebinger L, de Maayer P, Neumann A.	Front Bioeng Biotechnol	10.3389/fbioe.2019.00433	2019
	Clostridium strain FAM25158, a unique endospore-forming bacterium related to Clostridium tyrobutyricum and isolated from Emmental cheese shows low tolerance to salt.	Princic L, Burtscher J, Sacken P, Krajnc T, Domig KJ.	Front Microbiol	10.3389/fmicb.2024.1353321	2024
	Antisense-acting riboswitches: A poorly characterized yet important model of transcriptional regulation in prokaryotic organisms.	Serrano-Gutierrez M, Merino E.	PLoS One	10.1371/journal.pone.0281744	2023
Metabolism	A Heterodimeric Reduced-Ferredoxin-Dependent Methylenetetrahydrofolate Reductase from Syngas-Fermenting Clostridium ljungdahlii.	Yi J, Huang H, Liang J, Wang R, Liu Z, Li F, Wang S.	Microbiol Spectr	10.1128/spectrum.00958-21	2021
	The Restriction-Modification Systems of Clostridium carboxidivorans P7.	Kottenhahn P, Philipps G, Bunk B, Sproer C, Jennewein S.	Microorganisms	10.3390/microorganisms11122962	2023
	Probing efficient microbial CO₂ utilisation through metabolic and process modelling.	Gorter de Vries PJ, Mol V, Sonnenschein N, Jensen TO, Nielsen AT.	Microb Biotechnol	10.1111/1751-7915.14414	2024
Metabolism	Traits of selected Clostridium strains for syngas fermentation to ethanol.	Martin ME, Richter H, Saha S, Angenent LT.	Biotechnol Bioeng	10.1002/bit.25827	2016
Metabolism	Microbial carbon use efficiency predicted from genome-scale metabolic models.	Saifuddin M, Bhatnagar JM, Segre D, Finzi AC.	Nat Commun	10.1038/s41467-019-11488-z	2019
Biotechnology	Microbial electrosynthesis of methane and acetate-comparison of pure and mixed cultures.	Hengsbach JN, Sabel-Becker B, Ulber R, Holtmann D.	Appl Microbiol Biotechnol	10.1007/s00253-022-12031-9	2022
Metabolism	Impact of formate on the growth and productivity of Clostridium ljungdahlii PETC and Clostridium carboxidivorans P7 grown on syngas.	Ramio-Pujol S, Ganigue R, Baneras L, Colprim J.	Int Microbiol	10.2436/20.1501.01.222	2014
	Genome Sequence of the Autotrophic Acetogen Clostridium autoethanogenum JA1-1 Strain DSM 10061, a Producer of Ethanol from Carbon Monoxide.	Bruno-Barcena JM, Chinn MS, Grunden AM.	Genome Announc	10.1128/genomea.00628-13	2013
	Functional dissection and modulation of the BirA protein for improved autotrophic growth of gas-fermenting Clostridium ljungdahlii.	Zhang C, Nie X, Zhang H, Wu Y, He H, Yang C, Jiang W, Gu Y.	Microb Biotechnol	10.1111/1751-7915.13884	2021
Genetics	Comparative Genomics Provides Insights Into Genetic Diversity of Clostridium tyrobutyricum and Potential Implications for Late Blowing Defects in Cheese.	Podrzaj L, Burtscher J, Domig KJ.	Front Microbiol	10.3389/fmicb.2022.889551	2022
Metabolism	Discovery of an ene-reductase for initiating flavone and flavonol catabolism in gut bacteria.	Yang G, Hong S, Yang P, Sun Y, Wang Y, Zhang P, Jiang W, Gu Y.	Nat Commun	10.1038/s41467-021-20974-2	2021
	Metabolic engineering of Clostridium ljungdahlii for the production of hexanol and butanol from CO₂ and H₂.	Lauer I, Philipps G, Jennewein S.	Microb Cell Fact	10.1186/s12934-022-01802-8	2022
Metabolism	Interactive Regulation of Formate Dehydrogenase during CO₂ Fixation in Gas-Fermenting Bacteria.	Zhang L, Liu Y, Zhao R, Zhang C, Jiang W, Gu Y.	mBio	10.1128/mbio.00650-20	2020
	Development of a metabolic pathway transfer and genomic integration system for the syngas-fermenting bacterium Clostridium ljungdahlii.	Philipps G, de Vries S, Jennewein S.	Biotechnol Biofuels	10.1186/s13068-019-1448-1	2019
	Domestication of the novel alcohologenic acetogen Clostridium sp. AWRP: from isolation to characterization for syngas fermentation.	Lee J, Lee JW, Chae CG, Kwon SJ, Kim YJ, Lee JH, Lee HS.	Biotechnol Biofuels	10.1186/s13068-019-1570-0	2019
	Nitrate Feed Improves Growth and Ethanol Production of Clostridium ljungdahlii With CO₂ and H₂, but Results in Stochastic Inhibition Events.	Klask CM, Kliem-Kuster N, Molitor B, Angenent LT.	Front Microbiol	10.3389/fmicb.2020.00724	2020
	Electron availability in CO₂ , CO and H₂ mixtures constrains flux distribution, energy management and product formation in Clostridium ljungdahlii.	Hermann M, Teleki A, Weitz S, Niess A, Freund A, Bengelsdorf FR, Takors R.	Microb Biotechnol	10.1111/1751-7915.13625	2020
Metabolism	Flux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC19718 unravels specific metabolic activities while degrading toxic compounds.	Canto-Encalada G, Tec-Campos D, Tibocha-Bonilla JD, Zengler K, Zepeda A, Zuniga C.	PLoS Comput Biol	10.1371/journal.pcbi.1009828	2022
Metabolism	Functional Expression of the Clostridium ljungdahlii Acetyl-Coenzyme A Synthase in Clostridium acetobutylicum as Demonstrated by a Novel In Vivo CO Exchange Activity En Route to Heterologous Installation of a Functional Wood-Ljungdahl Pathway.	Fast AG, Papoutsakis ET.	Appl Environ Microbiol	10.1128/aem.02307-17	2018
	A comprehensive review of microbial fuel cells considering materials, methods, structures, and microorganisms.	Jalili P, Ala A, Nazari P, Jalili B, Ganji DD.	Heliyon	10.1016/j.heliyon.2024.e25439	2024
	Growth and Product Formation of Clostridium ljungdahlii in Presence of Cyanide.	Oswald F, Zwick M, Omar O, Hotz EN, Neumann A.	Front Microbiol	10.3389/fmicb.2018.01213	2018
Metabolism	Flavonoid-Modifying Capabilities of the Human Gut Microbiome-An In Silico Study.	Goris T, Cuadrat RRC, Braune A.	Nutrients	10.3390/nu13082688	2021
	Synergistically applying 1-D modeling and CFD for designing industrial scale bubble column syngas bioreactors.	Siebler F, Lapin A, Takors R.	Eng Life Sci	10.1002/elsc.201900132	2020
Metabolism	Expanding the molecular toolkit for the homoacetogen Clostridium ljungdahlii.	Molitor B, Kirchner K, Henrich AW, Schmitz S, Rosenbaum MA.	Sci Rep	10.1038/srep31518	2016
Metabolism	Transcriptomic profiles of Clostridium ljungdahlii during lithotrophic growth with syngas or H₂ and CO₂ compared to organotrophic growth with fructose.	Aklujkar M, Leang C, Shrestha PM, Shrestha M, Lovley DR.	Sci Rep	10.1038/s41598-017-12712-w	2017
Enzymology	Occurrence of ferredoxin:NAD(+) oxidoreductase activity and its ion specificity in several Gram-positive and Gram-negative bacteria.	Hess V, Gallegos R, Jones JA, Barquera B, Malamy MH, Muller V.	PeerJ	10.7717/peerj.1515	2016
	Looking for the mechanism of arsenate respiration of Fusibacter sp. strain 3D3, independent of ArrAB.	Acosta-Grinok M, Vazquez S, Guiliani N, Marin S, Demergasso C.	Front Microbiol	10.3389/fmicb.2022.1029886	2022
Phenotype	Genome-Scale Metabolic Modeling Enables In-Depth Understanding of Big Data.	Passi A, Tibocha-Bonilla JD, Kumar M, Tec-Campos D, Zengler K, Zuniga C.	Metabolites	10.3390/metabo12010014	2021
	Hexanol biosynthesis from syngas by Clostridium carboxidivorans P7 - product toxicity, temperature dependence and in situ extraction.	Kottenhahn P, Philipps G, Jennewein S.	Heliyon	10.1016/j.heliyon.2021.e07732	2021
Metabolism	Converting carbon dioxide to butyrate with an engineered strain of Clostridium ljungdahlii.	Ueki T, Nevin KP, Woodard TL, Lovley DR.	mBio	10.1128/mbio.01636-14	2014
	Energy conservation under extreme energy limitation: the role of cytochromes and quinones in acetogenic bacteria.	Rosenbaum FP, Muller V.	Extremophiles	10.1007/s00792-021-01241-0	2021
	Comparison of Syngas-Fermenting Clostridia in Stirred-Tank Bioreactors and the Effects of Varying Syngas Impurities.	Oliveira L, Ruckel A, Nordgauer L, Schlumprecht P, Hutter E, Weuster-Botz D.	Microorganisms	10.3390/microorganisms10040681	2022
	Enhancing CO₂-Valorization Using Clostridium autoethanogenum for Sustainable Fuel and Chemicals Production.	Heffernan JK, Valgepea K, de Souza Pinto Lemgruber R, Casini I, Plan M, Tappel R, Simpson SD, Kopke M, Nielsen LK, Marcellin E.	Front Bioeng Biotechnol	10.3389/fbioe.2020.00204	2020
	The immune response modulated by inoculation of commensal bacteria at birth impacts the gut microbiota and prevents Salmonella colonization.	Kempf F, Drumo R, Chausse AM, Menanteau P, Kubasova T, Roche S, Lalmanach AC, Guabiraba R, Chaumeil T, Lariviere-Gauthier G, Caballero-Posadas I, Laroche B, Rychlik I, Virlogeux-Payant I, Velge P.	Gut Microbes	10.1080/19490976.2025.2474151	2025
Metabolism	Electrosynthesis of organic compounds from carbon dioxide is catalyzed by a diversity of acetogenic microorganisms.	Nevin KP, Hensley SA, Franks AE, Summers ZM, Ou J, Woodard TL, Snoeyenbos-West OL, Lovley DR.	Appl Environ Microbiol	10.1128/aem.02642-10	2011
	CO₂ fixation by anaerobic non-photosynthetic mixotrophy for improved carbon conversion.	Jones SW, Fast AG, Carlson ED, Wiedel CA, Au J, Antoniewicz MR, Papoutsakis ET, Tracy BP.	Nat Commun	10.1038/ncomms12800	2016
Metabolism	An Amino Acid Substitution in RNA Polymerase That Inhibits the Utilization of an Alternative Sigma Factor.	Wang Erickson AF, Deighan P, Garcia CP, Weinzierl ROJ, Hochschild A, Losick R.	J Bacteriol	10.1128/jb.00277-17	2017
Metabolism	Genomic analysis of carbon monoxide utilization and butanol production by Clostridium carboxidivorans strain P7.	Bruant G, Levesque MJ, Peter C, Guiot SR, Masson L.	PLoS One	10.1371/journal.pone.0013033	2010
	SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments.	Youngblut ND, Barnett SE, Buckley DH.	Front Microbiol	10.3389/fmicb.2018.00570	2018
Metabolism	Using gas mixtures of CO, CO₂ and H₂ as microbial substrates: the do's and don'ts of successful technology transfer from laboratory to production scale.	Takors R, Kopf M, Mampel J, Bluemke W, Blombach B, Eikmanns B, Bengelsdorf FR, Weuster-Botz D, Durre P.	Microb Biotechnol	10.1111/1751-7915.13270	2018
	A genetic system for Clostridium ljungdahlii: a chassis for autotrophic production of biocommodities and a model homoacetogen.	Leang C, Ueki T, Nevin KP, Lovley DR.	Appl Environ Microbiol	10.1128/aem.02891-12	2013
Metabolism	Extensive Identification of Bacterial Riboflavin Transporters and Their Distribution across Bacterial Species.	Gutierrez-Preciado A, Torres AG, Merino E, Bonomi HR, Goldbaum FA, Garcia-Angulo VA.	PLoS One	10.1371/journal.pone.0126124	2015
Metabolism	The Sporomusa type Nfn is a novel type of electron-bifurcating transhydrogenase that links the redox pools in acetogenic bacteria.	Kremp F, Roth J, Muller V.	Sci Rep	10.1038/s41598-020-71038-2	2020
Genetics	Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium.	Humphreys CM, McLean S, Schatschneider S, Millat T, Henstra AM, Annan FJ, Breitkopf R, Pander B, Piatek P, Rowe P, Wichlacz AT, Woods C, Norman R, Blom J, Goesman A, Hodgman C, Barrett D, Thomas NR, Winzer K, Minton NP.	BMC Genomics	10.1186/s12864-015-2287-5	2015
Transcriptome	The purine-utilizing bacterium Clostridium acidurici 9a: a genome-guided metabolic reconsideration.	Hartwich K, Poehlein A, Daniel R.	PLoS One	10.1371/journal.pone.0051662	2012
Genetics	Analysis of the Core Genome and Pan-Genome of Autotrophic Acetogenic Bacteria.	Shin J, Song Y, Jeong Y, Cho BK.	Front Microbiol	10.3389/fmicb.2016.01531	2016
Pathogenicity	Tolerance of Listeria monocytogenes to Quaternary Ammonium Sanitizers Is Mediated by a Novel Efflux Pump Encoded by emrE.	Kovacevic J, Ziegler J, Walecka-Zacharska E, Reimer A, Kitts DD, Gilmour MW.	Appl Environ Microbiol	10.1128/aem.03741-15	2016
Metabolism	Characterization and detection of a widely distributed gene cluster that predicts anaerobic choline utilization by human gut bacteria.	Martinez-del Campo A, Bodea S, Hamer HA, Marks JA, Haiser HJ, Turnbaugh PJ, Balskus EP.	mBio	10.1128/mbio.00042-15	2015
Metabolism	Identifying reaction modules in metabolic pathways: bioinformatic deduction and experimental validation of a new putative route in purine catabolism.	Barba M, Dutoit R, Legrain C, Labedan B.	BMC Syst Biol	10.1186/1752-0509-7-99	2013
Genetics	Barriers to genome editing with CRISPR in bacteria.	Vento JM, Crook N, Beisel CL.	J Ind Microbiol Biotechnol	10.1007/s10295-019-02195-1	2019
	Gut Microbiome of an 11th Century A.D. Pre-Columbian Andean Mummy.	Santiago-Rodriguez TM, Fornaciari G, Luciani S, Dowd SE, Toranzos GA, Marota I, Cano RJ.	PLoS One	10.1371/journal.pone.0138135	2015
Metabolism	Clostridium scindens: a human gut microbe with a high potential to convert glucocorticoids into androgens.	Ridlon JM, Ikegawa S, Alves JM, Zhou B, Kobayashi A, Iida T, Mitamura K, Tanabe G, Serrano M, De Guzman A, Cooper P, Buck GA, Hylemon PB.	J Lipid Res	10.1194/jlr.m038869	2013
	Analysis of anoxybacillus genomes from the aspects of lifestyle adaptations, prophage diversity, and carbohydrate metabolism.	Goh KM, Gan HM, Chan KG, Chan GF, Shahar S, Chong CS, Kahar UM, Chai KP.	PLoS One	10.1371/journal.pone.0090549	2014
Enzymology	Metabolic engineering of Clostridium autoethanogenum for selective alcohol production.	Liew F, Henstra AM, Kopke M, Winzer K, Simpson SD, Minton NP.	Metab Eng	10.1016/j.ymben.2017.01.007	2017
Enzymology	Characterization of two virulent phages of Lactobacillus plantarum.	Briggiler Marco M, Garneau JE, Tremblay D, Quiberoni A, Moineau S.	Appl Environ Microbiol	10.1128/aem.02565-12	2012
Enzymology	Bioinformatic characterization of glycyl radical enzyme-associated bacterial microcompartments.	Zarzycki J, Erbilgin O, Kerfeld CA.	Appl Environ Microbiol	10.1128/aem.02587-15	2015
Metabolism	Molecular Evolution of the Oxygen-Binding Hemerythrin Domain.	Alvarez-Carreno C, Becerra A, Lazcano A.	PLoS One	10.1371/journal.pone.0157904	2016
Metabolism	Deciphering Clostridium tyrobutyricum Metabolism Based on the Whole-Genome Sequence and Proteome Analyses.	Lee J, Jang YS, Han MJ, Kim JY, Lee SY.	mBio	10.1128/mbio.00743-16	2016
	Harnessing heterologous and endogenous CRISPR-Cas machineries for efficient markerless genome editing in Clostridium.	Pyne ME, Bruder MR, Moo-Young M, Chung DA, Chou CP.	Sci Rep	10.1038/srep25666	2016
Pathogenicity	The Exosporium Layer of Bacterial Spores: a Connection to the Environment and the Infected Host.	Stewart GC.	Microbiol Mol Biol Rev	10.1128/mmbr.00050-15	2015
	Development of Strong Anaerobic Fluorescent Reporters for Clostridium acetobutylicum and Clostridium ljungdahlii Using HaloTag and SNAP-tag Proteins.	Charubin K, Streett H, Papoutsakis ET.	Appl Environ Microbiol	10.1128/aem.01271-20	2020
Metabolism	Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen.	Liu JK, Lloyd C, Al-Bassam MM, Ebrahim A, Kim JN, Olson C, Aksenov A, Dorrestein P, Zengler K.	PLoS Comput Biol	10.1371/journal.pcbi.1006848	2019
Metabolism	Synthesis of Heterologous Mevalonic Acid Pathway Enzymes in Clostridium ljungdahlii for the Conversion of Fructose and of Syngas to Mevalonate and Isoprene.	Diner BA, Fan J, Scotcher MC, Wells DH, Whited GM.	Appl Environ Microbiol	10.1128/aem.01723-17	2018
Metabolism	A high gas fraction, reduced power, syngas bioprocessing method demonstrated with a Clostridium ljungdahlii OTA1 paper biocomposite.	Schulte MJ, Wiltgen J, Ritter J, Mooney CB, Flickinger MC.	Biotechnol Bioeng	10.1002/bit.25966	2016
Pathogenicity	Lactose-inducible system for metabolic engineering of Clostridium ljungdahlii.	Banerjee A, Leang C, Ueki T, Nevin KP, Lovley DR.	Appl Environ Microbiol	10.1128/aem.03666-13	2014
Metabolism	Kinetic studies on fermentative production of biofuel from synthesis gas using Clostridium ljungdahlii.	Mohammadi M, Mohamed AR, Najafpour GD, Younesi H, Uzir MH.	ScientificWorldJournal	10.1155/2014/910590	2014
Enzymology	The Rnf complex of Clostridium ljungdahlii is a proton-translocating ferredoxin:NAD+ oxidoreductase essential for autotrophic growth.	Tremblay PL, Zhang T, Dar SA, Leang C, Lovley DR.	mBio	10.1128/mbio.00406-12	2012
Metabolism	Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii.	Nagarajan H, Sahin M, Nogales J, Latif H, Lovley DR, Ebrahim A, Zengler K.	Microb Cell Fact	10.1186/1475-2859-12-118	2013
Metabolism	Metabolic response of Clostridium ljungdahlii to oxygen exposure.	Whitham JM, Tirado-Acevedo O, Chinn MS, Pawlak JJ, Grunden AM.	Appl Environ Microbiol	10.1128/aem.02491-15	2015
Metabolism	Interspecies Microbial Fusion and Large-Scale Exchange of Cytoplasmic Proteins and RNA in a Syntrophic Clostridium Coculture.	Charubin K, Modla S, Caplan JL, Papoutsakis ET.	mBio	10.1128/mbio.02030-20	2020
Metabolism	Optimization of carbon and energy utilization through differential translational efficiency.	Al-Bassam MM, Kim JN, Zaramela LS, Kellman BP, Zuniga C, Wozniak JM, Gonzalez DJ, Zengler K.	Nat Commun	10.1038/s41467-018-06993-6	2018
	CO₂ to succinic acid - Estimating the potential of biocatalytic routes.	Liebal UW, Blank LM, Ebert BE.	Metab Eng Commun	10.1016/j.mec.2018.e00075	2018
	Gas Fermentation-A Flexible Platform for Commercial Scale Production of Low-Carbon-Fuels and Chemicals from Waste and Renewable Feedstocks.	Liew F, Martin ME, Tappel RC, Heijstra BD, Mihalcea C, Kopke M.	Front Microbiol	10.3389/fmicb.2016.00694	2016
Metabolism	Characterization of Clostridium ljungdahlii OTA1: a non-autotrophic hyper ethanol-producing strain.	Whitham JM, Schulte MJ, Bobay BG, Bruno-Barcena JM, Chinn MS, Flickinger MC, Pawlak JJ, Grunden AM	Appl Microbiol Biotechnol	10.1007/s00253-016-7978-6	2016
Enzymology	Characterization of an acetoin reductase/2,3-butanediol dehydrogenase from Clostridium ljungdahlii DSM 13528.	Tan Y, Liu ZY, Liu Z, Li FL	Enzyme Microb Technol	10.1016/j.enzmictec.2015.06.011	2015
Metabolism	Physiological response of Clostridium ljungdahlii DSM 13528 of ethanol production under different fermentation conditions.	Xie BT, Liu ZY, Tian L, Li FL, Chen XH	Bioresour Technol	10.1016/j.biortech.2014.11.101	2014
	Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia.	Brown SD, Nagaraju S, Utturkar S, De Tissera S, Segovia S, Mitchell W, Land ML, Dassanayake A, Kopke M	Biotechnol Biofuels	10.1186/1754-6834-7-40	2014
Metabolism	UVC-mutagenesis in acetogens: resistance to methanol, ethanol, acetone, or n-butanol in recombinants with tailored genomes as the step in engineering of commercial biocatalysts for continuous CO(2)/H(2) blend fermentations.	Kiriukhin M, Tyurin M, Gak E	World J Microbiol Biotechnol	10.1007/s11274-013-1579-7	2014
Metabolism	RNA-seq-based comparative transcriptome analysis of the syngas-utilizing bacterium Clostridium ljungdahlii DSM 13528 grown autotrophically and heterotrophically.	Tan Y, Liu J, Chen X, Zheng H, Li F	Mol Biosyst	10.1039/c3mb70232d	2013
Enzymology	Characterization of two novel butanol dehydrogenases involved in butanol degradation in syngas-utilizing bacterium Clostridium ljungdahlii DSM 13528.	Tan Y, Liu J, Liu Z, Li F	J Basic Microbiol	10.1002/jobm.201300046	2013
	Evaluation of Clostridium ljungdahlii DSM 13528 reference genes in gene expression studies by qRT-PCR.	Liu J, Tan Y, Yang X, Chen X, Li F	J Biosci Bioeng	10.1016/j.jbiosc.2013.04.011	2013
Phylogeny	Clostridium luticellarii sp. nov., isolated from a mud cellar used for producing strong aromatic liquors.	Wang Q, Wang CD, Li CH, Li JG, Chen Q, Li YZ	Int J Syst Evol Microbiol	10.1099/ijsem.0.000641	2015

References

#5077	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 13528
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#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) .
#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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Clostridium ljungdahlii (DSM 13528, ATCC 55383, PETC)

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