Strain identifier
BacDive ID: 2802
Type strain: 
Species: Clostridium ljungdahlii
Strain Designation: PETC
Strain history: <- ATCC <- S. Barik, University of Arkansas Medical Sciences, Little Rock, USA; PETC
NCBI tax ID(s): 748727 (strain), 1538 (species)
version 8.1 (current version)
General
@ref: 5077
BacDive-ID: 2802
DSM-Number: 13528
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, motile
description: Clostridium ljungdahlii PETC is an anaerobe, spore-forming, mesophilic bacterium that was isolated from chicken yard waste.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 748727 | strain |
| 1538 | species |
strain history
- @ref: 5077
- history: <- ATCC <- S. Barik, University of Arkansas Medical Sciences, Little Rock, USA; PETC
doi: 10.13145/bacdive2802.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Clostridiaceae
- genus: Clostridium
- species: Clostridium ljungdahlii
- full scientific name: Clostridium ljungdahlii Tanner et al. 1993
@ref: 5077
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Clostridium
species: Clostridium ljungdahlii
full scientific name: Clostridium ljungdahlii Tanner et al. 1993
strain designation: PETC
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 91.786 | |
| 69480 | 99.999 | positive |
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 5077 | CLOSTRIDIUM LJUNGDAHLII MEDIUM (DSMZ Medium 879) | yes | https://mediadive.dsmz.de/medium/879 | 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) | yes | https://mediadive.dsmz.de/medium/640 | 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: 5077
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 5077 | anaerobe | |
| 69480 | anaerobe | 100 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 100 |
| 69480 | yes | 99.704 |
Isolation, sampling and environmental information
isolation
- @ref: 5077
- sample type: chicken yard waste
- geographic location: Arkansas
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Agriculture | #Livestock (Husbandry) |
| #Engineered | #Waste | #Solid waste |
| #Host | #Birds | #Chicken |
taxonmaps
- @ref: 69479
- File name: preview.99_1289.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_42;96_749;97_872;98_1018;99_1289&stattab=map
- Last taxonomy: Clostridium
- 16S sequence: FR733688
- Sequence Identity:
- Total samples: 18602
- soil counts: 2899
- aquatic counts: 1409
- animal counts: 13922
- plant counts: 372
Safety information
risk assessment
- @ref: 5077
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Clostridium ljungdahlii strain DSM 13528 16S ribosomal RNA gene, partial sequence | DQ911275 | 320 | ena | 748727 |
| 20218 | Clostridium ljungdahlii strain ATCC 55383 16S ribosomal RNA gene, partial sequence | GU139552 | 1471 | ena | 1538 |
| 5077 | Clostridium ljungdahlii partial 16S rRNA gene, type strain DSM13528T | FR733688 | 1499 | ena | 748727 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Clostridium ljungdahlii DSM 13528 | GCA_000143685 | complete | ncbi | 748727 |
| 66792 | Clostridium ljungdahlii DSM 13528 PETC | GCA_001636855 | scaffold | ncbi | 748727 |
| 66792 | Clostridium ljungdahlii DSM 13528 strain PETC | 748727.19 | wgs | patric | 748727 |
| 66792 | Clostridium ljungdahlii strain DSM 13528 | 1538.8 | complete | patric | 1538 |
| 66792 | Clostridium ljungdahlii PETC | 2740892543 | draft | img | 748727 |
| 66792 | Clostridium ljungdahlii PETC, DSM 13528 | 648028017 | complete | img | 748727 |
GC content
- @ref: 5077
- GC-content: 22-23
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| motile | yes | 85.587 | no |
| flagellated | no | 60.812 | no |
| gram-positive | yes | 61.287 | no |
| anaerobic | yes | 98.669 | no |
| aerobic | no | 98.08 | yes |
| halophile | no | 92.038 | no |
| spore-forming | yes | 93.048 | no |
| thermophile | no | 98.342 | yes |
| glucose-util | yes | 84.728 | no |
| glucose-ferment | yes | 55.05 | no |
External links
@ref: 5077
culture collection no.: DSM 13528, ATCC 55383
straininfo link
- @ref: 72328
- straininfo: 43583
literature
| Pubmed-ID | title | authors | journal | DOI | year | mesh | topic | topic2 |
|---|---|---|---|---|---|---|---|---|
| 23651807 | 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 | Biofuels/supply & distribution, Clostridium/*genetics, *Gene Expression, Gene Expression Profiling/*standards, Genes, Bacterial/genetics, *Real-Time Polymerase Chain Reaction, Reference Standards, Reproducibility of Results | ||
| 23720212 | 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 | Alcohol Oxidoreductases/chemistry/genetics/isolation & purification/*metabolism, Biotransformation, Butanols/*metabolism, Butyrates/metabolism, Clostridium/*enzymology/genetics, Coenzymes/metabolism, Enzyme Inhibitors/metabolism, Enzyme Stability, Gene Expression Profiling, Hydrogen-Ion Concentration, Kinetics, NADP/metabolism, Oxygen/metabolism, Real-Time Polymerase Chain Reaction, Sequence Homology, Amino Acid, Temperature | Enzymology | Metabolism |
| 24056499 | 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 | Biological Transport, Carbon/metabolism, Carbon Dioxide/metabolism, Carbon Monoxide/metabolism, Clostridium/*genetics/growth & development/*metabolism, Energy Metabolism, Fructose/metabolism, Gases/*metabolism, *Gene Expression Profiling, Gene Expression Regulation, Bacterial, Metabolic Networks and Pathways, RNA, Small Untranslated/metabolism, Sequence Analysis, RNA, *Transcriptome, Vitamin B 12/biosynthesis | Metabolism | Transcriptome |
| 24415498 | 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 | Acetone/metabolism, Alcohols/metabolism, Carbon Dioxide/metabolism, Chromosomes, Fungal, Clostridium/classification/genetics/*growth & development, Fatty Acids/metabolism, Fermentation/*radiation effects, Genes, Bacterial, Genetic Enhancement/*methods, Genome, Bacterial, Hydrogen/metabolism, Mutagenesis/genetics/*radiation effects, Reproducibility of Results | Metabolism | Genetics |
| 24655715 | 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 | |||
| 25496952 | 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 | Acids/pharmacology, Biotechnology/*methods, Calcium Carbonate/pharmacology, Carbon Dioxide/metabolism, Carbon Monoxide/metabolism, Clostridium/drug effects/genetics/growth & development/*physiology, Ethanol/*metabolism, *Fermentation/drug effects, Gene Expression Profiling, Gene Expression Regulation, Bacterial/drug effects | Metabolism | Pathogenicity |
| 26320708 | 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 | Acetoin/metabolism, Alcohol Oxidoreductases/chemistry/genetics/*metabolism, Amino Acid Sequence, Bacterial Proteins/chemistry/genetics/metabolism, Butylene Glycols/metabolism, Clostridium/*enzymology/genetics, Clostridium acetobutylicum/enzymology/genetics, Fermentation, Genes, Bacterial, Industrial Microbiology, Kinetics, Metabolic Engineering, Models, Molecular, Molecular Sequence Data, Phylogeny, Protein Conformation, Recombinant Proteins/chemistry/genetics/metabolism, Sequence Homology, Amino Acid | Enzymology | Metabolism |
| 26420591 | 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 | *Alcoholic Beverages, Bacterial Typing Techniques, Base Composition, China, Clostridium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology | Phylogeny | Genetics |
| 27866253 | 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 | Acetyl Coenzyme A/metabolism, Aldehyde Oxidoreductases/metabolism, Carbon Dioxide/metabolism, Carbon Monoxide/metabolism, Clostridium/*metabolism, Ethanol/*metabolism, Multienzyme Complexes/metabolism | Metabolism | Enzymology |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 5077 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13528) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-13528 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 72328 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID43583.1 | StrainInfo: A central database for resolving microbial strain identifiers |