Woolston Lab
Woolston Lab
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    • Home
    • Research
    • Lab Members
    • Resources
    • Publications
  • Home
  • Research
  • Lab Members
  • Resources
  • Publications

Resources

This section includes protocols we have developed and published (in more detail than can be provided in journal articles), as well as computational resources and a list of plasmids and strains we have developed and are happy to share with the broader community. We only ask that if these resources are useful to you, please cite our work.

Procedures

Eubacterium limosum Electroporation Protocol (pdf)

Download

Eubacterium limosum Competent Cell Preparation (pdf)

Download

Alcohol Oxidase / Purpald Assay for Methanol Quantification (docx) (docx)

Download

Plasmids and Strains

Eubacterium limosum EPS Knockout Strains

The extracellular polymeric substance produced by E. limosum can make this organism very difficult to work with. We have generated three different knockout strains:

  • epsABC/ptkA/tmkA replaced with catP selectable marker (Sanford et al, 2022, FEMS Micro Letters)
  • epsABC/ptkA/tmkA cleanly deleted via recombineering (Sanford et al, 2024, In Review)
  • epsABC/ptkA/tmkA deleted by insertion of catP followed by removal by Cre (Sanford et al, 2024, Biotechnology and Bioengineering)

Eubacterium limosum expression vectors

We generated a range of E. limosum vectors for constitutive or inducible expression (Sanford and Woolston, 2022). Promoters include:

  • nifJ (high expression)
  • thl (medium expression)
  • 2TetO1 (low expression, tightly regulated)

We also developed new selectable markers, including:

  • Tetracycline
  • Ampicillin

Clostridial recombinase (recT) library

As part of a project supported by the DOE Joint Genome Institute's Community Science Program, we synthesized a library of 57 RecT homologs for screening in Clostridia, codon optimized for expression in Eubacterium limosum. These are all on plasmids with the pIP404 ori, chloramphenicol resistance gene (catP), and with expression controlled by the p2TetO1 promoter originally developed for Clostridium acetobutylicum. As such, they should be broadly compatible with different Clostridial species. The whole library or individual plasmids are available upon request


Reference: Sanford et al, 2024, In Review

Recombinase Sequences (xlsx)

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Sulfide Biosensor

Detecting Hydrogen Sulfide in the Gut Microbiome

  

As part of a project supported by the NIH National Institute of Biomedical Imaging and Bioengineering, we developed a transcriptional biosensor for hydrogen sulfide. The sensor uses two plasmids: The first (pMF2-rSQR and pSH1-wSQR) encodes a sulfide:quinone oxidoreductase from either Rhodobacter capsulatus or Wolinella succinogenes that oxidizes sulfide to per- and polysulfides under aeroobic or anaerobic conditions, respectively. The second (pMF1-JSH-105-mKate) encodes the transcriptional regulator SqrR from Rhodobacter capsulatus that responds to polysulfides, and mKate as a readout driven by the Sqr promoter modified for expression in E. coli.


  Reference: Fernez et al, 2025, ACS Synthetic Biology. Link 

To request any of the above strains (or other published material not listed above), contact Prof. Woolston using the link below. Please include your shipping address, as well as a FedEx Account to cover shipping costs. If shipping costs are prohibitive, please let us know, and we will do our best to accommodate.

Contact us to request strains

E-mail

Computational Resources

All computer code used to support analysis and conclusions in our published work is available on our GitHub repository

GitHub

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