@article{jensen_deichmann_ma_vilandt_schiesaro_rojek_lengger_eliasson_vento_durmusoglu_et al._2022, title={Engineered cell differentiation and sexual reproduction in probiotic and mating yeasts}, volume={13}, ISSN={["2041-1723"]}, DOI={10.1038/s41467-022-33961-y}, abstractNote={Abstract}, number={1}, journal={NATURE COMMUNICATIONS}, author={Jensen, Emil D. and Deichmann, Marcus and Ma, Xin and Vilandt, Rikke U. and Schiesaro, Giovanni and Rojek, Marie B. and Lengger, Bettina and Eliasson, Line and Vento, Justin M. and Durmusoglu, Deniz and et al.}, year={2022}, month={Oct} }
 @article{siedler_rau_bidstrup_vento_aunsbjerg_bosma_mcnair_beisel_neves_2020, title={Competitive Exclusion Is a Major Bioprotective Mechanism of Lactobacilli against Fungal Spoilage in Fermented Milk Products}, volume={86}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.02312-19}, abstractNote={
            In societies that have food choices, conscious consumers demand natural solutions to keep their food healthy and fresh during storage, simultaneously reducing food waste. The use of “good bacteria” to protect food against spoilage organisms has a long, successful history, even though the molecular mechanisms are not fully understood. In this study, we show that the depletion of free manganese is a major bioprotective mechanism of lactobacilli in dairy products. High manganese uptake and intracellular storage provide a link to the distinct, nonenzymatic, manganese-catalyzed oxidative stress defense mechanism, previously described for certain lactobacilli. The evaluation of representative
            Lactobacillus
            species in our study identifies multiple relevant species groups for fungal growth inhibition via manganese depletion. Hence, through the natural mechanism of nutrient depletion, the use of dedicated bioprotective lactobacilli constitutes an attractive alternative to artificial preservation.
          }, number={7}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Siedler, Solvej and Rau, Martin Holm and Bidstrup, Susanne and Vento, Justin M. and Aunsbjerg, Stina Dissing and Bosma, Elleke F. and McNair, Laura M. and Beisel, Chase L. and Neves, Ana Rute}, year={2020}, month={Apr} }
 @misc{vento_crook_beisel_2019, title={Barriers to genome editing with CRISPR in bacteria}, volume={46}, ISSN={["1476-5535"]}, url={https://doi.org/10.1007/s10295-019-02195-1}, DOI={10.1007/s10295-019-02195-1}, abstractNote={Abstract}, number={9-10}, journal={JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY}, publisher={Springer Science and Business Media LLC}, author={Vento, Justin M. and Crook, Nathan and Beisel, Chase L.}, year={2019}, month={Oct}, pages={1327–1341} }
 @article{leenay_vento_shah_martino_leulier_beisel_2019, title={Genome Editing with CRISPR-Cas9 in Lactobacillus plantarum Revealed That Editing Outcomes Can Vary Across Strains and Between Methods}, volume={14}, ISSN={["1860-7314"]}, DOI={10.1002/biot.201700583}, abstractNote={Lactic-acid bacteria such as Lactobacillus plantarum are commonly used for fermenting foods and as probiotics, where increasingly sophisticated genome-editing tools are employed to elucidate and enhance these microbes' beneficial properties. The most advanced tools to date utilize an oligonucleotide or double-stranded DNA donor for recombineering and Cas9 for targeted DNA cleavage. As the associated methods are often developed in isolation for one strain, it remains unclear how different Cas9-based editing methods compare across strains. Here, this work directly compares two methods in different strains of L. plantarum: one utilizing a plasmid-encoded recombineering template and another utilizing an oligonucleotide donor and an inducible DNA recombinase. This comparison reveals one instance in which only the recombineering-template method generates desired edits and another instance in which only the oligo method generates desired edits. It is further found that both methods exhibit highly variable success editing the same site across multiple L. plantarum strains. Finally, failure modes are identified for the recombineering-template method, including a consistent genomic deletion and reversion of a point mutation in the recombineering template. This study therefore highlights surprising differences for Cas9-mediated genome editing between methods and related strains, arguing for the need for multiple, distinct methods when performing CRISPR-based editing in bacteria.}, number={3}, journal={BIOTECHNOLOGY JOURNAL}, author={Leenay, Ryan T. and Vento, Justin M. and Shah, Malay and Martino, Maria Elena and Leulier, Francois and Beisel, Chase L.}, year={2019}, month={Mar} }