Tuning interdomain conjugation toward in situ population modification in yeasts

The ability to modify and control natural and engineered microbiomes is essential for biotechnology and biomedicine. Fungi are critical members of most microbiomes, yet technology for modifying the fungal members of a microbiome has lagged far behind that for bacteria. Interdomain conjugation (IDC) is a promising approach, as DNA transfer from bacterial cells to yeast enables in situ modification. While such genetic transfers have been known to naturally occur in a wide range of eukaryotes, and are thought to contribute to their evolution, IDC has been understudied as a technique to control fungal or fungal-bacterial consortia. One major obstacle to widespread use of IDC is its limited efficiency. In this work, we utilize interactions between genetically tractable Escherichia coli and Saccharomyces cerevisiae to control the incidence of IDC. We test the landscape of population interactions between the bacterial donors and yeast recipients to find that bacterial commensalism leads to max...,
Data was collected as described in the Materials and Methods section of Stindt, et al.
, MATLAB, All data here to be used in conjunction with custom MATLAB scripts found at [https://github.com/mccleanlab/Stindt_2023](https://github.com/mccleanlab/Stindt_2023)

## The following three data files contain all analyzed data used for plotted figures in Stindt et. al. 2023:

\__Consolidated_Data.mat includes source data for Figures 1-3, 5-7, SI Figures 2-7, 13-20. Compiled data is from analyzed flow cytometry, fluorimetry, and image analyses, with experiments organized by Plate numbers and experiment date. Use this data with All_plots script to generate most figures. \"All_plots\" script also specifies which experimental info (plate, date) corresponds to each figure.

\__Conjugation_Clump_Data.mat includes image analysis and fluorimetry data used for model fitting in Figure 4, SI Figures 8-12. For use with modeling scripts in the GitHub repository for this paper.

AllFits.mat includes all saved model parameters used in Figure 4, SI Figures 8-12. For use with modeling scripts in the GitHub r...