realized plasmid host range in surface-associated microbial systems
Description
A dataset accompanying the manuscript titled “Horizontal and vertical gene transfer jointly shape the realized plasmid host range in surface-associated microbial systems” (or similar; you should insert the manuscript title if finalized). The data comprises measurements and observations of plasmid transfer and host‐range in microbial biofilms (surface‐associated microbial systems). It includes [insert type of files: e.g., spreadsheets of host–plasmid interactions, raw counts, metadata describing isolates/samples, protocols used, etc.]. The dataset enables users to explore the realized host range of plasmids in a surface‐associated environment, reproduce the analyses, and potentially extend the findings.
Files
Steps to reproduce
Experimental data: Surface-associated conjugation assays were performed by mixing donor and recipient communities on membrane filters placed on agar media with varying nutrient concentrations (1×SWW, 10×SWW, LB). Samples were incubated under specified temperatures, and transconjugant cells were quantified using GFP fluorescence, microscopy, and FACS. Community compositions were determined by 16S rRNA gene amplicon sequencing. Standard protocols for sample preparation, plating, fluorescence imaging, and FACS gating are included in the paper. Simulation data: Individual-based simulations were performed using CellModeller with custom Python scripts. Simulations independently varied recipient growth rate distributions, conjugation and probability distributions. All simulation configuration files, and output CSVs are included. Simulations can be reproduced by running the provided CellModeller model scripts on a Python environment configured with OpenCL support. Refer to the manuscript’s Methods and Supplementary Information for detailed procedures, software versions, and statistical workflows.
Institutions
- Hokkaido Daigaku