The dataset contains the following directories: All_raw_MAGs: all cross-assembled MAGs per community, with a text file for their BAT annotation results. Cross-assembly was done by combining all time points. Candidatus_Saccharibacterium_MAGs: identified nanobacterium MAGs from various communities. Cellvibrio_MAGs: identified cellvibrio spp. across communities. Cellvibrio_Plasmids: Cp plasmids belonging to Cellvibrio (C1) which transferred from communities 8 to 4, 6, 9, and 10 (in horizontal communities) Interactive_Dataset: HTML5 (Plotly) graphs to explore all xenotypic sequences and MAG abundance plots Rscript_mock_data: R script used to design the mock data for the benchmark set. And a single spreadsheet (Xenoseq_mastersheet.xlsx, Supplementary Table 1) of data discussed in the main text.