Farm-level characteristics shape the microbial community structure of compost-bedded pack dairy barns

The repository includes: Species-level taxonomic abundance table generated from shotgun metagenomic sequencing, sample metadata, including farm identifier, tilling depth, tillage equipment type, antimicrobial resistance (AMR) class abundance table, virulence-associated function abundance table.

Samples were collected from eight commercial CBP dairy farms managed under deep and shallow tilling practices using either rototillers or cultivators. Sequence data were processed using a standardized shotgun metagenomic analysis pipeline, and downstream functional annotations were generated using established reference databases. These processed datasets were used for taxonomic, functional, AMR, and virulence analyses reported in the associated manuscript.